Progress 11/16/14 to 11/15/19
Outputs
Target Audience:Genes are the centerpiece for studies of a trait or biological process that they control and also for development of technologies enabling enhanced breeding for the trait that they control. We previously developed a novel genome-wide high-throughput system, gExpress, to clone the genes or QTLs controlling agronomic traits. The goals of this research project were to use this new gene cloning technology to genome-wide and high-throughput clone the genes controlling agronomic traits in crops and use the cloned genes to decipher the molecular mechanisms underlying agronomic traits or biological processes. We also developed new breeding methods, such as gene-based breeding (GBB), and genic toolkits for enhanced breeding in crops important to the USA and the State of Texas, such as cotton and maize by making full use of the new knowledge, new cloned genes, the state-of-the-art technologies, such as high-through DNA sequencing and bioinformatics tools, and the new concepts, new strategies and new methods of systems genomics and systems biology that study biology and develop tools in an integrated manner. Therefore, this project targeted the following audiences: Research scientists in plant molecular biology and biotechnology. The cloned genes and the discovered new knowledge promote many areas of plant molecular biology and biotechnology research, including development of new methods for enhanced plant genetic improvement, such as gene editing, gene regulation, and genetic engineering. Plant breeders. Not only was this project accomplished in collaboration with 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), but also the knowledge and gene toolbox developed through this project dramatically enhances crop plant breeding and revolutionizes the current breeding methods. Graduate students. First, numerous graduate students who were majoring in plant breeding were directly involved in this project. Second, the knowledge and tools developed through the project have been extended to classrooms, thus educating new generation breeders and agronomists for enhanced plant breeding and enhanced crop production, such as gene-based production or molecular precision agriculture. Research scientists in animal science and human medicine. The findings and methodologies of this project are applicable to research of livestock and humans, thus promoting livestock research and breeding, and human medicine. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?This project helped pioneer one new discipline, systems biology, and pioneered two new disciplines, systems genomics and gene-based breeding (GBB), thus making significant contributions to science and technologies. The results of the project will revolutionize the current biological science research, human medicine research, and plant and animal breeding. Therefore, this project provided a unique opportunity in training students and professionals in these new disciplines and cutting-edge research: This project has trained three postdoctoral scientists, 27 graduate students, six visiting scholars and a number of students in classroom: 1. Postdocs Yang Zhang, September 2013 - July 2015. Delin Xu, October 2016 - October 2018 Yun-Hua Liu, September 2014 - December 2019 2. Graduate Students Kari Hugie, Ph.D. in Plant Breeding, graduated in 2015 Daman Bhangu, M.S. in Plant Breeding, graduated in 2015 Jingjia Li, M.S. in Plant Breeding, graduated in 2016 Laura L. Masor, Ph.D. in Plant Breeding, graduated in 2016 Lorin M. Harvey, M.S. in Plant Breeding, graduated in 2016 Angira Brijesh, Ph.D. in Plant Breeding, graduated in 2016 Xiangkun Gu, Ph.D. in Molecular and Environmental Plant Science, graduated in 2017 Nancy J. Wahl, 2017, Ph.D. in Genetics, graduated in December 2017 Vishal Saitwal, Ph.D. in Plant Breeding, graduated in September 2017 Victoria L. Morrison, M.S. in Professional Program in Biotechnology, graduated in 2018. Murat Aci, M.S. in Plant Breeding, graduated in May 2018 Kotilingam Konda, Ph.D. in Plant Breeding, graduated in August 2018. Homa Zarghami, Ph.D., in Molecular and Environmental Plant Sciences, 2014 - Mitchell Schumann, Ph.D. in Plant Breeding, 2014 - Daman Bhangu, Ph.D. in Plant Breeding, 2015 - Jamshaid Ali Junaid, Ph.D. in Plant Breeding, 2015 - Jingjia Li, Ph.D. in Ecosystem Science and Management, 2015 - Daman Bhangu, Ph.D. in Plant Breeding, 2015 - Kotilingam Konda, Ph.D. in Plant Breeding, 2015 - Murat Aci, M.S. in Plant Breeding, 2016 - Ali Ullrich, M.S. in Plant Breeding, 2016 - Mustafa Cilkiz, Ph.D. in Molecular and Environmental Plant Sciences, 2017 - Selfinaz K Velioglu, M.S. in Plant Breeding, 2017 - Xuan Lin, Ph.D. in Molecular and Environmental Plant Science, 2017 - Salma Bibi, M.S., in Molecular and Environmental Plant Science, 2017 - Gali Bai, M.S. in Molecular and Environmental Plant Science, 2018 - Mehmet Dogan, M.S. in Plant Breeding, 2018 - 3. Visiting scholars Dr. Yadong Zhang, Jiangsu Academy of Agricultural Sciences, China Dr. Xiaoli Qi, Jiamusi University, China Yasemin Özhan, Ede University, Turkey Dr. Jianmin Song, Shandong Academy of Agricultural Sciences, China Dr. Wei Zhou, Hunan Agricultural University, China Dr. Quang Qiao, University of Guizhou, China 4. Classroom teaching SCSC, GENE, BIOT and MEPS 654 - Analysis of Complex Genomes (lectures) SCSC, GENE, BIOT and MEPS 655 - Analysis of Complex Genomes (labs) SCSC 685 (602) - Directed Studies MEPS 691 (618) - Research SCSC 691 (606) - Research 5. Workshops and seminars Co-organized the Systems Genomics and Analysis of Complex Genomes workshops in the annual International Plant & Animal Genome Conference, San Diego, California; Invited to present eight lectures and seminars at national or international conferences or institutions. 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 Genomics, Food Chemistry, Crop Science, Plant Breeding, Nature Communications, PLoS ONE, Plant Breeding, Frontiers in Plant Science, Molecular Genetics and Genomics, and Frontiers of Agricultural Science and Engineering Presented the results and achievements of this project at national and international professional conferences such as the annual International Plant & Animal Genome Conference, Annual Meeting of American Society of Crop Science, American Society of Agronomy and American Society of Soil Science, National Association of Plant Breeders Meeting, and Beltwide Cotton Conference. Incorporated the findings and discoveries of this project into the classroom teaching such as SCSC, GENE, BIOT and MEPS 654 - Analysis of Complex Genomes (lectures), SCSC, GENE, BIOT and MEPS 655 - Analysis of Complex Genomes (labs), SCSC 685 (602) - Directed Studies, MEPS 691 (618) - Research and SCSC 691 (606) - Research Incorporated the findings and discoveries of this project into training of students, postdoctoral associates and junior scientists. We trained 27 graduate students, three postdoctoral associates and six junior scientists during this period of the project. Directly delivered the new knowledge, resources and tools developed in this project to users such as breeders and researchers nationwide through collaboration with companies, such as Monsanto and BioNano Genomics, patent commercialization and invention disclosure. Directly delivered the new knowledge, resources and tools developed in this project to users such as breeders and researchers nationwide through collaboration. What do you plan to do during the next reporting period to accomplish the goals?
Nothing Reported
Impacts
What was accomplished under these goals?
Genes are the core of all biological processes and morphological and physiological characters of all living organisms, including humans, plants, animals and microorganisms. They essentially determine every aspect of human's life, including, but not limited to, human's life span, intelligence, creativity, pleasure, health, medicine, food, clothe, household use, shelter and living environments. Nothing can replace the importance and roles of genes in human's life. Therefore, genes are the keys to understanding human themselves - life span, intelligence, creativity, health and medicine, and the biological mechanisms underlying the production of human food and other well-being dependents, such as crops, livestock, trees, and other organisms. Importantly, genes are also the keys to designing and developing new or advanced technologies to continuously improve human life span, intelligence, creativity, health and medicine, and to continuously improve crop and livestock productivity and quality to sustain the security of increasing global population's food and other supplies. Molecular biology research has been pursued for over 60 years. A number of technologies, such as map-based cloning and gene editing, have been developed to identify and clone the genes controlling the characters or traits of importance to human life span, intelligence, creativity, health, diseases and medicine, and the genes controlling the traits of importance to human food production in crops and livestock. Nevertheless, only a very limited number of these genes have been cloned worldwide to date. For instance, human has 22,000 - 30,000 genes, of which only fewer than 1,000 genes are estimated to be cloned. Bread wheat has 50,000 - 60,000 genes, of which only fewer than a hundred are estimated to be cloned. There is an absence or little has been known of how the genes controlling a biological trait function to shape the performance of the trait because a vast majority of biological traits or processes are controlled by numerous genes. This may explain why the biotechnology revolution has not yet come, even though it was proposed 30 years ago. In contrast, the IT (Information Technology) revolution that was proposed at almost the same time as the biotechnology revolution has already gone through a few of revolutionary waves. This project has, for the first time worldwide, demonstrated the ability, utility and efficiency of the novel technology (named the gExpress technology) that we invented in previous studies for genome-wide high-throughput and rapid cloning of genes controlling a simple or complex trait or involved in a biological process in a species. Within the five-year period of this project, we cloned a large number of genes controlling corn grain yield and grain yield and quality traits, and a large number of genes controlling cotton fiber yield and fiber quality and yield traits using the gExpress technology. We demonstrated the utility and efficiency of the cloned genes for enhanced breeding using the cloned corn grain yield genes and cotton fiber length genes. We, for the first time, proposed and demonstrated gene-based breeding, an innovative and revolutionary technology that is extremely powerful and efficient for plant and animal breeding. The findings of these studies also led us to propose gene-based agriculture or molecular precision agriculture that manages crop production, such as irrigation and fertilization, through managing activities of the genes controlling the objective traits such as yield and quality. Using the cloned genes, we deciphered the molecular mechanisms of several biological traits or processes of agronomic importance. The gExpress technology is not only reliable and high-throughput, but importantly, it is also readily applicable to cloning of the genes controlling any trait in a species, including plants, animals, humans and microorganisms, regardless of its genome size, complexity, ploidy level and knowledge; therefore, this project has demonstrated that it is feasible to clone most, if not all, of the genes of a species and determine their biological functions through our gExpress technology, including crops, livestock and humans. As genes are the keys to biotechnology revolution, this project sheds bright light on the next green revolution in crop improvement and production as well as human health and medicine biotechnology revolution: from the current phenotypic medicine (i.e., treat a human disease or cancer after it is seen or detected) to gene-based medicine (i.e., treat a human disease or cancer based on the activities of the genes involved in the disease before it is seen or detected). Listed below are the major accomplishments of this project in the five-year period: We cloned a total of 19,961 genes controlling 22 agronomic traits, including 9,007 genes from corn and 10,954 genes from cotton. The 9,007 corn genes include 1,501 genes controlling inbred grain yield, 137 genes controlling hybrid grain yield, 1,235 genes controlling kernel weight, 722 genes controlling ear weight, 652 genes controlling ear length, 725 genes controlling kernel row length, 346 genes controlling ear diameter, 286 genes controlling cob diameter, 344 genes controlling kernel row number, 259 genes controlling kernel moisture, 419 genes controlling starch content, 427 genes controlling protein content, 446 genes controlling fat content, 527 genes controlling phosphorus content, and 981 genes controlling grain yield heterosis. The cotton 10,954 genes include 3,140 genes controlling lint yield, 2,494 genes controlling seed yield, 1,240 genes controlling lint percentage, 474 genes controlling fiber length, 1,078 genes controlling fiber strength, 725 genes controlling fiber uniformity, 742 genes controlling fiber elongation, and 881 genes controlling micronaire. The number of the genes cloned through this project is probably a few-fold more than the total number of genes cloned from plants, animals and humans worldwide in the past 40 years. We, for the first time, deciphered the molecular mechanisms of crop yield (corn), crop quality (cotton), quantitative genetics (corn and cotton), grain yield heterosis (corn), and plant polyploidization (cotton) using the cloned genes. It has been documented that most traits or biological processes of agronomic importance are quantitative traits, i.e., the traits that are inherited quantitatively and can be only quantified by measurement; heterosis or hybrid vigor is the molecular basis of hybrid varieties that have been widely used in production of corn, sorghum, vegetables, fruit trees and livestock; and a majority of flowering plants, including field crops, vegetables and fruit trees, are polyploids. The molecular knowledges of these traits are essential to design technologies and methodologies for enhanced breeding, such as gene-based breeding and gene-editing, and for enhanced crop production such as gene-based agriculture. We established gene-based breeding (GBB), a new discipline that is extremely powerful and efficient for plant and livestock breeding. We first demonstrated the utility and efficiency of the cloned genes for enhanced plant breeding in corn using the 1,501 ZmINGY (inbred line grain yield) genes and 137 ZmF1GY (hybrid grain yield) genes, and in cotton using the 474 GFL (fiber length) genes. Based on these research results, we proposed and established GBB in corn and cotton. Furthermore, we investigated the genetic potentials of GBB for crop improvement and found that the present best varieties could be further improved by 73% - 118% with GBB. We demonstrated that GBB is from several to hundreds-fold more powerful and more efficient than the breeding methods currently used in plant breeding programs. Therefore, GBB established in this project will continuously and substantially improve modern crops, thus promoting the next green revolution and helping feed the world.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2019
Citation:
Wahl NJ, Murray SC, Zhang H-B, Zhang MP, Dickens CM, Isakeit TS. 2019. Maize kernel development stage the primary factor in differential gene expression in response to two methods of field inoculation with Aspergillus flavus. bioRxiv 617241.
- Type:
Journal Articles
Status:
Published
Year Published:
2016
Citation:
Fu Y, Xia Z, Wang S, Chen X, Lu C, Luo M, Zhang H-B, Wang W. 2016. A bacterial artificial chromosome-based physical map of Manihot esculenta ssp. flabellifolia. Frontiers of Agricultural Science and Engineering 3:321-329.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2019
Citation:
Cilkiz M, Zhang Y, Zhang MP, Abbo S, Sherman A, Coyne CJ, Vandemark GJ, Zhang H-B. 2019. The molecular mechanisms underlying plant vernalization revealed by systems analysis of transcriptomes in chickpea and related species. The 2019 ASA-CSSA-SSSA International Annual Meeting, Nov. 10-13, San Antonio, Texas.
- Type:
Journal Articles
Status:
Published
Year Published:
2019
Citation:
Liu Y-H, Zhang MP, Sze S-H, Smith CW, Zhang H-B. 2019. Continued genetic improvement of cotton through gene-based breeding. The 2019 ASA-CSSA-SSSA International Annual Meeting, Nov. 10-13, San Antonio, Texas.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2019
Citation:
Zhang MP, Liu Y-H, Scheuring CF, Qi X, Pekar J, Sze S-H, Xu W, Murray SC, Zhang H-B. 2019. Development and utilization of gene-based breeding (GBB) for enhanced and continued genetic improvement in maize. The 2019 ASA-CSSA-SSSA International Annual Meeting, Nov. 10-13, San Antonio, Texas.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2019
Citation:
Zhang MP, Liu Y-H, Chang C-S, Zhi H, Wang S, Xu W, Smith CW, Zhang H-B. 2019. Quantification of gene expression while taking into account RNA alternative splicing. International Plant & Animal Genome Conference XXVII, W1068.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2019
Citation:
Zhang MP, Liu Y-H, Scheuring CF, Qi X, Pekar J, Sze S-H, Xu W, Murray SC, and Zhang H-B. 2019. Development of a gene-based breeding system in maize: accurate prediction of hybrid grain yields from their parents. International Plant & Animal Genome Conference XXVII, PE0822.
|
Progress 10/01/17 to 09/30/18
Outputs
Target Audience:Genes are the centerpiece for studies of a trait or biological process that they control and for development of technologies enabling enhanced breeding for the trait that they determine. We previously developed a novel genome-wide high-throughput system, gExpress, to clone the genes or QTLs controlling agronomic traits. The goals of this research project are to use this new gene cloning system to genome-wide and high-throughput clone the genes controlling agronomic traits in crops and use the cloned genes to decipher the molecular mechanisms underlying agronomic traits or biological processes. We will also develop new breeding methods, such as gene-based breeding (GBB), and genic toolkits for enhanced breeding in crops important to the USA and the State of Texas, such as cotton, maize, wheat, soybean and rice, by making full use of the new knowledge, new cloned genes, the state-of-the-art technologies, such as high-through DNA sequencing and bioinformatics tools, and the new concepts, new strategies and new methods of systems genomics and systems biology that study biology and develop tools in an integrated manner. To these ends, we are collaborating 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, such as cotton breeding and maize breeding. 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 helped pioneer and develop three novel disciplines: systems genomics, systems biology and gene-based breeding (GBB), and establish a new molecular basis of biology and genetics: The DNA "Jigsaw Puzzle" Structure Model. Therefore, it is making a revolutionary contribution to science and technologies. These results will revolutionize current biological science, human medicine, and plant and animal breeding. Therefore, this project has provided a unique opportunity in training students and professionals in these new disciplines and innovation research: This project has trained 2 postdoctoral scientists, 15 graduate students, 3 visiting scholars and a number of students in classroom: a. Postdocs: Yun-Hua Liu Delin Xu b. Graduate Students: Nancy J. Wahl, 2017, Ph.D. in Genetics, graduated in December 2017 Murat Aci, M.S. in Plant Breeding, graduated in May 2018 Kotilingam Konda, Ph.D. in Plant Breeding, graduated in August 2018. Victoria L. Morrison, M.S. in Professional Program in Biotechnology, graduated in December 2018. Daman Bhangu, Ph.D. in Plant Breeding, 2015 - present Ali Ullrich, M.S. in Plant Breeding, 2016 - present Mustafa Cilkiz, Ph.D. in Molecular and Environmental Plant Sciences, 2017 - present Gali Bai, M.S. in Molecular and Environmental Plant Science, 2018 - present Mehmet Dogan, M.S. in Plant Breeding, 2018 - present Homa Zarghami, Ph.D., in Molecular and Environmental Plant Sciences, 2014 - present Selfinaz K Velioglu, M.S. in Plant Breeding, 2017 - present Jamshaid Ali Junaid, Ph.D. in Plant Breeding, 2015 - present Xuan Lin, Ph.D. in Molecular and Environmental Plant Science, 2017 - present Salma Bibi, M.S., in Molecular and Environmental Plant Science, 2017 - present Jingjia Li, Ph.D. in Ecosystem Science and Management, 2015 - present c. Visiting scholars: Dr. Jianmin Song, Shandong Academy of Agricultural Sciences, China Dr. Wei Zhou, Hunan Agricultural University, China Dr. Quang Qiao, University of Guizhou, China d. Classroom teaching: SCSC, GENE, BIOT and MEPS 654 - Analysis of Complex Genomes (lectures) SCSC, GENE, BIOT and MEPS 655 - Analysis of Complex Genomes (labs) 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 Genomics, Food Chemistry, Crop Science, Plant Breeding, and Nature Communications. Presented the results and achievements of this project at national and international professional conferences such as the International Plant & Animal Genome Conference. 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 trained 15 graduate students and 2 postdoctoral associates during this period of the project. Directly delivered the new knowledge, resources and tools developed in this project to users such as breeders and researchers nationwide through collaboration. What do you plan to do during the next reporting period to accomplish the goals? Prepare 4 - 5 manuscripts from the results obtained in the previous years and publish them in peer-reviewed renowned journals; Extend the gene-based breeding (GBB) system developed for enhanced and accelerated breeding for grain yield to other agronomic traits; Promote the gene-based breeding (GBB) system in application in maize and cotton breeding programs nationwide and worldwide; and Continue the practice of GBB for cotton fiber length and GBB for maize F1 hybrid grain yield.
Impacts
What was accomplished under these goals?
During this period of the project (09/01/2017 - 08/31/2018), we have accomplished the followings under these goals: We developed a novel, simple, powerful and efficient method for accurate prediction of complex traits and for gene-based breeding (GBB) using the 474 fiber length genes that we previously cloned. We demonstrated that the present best cultivars could be large-scale and continuously improved (>120%) and GBB is the method of choice to realize the continued and large-scale crop improvement, thus promoting next green revolution and helping secure the world's food supplies. We identified 525 candidate genes that differentiate the fiber quality and yield traits between Upland cotton and Sea Island cotton. Using these candidate genes, we deciphered the molecular mechanisms of fiber trait differentiation in cottons. We were developing a plant breeder affordable and extremely high-throughput genotyping method and procedure using modern high-throughput sequencing technologies. The purpose of this study is to practically realize GBB in crop breeding programs. The research is currently under validation of the method and procedure. Once it is developed and validated, the cost of genotyping a sample using Illumina HiSeq 4000 will be reduced to <$2.00 from the current >$200 per sample, with a throughput of 80,000 samples per flow cell. We previously developed a maize inbred parent/hybrid population consisting of 205 inbred parents and their 227 F1 hybrids from the U.S. maize core inbred lines representing the U.S. public corn breeding gene pool and identified by USDA/ARS. In this period of the project, we conducted multiple-replicated field trials on this inbred parent/hybrid population at College Station and Lubbock, TX and phenotyped 21 agronomic traits and their mid-parent heterosis and better-parent heterosis. These traits included grain yield per plant, number of ears per plant, plant height, ear height, flowering date, maturity date, ear weight, grain weight per ear, number of kernels per ear, ear length, ear diameter, ear kernel length, number of kernel rows, cob diameter, 500-kernel weight, moisture, starch content, protein content, fat content, phosphorous content and heat tolerance. We was conducting gene-based breeding (GBB) for high-yielding hybrids using the 302 U.S. corn core inbred lines and developed seven hybrids that gave higher grain yields than the current Texas commercial hybrids by >10%. We deciphered the genetic basis of rice grain cooking quality by genome-wide association study (GWAS) with nearly 20,000 SNPs using the 216 U.S. rice core germplasm lines identified by USDA/ARS. We identified new germplasm lines and new SNP markers for enhanced rice cooking quality breeding. We deciphered the molecular mechanisms underlying soybean domestication by comparative analysis of the transcriptomes between cultivated and wild soybeans. We deciphered the molecular mechanisms underlying vernalization and flowering in chickpea by transcriptome analysis of chickpea and related species.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2019
Citation:
Zhang MP, Cui Y, Liu Y-H, Xu W, Sze S-H, Murray SC, Xu S, Zhang H-B. 2019. Accurate prediction of maize grain yield using its contributing genes for gene-based breeding. Genomics. doi:10.1016/j.ygeno.2019.02.001
- Type:
Journal Articles
Status:
Published
Year Published:
2019
Citation:
Mugabe D, Coyne CJ, Piakowski J, Zheng P, Ma Y, Landry E, McGee R, Main D, Vandemark, Zhang H-B, Abbo A. 2019. Quantitative trait loci for cold tolerance in chickpea. Crop Sci 59:1-10.
- Type:
Journal Articles
Status:
Published
Year Published:
2019
Citation:
Song J-M, Arif M, Zhang MP, Sze S-H, Zhang H-B. 2019. Phenotypic and molecular dissection of grain quality using the USDA rice mini-core collection. Food Chemistry 284:312-322.
- Type:
Journal Articles
Status:
Published
Year Published:
2019
Citation:
Zhang X, Yuan J, Sun Y, Li S, Gao Y, Yu Y, Liu C, Wang Q, Lv X, Zhang X, Ma KY, Wang X, Lin W, Wang L, Zhu X, Zhang C, Zhang J, Jin S, Yu K, Kong J, Xu P, Chen N, Zhang H-B, Sorgeloos P, Sagi A, Warren A, Liu Z, Wang L, Ruan J, Chu K, Liu B, Li F, Xiang J. 2019. Penaeid shrimp genome provides insights into benthic adaptation and frequent molting. Nature Comm 10:356.
- Type:
Journal Articles
Status:
Published
Year Published:
2018
Citation:
Zhang MP, Liu Y-H, Chang C-S, Zhi H, Wang S, Xu W, Smith CW, Zhang H-B. 2018. Quantification of gene expression while taking into account RNA alternative splicing. Genomics https://doi.org/10.1016/j.ygeno.2018.10.009
- Type:
Journal Articles
Status:
Published
Year Published:
2018
Citation:
van-Oss R, Gopher A, Kerem, Peleg Z, Lev-Yadun S, Sherman A, Zhang H-B, Vandemark G, Coyne CJ, Reany O, Abb S. 2018. Independent selection for seed free tryptophan content and vernalization response in chickpea domestication. Plant Breed 137:290-300.
- Type:
Theses/Dissertations
Status:
Published
Year Published:
2018
Citation:
Aci, Murat. 2018. Molecular mechanisms of crop domestication revealed by comparative analysis of the transcriptomes between cultivated and wild soybeans. M.S. Thesis, Texas A&M University, College Station, Texas.
- Type:
Journal Articles
Status:
Published
Year Published:
2018
Citation:
Konda, Kotilingam. 2018. Genetic analysis of indica rice (Oryza sativa L.) genotypes for hybrid seed production traits and brown plant hopper (BPH) resistance to identify parental lines. Ph.D. dissertation, Texas A&M University, College Station, Texas.
- Type:
Theses/Dissertations
Status:
Published
Year Published:
2017
Citation:
Wahl, Nancy J. 2017. Identification of genetic components to resistance to aflatoxin production in pre-harvest maize. Ph.D. dissertation, Texas A&M University, College Station, Texas.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2018
Citation:
Zhang M, Liu H-Y, Zhang H-B. 2018. Genome-wide high-throughput cloning of the genes important to plants, animals and humans: from traits to genes to mechanisms to trait prediction to gene-based breeding/medicine. 2018 International Sesame Genetics and Breeding Symposium, Zhengzhou, China, August 23-24, 2018.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2018
Citation:
Liu Y-H, Xu Y, Zhang M, Cui Y, Sze S-H, Smith CW, Xu S, Zhang H-B. 2018. Accurate prediction of fiber length using its contributing genes for gene-based breeding in cotton. International Plant & Animal Genome Conference XXVI, W022.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2018
Citation:
Zhao M, Li X, Lin Y, Wang Y, Qin J, Han Y, Wang K, Sun C, Yin R, Wang Y, Zhang H-B, Zhang M. 2018. Molecular mechanisms of ginsenoside biosynthesis revealed by genome-wide systems analysis of the genes significantly associated with ginsenoside contents in Panax ginseng C.A. Meyer. International Plant & Animal Genome Conference XXVI, W999.
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Progress 10/01/16 to 09/30/17
Outputs
Target Audience:Genes are the centerpiece for studies of a trait or biological process that they control and for development of technologies enabling enhanced breeding for the trait that they determine. We previously developed a novel genome-wide high-throughput system, gExpress, to clone the genes or QTLs controlling agronomic traits. The goals of this research project are to use this new gene cloning system to genome-wide and high-throughput clone the genes controlling agronomic traits in crops and use the cloned genes to decipher the molecular mechanisms underlying agronomic traits or biological processes. We will also develop new breeding methods, such as gene-based breeding (GBB), and genic toolkits for enhanced breeding in important crops such as cotton, maize, wheat, soybean and rice by making full use of the new knowledge, new cloned genes, the state-of-the-art technologies such as high-through DNA sequencing, computer and bioinformatics, and the new concepts, new strategies and new methods of systems genomics and systems biology. To these ends, we are collaborating 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?The results of this project has helped pioneer systems genomics, systems biology and gene-based breeding (GBB), thus making a significant contribution to science and technologies. These results will revolutionize current biological science research, human medicine research and plant and animal breeding. Therefore, this project has provided a unique opportunity in training students and professionals in these new disciplines and cutting edge research: This project has trained 2 postdoctoral scientists, 9 graduate students, three visiting scholars and a number of students in classroom: Postdocs Yun-Hua Liu, September 2014 - August 2017 Delin Xu, October 2016 - present Graduate Students Vishal Saitwal, Ph.D. in Plant Breeding, graduated in September 2017 Xiangkun Gu, Ph.D. in Molecular and Environmental Plant Science, graduated in June 2017 Mitchell Schumann, Ph.D. in Plant Breeding, 2014 - present Daman Bhangu, Ph.D. in Plant Breeding, 2015 - present Kotilingam Konda, Ph.D. in Plant Breeding, 2015 - present Ali Ullrich, M.S. in Plant Breeding, 2016 - present Murat Aci, M.S. in Plant Breeding, 2016 - present Mustafa Cilkiz, Ph.D. in Molecular and Environmental Plant Sciences, 2017 - present Homa Zarghami, Ph.D., in Molecular and Environmental Plant Sciences, 2014 - present Visiting scholars Dr. Jianmin Song, Shandong Academy of Agricultural Sciences, China Dr. Wei Zhou, Hunan Agricultural University, China Dr. Quang Qiao, University of Guizhou, China Classroom teaching SCSC, GENE, BIOT and MEPS 654 - Analysis of Complex Genomes (lectures) SCSC, GENE, BIOT and MEPS 655 - Analysis of Complex Genomes (labs) 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 Frontiers in Plant Science, Theoretical and Applied Genetics, and Functional and Integrative Genomics. Presented the results and achievements of this project at national and international professional conferences such as the International Plant & Animal Genome Conference and National Association of Plant Breeders Meeting. 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 9 graduate students and 2 postdoctoral associates during this period of the project. Directly delivered the new knowledge, resources and tools developed in this project to users such as breeders and researchers nationwide through collaboration with companies such as patent commercialization and invention disclosure. What do you plan to do during the next reporting period to accomplish the goals? Prepare 4 - 5 manuscripts from the results obtained in the FY 2016/2017 and publish them in peer-reviewed renowned journals; Package the gene-based breeding (GBB) system for enhanced and accelerated breeding for grain yield and 12 grain yield and quality traits; Promote the maize gene-based breeding (GBB) system in applications in maize breeding nationwide and worldwide; Decipher the molecular mechanisms underlying maize 500-kernel weight, maize grain yield heterosis and cotton fiber strength; and Practice GBB for cotton fiber length and GBB for maize F1 hybrid grain yield.
Impacts
What was accomplished under these goals?
During this period of the project (09/01/2016 - 08/31/2017), we have accomplished the followings under these goals: We have cloned and validated 10,480 genes controlling seven cotton fiber quality and yield traits. These genes include 1,078 genes for fiber strength (GSTR), 725 genes for fiber uniformity (GUNIF), 742 genes for fiber elongation (GELO), 881 genes for micronaire (GMIC), 3,140 genes for lint yield (GLY), 1,420 genes for lint percentage (GLP) and 2,494 genes for seed yield (GSY). We cloned and validated 7,369 genes controlling 12 maize individual grain yield and quality component traits and grain yield heterosis. These genes include 1,235 genes for 500-kernel weight (ZmINKW), 722 genes for ear weight (ZmINEW), 652 genes for ear length (ZmINEL), 725 genes for ear row length (ZmINERL), 346 genes for ear diameter (ZmINED), 286 genes for cob diameter (ZmINCD), 344 genes for kernel row number (ZmINKRN), 259 genes for seed moisture (ZmINMo), 419 genes for seed starch content (ZmINSt), 446 genes for seed fat content (ZmINFa), 427 genes for seed protein content (ZmINPr), 527 genes for seed phosphorous content (ZmINP) and 981 genes for grain yield heterosis (ZmF1GYH). We have demonstrated gene-based breeding (GBB) for enhanced fiber length breeding in cotton using the 474 cotton fiber length (GFL) genes that we previously cloned using our genome-wide high-throughput gene and QTL cloning method. The result showed that GBB is extremely powerful and efficient for enhanced and accelerated breeding in cotton, thus demonstrating that GBB enables promoting the next green revolution in crop production. We have demonstrated gene-based breeding (GBB) for enhanced inbred and F1 hybrid grain yield breeding in maize using the cloned maize inbred grain yield (ZmINGY) and F1 hybrid grain yield (ZmF1GY) genes. The result also showed that GBB is extremely powerful and efficient for enhanced and accelerated inbred and F1 hybrid grain yield breeding in maize, thus demonstrating that GBB promises to promote the next green revolution in crop production. We have resolved a long-standing and serious problem in gene research - quantification of transcript and gene expressions. We found that it is impossible or care must be taken to properly quantify individual transcript and gene expressions by real-time quantitative PCR (qPCR) that is currently used as the "standard" method for transcript and gene expression quantification, microarray, Northern hybridization, or serial analysis of gene expression (SAGE), when a gene is subjected to RNA alternative splicing. Full-length or shotgun RNA sequencing (RNA-seq) is the only method of choice for proper quantification of transcript and gene expressions. Based on these results, it is highly likely that over 50% of research articles containing gene expression analysis published to date in all professional journals have serious errors. These results have not only revolved the long-standing and serious problem in gene expression quantification, importantly, they will also provide a proper and better approach for gene research.
Publications
- Type:
Theses/Dissertations
Status:
Published
Year Published:
2017
Citation:
Gu, Xiangkun, 2017. Dissection of the genetic basis underlying wax biosynthesis in hexoploid wheat using bi-parental linkage mapping and genome-wide association mapping. Ph.D. Dissertation, Texas A&M University, College Station, Texas
- Type:
Theses/Dissertations
Status:
Submitted
Year Published:
2017
Citation:
Saitwal, Vishal M. 2017. Heterosis and combining ability for yield and fibre qualities of upland cotton under high density planting conditions for India. Ph.D. Dissertation, Texas A&M University, College Station, Texas
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2017
Citation:
Zhang MP, Cui Y, Liu Y-H, Xu W, Sze S-H, Xu S, Zhang H-B. 2017. Gene-based Breeding in Maize: Grain Yield Breeding by Effectively Using the Genes Controlling the Targeted Trait. International Plant & Animal Genome Conference XXV, P0712.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2017
Citation:
Liu Y-H, Xu Y, Zhang MP, Sze S-H, Smith CW, Xu S, Zhang H-B. 2017. Development of a gene-based breeding system in cotton: a new method powerful and efficient for enhanced fiber quality breeding. International Plant & Animal Genome Conference XXV, P0564.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2017
Citation:
Zhang MP, Wang Y, Wang Y, Wang K, Lin Y, Yin R, Zhao M, Qin J, Zhang H-B, Sun C. 2017. Molecular mechanisms underlying ginsenosides biosynthesis: genome-wide cloning and analysis of genes involved in ginsenoside biosynthesis from Jilin ginseng, Panax ginseng C.A. Meyer. International Plant & Animal Genome Conference XXV, P0226.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2017
Citation:
Zhang MP, Liu Y-H, Zhang H-B, 2017. Helping feed the world through gene-based breeding. Case study: Maize. 2017 Summit Forum on Wheat Diseases and Control Technology, August 25 27, 2017, Baoding, China.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2017
Citation:
Liu Y-H, Xu Y, Zhang MP, Cui Y, Sze S-H, Hague SS, Smith CW, Xu S, Zhang H-B. 2017. A gene-based breeding (GBB) system for enhanced and accelerated breeding in cotton. 2017 Annual NAPB Meeting, August 7-10, 2017, University of California, Davis, CA.
|
Progress 10/01/15 to 09/30/16
Outputs
Target Audience:Genes are the centerpiece for studies of a trait or biological process that they control and for development of toolkits enabling enhanced breeding for the trait that they determine. We previously developed a novel genome-wide high-throughput system, gExpress, to clone the genes or QTLs controlling agronomic traits. The goals of this research project are to use this new gene cloning system to genome-wide and high-throughput clone the genes controlling agronomic traits in crops and use the cloned genes to decipher the molecular mechanisms underlying agronomic traits or biological processes. We will also develop new breeding methods and genic toolkits for enhanced breeding in important crops such as cotton, maize, wheat, soybean and rice by making full use of the new knowledge, new cloned genes, the state-of-the-art technologies such as high-through DNA sequencing, computer and bioinformatics, and the new concepts, new strategies and new methods of systems genomics and systems biology. To these ends, we are collaborating 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?The results of this project have helped pioneer systems genomics, systems biology and gene-based breeding, thus making a significant contribution to science and technologies. These results will revolutionize current biological science research, human medicine research and plant and animal breeding. Therefore, this project has provided a unique opportunity in training students and professionals in these new disciplines and cutting edge research: This project has trained 2 postdoctoral scientists, 10 graduate students, three visiting scholars and a number of students in classroom: Postdocs Yang Zhang, September 2013 - July 2015. Yun-Hua Liu, September 2014 - present Graduate Students Kari Hugie, Ph.D. in Plant Breeding, graduated in 2015 Jingjia Li, M.S. in Plant Breeding, graduated in 2016 Laura L. Masor, Ph.D. in Plant Breeding, graduated in 2016 Lorin M. Harvey, M.S. in Plant Breeding, graduated in 2016 Angira Brijesh, Ph.D. in Plant Breeding, graduated in 2016 Daman Bhangu, M.S. in Plant Breeding, graduated in 2015 Mitchell Schumann, Ph.D. in Plant Breeding, 2014 - present Vishal Saitwal, Ph.D. in Plant Breeding, 2014 - present Daman Bhangu, Ph.D. in Plant Breeding, 2015 - present Ali Ullrich, M.S. in Plant Breeding, 2016 - present Visiting scholars Dr. Yadong Zhang, Jiangsu Academy of Agricultural Sciences, China Dr. Xiaoli Qi, Jiamusi University, China Yasemin Özhan, Ede University, Turkey Classroom teaching SCSC, GENE, BIOT and MEPS 654 - Analysis of Complex Genomes (lectures) SCSC, GENE, BIOT and MEPS 655 - Analysis of Complex Genomes (labs) 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 PLoS ONE, Plant Breeding, Frontiers in Plant Science, and Molecular Genetics and Genomics. Presented the results and achievements of this project at national and international professional conferences such as the International Plant & Animal Genome Conference, Agronomy Meeting and Beltwide Cotton Conferences. 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 10 graduate students and 2 postdoctoral associates during this period of the project. Directly delivered the new knowledge, resources and tools developed in this project to users such as breeders and researchers nationwide through collaboration with companies such as Monsanto and BioNano Genomics, patent commercialization and invention disclosure. What do you plan to do during the next reporting period to accomplish the goals? Prepare 4 - 5 manuscripts from the results obtained in the FY 2015/2016 and publish them in peer-reviewed renowned journals; Clone and validate the genes controlling maize 500-kernel weight, maize grain yield heterosis and cotton fiber strength; Decipher the molecular mechanisms underlying these traits (500-kernel weight, grain yield heterosis and fiber strength; and Integrate the cotton genome sequence assembly that we previously developed with our cotton SNP genetic map and an optical physical map under development in collaboration with BioNano Genomics.
Impacts
What was accomplished under these goals?
During this period of the project (09/01/2015 - 08/31/2016), we have accomplished the followings under these goals: We have cloned and validated 474 genes controlling cotton fiber length (GFL), 185 genes controlling cotton fiber length heterosis (GFLH), 1,501 genes controlling maize inbred grain yield (ZmINGY) and 137 genes controlling F1 hybrid grain yield (ZmF1GY). This number of genes is probably more than the total number of genes cloned from all species worldwide in the past 30 years. We have deciphered the molecular mechanisms of quantitative genetics, maize grain yield, cotton fiber quality and cotton and wheat polyploidization. We have developed and validated a gene-based breeding system for enhanced inbred and F1 hybrid grain yield breeding in maize and a gene-based breeding system for enhanced fiber length breeding in cotton. We have constructed a super dense genetic map consisting of 145,396 SNPs for cotton, with an average density of one SNP in every 17 kb, and mapped 209 QTLs (LOD ≥ 5.00) controlling fiber length (45), strength (36), uniformity (26), elongation (46), lint percentage (32), lint yield (16) and 100-seed weight (8). We have constructed a genetic map of cowpea consisting of 4,154 SNPs, with an average density of one SNP per 149 kb, and mapped 131 QTLs controlling heat tolerance, drought tolerance, biomass yield, flowering date, plant height and 100-seed weight.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2015
Citation:
Zhang MP, Rong Y, Lee M-K, Zhang Y, Stelly DM, Zhang H-B. 2015. Phylogenetic analysis of Gossypium L. using restriction fragment length polymorphism of repeated sequences. Mol Genet Genomics 290:18591872.
- Type:
Journal Articles
Status:
Published
Year Published:
2015
Citation:
Van Oss R, Abbo S, Eshed R, Sherman A, Coyne C, Vandemark G, Zhang H-B, Peleg Z. 2015. Genetic relationship in Cicer sp. expose evidence for geneflow between the cultigen and its wild progenitor. PLoS ONE 10(10): e0139789.
- Type:
Journal Articles
Status:
Published
Year Published:
2016
Citation:
Van Oss R, Sherman A, Shtienberg D, Zhang H-B, Vandemark G, Coyne C, Abbo S. 2016. Vernalization response of domesticated x wild chickpea progeny is subject to strong genotype by environment interaction. Plant Breeding 135:102-110.
- Type:
Journal Articles
Status:
Published
Year Published:
2016
Citation:
Ji R, Wang Y, Cheng Y, Zhang M, Zhang H-B, Zhu L, Fang J, Zhu-Salzman K. 2016. Transcriptome analysis of green peach aphid (Myzus persicae): Insight into developmental regulation and inter-species divergence. Front Plant Sci 7:1562.
- Type:
Theses/Dissertations
Status:
Published
Year Published:
2016
Citation:
Jingjia Li, M.S., 2016. Cloning and system analysis of genes controlling grain yield using ear leaf in maize. M.S. thesis, Texas A&M University, College Station, Texas.
- Type:
Theses/Dissertations
Status:
Published
Year Published:
2016
Citation:
Harvey, LM. 2016. QTL analysis of yield components in cotton. M.S. thesis, Texas A&M University, College Station, Texas.
- Type:
Theses/Dissertations
Status:
Published
Year Published:
2015
Citation:
Hugie, KL. 2015. Evaluation of conventional and marker-assisted breeding methods for the improvement of fiber quality in Gossypium spp. Ph.D. dissertation, Texas A&M University, College Station, Texas.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2015
Citation:
Masor LL, Hays DB, Singh BB, Zhang H-B, Zhang MP. 2015. Molecular mapping of drought tolerance genes in cowpea (Vigna unguiculata L. Walp). Texas A&M Plant Breeding Symposium. Poster presentation, College Station, TX. Feb. 2015.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2015
Citation:
Masor LL, Hays DB, Singh BB, Zhang H-B, Zhang MP. 2015. Molecular mapping of drought tolerance genes in cowpea (Vigna unguiculata L. Walp). Oregon State University Plant Breeding Seminar (Oral), Corvallis, OR. June 2015.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2015
Citation:
Masor LL, Scheuring CF, Zhang Y, Angira B, Zhang MP, Zhang H-B, Singh BB. 2015. Molecular mapping of drought tolerance genes in cowpea (Vigna unguiculata L. Walp). National Association of Plant Breeders Annual Meeting. Poster presentation, Pullman, WA. Aug. 2015.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2015
Citation:
Masor LL, Scheuring CF, Zhang Y, Angira B, Zhang MP, Zhang H-B, Singh BB. 2015. Molecular mapping of drought tolerance genes in cowpea (Vigna unguiculata L. Walp). Student Organic Seed Symposium. Oral presentation, Madison, WI. Aug. 2015.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2015
Citation:
Masor LL, Scheuring CF, Zhang Y, Angira B, Zhang MP, Zhang H-B, Singh BB. 2015. Molecular mapping of drought tolerance genes in cowpea (Vigna unguiculata L. Walp). American Society of Agronomy Annual Meeting. Oral presentation, Minneapolis, MN. Nov. 2015.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2015
Citation:
Hugie, K., D. Fang, P. Li, W. Smith, H-B. Zhang, S. Hague, and D. Jones. 2015. Identification of robust microsatellite markers for fiber length and strength in Gossypium spp. 2015 Beltwide Cotton Conferences. San Antonio, Texas, January 5 7, 2015.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2015
Citation:
Liu B, Hastie A, Qiu Z, Qi A, Muhantay G, Chan S, Wang J, Liang X, Qiu M, Hu S, Wang X, Li L, Li A, Zhang H-B, Miller D, Antczak D, Kalbfleisch T, Cao H, Bailey E. 2015. Towards a high-standard reference genome of horses with whole genome physical mapping and the integration of genome sequences. International Plant & Animal Genome Conference XXIII, P0319.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2015
Citation:
Angira B, Masor L, Zhang Y, Scheuring CF, Zhang YD, Singh BB, Zhang H-B, Hays DB, Zhang MP. 2015. Molecular Mapping of Heat Tolerance in Cowpea. American Society of Agronomy Annual Meeting. Crop Breeding and Genetics: II. Poster 521. Minneapolis, MN. Nov. 2015.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2015
Citation:
Zhang Y, Liu Y-H, Zhang MP, Zhang Q, Xu SS, Smith CM, Hague SS, Frelichowski J, Zhang H-B. 2015. The molecular mechanisms of plant polyploidization revealed by systems analysis of the genomes and transcriptomes of wheat, cotton and related species. International Plant & Animal Genome Conference XXIII, W016.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2015
Citation:
Liu Y-H, Zhang MP, Zhang Y, Smith CW, Hague SS, Sze S-H, Zhu J, Frelichowski J, Zhang H-B. 2015. The molecular mechanisms of crop quality: cloning and systems analysis of 474 genes controlling fiber length in cotton, Gossypium hirsutum L. and G. barbadense L. International Plant & Animal Genome Conference XXIII, W848.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2015
Citation:
Zhang MP, Liu Y-H, Zhang Y, Xu W, Smith CW, Murray S, Hague SS, Sze S-H, Frelichowski J, Zhang H-B. 2015. Molecular mechanisms of quantitative genetics revealed by cloning and systems analysis of 474 genes controlling fiber length in cotton and 1,501 genes controlling grain yield in maize. International Plant & Animal Genome Conference XXIII, W685.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2016
Citation:
Liu Y-H, Zhang MP, Zhang Y, Smith CW, Hague SS, Zhang H-B. 2016. Systems analysis of 1,090 GSTR genes reveals that epistasis plays important roles in cotton fiber strength. International Plant & Animal Genome Conference XXIV, W930.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2016
Citation:
Zhang MP, Liu Y-H, Zhang Y, Zhi H, Xu W, Murray S, Zhang H-B. 2016. Molecular mechanisms regulating heterosis: systems analysis of 981 ZMHET genes controlling grain yield heterosis in maize, Zea mays L. International Plant & Animal Genome Conference XXIV, W933.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2016
Citation:
Zhang Y, Scheuring CF, Angira B, Masor LL, Liu Y-H, Zhang YD, Singh BB, Zhang H-B, Hays D, Zhang MP. 2016. Molecular mapping of the genome and agronomic traits in cowpea. International Plant & Animal Genome Conference XXIV, W1014.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2016
Citation:
Singh BB, Angira B, Masor LL,Zhang MP, Zhang H-B, Foster JL, Asiwe JA, Singh YV, Hays D. 2016. Breeding next generation cowpea varieties for adaptation to changing climates and cropping systems. Joint Pan-African Grain Legume and World Cowpea Conference 2016, Feb. 28 March 4, 2016, Livingstone, Zambia (poster presentation) http://gl2016conf.iita.org/index.php/presentations/.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2016
Citation:
Harvey L, Zhang Y-D, Scheuring C, Liu Y-H, Zhang MP, Smith SW, Stelly D, Yang S-P, Caldwell D, Kerstetter R, Hague S, Zhang H-B. 2016. Molecular mapping of fiber yield component traits using an ultra-high-density SNP genetic map of cultivated tetraploid cottons. 2016 Beltwide Cotton Conferences, January 5-6, 2016, New Orleans, LA.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2016
Citation:
Angira B, Masor L, Zhang Y, Scheuring CF, Zhang YD, Singh BB, Zhang H-B, Hays DB, Zhang MP. 2016. Molecular mapping of heat tolerance in cowpea. Joint Pan-African Grain Legume and World Cowpea Conference 2016, Feb. 28 March 4, 2016, Livingstone, Zambia (invited oral presentation) http://gl2016conf.iita.org/index.php/presentations/.
|
Progress 11/16/14 to 09/30/15
Outputs
Target Audience:The goals of this research project are to large-scale clone the genes controlling agronomic traits in crops and use the cloned genes to decipher the molecular basis and regulation mechanisms underlying agronomic traits or biological processes. These include the molecular basis and regulatory mechanisms affecting crop yield, quality, abiotic stress tolerance, biotic stress tolerance, quantitative genetics, heterosis, polyploidization and crop domestication. We will also develop new toolkits for enhanced breeding in important crops such as cotton, maize, wheat, soybean and rice by making full use of the new knowledge, new cloned genes, the state-of-the-art technologies such as high-through DNA sequencing, computer and bioinformatics, and the new concepts, new strategies and new methods of systems genomics and systems biology. This project collaborates 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), Dr. B.B. Singh (cowpea breeder), Dr. David M. Stelly (cotton geneticist) and Dr. Jorge Da Silva (sugarcane breeder). Therefore, the knowledge and tools developed through the project have been directly transferred and immediately used in their breeding programs. Furthermore, each of their program and the PI program have numerous graduate students who are majoring in plant breeding and are 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, and professional training. We analyzed the 474 cotton fiber length genes (GFL), 756 cotton fiber strength genes (GSTR), 1,501 maize grain yield genes (ZmGY) and 981 maize grain yield heterosis genes (ZmHET) in a systems manner and for the first time, deciphered the molecular mechanisms of heterosis, crop yield, quality and plant polyploidization. The findings have significantly advanced our understanding of heterosis, crop yield, quality and plant polyploidization. This project has trained three junior scientists and four graduate students. How have the results been disseminated to communities of interest?The results and achievements of this project obtained so far have been disseminated to communities of interest through numerous methods: Filed a patent entitled "gExpress: Concepts, strategies and method for genome-wide high-throughput cloning of genes controlling quantitative traits" Presented the results and achievements of this project at national and international professional conferences such as the International Plant & Animal Genome Conference, Annual Beltwide Cotton Conference and Annual American Society of Agronomy Annual Meeting. 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 4 graduate students, 1 postdoctoral associate and 3 junior scientists in 2015. Directly delivered the new knowledge, resources and tools developed in this project to users such as breeders and researchers nationwide. For instance, we have proposed and are developing a gene-based breeding system in maize and cotton with breeders and a molecular precision agriculture system with agronomists using the cloned genes. What do you plan to do during the next reporting period to accomplish the goals?We plan to complete the following during the next reporting period: Publish the gExpress system for high-throughput cloning of genes controlling quantitative traits, the gGet package, the cloned maize grain yield genes, the cloned cotton fiber length genes, and the molecular mechanisms of quantitative genetics, maize grain yield, cotton fiber length and plant polyploidization. Prepare the manuscripts for the cotton SNP genetic map and fiber trait QTL mapping. Prepare the manuscripts for the cowpea SNP genetic map and agronomic trait QTL mapping, especially heat tolerance and drought tolerance QTL mapping. Clone the genes controlling cotton fiber elongation, fiber uniformity, lint yield, lint percentage and 100-seed weight. Continue the systems analysis of cotton fiber strength genes, maize grain yield heterosis genes and maize 500-kernal weight genes in order to decipher their underlying molecular mechanisms. Work toward development of a gene-based breeding system in cotton.
Impacts
What was accomplished under these goals?
This project was hatched in November 2016. So far we have accomplished the following: Developed an R package, named "gGet", for genome-wide high-throughput cloning and validation of genes controlling quantitative traits. Cloned 1,501 genes controlling maize grain yield (ZmGY) and using the cloned genes, deciphered the molecular mechanism of quantitative genetics and crop grain yield. Cloned 474 genes controlling cotton fiber length (GFL) and using the cloned genes, deciphered the molecular mechanism of quantitative genetics and cotton fiber length (crop quality). Cloned 756 genes controlling cotton fiber strength, named GSTR for Gossypium fiber strength and deciphered the molecular mechanisms of fiber strength. Each GSTR has an effect on fiber strength varying from 3.7% - 14.2%. However, 664 (87.8%) of them resulted in decreased fiber strength and 92 (12.2%) resulted in increased fiber strength, when turned on or up-regulated in 10-dpa developing fibers. It was also found that 29 of the GSTR genes were in the list of GFL genes. Cloned 981 gene controlling maize grain yield heterosis (ZmHET) and deciphered the molecular mechanism of plant heterosis. Cloned 1,610 genes controlling maize 500-kernel weight (ZmKW). The molecular mechanisms of kernel size is under analysis. Constructed a new genetic map of 145,396 SNPs for cotton consisting of 26 linkage groups and spanning 5,037 cM. Using the map, we mapped 209 QTLs (LOD ≥ 5.00) controlling cotton fiber length (45), strength (36), uniformity (26), elongation (46), lint percentage (32), lint yield (16) and 100-seed weight (8). Constructed a new genetic map of 4,154 SNPs for cowpea consisting of 11 linkage groups and spanning 1,084.65 cM, with a density of one SNP marker in approximately 0.26 cM or 149 kb. Using the map, we mapped 110 QTLs (LOD ≥ 3.00) controlling cowpea heat tolerance (7), drought tolerance (34), biomass (13), days to flower (29), plant height (24), and 100-seed weight (3).
Publications
- Type:
Journal Articles
Status:
Awaiting Publication
Year Published:
2015
Citation:
Van Oss R, Sherman A, Shtienberg D, Zhang H-B, Vandemark G, Coyne C, Abbo S. 2015. Vernalization response of domesticated x wild chickpea progeny is subject to strong genotype by environment interaction. Plant Breeding (in press).
- Type:
Journal Articles
Status:
Published
Year Published:
2015
Citation:
Van Oss R, Abbo S, Eshed R, Sherman A, Coyne C, Vandemark G, Zhang H-B, Peleg Z. 2015. Genetic relationship in Cicer sp. expose evidence for geneflow between the cultigen and its wild progenitor. PLoS ONE 10(10): e0139789.
- Type:
Journal Articles
Status:
Published
Year Published:
2015
Citation:
Zhang MP, Rong Y, Lee M-K, Zhang Y, Stelly DM, Zhang H-B. 2015. Phylogenetic analysis of Gossypium L. using restriction fragment length polymorphism of repeated sequences. Mol Genet Genomics 290:18591872.
- 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:
Published
Year Published:
2014
Citation:
Liu Y-H, Zhang MP, Huang JJ, Zhang H-B. 2014. DNA is structured as a linear Jigsaw Puzzle in the genomes of Arabidopsis, rice and budding yeast. Genome 57:9-19.
- Type:
Theses/Dissertations
Status:
Published
Year Published:
2015
Citation:
Hugie, K. L. 2015. Evaluation of conventional and marker-assisted breeding methods for the improvement of fiber quality in Gossypium spp. Ph.D. Dissertation, Texas A&M University, College Station, Texas
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2015
Citation:
Zhang MP, Liu Y-H, Zhang Y, Xu W, Smith CW, Murray S, Hague SS, Sze S-H, Frelichowski J, Zhang H-B. 2015. Molecular mechanisms of quantitative genetics revealed by cloning and systems analysis of 474 genes controlling fiber length in cotton and 1,501 genes controlling grain yield in maize. International Plant & Animal Genome Conference XXIII, W685.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2015
Citation:
Liu Y-H, Zhang MP, Zhang Y, Smith CW, Hague SS, Sze S-H, Zhu J, Frelichowski J, Zhang H-B. 2015. The molecular mechanisms of crop quality: cloning and systems analysis of 474 genes controlling fiber length in cotton, Gossypium hirsutum L. and G. barbadense L. International Plant & Animal Genome Conference XXIII, W848.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2015
Citation:
Zhang Y, Liu Y-H, Zhang MP, Zhang Q, Xu SS, Smith CM, Hague SS, Frelichowski J, Zhang H-B. 2015. The molecular mechanisms of plant polyploidization revealed by systems analysis of the genomes and transcriptomes of wheat, cotton and related species. International Plant & Animal Genome Conference XXIII, W016.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2015
Citation:
Liu B, Hastie A, Qiu Z, Qi A, Muhantay G, Chan S, Wang J, Liang X, Qiu M, Hu S, Wang X, Li L, Li A, Zhang H-B, Miller D, Antczak D, Kalbfleisch T, Cao H, Bailey E. 2015. Towards a high-standard reference genome of horses with whole genome physical mapping and the integration of genome sequences. International Plant & Animal Genome Conference XXIII, P0319.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2015
Citation:
Hugie, K. L., D. Fang, P. Li, W. Smith, H-B. Zhang, S. Hague, and D. Jones. 2015. Identification of robust microsatellite markers for fiber length and strength in Gossypium spp. Beltwide Cotton Conference.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2015
Citation:
Masor LL, Scheuring CF, Zhang Y, Angira B, Zhang MP, Zhang H-B, Singh BB. 2015. Molecular mapping of drought tolerance genes in cowpea (Vigna unguiculata L. Walp). American Society of Agronomy Annual Meeting. Oral presentation, Minneapolis, MN. Nov. 2015.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2015
Citation:
Masor LL, Scheuring CF, Zhang Y, Angira B, Zhang MP, Zhang H-B, Singh BB. 2015. Molecular mapping of drought tolerance genes in cowpea (Vigna unguiculata L. Walp). Student Organic Seed Symposium. Oral presentation, Madison, WI. Aug. 2015.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2015
Citation:
Masor LL, Scheuring CF, Zhang Y, Angira B, Zhang MP, Zhang H-B, Singh BB. 2015. Molecular mapping of drought tolerance genes in cowpea (Vigna unguiculata L. Walp). National Association of Plant Breeders Annual Meeting. Poster presentation, Pullman, WA. Aug. 2015.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2015
Citation:
Masor LL, Hays DB, Singh BB, Zhang H-B, Zhang MP. 2015. Molecular mapping of drought tolerance genes in cowpea (Vigna unguiculata L. Walp). Oregon State University Plant Breeding Seminar (Oral), Corvallis, OR. June 2015.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2015
Citation:
Masor LL, Hays DB, Singh BB, Zhang H-B, Zhang MP. 2015. Molecular mapping of drought tolerance genes in cowpea (Vigna unguiculata L. Walp). Texas A&M Plant Breeding Symposium. Poster presentation, College Station, TX. Feb. 2015.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2015
Citation:
Angira B, Masor L, Zhang Y, Scheuring CF, Zhang YD, Singh BB, Zhang H-B, Hays DB, Zhang MP. 2015. Molecular Mapping of Heat Tolerance in Cowpea. American Society of Agronomy Annual Meeting. Crop Breeding and Genetics: II. Poster 521. Minneapolis, MN. Nov. 2015.
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