Progress 06/08/09 to 06/07/14
Outputs
Target Audience: One of the research goals of this project is to develop new knowledge and new tools for accelerated plant genetic improvement and for enhanced productivity and effectiveness of crop production, and simultaneously address ecological concerns in agricultural production and utilization. This project has collaborated with several plant breeders, including Dr. C. Wayne Smith (cotton breeder), Dr. Stave Hague (cotton breeder), Dr. Wenwei Xu (maize breeder), Dr. Seth Murray (maize breeder), and Dr. B.B. Singh (cowpea breeder). Therefore, the knowledge and tools developed through the project have been directly transferred and immediately used in their breeding programs. Furthermore, each of them has numerous graduate students who are majoring in plant breeding and is interacted with many breeders and end-product users nationwide. The knowledge and tools developed through the project have been further extended to classrooms, enhanced plant breeding and enhanced crop production. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided? This project has made significant contributions to science and technologies, thus revolutionizing current biological science research, human medicine research and plant and animal breeding. This project established the DNA "Jigsaw Puzzle" Structure Model as the molecular basis of biology and genetics. This discovery provides a novel and comprehensive molecular basis of genetics, variation, abundance, diversity and complexity of all living organisms, thus revolutionizing the knowledge, concepts and strategies currently used in biology, breeding and medicine. A monographic book entitled "The Molecular Basis of Biology: DNA "Jigsaw Puzzle" Structure Model" about the findings currently is in preparation, invited by a world's well-known publisher, Springer Verlag. This project helped pioneer the new disciplines of biology: systems genomics and systems biology, which represents the next era of biology research. The new and high-throughput gene and QTL cloning system that we developed not only allows rapid and efficient cloning of the genes controlling many traits of economical and/or biological importance in plants, animals, humans and microorganisms, but also allow comprehensively deciphering the molecular bases and regulation mechanisms of many economical and/or biological important traits, biological processes and problems, thus revolutionizing the current biology, genomics, systems genomics and systems biology research, current molecular breeding and current crop production (such as gene-based crop production and molecular farming). This project developed the whole-genome integrated physical/genetic maps of turkey, chickpea and cotton, the whole genome sequences of turkey and upland cotton, and a huge amount of RNA-seq and RAD seq data for the crops important in agriculture. These maps and sequences provide resources and tools for high-throughput development of SNPs, especially genic SNP markers, genetic map construction, gene and QTL cloning, and comparative genome analysis. How have the results been disseminated to communities of interest? The results and achievements of this project have been disseminated to communities of interest through numerous methods: Published the results and achievements of this project in publicly readily accessible, internationally-well recognized peer-reviewed journals, such as BMC Genomics, PLoS ONE, PLoS Biology, Nucleic Acids Research, Nature Protocols, Nature Communications, Genome, Molecular Breeding, etc. Presented the results and achievements of this project at national and international professional conferences such as the International Plant & Animal Genome Conference. Presented the results and achievements of this project at national and international institutions such as University of Maryland, Chinese Academy of Sciences and Vietnam Academy of Science and Technology. Incorporated the findings and discoveries of this project into the classroom teaching such as SCSC, GENE and MEPS 654 - Analysis of Complex Genomes (lectures) and SCSC, GENE and MEPS 655 - Analysis of Complex Genomes (labs). Incorporated the findings and discoveries of this project into training of students, postdoctoral associates and junior scientists. We have trained numerous students, postdoctoral associates and junior scientists during the five-year period of this project. Directly delivered the new knowledge, resources and tools developed in this project to users such as breeders and researchers nationwide such as the RAD sequences that we developed. What do you plan to do during the next reporting period to accomplish the goals?
Nothing Reported
Impacts
What was accomplished under these goals?
This project was from June 8, 2009 to June 07, 2014. During the five-year period of the project, we have far more exceeded the proposed research objectives. The major accomplishments are summarized below: We have successfully developed the whole-genome integrated physical/genetic maps of turkey, chickpea and cotton, and sequenced the whole genomes of turkey and upland cotton. Furthermore, we have sequenced and profiled the transcriptomes for a total of 250 cotton and related species lines (350 Gb), 300 maize inbred lines (420 Gb), 100 wheat and related species lines (140 Gb), 60 pairs of chickpea and related species lines (160 Gb), and 24 cultivated and wild soybean lines (31 Gb). Together, we have sequenced and profiled the transcriptomes for a total of 794 plant lines with a total of 1,101 Gb sequences. Moreover, we have generated the BamHI RAD sequences for 182 cowpea lines (24 Gb), 351 cotton lines (491 Gb and 216 rice lines (108 Gb). Together, we have generated the BamHI RAD sequences for a total of 749 plant lines with a total of 605 Gb sequences. We have re-established the molecular basis of biology and genetics: The DNA "Jigsaw Puzzle" Structure Model. We discovered and established the "Jigsaw Puzzle" DNA structure model as the new molecular basis of genetics and biology. This DNA structure model has been tested using a large number of plant, animal and microbe species. We found that the variations of types, copy numbers, ratios, arrays or sequences, interactions and mutations (including gene mutation) of genome-constituting fundamental functional elements (FFE), including genes (GEN), DNA transposable elements (DTE), retro-transposable elements (RTE), simple sequence repeats (SSR) and low complex repeats (LCR), are the molecular basis of living organism's genetics, variation, diversity, abundance and complexity. We helped pioneer systems genomics and systems biology. We first established the DNA "Jigsaw Puzzle" Structure Model as the molecular basis of systems genomics and systems biology. Then, we developed a novel high-throughput system to clone the genes and QTLs controlling agronomic traits (submitted for filing a patent). Using the new gene/QTL cloning method, a large number of the genes controlling agronomic traits can be cloned within a few scientist years. Using the new gene/QTL cloning method, we have successfully cloned 474 genes controlling cotton fiber length (named GFL genes) and 1,501 gene controlling maize grain yield (named ZmGY genes), probably more than the total number of agronomic genes cloned from all crops in the past 20 years worldwide. We are currently cloning the genes controlling seven other cotton fiber quality and yield traits, and 13 other maize grain yield and quality traits. The throughput and efficiency of the new gene and QTL cloning method is over 1,000-fold higher than the current gene cloning methods such as map-based cloning, insertional and chemical-induced mutagenesis, RNA interference (RNAi), and gene overexpression. Furthermore, this new gene and QTL cloning system is applicable to clone the genes and QTLs controlling any trait in any organisms with the same efficiency, regardless of genome sizes, genome complexities, whether the genomes were previously subjected to research, and whether there is a genetic transformation system developed or not. Using the cloned genes from maize and cotton, we have deciphered the molecular mechanisms of quantitative genetics, crop yield, crop quality, heterosis and polyploidization, and is developing a gene-based breeding system in cotton and maize. In comparison, the gene-based breeding system is far more powerful and far more efficient than the current marker- or genomics-assisted breeding method, with which the performance of a breeding line can be 100% predicted (R2 = 1.000; P = 0.0000).
Publications
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2014
Citation:
Liu Y-H, Zhang MP, Zhang Y, Smith CW, Hague SS, Sze S-H, Zhu J, Frelichowski J, Zhang H-B. 2014. Molecular Basis of Quantitative Genetics Revealed by Cloning and Systems Analysis of 474 Genes Controlling Fiber Length in Cotton. Agricultural Bioscience International Conference, Saskatoon, Sastatchewan, Canada, October 5 8, 2014.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2014
Citation:
Liu Y-H, Zhang MP, Zhang Y, Smith CW, Hague SS, Sze S-H, Zhu J, Frelichowski J, Zhang H-B. 2014. The molecular basis and regulation mechanisms of fiber length revealed by large-scale cloning and systems analysis of genes controlling the trait. The International Cotton Genome Initiative Research Conference, Wuhan, Hubei, China, September 25-28, 2014.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2014
Citation:
Liu B, Qi A, Hastie A, Muhantay G, Chan S, Liang X, Wei W, Wang M, Wang J, Dong L, Liu J, Qiu M, Li L, Li A, Zhang H-B, Hu S, Cao H. 2014. High throughput physical mapping of the horse genomes using single molecule nanochannel arrays and its integration with the horse genome sequence assemblies. The 34th International Society for Animal Genetics Conference, Xian, China, July 28 August 1, 2014
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2014
Citation:
Coyne CJ, McGee RJ, Piaskowski JL, Abbo S, Vandemark G, Zhang H-B. 2014. Screening chickpea for cold tolerance under controlled conditions. The 6th International Food Legumes Research Conference and the 7th International Conference on Legume Genetics and Genomics. July 7 11, 2014, Saskatoon, Canada
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2014
Citation:
Zhang Y, Zhang MP, Abbo S, Sherman A, Shtienberg D, Coyne CJ, Vandemark GJ, Zhang H-B. 2014. Molecular Basis of Plant Vernalization Revealed by Systems Analysis of the Genes Controlling the Process in Chickpea. International Plant & Animal Genome Conference XXII, P365
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2014
Citation:
Liu Y-H, Zhang MP, Zhang Y, Smith CW, Hague S, Sze S-H, Zhu J, Frelichowski J, Zhang H-B. 2014. Large-scale Cloning and Characterization of Genes Controlling Fiber Length for Deciphering of the Molecular Basis of Fiber Quality and Development of a Gene-based Breeding System in Cotton. International Plant & Animal Genome Conference XXII, P474
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2014
Citation:
Zhang MP, Zhi H, Chang F, Zhang Y, Liu Y-H, Zhu J, Xu W, Murray SC, Zhang H-B. 2014. Large-scale cloning and characterization of genes controlling grain yield for deciphering of the molecular basis of grain yield and development of a gene-based breeding system in maize. International Plant & Animal Genome Conference XXII, P875
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2014
Citation:
Zhang Y, Zhang MP, Zhang Q, Liu Y-H, Xu SS, Zhang H-B. 2014. Systems genomics analysis of wheat and its related species has revealed the molecular basis of plant polyploidization. International Plant & Animal Genome Conference XXII, W821
- Type:
Journal Articles
Status:
Published
Year Published:
2014
Citation:
Liu Y-H, Zhang MP, Huang JJ, Zhang H-B.(2014) DNA is structured as Jigsaw Puzzle in the genomes of Arabidopsis, rice and yeast. Genome 57:9-19.
- Type:
Theses/Dissertations
Status:
Published
Year Published:
2014
Citation:
Liu, Y.-H. 2014. Molecular basis of quantitative genetics revealed by cloning and analysis of 474 genes controlling fiber length in cotton. Ph.D. Dissertation, Texas A&M University, College Station, Texas
- Type:
Journal Articles
Status:
Published
Year Published:
2014
Citation:
Wang W, Feng B, Xiao J, Xia Z, Zhou X, Li P, Zhang W, Wang Y, M�ller BL, Zhang P, Luo M-C, Xiao G, Liu J, Yang J, Chen S, Rabinowicz PD, Chen X, Zhang H-B, Ceballos H, Lou Q, Zou M, Carvalho LJCB, Zeng C, Xia J, Sun S, Fu Y, Wang H, Lu C, Ruan M, Zhou S, Wu Z, Liu H, Kannangara RM, J�rgensen K, Neale RL, Bonde M, Heinz N, Zhu W, Wang S, Zhang Y, Pan K, Wen M, Ma P-A, Li Z, Hu M, Liao W, Hu W, Zhang S, Pei J, Guo A, Guo J, Zhang J, Zhang Z, Ye J, Ou W, Ma Y, Liu X, Tallon LJ, Galens K, Ott S, Huang J, Xue J, An F, Yao Q, Lu X, Fregene M, L�pez-Lavelle LAB, Wu J, You FM, Chen M, Hu S, Wu G, Zhong S, Ling P, Chen Y, Wang Q, Liu G, Liu B, Li K, Peng M. (2014) Cassava genome from a wild ancestor to cultivated varieties. Nature Communications 5:5110.
- Type:
Journal Articles
Status:
Awaiting Publication
Year Published:
2014
Citation:
1. Zhang MP, Rong Y, Lee M-K, Zhang Y, Stelly DM, Zhang H-B. (2014) Phylogenetic analysis of Gossypium L. using restriction fragment length polymorphism of repeated sequences. Mol Genet Genomics (accepted)
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2014
Citation:
Masor LL, Hays DB, Singh BB, Zhang H-B, Zhang MP. 2014. Molecular mapping of drought tolerance genes in cowpea (Vigna unguiculata L. Walp). 8th Annual Plant Breeding Coordinating Committee Meeting and 4th Annual National Association of Plant Breeders Meeting. August 5-8, 2014 in Minneapolis, MN.
|
Progress 01/01/13 to 09/30/13
Outputs
Target Audience: Plant breeders and researchers: Eight breeders and 18 researchers have requested for and used the DNA markers, BAC and BIBAC libraries and physical maps that we developed through this project in FY 2012/2013 for their research and breeding programs. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided? Three graduate students and two junior prefessionals have been trained through this project in 2013. How have the results been disseminated to communities of interest? The research results of this project were disseminated mainly through the follwoing three approaches: 1. The results have been presented at professional conferences in the field of this project; 2. The results have been published in professional peer-reviewed journals; and 3. The results have been made available and disseminated to the public and private researchers. The research results included not only scientific disoveries (such as the DNA "Jigsaw Puzzle" Structure Model) and new or advanced technologies (e.g., the high-throughput gene and QTL cloning systems, but also the resources and tools for advanced genetics research and breeding (e.g., BAC and BIBAC libraries, genome physical maps and DNA markers). What do you plan to do during the next reporting period to accomplish the goals? We plan to accomplish the following research goals during the next reporting period: 1. Disclose the novel high-throughput gene and QTL cloning system that we have developed through this research, or publish it in an peer-reviewed journal and disseminate to the public for enhanced agricultural and life sciences research; 2. Clone >1,000 genes controling cotton fiber yield and quality traits, maize grain yield and quality traits and chickpea winter hardiness; 3. Publish and file the 474 cotton fiber length genes, 1,253 maize grain yield genes and 606 chickpea vernalization genes for patents; 4. Decipher the molecular mechanisms of heterosis in maize, plant polyploidization in cotton and wheat, and crop domestication in soybean and chickpea; 5. Prepare and publish 2 - 3 research articles in the molecular basis of genetics, biology and breeding: The DNA "Jigsaw Puzzle" Structure Model; and 6. Accomplish the genotyping works of cotton and cowpea genetic mapping using the high-throughput RAD-seq technology.
Impacts
What was accomplished under these goals?
Outputs: The goals of this project are to advance the body of knowledge in crop genomics and genetics, develop revolutionary, readily usable gene/QTL cloning systems in crops, isolate and characterize genes and QTLs important to agriculture, and to generate molecular toolkits enabling enhanced crop genetic improvement and breeding. To these ends, we have worked in several aspects of molecular genetics, genomics, systems genomics and systems biology: [1] Development of genomic resources necessary for gene discovery - Large-insert BAC and BIBAC libraries are essential for advanced genomics, genetics and breeding research. We helped pioneer the theory and technology of high-molecular-weight recombinant DNA, and developed >200 BAC and BIBAC libraries for different species of economical importance. These libraries have provided resources and tools essential for accelaerated genomics, genetics and breeding research. [2] Genome physical mapping with BACs - It is the centerpiece of genomics research and crucial to development of the readily usable gene cloning systems. We helped pioneer the theory and technology of genome physical mapping with BACs and developed the BAC physical maps of indica rice, soybean, japonica rice, Arabidopsis, chicken, Ustilago maydis, Penicillium chrysogenum, Phytophthora sojae, chickpea, cotton, turkey, scallop and red algae. In 2013, we worked toward development of a roboust integrated physical/genetic map of Upland cotton and sequencing the Upland genome. So far, we have developed the first draft of the Upland cotton genome sequence. [3] Functional genomics - We helped pioneer Systems Genomics and Systems Biology in crop plants and developed a novel and high-throughput system of cloning genes and QTLs controlling important agronomic traits. Using the system, hunderds of genes controlling different traits can be cloned, the gene networks controlling the traits can be constructed and the molecular bases underlying the traits can be deciphered by a scientist within a few years. The gene and QTL cloning efficiency of the system is >1,000-fold higher than those widely used today. In 2013, we continued cloning and characterization of genes and QTLs controlling different traits of cotton fiber quality and yield, corn grain yield and quality, and chickpea vernalization and winter hardiness using the new gene/QTL cloning system. So far, we have cloned and characterized 474 genes controlling cotton fiber length, 1,253 genes controlling maize grain yield and 606 genes controlling chickpea vernalization. Moreover, we have also made significant progress in deciphering the molecular mechanisms of crop yield and quality (maize and cotton), plant heterosis (maize), plant polyploidization (wheat and cotton) and crop demostication (chickpea and soybean). [4] Re-establishing the molecular basis of genetics and biology - Genome research has raised a question: how DNA makes the abundance, diversity and complexity of living organisms. We previously established a novel DNA structure model named “Jigsaw Puzzel” structure (i.e., DNA biological structure) to explain these phenomena and experimentally tested two features of the structure model: the content variation of genome (“Jigsaw Puzzle” structure)-constituent fundemantal function element (FFE), and FFE array/re-array. In 2013, we wrote the manuscript and submitted for publication of the results from the experimental test of the third feature of the DNA structure model: FFE interaction and network, and further developed the model using maize, soybean, wheat and related species. One manuscript was published and two manuscripts were submitted for publication in this research area. Impacts: The impacts of this project on science and technology are huge and broad. The major achievements of this project obtained so far include, but are not limited to, [1] pioneered and developed the theory and technology of high-molecular-weight recombinant DNA; [2] pioneered and developed the theory, strategy and technology of genome physical mapping with BACs; [3] pioneered and developed the new theory, new strategy and new technology of high-throughput gene/QTL cloning and gene network construction controlling traits of interest, and deciphered the molecular basis of heterosis in maize; [4] discovered and established the DNA “Jigsaw Puzzel” structure model as the new molecular basis of genetics and biology; [5] helped pioneer Systsms Genomics and Systems Biology; [6] developed a largest collection of BAC and BIBAC libraries worldwide (>200 libraires); and [7] constructed the whole-genome physical maps for 12 species. The high-molecular-weight recombination DNA and genome physical mapping technologies have emerged the core genome technologies for and have been widely used in modern genomics, genetics and breeding research in both public and private domains worldwide. The BAC libraries and physical maps have been widely distributed and used as essential resources, tools and infrastruture in genomics, genetics and breeding research of crop plants, farm animals and human in discovery and isolation of genes and QTLs important to agriculture, determination of the position, structure, function and expression of every crop plant gene, targeted generation of DNA markers for agronomic genes and QTLs of importance for plant breeding and germplasm analysis, whole genome sequencing and assembly, and development of revolutionary and new means for high-yield, high-quality and high-efficiency crop breeding and production. The new concepts, new strategies and new technologies for high-throughput gene/QTL cloning and network construction will allow large-scale cloning of genes/QTLs controlling all major traits of agronomic importance rapidly and deciphering the molecular basis of many, if not all, of the traits and biological phenomena important to agriculture. These include, but are not limited to, crop yield, quality, abotic stress, disease resistance, efficiency of water, fertilizer and mineral uses, heterosis, polyploidization and domestication. Using these new technologies, we are working toward to cloning the genes of these traits in maize, cotton and chickpea. Hence, they will significantly contribute to the U.S. increased agricultural productivity, cleaner living environments and enhanced agricultural competitive ablity. The new DNA “Jigsaw Puzzel” structure model that we discovered and the new gene/QTL cloning system and research method that we developed through this project provide a novel theory, novel molecular basis of genetics and biology and novel research method for all living organisms; therefore, it will revolutionize our knowledge, concepts and strategies currently used and promote research and discoveries in all areas of biology, plant breeding, animal breeding and human medicine.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2013
Citation:
Qin J, Scheuring CF, Wei G, Zhi H, Zhang, MP, Huang JJ, Zhou X, Galbraith DW, Zhang H-B. 2013. A repertoire of genes differentially expressed in developing ear shoots between a superior hybrid and its parental inbreds in maize. Mol Genet Genomics 288:691-705.
- Type:
Journal Articles
Status:
Published
Year Published:
2013
Citation:
Zhai J, Wang Y, Sun C, Jiang S, Wang K, Zhang Y, Zhang H-B, Zhang MP. 2013. A plant-transformation-competent BIBAC library of ginseng (Panax ginseng C.A. Meyer) for functional genomics research and characterization of genes involved in ginsenoside biosynthesis. Molecular Breeding 31: 685-692.
- Type:
Journal Articles
Status:
Published
Year Published:
2013
Citation:
Lee M-K, Zhang Y, Zhang MP, Goebel M, Kim HJ, Triplett BA, Stelly DM, Zhang H-B. 2013. Construction of a plant-transformation-component BIBAC library and genome sequence analysis of polyploid Upland cotton (Gossypium hirsutum L.). BMC Genomics 14:208. doi:10.1186/1471-2164-14-208.
- Type:
Journal Articles
Status:
Published
Year Published:
2013
Citation:
Liu Y-H, Zhang MP, Huang JJ, Zhang H-B. 2013. DNA is structured as Jigsaw Puzzle in the genomes of Arabidopsis, rice and yeast. Genome (online and in press).
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2013
Citation:
Zhang MP, Wu C, Liu Y-H, Zhang Y, Lee M-K, Zhang H-B. 2013. Re-establishing the Molecular Basis of Genetics and Biology: The DNA Jigsaw Puzzle Structure Model. International Plant & Animal Genome Conference XXI. W764.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2013
Citation:
Zhang MP, Rong Y, Liu Y-H, Zhang Y, Zhang H-B. 2013. Molecular Mechanisms of Genome Variation and Evolution of Cotton and Related Species Revealed by Systems Genomics Analysis. International Plant & Animal Genome Conference XXI. P0452.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2013
Citation:
Su X, Qin J, Zhang MP, Zhang H-B. 2013. Significant Variation in Number of Genes in the NBS-encoding Gene Family among Inbred Lines and in a Segregating Population of Maize, Zea mays L. International Plant & Animal Genome Conference XXI. P0125.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2013
Citation:
Zhang Y, Zhang MP, Zhang Q, Liu Y-H, Xu SS, Zhang H-B. 2013. Molecular Mechanisms of Polyploid Plant Formation and Evolution Revealed by Systems Genomics Analysis. International Plant & Animal Genome Conference XXI. P0275.
|
Progress 01/01/12 to 12/31/12
Outputs
OUTPUTS: The goals of this project are to advance the body of knowledge in crop genomics and genetics, develop revolutionary, readily usable gene/QTL cloning systems in crops, isolate and characterize genes and QTLs important to agriculture, and to generate molecular toolkits enabling enhanced crop genetic improvement and breeding. To these ends, we have worked in several aspects of molecular genetics, genomics, systems genomics and systems biology: [1] Development of genomic resources necessary for gene discovery - Large-insert BAC and BIBAC libraries are essential for advanced genomics, genetics and breeding research. We helped pioneer the theory and technology of high-molecular-weight recombinant DNA, and developed >200 BAC and BIBAC libraries for different species of economical importance. These libraries have provided resources and tools essential for accelaerated genomics, genetics and breeding research. In 2012, we developed BIBAC libraries for sesame and ginseng, sequenced >10,000 cotton BIBAC ends and published the cotton BIBAC library. [2] Genome physical mapping with BACs - It is the centerpiece of genomics research and crucial to development of the readily usable gene cloning systems. We helped pioneer the theory and technology of genome physical mapping with BACs and developed the BAC physical maps of indica rice, soybean, japonica rice, Arabidopsis, chicken, Ustilago maydis, Penicillium chrysogenum, Phytophthora sojae, chickpea, cotton, turkey, scallop and red algae. In 2012, we published the Upland cotton physical map and worked toward development of a roboust integrated physical/genetic map of Upland cotton. [3] Functional genomics - We helped pioneer Systems Genomics and Systems Biology in crop plants and developed a novel and high-throughput system of cloning genes and QTLs controlling important agronomic traits. Using the system, hunderds of genes controlling different traits can be cloned, the gene networks controlling the traits can be constructed and the molecular bases underlying the traits can be deciphered by a scientist within a few years. The gene and QTL cloning efficiency of the system is >1,000-fold higher than those widely used today. In 2012, we continued cloning and characterization of genes and QTLs controlling different traits of cotton fiber quality and yield, and corn grain yield and quality using the new gene/QTL cloning system. [4] Re-establishing the molecular basis of genetics and biology - Genome research has raised a question: how DNA makes the abundance, diversity and complexity of living organisms. We previously established a novel DNA structure model named "Jigsaw Puzzel" structure (i.e., DNA biological structure) to explain these phenomena and experimentally tested two features of the structure model: the content variation of genome ("Jigsaw Puzzle" structure)-constituent fundemantal function element (FFE), and FFE array/re-array. In 2012, we accomplished the experimental test of the third feature of the DNA structure model: FFE interaction and network, and further developed the model using maize, wheat and related species. Three manuscripts in this area were prepared for publication. PARTICIPANTS: PD: Hongbin Zhang Personnel who worked in the project in the FY 2012: Yang Zhang (Assistant Research Scientist), Chantel Scheuring (Research Associate), Yun-Hua Liu (Graduate Student), Fisher Chang (Graduate Student) and Meiping Zhang (Associate Research Scientist). Collaborators: C. Wayne Smith, Professor of Cotton Genetics and Breeding, Texas A&M University David M. Stelly, Professor of Cotton Genetics, Texas A&M University Steve Hague, Associate Professor of Cotton Breeding, Texas A&M University Wenwei Xu, Associate Professor of Maize Genetics and Breeding, Texas A&M University Seth Murray, Assistant Professor of Maize Genetics and Breeding, Texas A&M University TARGET AUDIENCES: Not relevant to this project. PROJECT MODIFICATIONS: Not relevant to this project.
Impacts
The impacts of this project on science and technology are huge and broad. The major achievements of this project obtained so far include, but are not limited to, [1] pioneered and developed the theory and technology of high-molecular-weight recombinant DNA; [2] pioneered and developed the theory, strategy and technology of genome physical mapping with BACs; [3] pioneered and developed the new theory, new strategy and new technology of high-throughput gene/QTL cloning and gene network construction controlling traits of interest, and deciphered the molecular basis of heterosis in maize; [4] discovered and established the DNA "Jigsaw Puzzel" structure model as the new molecular basis of genetics and biology; [5] helped pioneer Systsms Genomics and Systems Biology; [6] developed a largest collection of BAC and BIBAC libraries worldwide (>200 libraires); and [7] constructed the whole-genome physical maps for 12 species. The high-molecular-weight recombination DNA and genome physical mapping technologies have emerged the core genome technologies for and have been widely used in modern genomics, genetics and breeding research in both public and private domains worldwide. The BAC libraries and physical maps have been widely distributed and used as essential resources, tools and infrastruture in genomics, genetics and breeding research of crop plants, farm animals and human in discovery and isolation of genes and QTLs important to agriculture, determination of the position, structure, function and expression of every crop plant gene, targeted generation of DNA markers for agronomic genes and QTLs of importance for plant breeding and germplasm analysis, whole genome sequencing and assembly, and development of revolutionary and new means for high-yield, high-quality and high-efficiency crop breeding and production. The new concepts, new strategies and new technologies for high-throughput gene/QTL cloning and network construction will allow large-scale cloning of genes/QTLs controlling all major traits of agronomic importance rapidly and deciphering the molecular basis of many, if not all, of the traits. These traits include, but are not limited to, crop yield, quality, abotic stress, disease resistance, and efficiency of water, fertilizer and mineral uses. Using these new technologies, we are working toward to cloning the genes of these traits in maize and cotton. Hence, they will significantly contribute to the U.S. increased agricultural productivity, cleaner living environments and enhanced agricultural competitive ablity. The new DNA "Jigsaw Puzzel" structure model that we discovered through this project provides a novel theory and novel molecular basis of genetics and biology of all living organisms; therefore, it will revolutionize our knowledge, concepts and strategies currently used and promote research and discoveries in all areas of biology, plant breeding, animal breeding and human medicine.
Publications
- Zhang, M.P., Zhang, Y., Huang, J.J., Lee, M.-K., Zhang, X.J., Stelly, D.M., and Zhang H.-B. (2012). Physical mapping of polyploid genomes: A BIBAC physical map of allotetraploid Upland cotton, PLoS ONE, 7(3): e33644.
- Zhang, M.P., Zhang, Y., Scheuring, C.F., Wu, C.-C., Dong, J.J., and Zhang, H.-B. (2012). Preparation of megabase-sized DNA from a variety of organisms using the nuclei method for advanced genomics research, Nature Protocols, 7:467-478.
- Zhang, H.-B., Scheuring, C.F., Zhang, M.P., Zhang, Y., Wu, C.-C., Dong, J.J., and Li, Y. (2012). Construction of BIBAC and BAC libraries from a variety of organisms for advanced genomics research, Nature Protocols, 7:479-499. McGee, R., Piaskowski, J., Vandemark, G., Zhang, H.-B., Abbo S., and Coyne, C. (2012). Screening for winter-hardiness in a cultivated chickpea/wild relative RIL population (abstract), ASA-CSSA-SSSA International Annual Meeting, Cincinnati, OH. October 21-24, 2012
- Kim, H.J., Triplett, B.A., Zhang, H.-B., Lee, M.-K., Hinchliffe, D.J., Li, P., and Fang, D.D. (2012). Characterization of cellulose synthase catalytic subunit genes involved in secondary wall biosynthesis in Gossypium hirsutum L. (abstract), The International Cotton Genome Initiative Research Conference, Raleigh, NC. October 9-13, 2012.
- Hulse, A.M., Hoegenauer, K., Wang, F., Stelly, D.M., Ashrafi, H., van Deynze, A., Zhang, H.-B., Saski, C., Patterson, A.H., Schmutz, J., Chen, Z.J., Udall, J.A., Yu, J.Z., and Jones, D.C. (2012). Localization of allotetraploid Gossypium SNPs using physical mapping resources (abstract), The International Cotton Genome Initiative Research Conference, Raleigh, NC. October 9-13, 2012.
- Zhang, M.P., Liu, Y.-H., Zhang, Y., and Zhang, H.-B. (2012). Re-establishing the molecular basis of genetics and biology: Copy number variation and correlation of genome-constituent element families in Gossypium L. (abstract), The International Cotton Genome Initiative Research Conference, Raleigh, NC. October 9-13, 2012.
- Liu, Y.-H., Zhang, M.P., Zhang, Y., Smith, C.W., Hague, S.S., and Zhang, H.-B. (2012). Toward cloning of all major genes significant for cotton fiber yield and quality, and deciphering of the molecular basis of cotton fiber yield and quality (abstract), The International Cotton Genome Initiative Research Conference, Raleigh, NC. October 9-13, 2012.
- Zhang, Y., Zhang, M.P., Liu, Y.-H., Smith, C.W., Hague, S.S., Stelly, D.M., and Zhang, H.-B. (2012). Toward development of robust integrated physical and genetic maps for individual chromosomes of upland cotton for accurately sequencing its genome (abstract), The International Cotton Genome Initiative Research Conference, Raleigh, NC. October 9-13, 2012.
- Rong, Y., Zhang, M.P., Lee, M.-K., Stelly, D.M., and Zhang, H.-B. (2012). Reconstruction of the phylogenetic tree for gossypium l. and inference on the genomic origins of the AD-genome species by genome-wide analysis (abstract), The International Cotton Genome Initiative Research Conference, Raleigh, NC. October 9-13, 2012.
- Zhang, Y., Li, X., Zhang, M.P., and Zhang, H.-B. (2012). Size variation, evolution and regulation of nucleotide-binding site (NBS)-encoding gene family in wheat and related species (abstract), International Plant & Animal Genome Conference XX. P300. . San Diego, CA. January 15-18, 2012.
- Zhang, M.P., Zhang, Y., Huang, J.J., Lee, M.-L., Zhang, X., Stelly, D.M., and Zhang, H.-B. (2012). Genome physical mapping of polyploids: Construction and characterization of a BIBAC physical map of cultivated tetraploid cotton, Gossypium hirsutum L. (abstract), International Plant & Animal Genome Conference XX. W432. . San Diego, CA. January 15-18, 2012.
- Zhang, M.P., Zhang, Y., Lee, M.-K., and Zhang, H.-B. (2012). A genome is a system: Interactions among the elements constituting the plant genomes (abstract), International Plant & Animal Genome Conference XX. W699. San Diego, CA. January 15-18, 2012.
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Progress 01/01/11 to 12/31/11
Outputs
OUTPUTS: The goals of this project are to develop revolutionary, readily usable gene cloning systems in crop plants, to isolate and characterize genes and QTLs important to agriculture, to generate molecular tools for efficient utilization of agronomic genes and QTLs in crop genetic improvement, and to advance the body of knowledge in genomics and genetics. To these ends, we have been working in several aspects of molecular genetics, genomcis and systems biology: [1] Development of genomic resources for gene discovery - Large-insert BAC and BIBAC libraries are essential for advanced genomics and genetics research. We helped pioneer the theory and technology of high-molecular-weight (HMW) recombinant DNA, and developed >200 BAC libraries for different species of economical importance, which have provided essential resources for accelerated genomics research and gene/QTL cloning. In 2011, we developed a BIBAC library for Bamboo (172,800 clones), completed the analysis of cotton and watermelon BIBAC libraries, published two protocol articles in Nature Protocols (Impact Factors = 8.449), and submitted a research article in the cotton BIBAC library for peer-reviewed publication. [2] Genome physical mapping with BACs - It is the centerpiece of genomics research and crucial to development of the readily usable gene cloning systems. We helped pioneer the theory and technology of genome physical mapping with BACs and developed the BAC physical maps of indica rice, soybean, japonica rice, Arabidopsis, chicken, Ustilago maydis, Penicillium chrysogenum, Phytophthora sojae, chickpea, cotton, turkey, scallop and red algae. In 2011, we published the comparative physical map of turkey with chicken, and prepared a research article for the cotton physical map (submitted). [3] Functional genomics - We are developing a large-scale high-throughput system of cloning genes and QTLs for agronomic traits in maize and cotton to translate functional genomics research results into enhanced crop genetic improvement. In 2011, we completed the field phentotypeing works of the cotton ELS RIL population and the maize population of heterosis study, and started the lab work on the two populations to clone the genes and QTLs contributing to the major agronomic traits of cotton and maize. [4] DNA structure - Genome sequencing and research have raised a question about how DNA makes the abundance, diversity and complexity of living organisms. We previously proposed a novel DNA structure model named "Jigsaw Puzzel" structure (i.e., DNA biological structure) to explain these phenomena, based on the comprehensive analysis of the genomes of Arabidopsis, rice and yeast. In 2011, we accomplished the research in the size variations of 49 families of genes, DNA transposable elements, retra-transposable elemments, simple sequence repeats and low complex repeats in 206 lines of Gossypium, Glycine and Oryza, discovered a novel molecular basis of genetic variation and prepared a research article for peer-reviewed journal (submitted). We have also prepared a research article in gene number variation, evolution and regulation of the 5S rRNA gene family (submitted). PARTICIPANTS: PDs: Hongbin Zhang Personnel who worked in the project in the FY 2011: Yang Zhang (Postdoc/Assistant Research Scientist), Chantel Scheuring (Research Associate), Yun-Hua Liu (Graduate Student), Fisher Chang (Graduate Student), and Meiping Zhang (Assistant/Associate Research Scientist). TARGET AUDIENCES: Nothing significant to report during this reporting period. PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.
Impacts
The impacts of this project on both sicience and technology are huge and broad. The major achievements of this project so far include, but are not limited to, [1] pioneered and developed the theory and technology of HMW recombinant DNA; [2] pioneered and developed the theory, strategy and technology of genome physical mapping with BACs, [3] pioneered and developed the new theory, new strategy and new technology of large-scale gene identification and gene network construction controlling traits of interest, and deciphered the molecular basis of heterosis in maize; [4] discovered and tested the DNA "Jigsaw Puzzel" structure model as the molecular basis of biology, [5] developed a largest collection of BAC and BIBAC libraries worldwide (>200 libraires), and [6] constructed the whole-genome physical maps of 12 species. The HMW recombination DNA and genome physical mapping technologies have emerged the core ones for and been widely used in modern genomics research in both public and private domains worldwide. The BAC libraries and physical maps have been widely used as essential resources, tools and infrastruture in genomics research of crop plants, farm animals and human in discovery and isolation of genes and QTLs important to agriculture, determination of the position, structure, function and expression of every crop plant gene, targeted generation of DNA markers for agronomic genes and QTLs of importance for plant breeding and germplasm diagnostics, whole genome sequencing and development of revolutionary and new means for high-yield, high-quality and high-efficiency crop breeding and production. The new concepts, new strategies and new technologies for large-scale gene identification and network construction will allow large-scale cloning genes controlling all major traits of agronomic importance rapidly and deciphering the molecular basis of many, if not all, of the traits. These traits include, but are not limited to, yield, quality, stress and disease resistances, and efficiency of water, fertilizer and mineral uses. Using these new technologies, we are working toward to cloning the genes of these traits in maize and cotton. Hence, they will significantly contribute to the U.S. increased agricultural productivity, cleaner living environments and enhanced agricultural competitive ablity. The new DNA "Jigsaw Puzzel" structure model that we discovered through this project will provide novel theory and basis of biology of all living organisms; therefore, they will revolutionize our knowledge, concepts and strategies currently used in all areas of biological research, plant breeding, animal breeding and human medicine.
Publications
- Zhang, M.P., Lee, M.-K., Rong, Y., Liu, Y.-H., Zhang, Y., Wu, Y.-H., Zhang, H.-B. 2011. Copy Number Variation, Evolution and Regulation of Transposable Element Families in Plants. International Plant & Animal Genome Conference XIX. W584.
- Kim, H.J., Triplett, B.A., Zhang, H.-B., Lee, M.-K., Hinchliffe, D.J., Li, P., Fang, D.D. (2011) Cloning and characterization of homoeologous cellulose synthase catalytic subunit 2 genes from allotetraploid Gossypium hirsutum. Gene 494:181-189.
- Zhang, X., Zhao, C., Huang, C., Duan, H., Huan, P., Liu, C., Zhang. X., Zhang, Y., Li, F., Zhang, H.-B., Xiang, J. (2011) A BAC-based physical map of Zhikong scallop (Chlamys farreri Jones et Preston). PLoS ONE 6: e27612.
- Zhang, Y., Zhang, X., OHare, T.H., Payne, W.S., Dong, J.J., Scheuring, C.F., Zhang, M.P., Huang, J.J., Delany, M., Zhang, H.-B., Dodgson, J.B. (2011) A comparative physical map reveals the pattern of chromosomal evolution between the turkey (Meleagris gallopavo) and chicken (Gallus gallus) genomes. BMC Genomics 12:447.
- Zhang, M.P., Chang, Y.-L., Stelly, D.M., Zhang, H.-B. 2011. BIBAC as a Tool for Large-scale Functional Analysis of Genomes. International Plant & Animal Genome Conference XIX. W355.
- Zhang, Y., Lee, M.-K., Zhang, X., Payne, B., Park. H.J., Dong, J.J., Scheuring, C., Zhang, M.P., Delany, M.E., Dodgson, J., Zhang, H.-B. 2011. A BAC-based Integrated Physical, Genetic and Comparative Map of the Turkey, Chicken and Human Genomes. International Plant & Animal Genome Conference XIX. W470.
- Abbo, S., Sherman, A., Zhang, H.-B. 2011. The potential for introgression of adaptive traits in chickpea. International Plant & Animal Genome Conference XIX. W283.
- Zhang, X., Zhao, C., Huang, C., Duan, H., Huan, P., Liu, C., Li, F., Zhang, H.-B., Xiang, J. 2011. A first-generation BAC-based physical map of Zhikong scallop (Chlamys ferreri Jones et Preston). International Plant & Animal Genome Conference XIX. W039.
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Progress 01/01/10 to 12/31/10
Outputs
OUTPUTS: The goals of this project are to develop revolutionary, readily usable gene cloning systems in crop plants, to isolate and characterize genes and QTLs important to agriculture, to generate molecular tools for efficient utilization of agronomic genes and QTLs in crop genetic improvement, and to advance the body of knowledge in genomics and genetics. To these ends, we have been working in several aspects of genomcis and systems biology: [1] Development of genomic resources for gene discovery - Large-insert BAC and BIBAC libraries are essential for advanced genomics and genetics research. We helped pioneer the theory and technology of megabase-sized recombinant DNA. In 2010, we developed a BIBAC library for Populus euphratica Oliv. Together, we have developed a total of >200 BAC libraries through the project, which have provided essential resources for accelerated genomics research. [2] Genome physical mapping with BACs - It is the centerpiece of genomics research and crucial to development of the readily usable gene cloning systems. We helped pioneer the theory and technology of genome physical mapping with BACs and constructed the BAC physical maps of indica rice, soybean, japonica rice, Arabidopsis, chicken, Ustilago maydis, Penicillium chrysogenum, Phytophthora sojae, chickpea, and red algae. In 2010, we published the physical map of chickpea and the draft genome sequence of turkey, initiated the preparation of a research article for the cotton physical map, and completed the comparative map among turkey, chicken and human. [3] Functional genomics - We are developing genechip-assisted gene cloning and breeding systems in maize and cotton to translate functional genomics research results into enhanced crop genetic improvement. We previously identified 748 genes significant to heterosis in maize and >2,000 genes important to cotton fiber yield and quality. In 2010, we prepared a research article from the data of maize heterosis and submitted for publication. Moreover, we have completed development of new concepts, new strategies and new technologies for large-scale gene identification and network construction, and used them to have identified 39 genes controlling maize grain yield traits and re-examined the molecular basis of maize heterosis. Finally, we have augmented the cotton ELS RIL population and phenotyped their fiber quality and yield traits through a field trial. [4] DNA structure - Genome sequencing and research have raised a question about how DNA makes the abundance, diversity and complexity of living organisms. We previously proposed a novel DNA structure model named "Jigsaw Puzzel" structure to explain these phenomena, based on the comprehensive analysis of the genomes of Arabidopsis, rice and yeast. In 2010, we continued to develop and test the model using Oryza, Gossypium, Glycine, Triticum and Zea. We published the results in the gene numner variation, evolution and regulation of the NBS-LRR and receptor-like kinase gene families in Gossypium, Oryza and Glycine, and completed the study of gene number variation, evolution and regulation of the 5S rRNA gene family and five transposable element families in the genera. PARTICIPANTS: PIs/PDs: Hongbin Zhang Personnel who worked in the project in the FY 2010: Yang Zhang (postdoc), Chantel Scheuring (research associate), James Huang (graduate student), Yun-Hua Liu (graduate student), Hui Zhi (graduate student), Jun Qin (visiting scientist), and Meiping Zhang (visiting professor). TARGET AUDIENCES: Nothing significant to report during this reporting period. PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.
Impacts
The impacts of this project on both sicience and technology are huge and broad. The major achievements of this project so far include, but are not limited to, [1] pioneered and developed the theory and technology of megbase-sized recombinant DNA; [2] pioneered and developed the theory, strategy and technology of genome physical mapping with BACs, [3] pioneered and developed the new theory, new strategy and new technology of large-scale gene identification and gene network construction controlling traits of interest, and deciphered the molecular basis of heterosis in maize; [4] discovered and tested the DNA "Jigsaw Puzzel" structure model as the molecular basis of biology, [5] developed a largest collection of BAC and BIBAC libraries worldwide (>200 libraires), and [6] constructed the whole-genome physical maps of 12 species. The megabase-sized recombination DNA and genome physical mapping technologies have emerged the major technologies for and been widely used in modern genomics research in both public and private domains worldwide. The BAC libraries and physical maps have been widely used as essential resources, tools and infrastruture in genomics research of crop plants, farm animals and human in discovery and isolation of genes and quantitative trait loci important to agriculture, determination of the position, structure, function and expression of every crop plant gene, targeted generation of DNA markers for agronomic genes and QTLs of importance for plant breeding and germplasm diagnostics, whole genome sequencing and development of revolutionary and new means for high-yield, high-quality and high-efficiency crop breeding and production. The new concepts, new strategies and new technologies for large-scale gene identification and network construction will allow large-scale cloning genes controlling traits of agronomic importance rapidly and deciphering the molecular basis of many, if not all, of the traits. These traits include, but are not limited to, yield, quality, stress and disease resistances, and efficiency of water, fertilizer and mineral uses. Hence, they will significantly contribute to the U.S. increased agricultural productivity, cleaner living environments and enhanced agricultural competitive ablity. The new DNA "Jigsaw Puzzel" structure model that we discovered through this project will provide novel theory and basis of biology of all living organisms; therefore, they will revolutionize our knowledge, concepts and strategies currently used in all areas of biological research, plant and animal breeding, and human medicine.
Publications
- Shao C-W, Chen S-L, Scheuring CF, Xu J-Y, Sha Z-X, Dong X-L, Zhang H-B. 2010. Construction of two BAC libraries of half-smooth tongue sole Cynoglossus semilaevis and isolation of clones containing candidate sex-determination genes. Marine Biotechnology 12:558-568.
- Budak H, Zhang H-B, Gupta PK Chalhoub B, James A, Liu C (eds.). 2009. Wet Laboratory Tools Widely Used in Plant Genomics. International Journal of Plant Genomics, Vol. 2009 (special issue) http://www.hindawi.com/journals/ijpg/contents.html
- Liu Y-H, Zhang M, Wu C, Huang JJ, Zhang H-B. 2010. DNA is structured as Jigsaw Puzzle. Plant & Animal Genomes XVIII Conference. P893.
- Zhang H-B, Huang JJ, Zhang M, Liu Y-H, Scheuring C, Stelly DM, Smith CW, Hague S. 2010. Towards a super-dense integrated map of the cotton genome. Plant & Animal Genomes XVIII Conference. P673.
- Zhang MP, Wu Y-H, Lee M-K, Liu Y-H, Rong Y, Santos TS, Wu C, Xie F, Nelson RL, Zhang H-B. 2010. A new source of genetic variation: intraspecific variation and evolution of gene family sizes in plants. Plant & Animal Genomes XVIII Conference. P227.
- Dalloul RA, Long JA, Zimin AV, Reed KM, Aslam L, Beal K, Blomberg LA, Burt DW, Crasta O, Crooijmans RPMA, Cooper K, Coulombe RA, De S, Delany ME, Dodgson JB, Dong JJ, Evans C, Flicek P, Florea L, Folkerts O, Groenen MAM, Harkins TT, Herrero J, Hoffmann S, Megens H-J, Jiang A, de Jong P, Kaiser P, Kim H, Kim K-W, Kim S, Langenberger D, Lee M-K, Lee T, Mane S, Marcais G, Marz M, McElroy AP, Modise T, Nefedov M, Notredame C, Paton IR, Payne WS, Pertea G, Prickett D, Puiu D, Qioa D, Raineri E, Salzberg SL, Schatz MC, Scheuring C, Schmidt CJ, Schroeder S, Smith EJ, Smith J, Sonstegard TS, Stadler PF, Tafer H, Tu Z, Van Tassell CP, Vilella AJ, Williams K, Yorke JA, Zhang L, Zhang H-B, Zhang X, Zhang Y, Reed KM. 2010. Multi-platform next generation sequencing of the domestic turkey (Meleagris gallopavo): Genome assembly and analysis. PLoS Biology 8:e1000475.
- Zhang MP, Wu Y-H, Lee M-K, Liu Y-H, Rong Y, Santos FS, Wu C-C, Xie F, Nelson RL, Zhang H-B. 2010. Numbers of genes in the NBS and RLK families vary by more than four-fold within a plant species and are regulated by multiple factors. Nucleic Acids Research 38:6513-6525.
- Zhang X, Scheuring CF, Zhang MP, Dong JJ, Zhang Y, Huang JJ, Lee M-K, Abbo S, Sherman A, Shtienberg D, Chen W, Muehlbauer F, Zhang H-B. 2010. A BAC/BIBAC-based physical map of chickpea, Cicer arietinum L. BMC Genomics 11:501. doi:10.1186/1471-2164-11-501.
- Xiang J, Li F, Zhang X, Wang B, Jiang H, Zhang L, Zhang Y, Zhang H-B. 2010. Some advances of omics studies in shrimp of China. Plant & Animal Genomes XVIII Conference. W054.
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Progress 01/01/09 to 12/31/09
Outputs
OUTPUTS: The goals of this project are to develop revolutionary, readily usable gene cloning systems in crop plants, to isolate and characterize genes and QTLs important to agriculture, to generate molecular tools for efficient utilization of agronomic genes and QTLs in crop genetic improvement, and to advance the body of knowledge in genomics and genetics. To these ends, we have been working in several aspects: [1] Development of genomic resources for gene discovery - Large-insert BAC and BIBAC libraries are essential for advanced genomics and genetics research. We helped pioneer the theory and technology of megabase-sized recombinant DNA. In 2009, we developed BAC/BIBAC libraries for Jatropha and ginseng. These libraries, along with >200 BAC libraries previously developed through the project, have provided essential resources for accelerated genomics research. [2] Genome physical mapping with BACs - It is the centerpiece of genomics research and crucial to development of the readily usable gene cloning systems. We helped pioneer the theory and technology of genome physical mapping with BACs and constructed the BAC physical maps of indica rice, soybean, japonica rice, Arabidopsis, chicken, Ustilago maydis, Penicillium chrysogenum, Phytophthora sojae and red algae. In 2009, we completed the physical maps of chickpea and cotton, and continued construction of the turkey physical map. [3] Functional genomics - We are developing array-assisted gene cloning and breeding systems in maize and cotton to translate functional genomics research results into enhanced crop genetic improvement. We previously identified 761 genes significant to heterosis in maize and >2,000 genes important to cotton fiber yield and quality. In 2009, we analyzed the data of maize heterosis and prepared a manuscript for publication. [4] Comparative genomics - Understanding of genome and its evolution is important not only for functional genomics research, but also for plant breeding. We are studying plant genome organization and evolution with integrated tools using Oryza, Gossypium and Glycine. We previously studied variation and evolution of the NBS-LRR and receptor-like kinase gene families in Gossypium, Oryza and Glycine. In 2009, we analyzed the data and prepared manuscripts for publication. [5] Isolation of agronomic genes - Our above research has allowed efficient cloning and analyzing genes of agronomic importance known only by phenotype. In 2009, we continued toward cloning of the genes for root-knot nematode resistance in cotton, Ascochyta blight resistance in chickpea, and everblooming (evb) in rose. We increased the RIL seeds for cotton root-knot nematode resistance and identified BAC/BIBAC contigs containing two QTLs for chickpea Ascochyta blight resistance and one QTL for days to first flower. [6] DNA structure - Genome sequencing and research have raised a question about how DNA makes the abundance, diversity and complexity of living organisms. We previously proposed a novel DNA structure model named "Jigsaw Puzzel" structure to explain these phenomena. In 2009, we further tested the model using rice and yeast, and prepared a research article for publication. PARTICIPANTS: PIs/PDs: Hongbin Zhang Personnel who worked in the project in the FY 2009: Yang Zhang (postdoc), Chantel Scheuring (research associate), James Huang (graduate student), Yun-Hua Liu (graduate student), Yen-Hsuan Wu (graduate student), Hui Zhi (graduate student),Jun Qin (visiting scientist), Xingpu Li (visiting scientist), and Meiping Zhang (visiting professor). TARGET AUDIENCES: Nothing significant to report during this reporting period. PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.
Impacts
The impacts of this project on both sicience and technology are huge and broad. The major achievements of this project so far include, but are not limited to, [1] pioneered and developed the theory and technology of megbase-sized recombinant DNA, [2] pioneered and developed the theory, technology and strategy of genome physical mapping with BACs, [3] discovered and tested the DNA "Jigsaw Puzzel" structure model, [4] developed one of the three largest collections of BAC and BIBAC libraries worldwide (>200 libraires), and [5] constructed the whole-genome physical maps of 12 species. These megabase-sized recombination DNA and genome physical mapping technologies have emerged the major technologies of choice for and been widely used in modern genomics research in both public and private domains worldwide. The BAC libraries and physical maps have been widely used as essential resources, tools and infrastruture in genomics research of crop plants, farm animals and humans in discovery and isolation of genes and quantitative trait loci important to agriculture, determination of the position, structure, function and expression of every crop plant gene, targeted generation of DNA markers for agronomic genes and QTLs of importance for plant breeding and germplasm diagnostics, whole genome sequencing and development of revolutionary and new means for high-yield, high-quality and high-efficiency crop breeding and production. Using these tools, we are analyzing the genes involved in several biological processes extremely important to agriculture, such as heterosis, fiber development, biotic stress and plant flowering. Isolation of the genes and understaunding of the processes will greatly promote crop genetic improvement, thus contributing to the U.S. increased agricultural productivity, cleaner living environments and enhanced agricultural competitive ablity. The new DNA "Jigsaw Puzzel" structure model and its evolutionary mechanisms we discovered through this project will provide novel theory and basis of genetics and evolution of all living organisms; therefore, they will revolutionize our knowledge, concepts and strategies currently used in all areas of biological research, plant and animal breeding, and human medicine.
Publications
- Yasukochi Y, Tanaka-Okuyama M, Shibata F, Yoshido A, Marec F, Wu C, Zhang H-B, Goldsmith MR, Sahara K. 2009. Extensive conserved synteny of genes between the karyotypes of Manduca sexta and Bombyx mori revealed by BAC-FISH mapping. PLoS ONE 4:e7465.
- Larson SR, Scheuring C, Kaur P, Cliften PF, Mott IW, Bushman BS, Dong JJ, Zhang Y, Zhang X, Kiani M, Wu Y-H, Liu Y-H, Zhang H-B, Chatterton NJ, Wang R R-C. 2009. BAC library development for allotetraploid Leymus (Triticeae) wildryes enables comparative genetic analysis of lax-barrenstalk1 orthogene sequences and growth habit QTLs. Plant Science 177:427-438.
- Zhang H-B, Liu Y-H, Wu C, Huang JJ, Wang S. 2009. A new DNA Jigsaw Puzzle structure model. Plant & Animal Genome XVII Conference. W218.
- Zhang H-B, Chang Y-L. 2009. BIBAC as a tool for large-scale functional analysis of genomes. Plant & Animal Genome XVII Conference. W299.
- Zhang X, Scheuring C, Huang JJ, Lee M-K, Zhang Y, Abbo S, Muehlbauer F, Sherman A, Shtienberg D, Chen W, Zhang H-B. 2009. A first generation BAC/BIBAC-based integrated physical and genetic map of chickpea (Cicer arietinum L.). Plant & Animal Genome XVII Conference. Cool Season Legumes Workshop.
- Lee M-K, Zhang X, Zhang Y, Payne B, Dong JJ, Park HJ, Scheuring C, Delany ME, Dodgson J, Zhang H-B. 2009. Toward a robust BAC-based physical and comparative map of the turkey genome. Plant & Animal Genome XVII Conference. P520.
- Zhang M, Sun C, Wang Z, Zhang H-B. 2009. Toward comprehensive understanding of the ginseng genome: Construction and characterization of a plant-transformation-competent BIBAC library of Jilin ginseng. Plant & Animal Genome XVII Conference. P053.
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Progress 01/01/08 to 12/31/08
Outputs
OUTPUTS: The goals of this project are to develop revolutionary, readily usable gene cloning systems in crop plants, to isolate and characterize genes and QTLs important to agriculture, to generate molecular tools for efficient utilization of agronomic genes and QTLs in crop genetic improvement, and to advance the body of knowledge in genomics and genetics. To these ends, we have been working in several aspects. 1. Development of genomic resources for gene discovery - Large-insert BAC and BIBAC libraries are essential for advanced genomics and genetics research. We helped pioneer the theory and technology of the BAC and BIBAC library construiction. In 2008, we developed BAC/BIBAC libraries for chickpea, watermelon, banana turkey and shrimp. These libraries, along with the nearly 200 BAC libraries we previously developed through the project, have provided essential resources for accelerated genomics research. 2. Genome physical mapping with BACs - Genome physical mapping is the centerpiece of genomics research and crucial for development of the readily usable gene cloning systems. We helped pioneer the theory, technology and strategy of genome physical mapping with BACs and constructed the BAC physical maps of indica rice, soybean, japonica rice, Arabidopsis, chicken, Ustilago maydis, Penicillium chrysogenum, Phytophthora sojae and red algae. In 2008, we continued the construction of the physical maps of turkey, cotton and chickpea. The first-generation physical maps have been generated for the species. 3. Functional genomics - Development of the BAC libraries and physical maps has promoted the research of functional genomics. We are developing array-assisted gene cloning and breeding systems in maize and cotton to translate functional genomics research results into enhanced crop genetic improvement. We previously identified over 2100 genes significant to heterosis in maize and over 4,000 genes important to cotton fiber yield and quality. In 2008, we analyzed the data and prepared manuscripts for publication. 4. Comparative genomics - Understanding of genome and its evolution is important not only for functional genomics research, but also for plant breeding. We are studying plant genome organization and evolution with integrated genomics tools using Oryza, Gossypium and Glycine as materials. We previously studied evolution of the NBS-LRR-encoding gene family in Gossypium. Oryza and Glycine. In 2008, we analyzed the data and prepared manuscripts for publication. 5. Isolation of agronomic genes - Our above research has allowed efficient tagging, cloning and analyzing genes of agronomic importance known only by phenotype. In 2008, we continued toward cloning of the genes for root-knot nematode resistance in cotton, Ascochyta blight resistance in chickpea, and everblooming (evb) in rose. 6. DNA structure - Genome sequencing and research have raised a question about how DNA makes the abundance, diversity and complexity of living organisms. We previously proposed a novel DNA structure model named linear "Jigsaw Puzzel" structure to explain these phenomena. In 2008, we further tested the model using rice and yeast. PARTICIPANTS: PIs/PDs: Hongbin Zhang Personnel who worked in the project in the FY 2008: Xiaojun Zhang (postdoc), Yang Zhang (postdoc), Chantel Scheuring (research associate), James Huang (graduate student), Yun-Hua Liu (graduate student), Yen-Hsuan Wu (graduate student), and Meiping Zhang (visiting professor) TARGET AUDIENCES: Not relevant to this project. PROJECT MODIFICATIONS: Not relevant to this project.
Impacts
The impacts of this project on both sicience and technology are huge and broad. The major achievements of this project so far include, but not limited to, [1] pioneering and development of the theory and technology of megbase-size recombinant DNA, [2] pioneering and development of the theory, technology and strategy of genome physical mapping with BACs, [3] discovery and test of the novel DNA "Jigsaw Puzzel" structure model, [4] development of one of the three largest collections of BAC and BIBAC libraries worldwide (~200 libraires), and [5] construction of most (12 physical maps) of whole-genome physical maps available in the world. These megabase-size recombination DNA and genome physical mapping technologies have emerged the major technologies of choice for and been widely used in modern genomics research in both public and private domains worldwide. The BAC libraries and physical maps have been widely used as essential resources, tools and infrastruture in genomics research of crop plants, farm animals and humans in discovery and isolation of genes and quantitative trait loci important to agriculture, determination of the position, structure, function and expression of every crop plant gene, targeted generation of DNA markers for agronomic genes and QTLs of importance for plant breeding and germplasm diagnostics, and development of revolutionary and new means for high-yield, high-quality and high-efficiency crop breeding and production. Using these tools, we are analyzing the genes involved in several biological processes extremely important to agriculture, such as heterosis, fiber development, biotic stress and plant flowering. Isolation of the genes and understaunding of the processes will greatly promote crop genetic improvement, thus contributing to the U.S. increased agricultural productivity, cleaner living environments and enhanced agricultural competitive ablity. The new DNA "Jigsaw Puzzel" structure model and its evolutionary mechanisms we discovered through this project will provide novel theory and basis of genetics and evolution of all living organisms; therefore, they will revolutionize our knowledge, concepts and strategies currently used in all areas of biological research, plant and animal breeding, and human medicine.
Publications
- Zhang Y, Zhang X, Scheuring CF, Zhang H-B, Li F, Xiang J. 2008. Construction of bacterial artificial chromosome libraries for Zhikong Scallop Chlamys farreri. Chinese J. Oceanology and Limnology 26:215-218.
- Zhang H-B, Scheuring CF, Dong J, Wu C, Zhang M, Zhang X, Zhang Y. 2008. Handbook of Megabase-sized Recombinant DNA Technology: Construction and Manipulation of Bacteria-based Large-insert DNA Libraries. Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, China
- Zhang MP, Li Y, Zhang H-B. 2008. Isolation of megabase-sized DNA fragments from plants. In: Handbook of Nucleic Acid Purification. D. Liu (ed.). Taylor & Francis Group, LLC, Florida, USA, pp. 513-524.
- Lee M-K, Payne B, Dong J, Park H-J, Zhang X, Dodgson, Zhang H-B. 2008. First-generation physical and comparative map of the turkey genome constructed by BAC fingerprint analysis with capillary electrophoresis. Plant & Animal Genome XVI Conference. W284.
- Goebel MR, Alabady MS, Dabney AR, Smith CW, Wilkins TA, Zhang H-B. 2008. Comparative analysis of gene expression in developing fibers between Upland and Sea Island cottons. Plant & Animal Genome XVI Conference. W223
- Zhang X, Scheuring, Huang J, Lee M-K, Abbo S, Meuhlbauer, Sherman A, Shtienberg D, Chen W, Zhang H-B. 2008. Toward a BAC/BIBAC-based integrated physical and genetic map of chickpea. Plant & Animal Genome XVI Conference. P387
- Zhang Y, Zhang X, Scheuring CF, Zhang H-B, Huan P, Li F, Xiang J. 2008. Construction and characterization of two bacterial artificial chromosome libraries of Zhikong Scallop, Chlamys farreri Jones et Preston, and identification of BAC clones containing the genes involved in its innate immune system. Marine Biotechnology 10:358-365.
- Zhang MP, Wu Y-H, Zhang H-B. 2008. New mechanisms of plant genome evolution revealed in genera Oryza and Glycine. Plant & Animal Genome XVI Conference. P229
- Rajesh PN, Avcioglu B, Nayak S, Winter P, Varshney R, McPhee K, Zhang H-B, Meuhlbauer F, Chen W. 2008. Integration of additional molecular markers and genetic analysis of Ascochyta blight resistance in chickpea. Plant & Animal Genome XVI Conference. P386
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Progress 01/01/07 to 12/31/07
Outputs
OUTPUTS: The goals of this project are to develop revolutionary, readily usable gene cloning systems in crop plants, to isolate and characterize genes and QTLs important to agriculture, to generate molecular tools for efficient utilization of agronomic genes and QTLs in crop genetic improvement, and to advance the body of knowledge in genomics and genetics. To these ends, we have been working in several aspects. 1. Development of genomic resources for gene discovery - Large-insert BAC and BIBAC libraries are essential for advanced genomics and genetics research. We helped pioneer the theory and technology of the BAC and BIBAC library construiction. In 2007, we developed BAC libraries for Phytophthora sojae and scallop. These libraries, along with the nearly 200 BAC libraries of different species previously developed through the project, have provided essential resources for accelerated genomics research. 2. Genome physical mapping with BACs - Genome physical mapping is the
centerpiece of genomics research and crucial for development of the readily usable gene cloning systems. We helped pioneer the theory, technology and strategy of genome physical mapping with BACs and constructed the BAC physical maps of indica rice, soybean, japonica rice, Arabidopsis, chicken, Ustilago maydis, Penicillium chrysogenum, Phytophthora sojae and red algae. In 2007, we continued the construction of the comparative physical map of turkey-chicken and the physical map of cotton and worked toward development of a physical map of chickpea. 3. Functional genomics - Development of the BAC libraries and physical maps has promoted the research of functional genomics. We are developing array-assisted gene cloning and breeding systems in maize and cotton to translate functional genomics research results into enhanced crop genetic improvement. We previously identified over 2100 genes significant to heterosis in maize. In 2007, we identified over 4,000 genes important to cotton fiber
yield and quality. 4. Comparative genomics - Understanding of genome and its evolution is important not only for functional genomics research, but also for plant breeding. We are studying plant genome organization and evolution with integrated genomics tools using Oryza, Gossypium and Glycine as materials. We previously studied evolution of the NBS-LRR-encoding gene family in Gossypium. In 2007, we extended this study in Oryza and Glycine. 5. Isolation of agronomic genes - Our above research has allowed efficient tagging, cloning and analyzing genes of agronomic importance known only by phenotype. In 2007, we continued toward cloning of the genes for root-knot nematode resistance in cotton, Ascochyta blight resistance in chickpea, and everblooming (evb) in rose. 6. DNA structure - Genome sequencing and research have raised a question about how DNA makes the abundance, diversity and complexity of living organisms. In 2000, we proposed a novel DNA structure model named linear "Jigsaw
Puzzel" structure to explain these phenomena. In 2006, we completed the test of the novel DNA "Jigsaw Puzzel" structure model. In 2007, we extended this research to rice and yeast to further test the model.
PARTICIPANTS: PIs/PDs: Hongbin Zhang Personnel who worked in the project in the FY 2007: Mi-Kyung Lee (assistant research scientist), Jenifer J. Dong (research assistant),(Xiaojun Zhang (postdoc), Chantel Scheuring (research associate), Mark Goebel (graduate student), James Huang (graduate student), Yun-Hua Liu (graduate student), Yen-Hsuan Wu (graduate student), Meiping Zhang (visiting professor) and Yang Zhang (visiting student)
Impacts
The impacts of this project on both sicience and technology are huge and broad. The major achievements of this project so far include, but not limited to, [1] pioneering and development of the theory and technology of megbase-size recombinant DNA, [2] pioneering and development of the theory, technology and strategy of genome physical mapping with BACs, [3] discovery and test of the novel DNA "Jigsaw Puzzel" structure model, [4] development of one of the three largest collections of BAC and BIBAC libraries worldwide (~200 libraires), and [5] construction of most (9 physical maps) of whole-genome physical maps available in the world. These megabase-size recombination DNA and genome physical mapping technologies have emerged the major technologies of choice for and been widely used in modern genomics research in both public and private domains worldwide. The BAC libraries and physical maps have been widely used as essential resources, tools and infrastruture in genomics
research of crop plants, farm animals and humans in discovery and isolation of genes and quantitative trait loci important to agriculture, determination of the position, structure, function and expression of every crop plant gene, targeted generation of DNA markers for agronomic genes and QTLs of importance for plant breeding and germplasm diagnostics, and development of revolutionary and new means for high-yield, high-quality and high-efficiency crop breeding and production. Using these tools, we are analyzing the genes involved in several biological processes extremely important to agriculture, such as heterosis, fiber development, biotic stress and plant flowering. Isolation of the genes and understaunding of the processes will greatly promote crop genetic improvement, thus contributing to the U.S. increased agricultural productivity, cleaner living environments and enhanced agricultural competitive ablity. The new DNA "Jigsaw Puzzel" structure model and its evolutionary mechanisms
we discovered through this project will provide novel theory and basis of genetics and evolution of all living organisms; therefore, they will revolutionize our knowledge, concepts and strategies currently used in all areas of biological research, plant and animal breeding, and human medicine.
Publications
- Zhang H-B. 2007. Map-based cloning of genes and quantitative trait loci. In: Principles and Practices of Plant Genomics, Vol.: Genome Mapping. C. Kole and AG Abbott (eds.). Science Publishers, New Hampshire, USA. pp. 229-267.
- Zhang H-B, Lee M-K, Scheuring C, Rong Y, Goebel M, Wu Y-H, Zhang L, Stelly DM, Smith CW. 2007. Toward comprehensive understanding of the cotton genome in structure, organization, function and evolution. Proceedings of the World Cotton Research Conference-4, September 10 -14, Lubbock, Texas, USA.
- Goebel M, Alabady M, A Dabney A, Smith CW, Wilkins TA, Zhang H-B. 2007. Comaprative analysis of gene expression in developing fibers between Upland and Sea Island cottons. The World Cotton Research Conference-4, 10-14 September, 2007, Lubbock, Texas, USA.
- Rong Y, Lee M-K, Percival AE, Stelly DM, Zhang H-B. 2007. Inferences on phylogeny and origin of polyploidy Gossypium genomes from nuclear repetitive DNA sequence variation. The World Cotton Research Conference-4, 10-14 September, 2007, Lubbock, Texas, USA.
- Wu Y-H, Lee M-K, Zhang H-B. 2007. Impacts of domestication, breeding and polyploidization on plant genome evolution revealed in Gossypium: The NBS-LRR-encoding gene family. The World Cotton Research Conference-4, 10-14 September, 2007, Lubbock, Texas, USA.
- Lee M-K, Scheuring C, He L, Goebel M, Kim HJ, Triplett B, Zhang H-B. 2007. BAC and BIBAC library resources of upland cotton for genome analysis, and gene and QTL cloning and characterization in cottons. The World Cotton Research Conference-4, 10-14 September, 2007, Lubbock, Texas, USA.
- Zhang H-B. 2007. A novel DNA structure model providing an explanation for the abundance, diversity and complexity of living organisms. The 49th Annual Maize Genetics Conference, 22-25 March 2007, St. Charles, Illinois. P127.
- Sahara K, Yoshido A, Marec F, Fukova I, Zhang H-B, Wu C-C, Goldsmith MR, Yasukochi Y. 2007. Conserved synteny of genes between chromosome 15 of Bombyx mori and a chromosome of Manduca sexta shown by five-color BAC-FISH. Genome 50: 1061-1065.
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Progress 01/01/06 to 12/31/06
Outputs
The goals of this project are to develop revolutionary, readily usable gene cloning systems in crop plants, to isolate and characterize genes and QTLs important to agriculture, and to generate molecular tools for efficient utilization of agronomic genes and QTLs in crop genetic improvement. To these ends, we have been working in several aspects. 1. Development of genomic resources for gene discovery - Large-insert BAC libraries are essential for advanced genomics and genetics research. In 2006, we developed BAC libraries for sweatpotato and Leymus. These libraries, along with the nearly 200 BAC libraries of different species previously developed through the project, have provided essential resources for accelerated genomics research. 2. Genome physical mapping with BACs - Genome physical mapping is the centerpiece of genomics research and crucial for development of the readily usable gene cloning systems. BAC-based maps are essential for large-scale gene mapping,
targeted DNA marker development, and discovery, cloning and characterization of every gene in the species. We helped pioneer the technologies of genome physical mapping with BACs and constructed the BAC physical maps of indica rice, soybean, japonica rice, Arabidopsis, chicken, Ustilago maydis, Penicillium chrysogenum, and Phytophthora sojae. In 2006, we constructed a comparative physical map of turkey-chicken and a physical map of red algae, and continued developing the physical map of cotton. 3. Functional genomics - Development of the BAC libraries and physical maps has promoted the research of functional genomics. We are developing array-assisted breeding systems in maize and cotton to translate functional genomics research results into enhanced crop genetic improvement. In 2006, we identified over 2100 genes potentially contributing to heterosis in maize and were conducting association analysis between fiber traits and fiber gene expression in cotton. 4. Comparative genomics -
Comparartive genomics research enables the genome research results of the model species to be used in agricultural species. In 2006, we continued comparative analysis between Arabidopsis and cotton, and the evolutionary studies of genome sizes and the NBS-LRR-encoding gene family in Gossypium. 5. Isolation of agronomic genes - The above research results have allowed efficient tagging, cloning and analyzing genes of agronomic importance known only by phenotype. In 2006, we continued toward cloning of the genes for root-knot nematode resistance in cotton, Ascochyta blight resistance in chickpea - a model system of quantitative resistance in plants, and everblooming (evb) in rose - a unique phenomonon in flowering plants. 6. DNA structure - Genome sequencing and research has raised a question about how DNA makes the abundance, diversity and complexity of living organisms. In 2000, we proposed a novel DNA structure model and started testing the model. In 2006, we completed the test of the
novel DNA structure model and published the first article in the new field, which is expected to provide a basis of abundance, diversity and complexity of living organisms and a new concept for plant breeding.
Impacts
This project has allowed pioneering or developing the technologies of BAC and BIBAC library construction and genome physical mapping, and developed one of the three largest collections of genomic resources worldwide for gene discovery, cloning and analysis, and BAC physical maps of 10 species. The technologies developed have been widely used in genome research in both public and private domains. The BAC libraries and physical maps have been widely used as essential resources, tools and infrastruture in genomics research of crop plants, farm animals and humans in [1] discovery and isolation of genes and quantitative trait loci important to agriculture, [2] determination of the position, structure, function and expression of every crop plant gene, [3] targeted generation of DNA markers for agronomic genes and QTLs of importance for plant breeding and germplasm diagnostics, and [4] development of revolutionary and new means for high-yield, high-quality and
high-efficiency crop breeding and production. Using these tools, we are analyzing the genes involved in several biological processes extremely important to agriculture, such as heterosis, fiber development, biotic stress and plant flowering. Isolation of the genes and understaunding of the processes will greatly promote crop genetic improvement, thus contributing to the U.S. increased agricultural productivity, cleaner living environments and enhanced agricultural competitive ablity. The new DNA structure model we discovered will revolutionize our current concepts in genetics, genomics and breeding research.
Publications
- Anderson JC, Lee M-L, Zhang H-B, Klein PE, Stelly DM, Price HJ. 2006. The use of Cen38 in assessing evolutionary relationships in the genus Sorghum. International Plant & Animal Genome Conference XIV. P218
- Feng J, Vick BA, Zhang H-B, Lee M-K, Jan CC. 2006. Construction of two BAC and BIBAC libraries from sunflower and identification of linkage group-specific clones by overgo hybridization. International Plant & Animal Genome Conference XIV. W289
- Lichtenzveig J, Bonfil, DJ, Zhang H-B, Shtienberg D, Abbo S. 2006. Mapping quantitative trait loci associated with time to flowering and resistance to Didymella rabiei, the causal agent of Ascochyta blight. Theor. Appl. Genet. 113:1357-1369.
- Wu C, Wang S, Zhang H-B. 2006. Interactions among genomic structure, function and evolution revealed by comprehensive analysis of the Arabidopsis genome. Genomics 88:394-406.
- Feng J, Vick BA, Lee M-K, Zhang H-B, Jan CC. 2006. Construction of BAC and BIBAC libraries from sunflower and identification of linkage group-specific clones by overgo hybridization. Theor Appl Genet 113:23-32.
- Stevens MR, Coleman CE, Parkinson SE, Zhang H-B, Balzotti MR, Kooyman D, Arumuganathan K, Bonifacio A, Fairbanks DJ, Jellen EN, Maughan PJ, Stevens JJ. 2006. Construction of a quinoa (Chenopodium quinoa Wild.) BAC library and its use in identifying genes encoding seed storage proteins. Theor Appl Genet 112:1593-1600.
- He L, Du C, Li Y, Scheuring C, Zhang H.-B. 2006. Large-insert bacterial clone libraries and their applications. In: Aquaculture Genome Technologies. Z. Liu (ed.). Blackwell Publishing, Ames, Iowa, USA (in press)
- McPhee KE, Croser J, Sarma B, Ali SS, Amla D, Rajesh PN, Zhang H-B. 2006. Development of transgenics in chickpea. In: Chickpea. Yadav SS, Redden B, Chen W, Sharma B (eds.). CABI, UK (in press)
- Zhang H-B, Wu C, and Wang S. 2006. Beyond the double helix model: DNA structure revealed by comprehensive analysis of the Arabidopsis thaliana genome. The CAS Conferences on Marine Science and Technology, July 28 - August 1, 2006, Qingdao, China. P 97
- Scheuring C, Barthelson R, Galbraith DW, Betran J, Cothren JT, Zeng Z-B, Zhang H-B. 2006. Preliminary analysis of differential gene expression between a maize superior hybrid and its parents using the 57K maize gene-specific long-oligonucleotide microarray. The 48th Annual Maize Genetics Conference. 9 - 12 March, 2006. Pacific Grove, CA. P193
- Yesudas CR, Shultz JL, Zhang H-B, Wong GK-S, Lightfoot D. 2006. A catalog of duplicated regions from marker amplicon homologs and BAC DNA sequence analysis in soybean, a paleopolyploid genome. International Plant & Animal Genome Conference XIV. P33
- Li Y, Uhm T, Ren C, Wu C, Santos TS, Lee M-K, Yan B, Santos F, Zhang A, Xu Z, Scheuring C, Sanchez A, Millena AC, Nguyen HT, Kou H, Liu D, Zhang H-B. 2007. A plant-transformation-competent BIBAC/BAC-based map of rice for functional analysis and genetic engineering of its genomic sequence. Genome (in press)
- Broggini GAL, Le Cam B, Parisi L, Wu C, Zhang H-B, Gessler C, Patocchi A. 2007. Construction of a contig of BAC clones spanning the region of the apple scab avirulence gene Avr Vg. Fungal Genetics and Biology 44:44-51.
- Zhang X, Scheuring C, Tripathy S, Xu Z, Wu C, Ko A, Tian SK, Arredond F, Lee M-K, Santos AF, Zhang H-B, Tyler BM. 2006. An integrated BAC and genome sequence physical map of Phytophthora sojae. Molecular Plant-Microbe Interactions 19: 1302-1310.
- Tyler BM, Tripathy S, Zhang X, Dehal P, Jiang RHY, Aerts A, Arredondo FD, Baxter L, Bensasson D, Beynon JL, Chapman J, Damasceno CMB, Dorrance AE, Dou D, Dickerman AW, Dubchak IL, Garbelotto M, Gijzen M, Gordon SG, Govers F, Grunwald NJ, Huang W, Ivors KL, Jones RW, Kamoun S, Krampis K, Lamour KH, Lee M-K, Maclean DJ, McDonald WH, Medina M, Meijer HJG, Morris PF, Nordberg EK, Ospina-Giraldo MD, Phuntumart V, Putnam NH, Rash S, Rose JKC, Sakihama Y, Salamov AA, Savidor A, Scheuring CF, Smith BM, Sobral BWS, Terry A, Torto-Alalibo TA, Win J, Xu Z, Zhang H-B, Grigoriev IV, Rokhsar DS, Boore JL. 2006. Phytophthora genome sequences uncover evolutionary origins and mechanisms of pathogenesis. Science 313: 1261-1266.
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Progress 01/01/05 to 12/31/05
Outputs
The goals of this project are to develop revolutionary, readily usable gene cloning systems in crop plants, to isolate and characterize genes and QTLs important to agriculture, and to generate molecular tools for efficient manipulation and utilization of agronomic genes and QTLs in crop genetic improvement. To these ends, we have been working in several aspects. 1. Development of genomic resources for gene discovery - Large-insert BAC and BIBAC libraries are essential resources for advanced genomics and genetics research. In 2005, we developed BAC libraries for several plant and pest species. These libraries, together with the nearly 200 BAC and BIBAC libraries of different plant and animal species previously developed through the project, have provided essential resources for accelerated genomics research of crop plants. 2. Genome physical mapping with BACs - Availability of the BAC libraries allowed us to reconstruct the genomes with BAC clones, i.e., genome
physical mapping. Genome physical mapping is the centerpiece of genomics research and crucial for development of the readily usable gene cloning systems. BAC-based physical maps integrated with genetic maps are essential for large-scale gene mapping, targeted DNA marker development, and discovery, cloning and characterization of every gene in the species. We helped pioneer the technologies of genome physical mapping with BACs/BIBACs, and constructed the BAC physical maps of indica rice, soybean, japonica rice and Arabidopsis. In 2005, we constructed the BAC physical maps of Penicillium chrysogenum, and the soybean pathogen, Phytophthora sojae, and continued developing the BAC/BIBAC physical map of cotton and the comparative physical map of turkey-chicken-human. 3. Functional genomics - Development of the BAC libraries and genome physical maps has promoted the research of functional genomics. In 2005, we continued developing microarray-assisted breeding systems in maize and cotton to
translate the functional genomics research results into enhanced crop genetic improvement. We developed essential materials for functional and genetic dissection of heterosis in maize and identified over 800 genes potentially contributing to heterosis in maize. We also collected essential samples for association analysis between fiber traits and fiber gene expression in cotton. 4. Comparative genomics - Comparartive genomics research enables the genome research results of the model species to be used in agricultural species. In 2005, we continued working in comparative genomics between Arabidopsis and cotton, further refined the phylogeny of the cotton genus Gossypium, and studied the evolution of genome sizes and the NBS-LRR-encoding gene family in the genus. 5. Isolation of agronomic genes - The results of the above research have allowed efficient tagging, cloning and analyzing genes of agronomic importance known only by phenotype. In 2005, we continued tagging and cloning of the
genes for root-knot nematode resistance in cotton, Ascochyta blight resistance in chickpea - a model system of quantitative resistance in plants, and everblooming (evb) in rose - a unique phenomonon in flowering plants.
Impacts
This project has allowed pioneering or developing the technologies of BAC and BIBAC library construction and genome physical mapping, and developed one of the three largest collections of genomic resources worldwide for gene discovery, cloning and analysis, and BAC physical maps of seven species. The technologies developed have been widely used in genome research in both public and private domains. The BAC libraries and physical maps have been widely used as essential resources (e.g., BAC and BIBAC libraries), tools and infrastruture in genomics research of crop plants, farm animals and humans in [1] discovery and isolation of genes and quantitative trait loci important to agriculture, [2] determination of the position, structure, function and expression of every crop plant gene, [3] targeted generation of DNA markers for agronomic genes and QTLs of importance for plant breeding and germplasm diagnostics, and [4] development of revolutionary and new means for
high-yield, high-quality and high-efficiency crop breeding and production. Using these tools, we are analyzing the genes involved in several biological processes extremely important to agriculture, such as heterosis, fiber development, biotic stress and plant flowering. Isolation of the genes and understaunding of the processes will greatly promote crop genetic improvement, thus contributing to the U.S. increased agricultural productivity, cleaner living environments and enhanced agricultural competitive ablity.
Publications
- Shultz J, Kurunam D, Shopinski K, Iqbal MJ, Kazi S, Zobrist K, Bashir R, Yaegashi S, Lavu N, Afzal A, Yesudas C, Kassem MA, Wu C, Zhang H-B, Town CD, Meksem K, Lightfoot DA 2006 The soybean genome database (SoyGD): physical maps, genetic maps, homeologous regions, DNA markers, contig structures, EST content, BAC end sequences and contiguous DNA sequences of glycine max. Nucleic Acids Res. 34: D758 - D765.
- Stupar RM, Beaubien KA, Jin W, Song J, Lee M-K, Wu C, Zhang H-B, Han B, Jiang J. 2005. Structural diversity and differential transcription of the patatin gene family during potato tuber development. Genetics 105:051219
- Nam Y-W, Lee J-R, Son K-H, Lee M-K, Robbins MD, Chung S-M, Staub JE, Zhang H-B. 2005. Construction of two BAC libraries from cucumber (Cucumis sativus L.) and identification of clones linked to yield component quantitative trait loci. Theor. Appl. Genet. 111:150-161
- Ortiz-Vazquez E, Kaemmer D, Zhang H-B, Muth J, Rodriguez-Mendiola M, Arias-Castro C, James A. 2005. Construction and characterization of a plant transformation-competent BIBAC library of the black Sigatoka-resistant banana Musa acuminata cv. Tuu Gia (AA). Theor. Appl. Genet. 110:706-713
- Ren C, Xu ZY, Sun S, Lee M-K, Wu C, Scheuring C, Santos TS, and Zhang H-B. 2005. Genomic DNA Libraries and Physical Mapping. In: The Handbook of Plant Genome Mapping: Genetic and Physical Mapping. Meksem K and Kahl G (eds.). Wiley-VCH Verlag GmbH, Weinheim, Germany, pp 173-213 (Note that all other authors are students and postdoctoral associates of Zhang).
- Zhang H-B, Yan B, Chang Y-L, Dodgson JB, Lee M-K, Li Y, Lightfoot DA, Liu D, Meksem K, Nguyen HT, Ren C, Stelly DM, Sun S, Wu C, Xu Z, Zhang A. 2005. Whole genome physical mapping with BACs by fingerprint analysis: Lessons and tips. International Plant & Animal Genome Conference XIII. W201
- Yu JZ, Kohel RJ, Xu Z, Dong J, Zhang H-B, Stelly DM, Pepper AE, Cui P, Hoffman SM. 2005. Integrated genetic, physical and comparative mapping of the cotton genome. Proceedings of the Beltwide Cotton Improvement Conference. New Orleans, LA.
- Stevens MR, Coleman CE, Parkinson SE, Zhang H-B, Balzotti MB, Kooyman D, Arumuganathan K, Bonifacio A, Fairbanks DJ, Jellen EN, Maughan PJ, Stevens J. 2005. Construction of a quinoa BAC library and its use in identifying the 11S seed storage protein gene. International Plant & Animal Genome Conference XIII. P053
- Feng J, Jan CC, Vick BA, Zhang H-B. 2005. Construction and characterization of two complementary BAC and BIBAC libraries from cultivated sunflower (Helianthus annuus L.). International Plant & Animal Genome Conference XIII. P051
- Shopinski K, Shultz JL, Lavu N, Iqbal J, Town C, Wu C, Zhang H-B, Meksem K, Lightfoot DA. 2005. The genome browser for soybean: displaying a sequence framework and physical map. International Plant & Animal Genome Conference XIII. P875
- Yu JZ, Kohel RJ, Xu Z, Dong J, Zhang H-B, Stelly DM, Zhu Y, Covaleda L. 2005. Physical mapping of fiber initiation genes in cotton. International Plant & Animal Genome Conference XIII. P621
- Xu Z, Kohel RJ, Dong J, Zhang H-B, Stelly DM, Covaleda L, Koo P, Yu JZ. 2005. A syntenic study between cotton and Arabidopsis using integrated physical maps and conserved ortholog markers. International Plant & Animal Genome Conference XIII. P248
- Anderson JC, Lee M-K, Zhang H-B, Islam-Faridi MN, Stelly MD, Price HJ. 2005. Distribution Of Cen38 In The Genus Sorghum. International Plant & Animal Genome Conference XIII. P234
- Lightfoot D, Shultz J, Wu C, Zhang H-B, Liu B, Wong GK-S. 2005. DNA Sequence analysis of BACs from highly conserved homeologous regions in a paleopolyploid genome. International Plant & Animal Genome Conference XIII. P040
- Shultz J, Lavu N, Langin C, Shopinski K, Kazi S, Bashir R, Iqbal J, Afzal J, C Town, Meksem K, Zhang H, Wu C, Lightfoot D. 2005. Uses of the soybean sequence ready physical map. International Plant & Animal Genome Conference XIII. W205
- Wu C, Sun S, Lee M-K, Xu ZY, Ren C, and Zhang H-B. 2005. Whole genome physical mapping: An overview on methods for DNA fingerprinting. In: The Handbook of Plant Genome Mapping: Genetic and Physical Mapping. Meksem K and Kahl G (eds.). Wiley-VCH Verlag GmbH, Weinheim, Germany, pp 257-284 (Note that all other authors are postdoctoral associates of Zhang).
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Progress 01/01/04 to 12/31/04
Outputs
The goals of this project are to develop revolutionary, readily usable gene cloning systems in crop plants, to isolate and characterize genes and QTLs important to agriculture and to generate molecular tools for efficient manipulation and utilization of the genes and QTLs. To these ends, we have been working in several aspects. 1. Gene discovery resource development - Large-insert BAC and BIBAC libraries are essential for advanced genomics research, including targeted marker development, genome physical mapping and sequencing, and gene discovery, cloning, characterization and utilization. In 2004, we developed 6 BAC libraries. These new libraries with the privously developed over 100 BAC and BIBAC libraries provide essential resources for accelerated genomics research of crop plants. 2. Genome physical mapping - It is the centerpiece of genomics research and crucial for development of the readily usable gene cloning systems. Integrated physical maps are essential for
large-scale gene mapping, targeted marker development, and discovery, cloning and characterization of every gene in the species. We previoualy helped pioneer the technologies of genome physical mapping with BACs, and constructed the physical maps of indica rice, soybean, japonica rice and Arabidopsis. In 2004, we continued development of the cotton physical map, advanced the physical mapping technologies using the capillary electrophoresis technology, and constructed the physical maps of the penicillin-producing species, Penicillium chrysogenum and the soybean pathogen, Phytophthora sojae. 3. Functional genomics with emphasis on gene position, function, expression, organization and interaction -Structural genomics research has promoted the research of functional genomics. In 2004, we studied the DNA structure and organization using Arabidopsis and human as the model systems and continued the development of microarray-assisted breeding systems for maize and cotton to translate the
functional genomics research results into enhanced crop plant genetic improvement. 4. Comparative genomics -Comparative genomics research enables the genome research results of the model species to be used in agricultural species. In 2004, we continued working in comparative genomics between Arabidopsis and cotton, and initiated a comparative genomics project between chicken, turkey and human. We have also reconstructed the phylogeny of the cotton genus Gossypium and initiated projects in evolution of plant genome sizes and the NBS-LRR-encoding gene family in the Gossypium. 5. Isolation of agronomic genes - Many agronomic genes are known only by phenotype. To isolate such genes, we previously developed map-based cloning systems in crop plants. In 2004, we isolated and characterized all NBS-LLR-encoding resistance genes to different pathogens in cotton and continued mapping and cloning of the genes for root-knot resistance in cotton. Moreover, we started cloning and characterization of
the chickpea Ascochyta blight resistance genes, a model system of quantitative resistance in crop plants and the rose everblooming (evb) gene, the unique one controlling recurrently flowering in flowering plants.
Impacts
This project has provided essential resources (e.g., BAC and BIBAC libraries) for many crop plants and readily usable tools and infrastruture (e.g., integrated physical/genetic maps) in several major crop plants including soybean, indica rice, japonica rice and cotton. These resources, tools and infrastructures will significantly promote [1] discovery and isolation of a large number of genes and quantitative trait loci important to agriculture, [2] determination of the position, structure, function and expression of every crop plant gene, [3] targeted generation of DNA markers for agronomic genes/QTLs of importance for fine mapping and marker-assisted plant breeding and germplasm diagnostics, and [4] development of revolutionary and new means for high-yield, high-quality and high-efficiency crop breeding and production.
Publications
- Xu, Z., M. van den Berg, C. Scheuring, H. L. Colaveda, Lu, F. A. Santos, T. Uhm, M.-K. Lee, C. Wu, S. Liu, and H.-B. Zhang. 2004. Genome-wide physical mapping from large-insert clones by fingerprint analysis with capillary electrophoresis: A robust physical map of Penicillium chrysogenum. Nucleic Acids Res. (submitted)
- Stevens MR, Coleman CE, Parkinson SE, Zhang H-B, Balzotti MR, Kooyman D, Arumuganathan K, Bonifacio A, Fairbanks DJ, Jellen EN, Maughan PJ, Stevens JJ. 2004. Construction of a quinoa (Chenopodium quinoa Willd.) BAC library and its use in identifying genes encoding seed storage proteins. Mol. Genet. Genomics (submitted)
- Ortiz-Vazquez E, Kaemmer D, Zhang H-B, Muth J, Rodriguez-Mendiola M, Arias-Castro C, James A. 2004. Construction and characterization of a plant-transformation-competent BIBAC library of the Black Sigatoka resistant banana Musa acuminata cv. Tuu Gia (AA). Theor. Appl. Genet. (in press)
- Lichtenzveig J, Scheuring C, Dodge J, Abbo S, Zhang H-B. 2004. Construction of BAC and BIBAC libraries and their applications for generation of SSR markers for genome analysis of chickpea, Cicer arietinum L. Theor. Appl. Genet. (in press)
- Meksem K, Shultz J, Jyothi. LN, Jamai A, Henrich J, Kranz H, Arenz M, Schlueter T, Ishihara H, Tebbji F, Zhang H-B, Lightfoot DA. 2004. A BAC based physical map of the Ustilago maydis genome. Genome (in press)
- Wallis JW, Aerts J, Groenen MAM, Crooijmans RPMA, Layman D, Graves TA, Scheer DE, Kremitzki C, Fedele MJ, Mudd NK, Cardenas M, Higginbotham J, Carter J, Mcgrane R, Gaige T, Mead K, Walker J, Albracht D, Davito J, Yang S-P, Leong S, Chinwalla A, Sekhon M, Wylie K, Dodgson J, Romanov MN, Cheng H, De Jong PJ, Osoegawa K, Nefedov M, Zhang H-B, Mcpherson JD, Krzywinski M, Schein J, Hillier L, Mardis ER, Wilson RK, and Warren WC. 2004. A physical map of the chicken genome. Nature 432: 761-764.
- He LM, Du CG, Covaleda L, Robinson AF, Yu JZ, Kohel RJ, Zhang H-B. 2004. Cloning, characterization, and evolution of the NBS-encoding resistance gene analogue family in polyploid cotton (Gossypium hirsutm L.). Molecular Plant-Microbe Interactions 17: 1234-1241.
- Raudsepp T, Avni Santani A, Wallner B, Kata SR, Ren C, Zhang H-B, Womack JE, Skow LC, Chowdhary BP. 2004. A detailed physical map of the horse Y chromosome. Proc. Natl. Acad. Sci. USA 101: 9321-9326.
- Budiman, M.A., S-B. Chang, S. Lee, T.J. Yang, H-B. Zhang, H. de Jong and R.A. Wing 2004. Localization of jointless-2 gene in the centromeric region of tomato chromosome 12 based on high resolution genetic and physical mapping. Theor. Appl. Genet. 108:190-196.
- Wu C, Wang S, Xu Z, Zhang H-B. 2004. Interactions among genomic structure, function and evolution identified in Arabidopsis thaliana. Genome Research (submitted)
- Ortiz-Vazquez E, Kaemmer D, Rodriguez-Mendiola M, Zhang H-B, Arias-Castro C, James A. 2004. Construction of a binary bacterial artificial chromosome library of Musa acuminata TUU GIA. International Plant & Animal Genome Conference XII. P147.
- Wu C, Goldsmith M, Felipe Santos F, Cerrato J, Dodge J, Zhang H-B. 2004. Large-insert BAC libraries for fundamental studies in Lepidoptera. International Plant & Animal Genome Conference XII. P149.
- Xu Z, Covaleda L, Ding K, Wu C, Lee M-K, Scheuring C, Zhang H-B. 2004. A high-throughput BAC and BIBAC DNA isolation system for whole genome physical mapping and large-scale sequencing. International Plant & Animal Genome Conference XII. P188.
- Wu C, Sun S, Nimmakayala P, Santos F, Ding K, Meksem K, Lightfoot D, Zhang H-B. 2004. Toward a robust integrated physical, genetic and comparative map of the soybean genome. International Plant & Animal Genome Conference XII. P532.
- Santani AB, Raudsepp T, Wallner B, Ren C, Zhang H-B, Skow LC, Chowdhary BP. 2004. Developing BAC contigs over the euchromatic region of the horse Y chromosome. International Plant & Animal Genome Conference XII. P689.
- Xu Z, Yu J, Covaleda L, Dong J, Lee M-K, Ding K, Kohel RJ, Zhang H-B. 2004. Toward an integrated physical and genetic map of the cultivated cotton genome: physical map contig assembling and anchoring to its subgenomes. International Plant & Animal Genome Conference XII. P759.
- Shultz J, Iqbal J, Langin C, Nagajyothi L, Watson D, Zhang H-B, Meksem K, Town C, Lightfoot D. 2004. Physical map builds from recently duplicated genomes. International Plant & Animal Genome Conference XII. P918.
- Yu JZ, Kohel RJ, Zhang H-B, Stelly DM, Xu Z, Dong J, Covaleda L, Lee M-K, Lazo GR, Gupta P. 2004. Toward an integrated physical and genetic map of the cultivated allotetraploid cotton genome. International Plant & Animal Genome Conference XII. W147.
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Progress 01/01/03 to 12/31/03
Outputs
The goals of this project are to develop revolutionary, readily usable gene cloning systems in crop plants, to generate molecular tools for efficient manipulation and utilization of genes and QTLs important to agriculture and to isolate and characterize the genes and QTLs. Toward these goals, we have been working in several aspects. 1. Gene discovery resource development - Large-insert BAC and plant-transformation-competent BIBAC libraries are essential for genomics research, including targeted marker development, genome physical mapping and sequencing, and gene discovery, cloning, characterization and utilization. In 2003, we developed 16 new BAC and BIBAC libraries. Now we have over 100 BAC and BIBAC libraries, the largest collection of the libraries in the world. These libraries have provided essential resources for accelerated genomics research of crop plants. 2. Genome physical mapping - It is the centerpiece of genomics research and crucial for development of
the readily usable gene cloning systems. Studies have proven that integrated physical maps are essential platforms for large-scale gene mapping, targeted marker development, and discovery, cloning and characterization of every gene in the species. We helped pioneer the technologies of genome physical mapping with BACs, and constructed the BAC physical maps of indica rice, soybean, japonica rice and Arabidopsis. In 2003, we analyzed about 100,000 (6.1 x) cotton BACs and constructed 5,466 contigs for the physical map development of the cultivated cotton. 3. Functional genomics: gene position, function, expression, organization and interaction - Structural genomics research has promoted the research of functional genomics. In 2003, we studied interactions among the 26,000 genes of Arabidopsis and the structure, organization, function and evolution of its genome. We also initiated a project to associate tens of thousands of genes with agaronomic traits in maize and develop novel tools for
enhanced crop plant breeding and production using the functional genomics research results. 4. Comparative genomics - Development of the BAC libraries and physical maps has allowed study of genome organization and evolution at the genome-wide level. In 2003, we initiated a project to estimate the genomic relationships between the genomes of Arabidopsis and cotton to allow the genomics research results of the model species to be used in cotton. 5. Isolation of agronomic genes - Many agronomic genes are known only by phenotype. To isolate such genes, we previously developed map-based cloning systems in crop plants. In 2003, we continued mapping and cloning of the genes for root-knot resistance (RNR) in cotton, and developing of a RIL population of cotton for RNR gene fine mapping and cloning. 6. DNA markers and map development and gene/QTL mapping - To facilitate research of legume genomes, we are developing genomic tools for legume gene mapping and cloning, and genome analysis using
chickpea as a model. In 2003, we developed additional 300 SSR markers from BACs and constructed an SSR-based map for chickpea and mapped several genes and QTLs of agronomic importance in the species.
Impacts
This project has provided essential resources (e.g., BAC and BIBAC libraries) for many crop plants and readily usable tools and infrastruture (e.g., integrated physical/genetic maps) in several major crop plants including soybean, indica rice, japonica rice and cotton. These resources, tools and infrastructures will significantly promote [1] discovery and isolation of a large number of genes and quantitative trait loci important to agriculture, [2] determination of the position, structure, function and expression of every crop plant gene, [3] targeted generation of DNA markers for agronomic genes/QTLs of importance for fine mapping and marker-assisted plant breeding and germplasm diagnostics, and [4] development of revolutionary and new means for high-yield, high-quality and high-efficiency crop breeding and production.
Publications
- Chen Q, Sun S, Ye Q, McCuine S, Huff E, Zhang H-B. 2003. Construction of two BAC libraries from the wild Mexican diploid potato, Solanum pinnatisectum and identification of clones near the late blight and Colorado potato beetle resistance loci. Theor. Appl. Genet. (in press).
- Dvorak J, Anderson OD, Gill BS, Luo M-C, Zhang H-B, Deal K, Li W, You FM, Gu YQ, McGuire PE. 2003. Assessment of the insular organization of the wheat D genome by physical mapping. Plant & Animal Genome XI. P356
- Xu ZY, Sun S, Covaleda L, Ding K, Zhang A, Scheuring C, and Zhang H-B. 2003. Genome physical mapping with large-insert bacterial clones by fingerprint analysis: methodologies, source clone genome coverage and contig map quality. Nucleic Acids Res. (submitted).
- Li Y, Uhm T, Santos TS, Ren C, Lee M-K, Yen B, Sun S, Liu D, Nguyen HT, Zhang H-B. 2003. A plant-transformation-competent BIBAC-based integrated map of the rice genome for functional analysis and genetic engineering of the rice genome. Plant Cell (submitted)
- Goldsmith MR, McGovern C, Wu C, Zhang H-B, Mita K, Yasukochi Y, Shimada T, Sugasaki T, Okano K, Zeng P, Mills DR, and Marino SW. 2003. Resources for comparative linkage mapping in Lepidoptera. Insect Molecular Science
- Xu Z, Chang Y-L, Ding K, Covaleda L, Sun S, Wu C, Zhang H-B. 2003. Automated procedure for whole-genome physical mapping from large-insert BACs and BIBACs. Plant & Animal Genome XI. P115
- Li Y, Uhm T, Santos TS, Ren C, Lee M-K, Yan B, Santos F, Zhang A, Liu D, Zhang H-B. 2003. A Plant-transformation-competent BIBAC-based integrated physical map of japonica rice for functional analysis of the rice genome sequence. Plant & Animal Genome XI. P342
- Wu C, Sun S, Nimmakayala P, Santos F, Ding K, Meksem K, Lightfoot DA, Zhang H-B. 2003. A BAC/BIBAC-based physical map of the soybean genome. Plant & Animal Genome XI. P482
- Lee S, Chang S-B, Yang T-J, Budiman A, Zhang H-B, de Jong H, Wing RA. 2003. Localization of jointless-2 gene in the centromeric region of tomato chromosome 22 based on high resolution genetic and physical mapping. Plant & Animal Genome XI. P509
- Ren C, Lee M-K, Yan B, Ling P, Ding K, Cox B, Dodgson JB, Zhang H-B. 2003. A BAC-based physical map of the chicken genome. Plant & Animal Genome XI. P601
- Xu Z, Yu JZ, Covaleda L, Dong J, Lee M-K, Ding K, Kohel RJ, Zhang H-B. 2003. Toward an integrated physical and genetic map of the cotton genome: BAC fingerprinting and physical map construction. Plant & Animal Genome XI. P689
- Yu JZ, Kohel RJ, Zhang H-B, Stelly DM, Dong J, Xu Z, Covaleda L, Zhang L, Gao W, Steele NL. 2003. Integrative physical and genetic mapping of the cotton genome (Gossypium hirsutum L.). Plant & Animal Genome XI. W219
- Xu Z, Sun S, Covaleda L, Ding K, Zhang A, Zhang H-B. 2003. Whole-genome physical mapping with BACs: Fingerprinting methods, source clone genome coverage and map contig accuracy and size. Plant & Animal Genome XI. W224
- Stevens MR, Bonifacio A, Coleman CE, Jellen EN, Gardunia BW, Parkinson SE, Pratt C, Zhang H-B. 2003. Understanding the Chenopodium quinoa genome to facilitate quinoa breeding - a teach approach. Plant & Animal Genome XI. W326
- Lightfoot D, Meksem K, Zhang H-B. 2003. Accessing the soybean integrated physical and genetic map. Plant & Animal Genome XI. C2
- Shultz JL, Triwitayakom K, Jamai A, Iqbal J, Wu C, Tao Q, Nimmakayala P, Zhang H-B, Meksem K, Lightfoot D. 2003. The soybean integrated physical and genetic map: progress toward functional, high density gene maps. Plant & Animal Genome XI. P22
- Sun S, Xu Z, Wu C, Ding K, Zhang H-B. 2003. Genome properties and their influences on library construction and physical mapping. Plant & Animal Genome XI. P77
- Gehno J, Hively K, Young M, Zhang H-B, Lee M-K, Stevens M, Kooyman D. 2003. Construction of a llama BAC library with approximately four genome-equivalent coverage. Plant & Animal Genome XI. P172
- Fang X, Gu S, Xu Z, Chen F, Guo D, Zhang H-B, Wu N. 2003. Construction of a binary BAC library for an apomictic monosomic addition line of Beta corolliflora in sugar beet and identification of the clones derived from the alien chromosome. Theor. Appl. Genet. (in press).
- Wu C, Sun S, Padmavathi N, Santos FA, Springman R, Meksem K, Lightfoot D, Zhang H-B. 2003. A BAC and BIBAC-based physical map of the soybean genome. Genome Res. (in press).
- Ren C, Lee M-K, Yan B, Ding K, Cox B, Romanov MN, Price JA, Dodgson JB, Zhang H-B. 2003. A BAC-based physical map of the chicken genome. Genome Res. 13:2754-2758.
- Chang Y-L, Henriquez X, Preuss D, Copenhaver GP, and Zhang H-B. 2003. A plant transformation-competent binary BAC library of the Arabidopsis thaliana Landsberg ecotype for functional and comparative genomics. Theor. Appl. Genet. 106: 269-276
- Lightfoot, DA, Meksem K, Zhang H-B. 2003. Integrative physical mapping of the soybean genome. In: VandenBosch KA, and Stacey G. (eds.). Summaries of Legume Genomics Projects from around the Globe. Community Resources for Crops and Models. Plant Physiology 131: 19-20
- Ren C, Xu ZY, Sun S, Lee M-K, Wu C, and Zhang H-B. 2003. Genomic Libraries for Physical Mapping. In: Meksem K and Kahl G (eds.) Handbook of Plant Genome Mapping. Wiley-VCH Verlag GmbH, Weinheim, Germany (in press)
- Wu C, Sun S, Lee M-K, Xu ZY, Ren C, and Zhang H-B. 2003. Whole genome physical mapping: An overview on methods for DNA fingerprinting. In: Meksem K and Kahl G (eds.) Handbook of Plant Genome Mapping. Wiley-VCH Verlag GmbH, Weinheim, Germany (in press)
- Wu C, Xu Z, Zhang H-B. 2003. DNA Libraries. In: Meyers RA (ed.) Encyclopedia of Molecular Cell Biology and Molecular Medicine. Wiley-VCH Verlag GmbH, Weinheim, Germany (in press)
- Wu C, Nimmakayala P, Santos FA, Springman R, Meksem K, Lightfoot DA, Zhang H-B. 2003. Organization and evolution of TIR-NBS-LRR-encoding genes in the soybean genome. Mol. Genet. Genomics (submitted).
- Wu C, Nimmakayala P, Santos FA, Springman R, Tao Q, Meksem K, Lightfoot DA, Zhang H-B. 2003. Construction of a soybean bacterial artificial chromosome library for physical map-based genome sequencing. Theor. Appl. Genet. (submitted).
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Progress 01/01/02 to 12/31/02
Outputs
The goals of this project are to develop a revolutionary, readily usable gene cloning system in crop plants and isolate the genes and QTLs important to agriculture. Towards these goals, we have been working on the project in several aspects. 1. Gene discovery resource development - Large-insert BAC libraries are essential for genomics research, including marker development, genome physical mapping and sequencing, gene discovery, cloning, characterization and utilization. In 2002, we developed over 10 new BAC and BIBAC libraries and now we have over 90 BAC and BIBAC libraries, the largest collection of the libraries in the world. These libraries have provided essential resources for accelerated genomics research of crop plants. 2. Genome physical mapping - It is the centerpiece of genomics research and crucial for development of the readily usable gene cloning system. An integrated physical map will provide a powerful platform for large-scale gene mapping, target
marker development, and discovery, cloning and characterization of every gene in the species. We helped pioneer the technologies of genome physical mapping with BACs, and constructed the BAC physical maps of indica rice and Arabidopsis. In 2002, we constructed BAC/BIBAC-based physical maps of soybean and japonica rice and initiated the physical map development of the cultivated cotton. 3. Functional genomics: gene position, function, expression, organization and interaction - Development of the integrated physical maps has promoted the research of functional genomics. In 2002, we initiated a project of mapping 20,000 soybean EST genes to the soybean physical map. We studied the genome organization and evolution of disease resistance genes in indica rice and japonica rice, and were working in defense genomics of cotton. 4. Comparative genomics - Development of the BAC libraries and physical maps has allowed study of genome organization and evolution at the genome-wide level. We studied
genome organization and evolution of monocots (rice, maize and wheat) and dicots (Arabidopsis). 5. Isolation of agronomic genes - Many agronomic genes are known only by phenotype. To isolate such genes, we previously developed map-based cloning systems in crop plants. In 2002, we continued mapping and cloning of the genes for root-knot resistance (RNR) in cotton and everblooming in rose, and were developing a RIL population of cotton for RNR gene fine mapping and cloning. 6. DNA markers and map development and gene/QTL mapping - To facilitate research of legume genomes, we are developing genomic tools for legume gene mapping and cloning, and genome analysis using chickpea as a model. In 2002, we developed 170 new SSR markers from BACs and constructed an SSR-based map for chickpea and mapped several genes and QTLs of agronomic importance in the species.
Impacts
This project has so far provided readily usable, essential tools and infrastruture (e.g., BAC and BIBAC libraries and integrated physical/genetic maps) for [1] discovery and isolation of a large number of genes and quantitative trait loci important to agriculture, [2] determination of the position, structure, function and expression of every gene, [3] target generation of DNA markers for agronomic genes/QTLs of importance for fine mapping and marker-assisted plant breeding and germplasm diagnostics, and [4] development of revolutionary and new means for high-yield, high-quality and high-efficiency crop production.
Publications
- Wu C, Nimmakayala P, Santos FA, Springman R, Tao Q, Meksem K, Lightfoot DA, and Zhang H-B. 2003. Genome organization and evolution of TIR-NBS-LRR-encoding gene class in soybean. Genetics (submitted).
- Meksem K, Shultz J, Schlueter T, Zhang H-B, Lightfoot DA. 2003. A physical map of the Ustilago maydis genome: A tool for functional genomics. Genome Research (submitted).
- Snatos TS (Ph.D. dissertation). 2002. Genome organization and evolution of rice (Oryza sativa L.). Texas A&M University.
- Zhang H-B, He L, Zhang L, Lee M-K, Stelly DM, Covaleda LM, Robinson F, Yu J, Kohel RJ and Cook CG. 2002. Genomics research in cotton. Proc. of the 2002 Beltwide Cotton Conference, January 8 - 12, Atlanta, Georgia, USA.
- Zhang H-B, Yu JZ, Kohel RJ, Stelly DM, Xu Z-Y, Covaleda L, Ding K-J, Wu C-C, Lee M-K. 2002. Toward development of a whole-genome, BAC/BIBAC-based integrated physical/genetic map of the cotton genome using the Upland cotton genetic standard TM-1: BAC fingerprinting and physical map contig construction. Cotton Science 14:33.
- Yu JZ, Kohel RJ, Zhang H-B, Dong J-M, Sun S-K, Steele NL. 2002. Toward development of a whole-genome, BAC/BIBAC-based integrated physical/genetic map of the cotton genome using the Upland cotton genetic standard TM-1: BAC and BIBAC construction, SSR marker development and Physical/genetic map integration. Cotton Science 14:32.
- Meksem K, Shultz J, Jamai A, Zobrist K, Triwitakom K, Zhang H-B, Wu C, Iqbal MJ, Lightfoot DA. 2002. Development of physical maps integrated with genetic markers and ESTs: Prelude to genome sequencing and functional analysis. Plant, Animal and Microbe Genomes X. W146.
- Dong J, Kohel RJ, Zhang H-B and Yu J. 2002. Toward development of an integrated physical/genetic map of the cotton genome: large-scale generation of SSR markers from a BAC library of the cotton genetic standard line TM-1. Plant, Animal and Microbe Genomes X. P220.
- Wu C, Sun S, Padmavathi N, Santos FA, Springman R, Tao Q, Meksem K, Lightfoot D and Zhang H-B. 2003. A BAC and BIBAC-based physical map of the soybean genome. Plant Cell (submitted).
- Wu C, Xu Z and Zhang H-B. 2003. DNA Libraries. Encyclopedia of Molecular Cell Biology and Molecular Medicine (submitted).
- Hong YS, Hogan JR, Wang X, Sarkar A, Sim C, Loftus BL, Ren C, Huff ER, Carlile JL, Black K, Zhang H-B, Gardner MJ, Collins FH. 2003. Construction and characterization of a BAC library and generation of BAC end sequence-tagged connectors for genome sequencing of the malaria mosquito, Anopheles gambiae. Mol. Genet. Genomics. In press.
- Lee M-K, Ren CW, Yan B, Cox B, Zhang H-B, Romanov M, Sizemore FG, Suchyta SP, Peters E, Dodgson JB. 2003. Construction and characterization of three complementary BAC libraries for analysis of the chicken genome. Animal Genetics. In press.
- van Leeuwen H, Monfort A, Zhang H-B, Puigdomenech P. 2003. Identification and characterisation of a melon genomic region containing a resistance gene cluster from a constructed BAC library. Microcolinearity between Cucumis melo and Arabidopsis thaliana. Plant Mol. Biol. 51: 703-718.
- Tao Q, Wang A, Zhang H-B. 2002. One large-insert plant-transformation-competent BIBAC library and three BAC libraries of japonica rice for genome research in rice and other grasses. Theor. Appl. Genet. 105:1058-1066.
- Chauhan RS, Farman ML, Zhang H-B and Leong SA. 2002.Genetic and physical mapping of a rice blast resistance locus, Pi-CO39(t), that corresponds to the avirulence gene AVR1-CO39 of Magnaporthe grisea. Mol. Genet. Genomics 267: 603-612.
- Lichtenzveig J, Shtienberg D, Zhang H-B, Bonfil DJ and Abbo S. 2002. Biometric analyses of the inheritance of resistance to Dydimella rabiei in chickpea. Phytopathology 92: 417-423.
- Lightfoot, DA, Meksem K, Zhang H-B. 2003. Integrative physical papping of the soybean genome. In: VandenBosch KA, and Stacey G. (eds.). Summaries of Legume Genomics Projects from around the Globe. Community Resources for Crops and Models. Plant Physiology 131: 19-20.
- Zhang L, Dong J, Decanini LI, Lee M-K, Ren C, Yan B, Kohel RJ, Yu J, Zhang H-B and Stelly DM. 2002. Development of molecular cytogenetic markers in cotton. Plant, Animal and Microbe Genomes X. P285.
- McCuine SA and Zhang H-B. 2002. Integrated production and dissemination of large-insert, ordered and high-quality BAC and BIBAC libraries for accelerated genomics research. Plant, Animal and Microbe Genomes X. P86.
- Wu C, Santos T and Zhang H-B. 2002. Genome-wide organization and evolution of disease resistance gene families in plant genomes. Plant, Animal and Microbe Genomes X. W182.
- Luo M-C, Thomas C, Xu Z, Zhang H-B, Malandro M, Morgante M, McQuire PE and Dvorak J. 2002. Automated fingerprinting of BAC libraries for the construction of physical maps of large genomes. Plant, Animal and Microbe Genomes X. P120.
- Xu Z, Chang Y-L, Ding K, Covaleda L, Sun S, Wu C and Zhang H-B. 2002. Automation of the procedure for whole-genome physical mapping from large-insert random BACs and BIBACs. Plant, Animal and Microbe Genomes X. P123.
- Xu Z, Sun S, Ding K, Covaleda L and Zhang H-B. 2002. Accuracy of physical map assembly and fingerprinting methods. Plant, Animal and Microbe Genomes X. P148.
- Scheuring C, Lichtenzveig J, Abbo S and Zhang H-B. 2002. Generation of SSR markers from large-insert BACs for genetic map construction, gene and QTL mapping and integrated physical mapping of chickpea. Plant, Animal and Microbe Genomes X. P193.
- Wu C, Sun S, Padmavathi N, Santos FA, Springman R, Tao Q, Meksem K, Lightfoot D and Zhang H-B. 2002. Toward a whole-genome, BAC/BIBAC-based integrated physical and genetic map of the soybean genome: the first version of the integrated map. Plant, Animal and Microbe Genomes X. P486.
- Lee M-K, Ren C, Yan B, Cox B, Dodgson J and Zhang H-B. 2002. Development of a whole-genome, BAC-based integrated physical/genetic map of the chicken genome: I. Construction and characterization of source BAC libraries. Plant, Animal and Microbe Genomes X. P590.
- Ren C, Lee M-K, Yan B, Ling P, Ding K, Cox B, Dodgson JB and Zhang H-B. 2002. Development of a whole-genome, BAC-based integrated physical/genetic map of the chicken genome: II. BAC fingerprinting and physical map contig assembly. Plant, Animal and Microbe Genomes X. P591.
- Santos TS and Zhang H-B. 2002. Genome-wide organization and evolution of disease resistance gene families in the cultivated rice, oryza sativa L. Plant, Animal and Microbe Genomes X. P91.
- Xu Z, Deal KR, Li W, Covaleda L, Chang Y-L, Dvorak J, Luo M-C, Gill GS, Anderson OD and Zhang H-B. 2002. Construction and characterization of five large-insert BAC and BIBAC libraries of Aegilops tauschii, the diploid donor of the wheat D genome. Plant, Animal and Microbe Genomes X. P92.
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Progress 01/01/01 to 12/31/01
Outputs
The goals of this project are to develop a revolutionary, readily usable gene cloning system in crop plants and isolate the genes and QTLs important to agriculture. Towards these goals, we have been working on the project in several aspects. 1. Gene discovery resource development - Large-insert BAC libraries are essential for genomics research, including marker development, gene discovery, cloning, characterization and utilization. In 2001, we developed 10 new BAC libraries. We now have 80 BAC libraries, the largest collection of the libraries in the world. These libraries are playing a key role in accelerated genomics research. 2. Genome physical mapping - It is the centerpiece of genomics research and crucial for development of the readily usable gene cloning system. An integrated physical map will provide a "freeway" for large-scale gene mapping, target marker development, and discovery, cloning and characterization of every gene in the species. We helped pioneer
technologies of genome physical mapping with BACs, and constructed the BAC physical maps of indica rice and Arabidopsis. In 2001, we constructed the first-generation of the soybean physical map, completed all lab work for the physical maps of chicken and japonica rice, worked toward the physical map of wheat, and tested the feasibility of physical mapping of the cultivated cotton. 3. Functional genomics: gene position, function, expression, organization and interaction - Development of the integrated physical maps has promoted the research of functional genomics. In 2001 we started mapping of the 16,000 maize and 10,000 wheat unigenes (ESTs) and initiated a project of mapping 20,000 soybean EST genes to integrated physical maps. We studied the genome organization and evolution of disease resistance genes in soybean and were working in functional genomics of disease resistances in cotton, indica rice and japonica rice. 4. Comparative genomics - Development of the BAC libraries and
physical maps has allowed us to study genome organization and evolution at the genome-wide level. We studied genome organization and evolution of monocots (rice, maize and wheat) and dicots (Arabidopsis). 5. Bioinfomatics - To efficiently manipulate the data generated from genomics research, we created a database and a genomic information system for genomics of agricultural species. In 2001, we established a core facility for bioinfomatics of agricultural genomics, and created the database for soybean and chicken physical maps. 6. Isolation of agronomic genes - Many agronomic genes are known only by phenotype. To isolate such genes, we developed map-based cloning systems in crop plants. In 2001, we continued mapping and cloning of the genes for root-knot resistance (RNR) in cotton and everblooming in rose. 7. DNA markers and map development and gene/QTL mapping - To facilitate research of legume genomes, we are developing genomic tools for legume gene mapping and cloning, and genome
analysis using chickpea as a model. In 2001, we developed 142 new SSR markers from BACs and worked toward construction of an SSR-based map for chickpea and mapping of agronomic genes and QTLs in the species.
Impacts
This project will provide a revolutionary, novel and readily usable system for [1] discovery and isolation of a large number of genes and quantitative trait loci important to agriculture, [2] determination of the position, structure, function and expression of every gene, [3] generation of many types of DNA markers for any agronomic gene/QTL of importance through the entire genome for marker-assisted plant breeding and germplasm diagnostics, and [4] development of revolutionary and new means for high-yield, high-quality and high-efficiency crop production.
Publications
- Walker RL, Robbins MD, Wu C, Zhang H-B, Coleman CE, Jellen EN, and Stevens MR. 2001. Fine mapping of the Fr1 locus in tomato (Lycopersicon esculentum). Plant & Animal Genome IX. P525.
- Lee M-K, Ren C, Ling P, Cox B, Dodgson JB, and Zhang H-B. 2001. Towards a BAC-based physical map of the chicken genome. Plant & Animal Genome IX. P582.
- Vinatzer BA, Patocchi A, Tartarini S, Gianfranceschi L, Zhang H-B, Gessler C, and Sansavini S. 2001. Identification and characterization of a receptor-like gene cluster from the Vf scab resistance locus in apple. Plant & Animal Genome IX. W95.
- Zhang H-B, Tao Q, Chang Y-L, Chen H, and Schuering C. 2001. Development and applications of genome-wide BAC/BIBAC-based physical maps for accelerated research of agricultural genomes. Plant & Animal Genome IX. W126.
- Wu C, Nimmakayala P, Santos FA, Springman R, Ding K, Tao Q, Meksem K, Lightfoot DA, and Zhang H-B. 2001. Development of a BAC/BIBAC-based physical map of the soybean genome for accelerated genomics research. Plant & Animal Genome IX. W135.
- Lee M-K, Ren C, Ling P, Cox B, Dodgson JB, and Zhang H-B. 2001. Development of a BAC-based physical map of the chicken genome for high-throughput gene mapping and cloning. Plant & Animal Genome IX. W176.
- McCuine SA and Zhang H-B. 2001. Seventy large-insert, ordered and high-quality BAC and BIBAC libraries for accelerated plant and animal genomics research. Plant & Animal Genome IX. P78.
- Meksem K, Zobrist K, Schultz J, Zhang H-B. 2001. Development of physical maps integrated with genetic markers and EST: Preclude to genome sequencing. Plant & Animal Genome IX. P79.
- Chen Q, and Zhang H-B. 2001. Construction of two BAC libraries from a wild Mexican diploid potato: Solanum pinnatisectum. Plant & Animal Genome IX. P97.
- Dong J, Kohel RJ, Zhang H-B, and Yu J. 2001. Bacterial artificial chromosome (BAC) libraries constructed from the genetic standard of Upland cottons. Plant & Animal Genome IX. P104.
- Chauhan R, Farman M, Hirt J, Durfee T, Ronald P, Zhang H-B, Blattener F, and Leong S. 2001. Genomics of blast resistance in rice line CO39 corresponding to avirulence locus Avr1-Co39 of Magnaporthe grisea. Plant & Animal Genome IX. P386.
- Iqbal J, Triwitayakorn K, Njiti V, Shulz J, Meksem K, Zhang H-B, and Lightfoot D. 2001. Harvesting genetic variation: combining genome wide integrated genetic and physical maps with expression profiling. Plant & Animal Genome IX. W99.
- Wu C, Nimmakayala P, Santos FA, Springman R, Tao Q, Meksem K, Lightfoot DA, and Zhang H-B. 2001. The NBS-LRR gene family in the soybean genome is organized and evolves by a process of birth-and-death, super-cluster formation and adaptive selection. Plant Cell (submitted).
- Wu C, Nimmakayala P, Santos FA, Springman R, Tao Q, Meksem K, Lightfoot DA, and Zhang H-B. 2001. Construction and characterization of a large-insert BAC library of soybean for whole-genome physical mapping and large-scale genome sequencing. Theor. Appl. Genet. (submitted).
- Chang Y-L, Preuss D, and Zhang H-B. 2001. A plant transformation-competent binary BAC library of the Arabidopsis thaliana Landsberg ecotype for functional and comparative genomics. Theor. Appl. Genet. (submitted).
- Tao Q, Wang A, Zhang H-B. 2001. Four large-insert BAC and BIBAC libraries of japonica rice cv. Nipponbare and their applications in global genome physical mapping and sequencing, and large-scale functional analysis of rice genome sequence. Theor. Appl. Genet. (accepted).
- Lichtenzveig J, Shtienberg D, Zhang H-B, and Abbo S. 2001. Dydimella rabiei-Cicer arietinum pathosystem: biometrics analyses of the field response genetics. Phytopathology. In press.
- Chang Y-L, Tao Q, Scheuring C, Meksem K and Zhang H-B. 2001. An integrated map of Arabidopsis thaliana for functional analysis of its genome sequence. Genetics. 159: 1231-1242.
- Tao Q-Z, Chang Y-L, Wang J., Chen H, Schuering C, Islam-Faridi MN, Wang B, Stelly DM, and Zhang H-B. 2001. Bacterial artificial chromosome-based physical map of the rice genome constructed by restriction fingerprint analysis. Genetics 158: 1711-1724.
- Vinatzer, BA, Patocchi, A, Gianfranceschi, L, Tartarini, S, Zhang, H-B, Gessler, C, Sansavini, S. 2001. Apple contains receptor-like genes homologous to the Cladosporium fulvum resistance gene family of tomato with a cluster of genes cosegregating with Vf apple scab resistance. Molecular Plant-Microbe Interactions 14: 508-515.
- Chang Y-L (Ph.D. dissertation). 2001. An Integrated System for Large-scale Functional Analysis of the Genome Sequence in Arabidopsis thaliana. Texas A&M University.
- Chang Y-L, Tao Q, Schuering C, Meksem K, and Zhang H-B. 2001. A BAC/BIBAC-based physical map of Arabidopsis thanliana: A platform for large-scale functional analysis of the genome sequence. Plant & Animal Genome IX. P83.
- Wu C, Nimmakayala P, Santos FA, Springman R, Tao Q, Meksem K, Lightfoot DA, and Zhang H-B. 2001. Development of a BAC/BIBAC-based physical map of the soybean genome. Plant & Animal Genome IX. P85.
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Progress 01/01/00 to 12/31/00
Outputs
The goals of this project are to develop a revolutionary, readily usable gene cloning system in crop plants and isolate the genes and QTLs important to agriculture. Towards these goals, we are working from several aspects. Below are summarized our accomplishments in 2001. 1. Genomic resource development - Large-insert BAC libraries are essential for genomics research, including marker development, gene discovery, cloning, characterization and utilization. In 2000, we developed 20 new BAC libraries. We now have 70 BAC libraries, the largest collection of the BAC libraries in the world. These libraries are playing a key role in accelerated genomics research. 2. Genome physical mapping - It is the centerpiece of genomics research and the readily usable gene cloning system under development. An integrated physical map will provide a "freeway" for large-scale, high-throughput gene mapping, target marker development, and discovery, cloning and characterization of every gene
in the species. We demonstrated feasibility and developed strategies and techniques of genome physical mapping with BACs, and constructed the BAC physical maps of indica rice and Arabidopsis. In 2000, we worked towards the BAC physical maps of soybean, wheat, chicken, japonica rice, cotton and maize. The lab work for soybean physical map and 1/2 of the lab work for chicken and japonica rice physical maps were completed, and physical mapping of wheat, cotton and maize was initiated. 3. Functional genomics: gene position, function, expression, organization and interaction - Development of the integrated physical maps has allowed us to initiate research of functional genomics. We developed techniques to position EST clones to physical maps in a throughput of > 20,000 EST or cDNA clones per scientist year, and initiated mapping the 16,000 maize and 10,000 wheat unigenes (ESTs). We also initiated functional genomics of disease resistances in cotton using the microarray technique. 4.
Comparative genomics - Development of the BAC libraries and physical maps has allowed us to study genome organization and evolution at the genome-wide level. We studied genome organization and evolution of rice, maize and wheat. 5. Bioinfomatics - To efficiently manipulate the data generated from genomics research, we created a database and a genomic information system for genomics of agricultural species. In 2000, we created the database for soybean, chicken and wheat genomics. 6. Isolation of agronomic genes - Many agronomic genes are known only by phenotype. To isolate such genes, we developed map-based cloning systems in crop plants. In 2000, we continued mapping and cloning of the genes for root-knot resistance (RNR) in cotton and everblooming in rose. We identified 6 DNA markers for RNR, and developed three large mapping populations for cotton RNR and a mapping population for rose everblooming. 7. DNA markers and map development - To facilitate research of legume genomes, we are
developing genomic tools for legume gene mapping and cloning, and genome analysis using chickpea as a model. In 2000, we were developing SSR markers and map for chickpea and mapping several of genes and QTLs in the species.
Impacts
This project will provide a revolutionary, novel and readily usable system for [1] discovery and isolation of a large number of genes and quantitative trait loci important to agriculture, [2] determination of the position, structure, function and expression of every gene, [3] generation of all types of DNA markers through the entire genome for enhanced plant breeding and germplasm diagnostics, and [4] development of revolutionary and new means for high-yield, high-quality and high-efficiency crop production.
Publications
- Yu J, Kohel RJ, Zhang H-B, Dong J, and Decanini L. 2000. Construction of a cotton BAC library and its applications to gene isolation. Plant & Animal Genome VIII. P146.
- Tao Q, Wang A, and Zhang H-B. 2000. Three large-insert BAC libraries and one BIBAC library of rice cv. Nipponbare. Plant & Animal Genome VIII. P118.
- Chang Y-L, Santos TS, Q. Tao A. Wang L. He L, and Zhang H-B. 2000. Construction and characterization of two maize inbred line B73 BAC libraries. Plant & Animal Genome VIII. P124.
- Xu K, Xia Xu1, Zhang H-B, Deb R, Ronald PC, and Mackill DJ. 2000. Fine-scale mapping of the rice submergence tolerance gene. Plant & Animal Genome VIII. W2.
- Chang Y-L, Tao Q, Chen H, Wang J, Meksem K, and Zhang H-B. 2000. A genome-wide, large-scale genome sequencing- and plant transformation-ready BAC and BIBAC map of Arabidopsis thaliana. Plant & Animal Genome VIII. P147.
- Tao Q, Chang Y-L, Wang J, Chen H, Islam-Faridi MN, Scheuring C, Wang BB, Stelly DM, and Zhang H-B. 2000. The genome-wide physical maps of the rice and Arabidopsis genomes: Reliability and accessibility. Plant & Animal Genome VIII. W151.
- Zhang H-B, and Scheuring C. 2000. Fifty large-insert, ordered and high-quality BAC and BIBAC libraries for accelerated plant and animal genomics research. Plant & Animal Genome VIII. P112.
- Pecherer RM, Polacco M, Zhang H-B, Beavis WD, Cartner T, and Shroeder S. 2000. A comparison of maize and rice genome maps. Plant & Animal Genome VIII. P21.
- Tao Q, Chang Y-L, Wang J, Chen H, Islam-Faridi MN, Scheuring C, Wang BB, Stelly DM, and Zhang H-B. 2000. The genome-wide BAC physical map of the rice genome: Reliability and accessibility. Plant & Animal Genome VIII. P123.
- Wu C, Nimmakayala P, Tao Q, Santos FA, Meksem K, Lightfoot DA, and Zhang H-B. 2000. Toward development of a genome-wide, BAC and BIBAC physical map of the soybean genome. Plant & Animal Genome VIII. P137.
- Chen H, Tao Q, Chang Y-L, Zhang H-B. 2000. A web-based genomic information system for efficiently manipulating, displaying and accessing the BAC physical maps of genomes. Plant & Animal Genome VIII. C6.
- Zhang H-B. 2000. Construction and Manipulation of Large-insert Bacterial Clone Libraries - Manual. Texas A&M University, Texas, USA.
- Chen H (thesis). 2000. A web-based genomic information system for efficiently manipulating and accessing genome physical maps (the PI is the major professor of the student).
- He L (thesis). 2000. Identification of DNA marker for root-knot nematode resistant gene and characterization of disease resistance genes in cotton (the PI is the major professor of the student).
- Hume, M.E., Harvey, R.B., Stanker, L.H., Droleskey, R.L., Poole, T.L., and Zhang, H.-B. 2000. Genotypic variation among Arcobacter isolates from a farrow-to-finish swine facility. J. Food Prot. In press.
- Zhang, H.-B., and Wu, C.C. 2000. BACs as tools for genome sequencing. Plant Physiology and Biochemistry. In press
- Deng, Z., Tao, Q., Chang, Y.-L., Gmitter Jr., F.G., and Zhang, H.-B. 2000. Construction of a bacterial artificial chromosome (BAC) library for citrus and identification of BAC contigs containing citrus resistance gene candidates. Theor. Appl. Genet. In press.
- Zobrist, K., Meksem, K., Lightfoot, D.A., Wu, C., Santos, F.A., Nimmakayala, P., Tao, Q., and Zhang, H.-B. 2000. Integrative physical mapping of the soybean genome: A tool for rapid identification of economically important genes. Soybean Genetics Newsletter, 27:15-20.
- Wu C, Nimmakayala P, Santos FA, Meksem K, Lightfoot DA, and Zhang H-B. 2000. Toward development of a BAC/BIBAC-based physical map of the soybean genome: A platform for high-throughput gene mapping, gene cloning, marker development and large-scale genome sequencing. Soy2000 8th Biennial Conference of the Cellular and Molecular Biology of the Soybean. August 13 - 16, 2000. Lexington, Kentucky. PIII 15.
- Meksem K, Shulz J, Iqbal J, Ruben E, Triwitakorn TK, Zobrist K, Zhang H-B, and Lightfoot DA. 2000. Development of physical maps integrated with genetic markers and EST: Prelude to genome sequencing. Soy2000 8th Biennial Conference of the Cellular and Molecular Biology of the Soybean. August 13 - 16, 2000. Lexington, Kentucky. PIII 05.
- Brabson JS, Islam-Faridi MN, Zhang H-B, and Kinlaw CS. 2000. Mapping of pine BACs: Toward integration of genetic and physical maps. Plant & Animal Genome VIII. P349.
- Deng Z, Gmitter Jr. FG, Chen C, Huang S, Ling P, Yu C, and Zhang H-B. 2000. Potential applications of bacterial artificial chromosome libraries in isolation of disease resistance genes in citrus. Plant & Animal Genome VIII. W91.
- Deng, Z., Huang, S., Ling, P., Yu, C., Chen, C., Wendell, M.K., Zhang, H.-B., and Gmitter Jr., F.G. 2001. Fine genetic mapping and BAC contig development for the citrus tristeza virus resistance gene locus in Poncirus trifoliata (Raf.). Mol. Gen. Genet. In press.
- Deng Z, Huang S, Ling P, Tao Q, Zhang H-B, Chen C, Yu C, Wendell MK, and Gmitter Jr. FG. 2000. Genetic and physical mapping of the CTV resistance gene region and identification of putative resistance gene sequences. Plant & Animal Genome VIII. P148.
- Chauhan RS, Farman M, Hirt J, Ronald P, Zhang H-B, and Leong S. 2000. Genetic analysis and fine mapping of a locus for blast resistance in rice line, Co39, and construction of its BAC library. Plant & Animal Genome VIII. P181.
- He L, Yu Z, Bridges A, Robinson F, Kohel R, and Zhang H-B. 2000. Isolation and characterization of disease resistance (R) genes in cotton. Plant & Animal Genome VIII. P57.
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Progress 01/01/99 to 12/31/99
Outputs
The goals of this project are to develop a revolutionary, novel and readily usable gene cloning system in crop plants and isolate the genes important to agriculture. Below are summarized our significant findings and accomplishments toward these goals in 1999. 1. BAC and binary BAC (BIBAC) library development - Large-insert BAC libraries are essential for genomics research. In 1999, we developed 10 new large-insert BAC and BIBAC libraries. We now have 50 BAC and BIBAC libraries, the largest collection of the BAC libraries in the world. Currently, over 540 laboratories world-wide are using our BAC libraries in research. 2. Genome physical mapping - Genome physical mapping, i.e., reconstruction of genomes from large-insert, ordered DNA libraries, is the centerpiece of the readily used gene cloning system under development. A genome physical map will provide a "freeway" for targeted marker development, large-scale gene mapping, discovery, cloning, characterization and
utilization. In previous studies, we demonstrated the feasibility for and developed strategies and technologies of developing genome physical maps from ordered BAC libraries, and constructed the genome-wide BAC/BIBAC physical maps of the rice and Arabidopsis genomes. This is the first case in the world that the physical maps were so successfully developed from BACs, thus providing a paradigm for developing physical maps of other crop species. In 1999, we extensively tested the reliability of the rice and Arabidopsis BAC/BIBAC physical maps, integrated the BAC physical maps and genetic linkage maps for rice chromosomes 8, 11 and 12, created a new database especially for integrated genetic and physical maps of agricultural genomes, and developed a new, web-based genomics information system (GIS) for physical map manipulation and utilization. We initiated genome-wide integrated physical mapping of the soybean and chicken genomes, and completed about 1/2 of lab work for construction of
the soybean BAC/BIBAC physical map. 3. Isolation of agronomic genes - Many agronomic genes are known only by phenotype. To isolate such genes, we have developed map-based cloning systems in cotton, rice and rose. In 1999, we cloned the cotton genomic DNA sequences that potentially confer resistance to nematodes, fungi, bacteria and viruses, and sequenced and mapped some of the cotton disease resistance candidate clones to the existing cotton genetic map. We also worked towards molecular tagging and mapping of the gene for recurrent flowering in rose, which is unique in the plant kingdom and economically significant to recurrent production of flowers and fruits during seasons. 4. New technologies development - Because advance of science depends on technology, we continued the development of new technologies for plant genomics research in 1999, with special emphasis on large-insert BIBAC transformation in Arabidopsis and cotton. This technology will streamline positional cloning and
engineering of genes/QTLs of agronomic importance in plants. We have developed technologies and transformed a 120 kb soybean BIBAC into Arabidopsis. The transformation of BIBAC into cotton is under verification.
Impacts
This project will provide a revolutionary, novel and readily usable system for [1] discovery and isolation of a large number of genes and quantitative trait loci important to agriculture, [2] determination of the position, structure, function and expression of every gene, [3] generation of all types of DNA markers through the entire genome for enhanced plant breeding and germplasm diagnostics, and [4] development of revolutionary and new means for high-yield, high-quality and high-efficiency crop production.
Publications
- Patocchi A, Vinatzer BA, Gianfranceschi S, Zhang H-B, Sansavini S, Gessler C. 1999. Construction of a 550-kb BAC contig spanning the genomic region containing the apple scab resistance gene Vf. Mol. Gen. Genet. In press.
- Wu Y, Tulsieram L, Tao Q, Zhang H-B, Rothstein SJ. 1999. Construction of a large DNA insert library for Brassica napus using a conventional binary vector and identification of clones linked to a fertility restorer locus for Ogura CMS. Genome. In press
- Meksem, K., E. Ruben, K. Zobrist, D. Hyten, Q. Tao, H.-B. Zhang, and A. D. Lightfoot. 1999. Two plant transformation ready bacterial artificial chromosome libraries for soybean: Applications in chromosome walking and genome-wide physical mapping. Theor. Appl. Genet. In press
- Zhang, H.-B., M. A. Budiman, and R.A. Wing. 1999. Genetic mapping of jointless-2 to tomato chromosome 12 using RFLP and RAPD markers. Theor. Appl. Genet. In press
- Zwick MS, N. Islam-Faridi, H.-B. Zhang, G. L. Hodnett, M. I. Gomez, J. S. Kim, H. J. Price and D. M. Stelly. 1999. Distribution and sequence analysis of the centromere-associated repetitive element CEN38 of Sorghum bicolor. Proc. Natl. Acad. Sci. USA. In press
- Qiu, F., D. Jin, J. Fu, C. Zhang, W. Xie, R. Yang, H.-B. Zhang and B. Wang. 1999. Construction and characterization of a bacterial artificial chromosome library of thermo-sensitive genic male-sterile rice 5460S. Science in China, 42: 599-606.
- Scheuring C, Zhang H-B. 1999. The Texas A&M BAC Center - A Public Facility for Accelerated Plant Genomics Research. Plant & Animal Genome VII. P114.
- Gmitter Jr. FG, Chang Y-L, Deng Z, Huang S, Louzada ES, Zhang H-B. 1999. Construction of a deep bacterial artificial chromosome (BAC) library for mapping and cloning of agriculturally important genes in Poncirus and Citrus. Plant & Animal Genome VII. P111.
- He L, Bridges A, Robinson F, Cook CC, Zhang H-B. 1999. Toward map-based cloning of root-knot nematode resistant genes in cotton. Plant & Animal Genome VII. P84.
- Islam-Faridi MN, Williams C, Hodnett GL, Zhang H-B, Kim J-S, Hanson RE, Stelly DM, Price HJ. 1999. FISH of pCEN38 demonstrates common ancestry of sorghum and sugarcane subspecies. Plant & Animal Genome VII. W183.
- Lightfoot DA, Zhang H-B, Meksem K, Ruben E, Chancharoenchai K, Panzatopoulos P, Cregan P, Rao-Arelli P, Njiti V. 1999. Development of a genome integrated physical map: positional cloning of QTL from soybean. Plant & Animal Genome VII. W117.
- Santos TS, He L, Chang Y-L, Zhang H-B. 1999. Generation and characterization of a BAC library from the maize inbred line B73 for maize genomics research. Plant & Animal Genome VII. P97.
- Stelly DM, Crane CF, Hodnett GL, Price HJ, Zhang H-B, Kim J-S, Islam-Faridi MN, Gomez M, Zwick MS, Hanson RE. 1999. Polyploidization and repetitive elements in genome evolution. Plant & Animal Genome VII. W141.
- Chang Y-L, Tao Q, Wang J, Scheuring C, Meksem K, Zhang H-B. 1999. A large-scale plant transformation- and genome sequence-ready physical map of the Arabidopsis thaliana genome. Plant & Animal Genome VII.W29.
- Tao Q, Zhang H-B. 1999. Cloning and stable maintenance of DNA fragments over 300 kb in Escherichia coli with conventional plasmid-based vectors. Plant & Animal Genome VII. P119.
- Tao Q, Chang Y-L, Wang J, Chen H, Islam-Faridi MN, Scheuring C, Wang B, Stelly DM, and Zhang H-B. 1999. A large-scale sequence-ready physical map of the rice genome. Plant & Animal Genome VII. P93.
- Tao Q, Zhang H-B. 1999. Large DNA fragment cloning in bacteria beyond BACs and PACs. Plant & Animal Genome VII. W107.
- Tao Q, Chang Y-L, Wang J, Chen H, Islam-Faridi MN, Scheuring C, Wang B, Stelly DM, and Zhang H-B. 1999. Integrative physical mapping of genomes with large-insert bacterial clones: the sequence-ready physical map of the rice genome. Plant & Animal Genome VII. W111.
- Vinatzer AB, Sanasavini S, and Zhang H-B. 1999. Construction of an apple BAC library and its use for gene isolation. Plant & Animal Genome VII. W108.
- Meksem K, Lightfoot DA, Ruben E, Zhang H-B, Chancharoenchai K, Zobrist K, Panzatopoulos P, Rao-Arelli P. 1999. Soybean Gene Golfing: Positional cloning of the cyst nematode resistance loci in soybean. Plant & Animal Genome VII. P79.
- Meksem K, Zobrist K, Panzatopoulos I, Chancharoenchai K, Ruben E, Zhang H-B, Rao-Arelli P, Lightfoot DA. 1999. Development of genome integrated physical map; positional cloning of the cyst nematode resistance loci in soybean. Plant & Animal Genome VII. W112.
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Progress 01/01/98 to 12/31/98
Outputs
The focuses of this project are to develop readily used gene cloning systems in crop plants and isolate the genes important to agriculture. In 1998, we had made exciting progress. Below are summarized the significant findings and accomplishments. 1. BAC library development - Large-insert BAC libraries are essential genetic resources for genomics research, including gene discovery, cloning, study and utilization. In general, it takes 1 - 2 years for two personnel and costs $50,000 to $300,000 to develop a BAC library. In 1998, we developed 23 large-insert BAC libraries. Now the Texas A&M BAC Center has 40 BAC libraries, the largest collection of the BAC libraries in the world. Currently, over 400 laboratories world-wide are using our BAC libraries in research. 2. Genome physical mapping - Genome physical mapping, i.e., reconstruction of genomes from large-insert, ordered DNA libraries, is the centerpiece of modern genomics research. It is also the centerpiece of the
readily used gene cloning systems under development. A genome physical map will not only provide a most powerful organizational framework for all biological research results, such as linkage maps, DNA markers, genes, QTLs, ESTs, large-insert clones, repeat elements, etc., but also provide a "freeway" for marker development, gene mapping, discovery, cloning, study and utilization. In previous studies, we demonstrated the feasibility and developed strategies and technologies of developing genome physical maps from ordered BAC libraries. In 1998, we successfully developed the physical maps of the rice and Arabidopsis genomes. This is the first case in the world that the physical maps were so successfully developed from BACs. This will provide a paradigm for developing physical maps of other crop species, such as maize, cotton, wheat, etc. 3. Isolation of agronomic genes - Many agronomic genes are known only by phenotype. To isolate such genes, we have developed map-based cloning systems
in cotton, rice and rose. We isolated DNA markers and clones for and developed mapping populations for map-based cloning of the genes conferring resistance to the cotton root-knot nematode. To clone the gene conferring resistance to rice blast, we constructed a BAC contig containing the gene. We also initiated a research project to clone the gene for recurrent flowering in rose, which is unique in the plant kingdom and economically significant to recurrent production of flowers and fruits during seasons. 4. New technologies development - Advance of science depends on technology. Because of this, we had also emphasized the development of new technologies for plant genomics research in 1998. They are the new theory and concept for cloning of large fragments of plant and animal DNAs in bacteria, the techniques for cloning of binary BACs suitable for direct plant transformation for gene identification and engineering, the techniques for cloning BACs with average insert sizes from 200 to
500 kb, and the efficient strategies and corresponding techniques for ordering gene (EST or cDNA) clones to a physical map, with which about 40,000 EST or cDNA clones can be mapped to a physical map per scientist year.
Impacts
(N/A)
Publications
- Tao Q.-Z. and H.-B. Zhang. 1998. Cloning and stable maintenance of DNA fragments over 300 kb in Escherichia coli with conventional plasmid-based vectors. Nucleic Acids Res. 26: 4901-4909
- Dvorak, J., M.-C. Luo, Z.-L. Yang and H.-B. Zhang. 1998. The structure of Aegilops tauschii genepool and the evolution of hexaploid wheat. Theor. Appl. Genet. 97:657-670.
- Vinatzer, B. A., S. Sanasavini, and H.-B. Zhang. 1998. Construction and characterization of a BAC library of apple (Malus x domestica Borkh.). Theor. Appl. Genet. 97: 1183-1190.
- Hamilton, C. M., A. Frary, Y Xu, S. D. Tanksley and H.-B. Zhang. 1998. Construction of tomato genomic DNA libraries in a binary-BAC (BIBAC) vector. Plant J. In press
- Peng, K., H.-B. Zhang, and Q. Zhang. 1998. Highly efficient construction of a rice BAC library from variety Minghui 63 for cloning genes of agronomic importance. Acta Botanica Sinica In press.
- Moullet, O., H.-B. Zhang and E. S. Lagudah. 1998. Construction and characterisation of a large DNA insert library from the D genome of wheat. Theor. Appl. Genet. In press
- Meksem K, Ruben E, Hyten D, Zhang H-B and Lightfoot DA. 1998. Methods for physical mapping with directed microsatellite and AFLP markers. Theor. Appl. Genet. In press
- Zhang H-B. 1998. The Texas A&M BAC Center: Ten new BAC libraries constructed in 1997. Plant & Animal Genome VI. P15
- Meksem K, Lightfoot DA, and Zhang H-B. 1998. Development of genomes integrated physical map for gene golfing. Plant & Animal Genome VI. P16
- Tao Q, and Zhang H-B. 1998. Integrative physical mapping of crop genomes with bacterial artificial chromosomes. Plant & Animal Genome VI. P17
- Islam-Faridi MN, Chang Y-L, Zhang H-B, Kinlaw C, Doudrick RL, Neale DB, Echt C, Price HJ, and Stelly DM. 1998. Construction of a pine BAC library. Plant & Animal Genome VI. P18
- Chang Y-L, Wang J, Tao Q, Schuering C, and Zhang H-B. 1998. Rapid development of a physical map of the Arabidopsis genome with BACs. Plant & Animal Genome VI. P19
- Peng K, Zhang H-B, and Zhang Q. 1998. Highly efficient construction of a rice BAC library using variety Minghui 63 for cloning genes of agronomic importance. Plant & Animal Genome VI. P20
- Meksem K, Zhang H-B, and Lightfoot DA. 1998. Construction of a soybean transformation competent artificial chromosome library for the efficient isolation of soybean genes. Plant & Animal Genome VI. P26
- Mullet J, Klein R, Klein P, Cartinhour S, Dong J, Zhang H-B, Tao Q, Morishige D, Ulanch P, Childs K, Park B, Bennetzen J. 1998. Initial steps toward construction of integrated genetic/physical map of the sorghum genome. Plant & Animal Genome VI. W125
- Tao Q, Chang Y-L, Wang J, Islam-Faridi MN, Schuering C, Wang B, Peng K, Zhang Q, Stelly DM, and Zhang H-B. 1998. Toward development of an integrated physical map of the rice genome with BACs. Plant & Animal Genome VI. P403
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Progress 01/01/97 to 12/31/97
Outputs
The focus of my research is on development and implementation of readily-used systems to rapidly move from DNA markers to genes important to Texas agriculture. Significant progress has been made in 1997: 1. Large-insert BAC libraries development. We have established the Texas A&M BAC Center. In general, it takes 1 - 3 years for two personnel and costs 50,000 to 500,000 US dollars to develop a BAC library. In 1997, we developed 17 new BAC libraries for different crops, which has led to that the BAC Center has the largest collection of BAC libraries in the world. These BAC libraries are crucial resources for gene discovery, cloning and utilization. 2. New technologies development. A. New vectors for both large-insert library development and direct plant transformation - To expedite gene discovery, cloning and engineering, we have discovered a new system for large DNA fragment cloning superior over BACs and PACs and developed a series of vectors. B. Technologies for
genome physical mapping - Rapid and enhanced gene discovery, cloning and utilization will hinge on genome physical mapping. To accelerate physical mapping of genomes, we have developed a complete set of technologies (Invention No.: TAMUS1228) for rapid development of physical maps with BACs. These technologies will revolutionize current genome research. C. Technologies for large DNA fragment transformation in crop plants. The goals of this project are to develop a large DNA fragment transformation system in crops for accelerated positional cloning and engineering of agronomic genes. Cotton was transformed with BACs and potential transgenic seeds were obtained. This technology is still under development. 3. Development of integrated physical maps of plant genomes for rapidly "golfing" agronomically important genes. A. Grass crops - To rapidly move from DNA markers to genes, we are developing an integrated physical map for grass crops using rice as the reference species with our
technologies. In 1997, we have completed all lab work for developing a complete physical map of the rice genome. Now we are assembling the physical map of the rice genome from these BACs. B. The model species Arabidopsis thaliana - The genome of this species will be completely sequenced within a few years. However, the functions of over 70 percent of these sequences remain unknown. The goals of this project are to develop a system to rapidly determine gene function using the DNA sequences available. This involves development of general and functional physical maps for this species. In 1997, we have completed the lab work for developing the general physical map. Now we are assembling the general physical map and developing the functional physical map. 4. Positional cloning of agronomic genes and QTLs. A. Cotton - we have developed a research project in identification and isolation of genes for nematode resistance in cotton. B. Rice - we are working toward isolation of the genes for
heading date and for sheath blight resistance. We have generated the BAC contigs containing these genes and now are working toward identification of these genes.
Impacts
(N/A)
Publications
- Zhang, H.-B and R.A.Wing. 1997. Physical Mapping of the rice genome with BACs. Plant Mol Biol 35:115-127
- Chen, M., P. SanMiguel, A.C. de Oliveira, S.-S. Woo, H.-B. Zhang, R.A. Wing, and J.L. Bennetzen. 1997. Microcolinearity in sh2-homologous regions of the maize, rice and sorghum genomes. Proc. Natl. Acad. Sci. USA 94: 3431-3435
- Resta, P., H.-B. Zhang, J. Dubcovsky, and J. Dvorak. 1997. The origins of the genomes Triticum biunciale, T. ovatum, T. neglectum, T. columnare and T. rectum (Poaceae) based on variation in nuclear DNA sequences. Amer. J. Bot. (In press)
- Tao, Q., Y.-L. Chang, J. Wang, M.N. Islam-Faridi, K. Peng, Q. Zhang, B. Wang, D. M. Stelly, and H.-B. Zhang. 1997. Toward development of an integrated physical map of the rice genome with bacterial artificial chromosomes. The General Meeting of the International Program on Rice Biotechnology, September 15-19, 1997, Malacca, Malaysia. p111
- Zhang, H.-B. 1997. Toward development of a BAC Center for genome research. Plant & Animal Genome V. P36
- Vinatzer, B. A., S, Sansavini, H.-B. Zhang. 1997. Construction and characterization of an apple BAC library. Plant & Animal Genome V. P33
- Wang, J., R. A. White, R. A. Wing, and H.-B. Zhang. 1997. Toward map- based cloning of the Hd3a locus regulating rice heading date. The General Meeting of the International Program on Rice Biotechnology, September 15-19, 1997, Malacca, Malaysia. p250
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