Progress 03/01/06 to 03/27/08
Outputs
Progress Report Objectives (from AD-416) To identify and incorporate useful and important genes into improved cotton germplasm, to develop populations and/or methods that work towards improving useful and important traits, to broaden the genetic base of cotton through genetic improvement, to combat potential losses due to pests, diseases, and stresses imposed by the natural environment, to elucidate the underlying genetic basis of key seed and fiber traits to facilitate their incorporation into improved cotton germplasm, to increase the long-term economic value of germplasm available to cotton breeders and other researchers, and to develop an integrated genetic/physical map of the cotton genome and bridge the cotton genome with that of the model plant Arabidopsis. Approach (from AD-416) An interspecific mapping population of recombinant inbred (RI) lines will be developed and maintained. BAC libraries will be constructed and BAC clones will be evaluated for SSRs and fingerprinted for contig assembly into a physical map. SSR markers developed from the BAC clones will be screened for intraspecific polymorphism for germplasm characterization to enhance the germplasm evaluation process, mapped to the RI population, and used for the integration of the physical and genetic maps. A core marker set will be identified as the markers are screened and associated with the integrated genetic/physical map of cotton. Germplasm with useful characteristics will be identified through QTL analyses for such traits as disease and insect resistance and fiber and seed quality factors. Genetic control of these characteristics will be determined, and mapped to more efficiently identify and utilize diverse germplasm. Significant Activities that Support Special Target Populations Work under this project during FY 2008 resulted in significant progress in the development of cotton DNA markers, genome mapping, identification of Quantitative Trait Loci (QTL) for fiber and agronomic traits, and database enhancement. With cooperators, the project released data on 700 pairs of Gh Simple Sequence Repeat (SSR) primers to the public, and submitted their individual clone sequences to GenBank, CottonDB, and the Cotton Molecular Database (CMD). More than 200 Single Nucleotide Polymorphism (SNP) markers were analyzed and individually mapped on the cotton chromosomes. More than 2,600 newly fingerprinted Maxxa Bacterial Artificial Chromosome (BAC) clones that contained SSR loci were analyzed and integrated into the TM-1 fingerprint contig database. Integrated genetic, physical, and transcript maps were developed for selected Minimum Tiling Path (MTP) clones of homoeologous cotton chromosomes 12 and 26. Cotton genomic sequence data on some 200 such clones was obtained in collaboration with researchers in the U.S. and abroad. The complete sequences of these TM-1 MTP BAC clones are being analyzed. Mapping analysis and validation of approximately 1,500 SSR and SNP markers on 191 Recombinant Inbred Lines (RILs) of TM-1 x 3-79 cross was completed. Progress was made in migrating the CottonDB database to a new architecture that provides a more intuitive user interface for searches, and new sets of cotton genomic and genetic data have been added to the database. During the life of this project, a 12-genotype standardized panel for cotton marker development was established and DNA stocks were delivered as appropriate to the cotton research community. The TM-1 x 3- 79 RIL population was completed and its DNA stocks delivered to the research community, allowing coordinated consensus mapping of the cotton genome. With cooperation from the broader cotton research community, the project developed a draft version of an Upland cotton genome map that integrates 1,500 SSR and SNP markers, 6,000 BAC contigs, 100 QTL, and a genome-wide survey of the cotton transcriptome profile for 50,000 cotton Expressed Sequence Tag (EST) unigenes. This map provides the first Upland cotton genomic infrastructure for use in basic and applied cotton genetic studies to discover useful genes, and makes possible the sequencing of gene-rich islands or whole chromosomes of the Upland cotton genome. A detailed QTL analysis for fiber properties and yield components provided more than 80 genomic loci contributing to these traits, distributed among 13 At and 11 Dt chromosomes of the AD tetraploid genome. These QTL may contribute to the development of marker- assisted selection and molecular breeding for cotton improvement. The database, CottonDB, was improved in structure and content, and currently contains information on more than 450,000 genes, ESTs, and contig sequences; genetic and physical map data; nearly 10,000 DNA primers; and 9,000 germplasm accessions. This project expired in FY 2008 but was replaced by 6202-21000-030-00D which is continuing and expanding upon the work. (NP 301, Components 1, 2, Problem Statements 1.B, 2.B) Technology Transfer Number of Web Sites managed: 2
Impacts
(N/A)
Publications
- Chen, Z., Scheffler, B.E., Dennis, E., Triplett, B.A., Zhang, T., Chen, X., Stelly, D., Rabinowicz, P., Town, C., Arioli, T., Brubaker, C., Cantrell, R., Lacape, J., Ulloa, M., Chee, P., Gingle, A.R., Haigler, C.H., Percy, R. G., Saha, S., Wilkins, T., Wright, R.I., Van Deynze, A., Zhu, Y., Yu, S., Guo, W., Abdurakhmonov, I., Katageri, I., Ur-Rahman, M., Zafar, Y., Yu, J., Kohel, R.J., Wendel, J., Paterson, A. 2007. Towards Sequencing Cotton (Gossypium) Genomes. Plant Physiology. 145:1303-1310.
- Guo, Y., Saha, S., Yu, J., Jenkins, J.N., Kohel, R.J., Scheffler, B.E., Stelly, D.M. 2008. BAC-derived SSR chromosome locations in cotton. Euphytica. 161:361-370.
- An, C., Saha, S., Jenkins, J.N., Ma, D., Scheffler, B.E., Kohel, R.J., Yu, J., Stelly, D.M. 2008. Cotton (Gossypium spp.) R2R3-MYB transcription factors SNP identification, phylogenomic characterization, chromosome localization and linkage mapping. Theoretical and Applied Genetics. 161:1015-1026.
- Xu, Z., Kohel, R.J., Song, G., Cho, J., Alabady, M., Yu, J., Poo, K., Chu, J., Yu, S., Wilkins, T.A., Zhu, Y., Yu, J. 2008. Gene-rich islands for fiber development in the cotton genome. Genomics. 92:173-183.
- Xu, Z., Kohel, R.J., Song, G., Cho, J., Yu, J., Yu, S., Tomkins, J., Yu, J. 2008. An integrated genetic and physical map of homoeologous chromosomes 12 and 26 in Upland cotton (G. hirsutum L.). BMC Genomics. 9:108.
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Progress 10/01/06 to 09/30/07
Outputs
Progress Report Objectives (from AD-416) To identify and incorporate useful and important genes into improved cotton germplasm, to develop populations and/or methods that work towards improving useful and important traits, to broaden the genetic base of cotton through genetic improvement, to combat potential losses due to pests, diseases, and stresses imposed by the natural environment, to elucidate the underlying genetic basis of key seed and fiber traits to facilitate their incorporation into improved cotton germplasm, to increase the long-term economic value of germplasm available to cotton breeders and other researchers, and to develop an integrated genetic/physical map of the cotton genome and bridge the cotton genome with that of the model plant Arabidopsis. Approach (from AD-416) An interspecific mapping population of recombinant inbred (RI) lines will be developed and maintained. BAC libraries will be constructed and BAC clones will be evaluated for SSRs and fingerprinted for contig assembly into a physical map. SSR markers developed from the BAC clones will be screened for intraspecific polymorphism for germplasm characterization to enhance the germplasm evaluation process, mapped to the RI population, and used for the integration of the physical and genetic maps. A core marker set will be identified as the markers are screened and associated with the integrated genetic/physical map of cotton. Germplasm with useful characteristics will be identified through QTL analyses for such traits as disease and insect resistance and fiber and seed quality factors. Genetic control of these characteristics will be determined, and mapped to more efficiently identify and utilize diverse germplasm. Accomplishments Upland Cotton Genome Map: Cotton is a highly genetically complex crop plant; understanding the structural complexity and gene distribution within the cotton genome is necessary to support ongoing efforts by the broad cotton research and breeding community to improve the crop. Scientists in the Crop Germplasm Research Unit at the Southern Plains Agricultural Research Center, College Station, TX, in cooperation with many members of the larger cotton research community, developed a draft version of the Upland cotton genome map that integrates 1,200 SSR markers, 5,000 BAC contigs, 100 QTL, and a genome-wide survey of the cotton transcriptome profile for 50,000 cotton EST unigenes. This accomplishment is important because the map provides the first highly detailed synthesis of the Upland cotton genomic infrastructure which will be used by many in the cotton research community in the conduct of basic and applied cotton genetic studies. The map will effectively support efforts to discover useful genes in cotton germplasm collections, and to eventually sequence the gene-rich islands or whole chromosomes of the Upland cotton genome. (NP 301, Component 2, Problem Statement 2B) Permanent Mapping Population for the Cotton Genome: Research on cotton improvement in the U.S. is supported by a number of organizations, with relevant research being conducted at many locations; given the current focus on use of molecular biology techniques to genetically improve cotton, integration of research effort is critical for effective use of common resources. The establishment of a permanent mapping population for the cotton genome is essential because of the need to construct and integrate mapping activities with different marker sets from different laboratories. Scientists in the Crop Germplasm Research Unit at the Southern Plains Agricultural Research Center, College Station, TX, established, characterized, and released DNA stocks of a cotton population consisting of 191 recombinant inbred lines derived from a cross of TM-1 x 3-79, the genetic standards of Gossypium hirsutum and Gossypium barbadense, respectively. This accomplishment is important because it constitutes a critical foundation for the mapping of SSR and other molecular markers, as well as for the integrated cotton genome mapping with BAC clones and EST sequences. Availability of this mapping population will have major impact on the development of a consensus map of the cotton genome which will be productively used by the larger cotton research community. (NP 301, Component 1, Problem Statement 1B) Major Expansion of DNA Markers for Cotton: Development of new and improved cotton cultivars for U.S. farmers will require successful application of modern molecular biology techniques to the cotton germplasm pool. This will include significant expansion of the currently available DNA markers because of cotton�s low DNA polymorphism and the need for a large number of markers for germplasm characterization and gene discovery. Scientists in the Crop Germplasm Research Unit at the Southern Plains Agricultural Research Center, College Station, TX, in cooperation with many members of the larger cotton research community, developed 750 cotton BAC-derived SSR markers and 700 cotton genomic SSR markers, and released them to the research community via submission of the primer DNA sequences and associated information to GenBank, CottonDB, and/or the Cotton Microsatellite Database (CMD). This accomplishment is important because it greatly expands the collection of cotton molecular markers that are available to, and are portable among, all members of the cotton research community. The BAC-derived SSR marker set is of particular significance because it streamlines identification of new genes and QTLs in cotton, and will greatly facilitate the eventual integration of cotton genetic maps with BAC-based physical maps. (NP 301, Component 1, Problem Statement 1B) Technology Transfer Number of Non-Peer Reviewed Presentations and Proceedings: 10 Number of Newspaper Articles,Presentations for NonScience Audiences: 6
Impacts
(N/A)
Publications
- Blenda, A.V., Scheffler, J.A., Scheffler, B.E., Palmer, M., Lacape, J., Jesudurai, C., Jung, S., Muthukumar, S., Yellambalase, P., Ficklin, S., Staton, M., Eschelman, R., Ulloa, M., Saha, S., Burr, B., Lui, S., Zhang, T., Fang, D., Yu, J., Pepper, A.E., Kumpatla, S.P., Jacobs, J., Tomkins, J. P., Cantrell, R.G., Main, D. 2006. Cmo: a cotton microsatellite database resource for gossypium genomics. Biomed Central (BMC) Genomics.7:132
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Progress 10/01/05 to 09/30/06
Outputs
Progress Report 1. What major problem or issue is being resolved and how are you resolving it (summarize project aims and objectives)? How serious is the problem? Why does it matter? Cotton, a fiber and oilseed crop, ranks as the fourth most important cash crop in the U.S. for its fiber, and the second most important as a source of vegetable oil. As an introduced crop, cotton has a narrow genetic base that makes it vulnerable and limits the ability to make genetic advances. This project is focused on developing and utilizing genetic tools and other resources to improve cotton varieties for the American farmer. The genetic potential of cotton yields has not reached its full potential, current cotton yields are static if not declining, and genetic vulnerability is a concern as less than one percent of cotton germplasm has been explored. Cotton is a genetically complex organism that makes genetic manipulations and advancements very time intensive and requires the use
of sophisticated genetic methods; however, without such advancements U.S. cotton farmers cannot benefit substantially from exotic cotton germplasm. Therefore, a better understanding of the large, complex cotton genome and the public availability of sufficient genetic tools and information are urgently needed. This research falls under the Plant Genetic Resources, Genomics, and Genetic Improvement National Program (NP 301), and specifically addresses the Genomic Characterization and Genetic Improvement research component. Work under this project allows cotton researchers worldwide, public and private, to use updated cotton genomic tools and associated information (including DNA markers, DNA clones, and gene sequences) to identify agronomically useful genes from the exotic cotton germplasm available and to ultimately develop improved cotton cultivars that will benefit U.S. cotton producers and the textile industry. The American consumer benefits from the ongoing availability of
cotton products at stable prices. 2. List by year the currently approved milestones (indicators of research progress) Cotton genomics research and germplasm activities at the College Station Location have historically been conducted under a single project. However, with National Program Staff and Area Director concurrence, the genomics and germplasm activities were assigned to two separate projects in FY 2006; genomics research is covered by this project and germplasm activities under 6202-21000-024-00D. No new research objectives were introduced into the original OSQR-approved Project Plan; thus, genomics- focused milestones are addressed in the current report and germplasm- focused milestones are addressed in the companion -024 report. Year 1 (FY 2004): 1. Develop a panel of diverse U.S. cotton germplasm to identify DNA markers that are polymorphic. 2. Use the polymorphic DNA markers to characterize the diversity of U.S. germplasm. 3. Develop simple sequence repeat (SSR) markers
from bacterial artificial chromosome (BAC) clones to characterize cotton germplasm. 4. Develop a permanent Recombinant Inbred (RI) mapping population of TM- 1 x 3-79. 5. Map BAC-derived SSR markers on RI mapping population of TM-1 x 3-79. 6. Develop a core set of molecular markers as reference descriptors for characterization and evaluation studies. Year 2 (FY 2005): 1. Extend development of the polymorphic DNA markers to characterize the diversity of U.S. germplasm. 2. Use the polymorphic DNA markers to characterize the diversity of U.S. germplasm. 3. Continue to map BAC-derived SSR markers on RI mapping population of TM-1 x 3-79. 4. Continue development of a core set of molecular markers as reference descriptors for characterization and evaluation studies. Year 3 (FY 2006): 1. Extend development of the polymorphic DNA markers to characterize the diversity of U.S. germplasm. 2. Continue to use the polymorphic DNA markers to characterize the diversity of U.S. germplasm. 3.
Map additional BAC-derived SSR markers on RI mapping population of TM- 1 x 3-79 to extend definition of cotton genome. 4. Apply core set of molecular markers as reference descriptors in characterizing and evaluating important cotton productivity and quality traits. Year 4 (FY 2007): 1. Extend development of the polymorphic DNA markers to characterize the diversity of U.S. germplasm. 2. Continue to use the polymorphic DNA markers to characterize the diversity of U.S. germplasm. 3. Continue mapping of BAC-derived SSR markers on RI mapping population of TM-1 x 3-79 to extend definition of cotton genome. 4. Apply core set of molecular markers as reference descriptors in characterizing and evaluating important cotton productivity and quality traits. 5. Integrate genetic map data with existing genetic maps. 6. Provide relevant genomic data to appropriate public databases. FY 2008 (Year 5): 1. Extend development of the polymorphic DNA markers to characterize the diversity of U.S.
germplasm. 2. Continue to use the polymorphic DNA markers to characterize the diversity of U.S. germplasm. 3. Map additional BAC-derived SSR markers on RI mapping population of TM- 1 x 3-79 to extend definition of cotton genome. 4. Apply core set of molecular markers as reference descriptors in characterizing and evaluating important cotton productivity and quality traits. 5. Continue to integrate genetic map data with existing genetic maps. 6. Continue to provide relevant genomic data to appropriate public databases. 4a List the single most significant research accomplishment during FY 2006. Genetic Map of Important Cotton Markers Constructed: A portable genetic marker map of cotton was constructed. If the full genetic potential of cotton is to be identified and exploited in development of better cotton varieties, it is necessary that appropriate genetic techniques be developed to characterize the genetic diversity and control of important cotton productivity and quality
traits. Scientists in the Crop Germplasm Research Unit at the Southern Plains Agricultural Research Center, College Station, Texas, in cooperation with many other members of the cotton research community, constructed a portable genetic map of approximately 1,200 SSR markers based on the TM-1 x 3-79 RIL cotton mapping population. This accomplishment is important because it lays an important foundation for effective genetic characterization of cotton germplasm, and will contribute substantially to the development of more productive cotton varieties that will increase the profitability of U.S. cotton farmers. (NP 301; Component 2, Genomic Characterization and Genetic Improvement; ARS Strategic Plan Performance Measure 1.2.8) 4b List other significant research accomplishment(s), if any. Genome Survey of Upland Cotton Completed: A genome-wide genetic survey of Upland cotton was completed and the information made available to cotton researchers worldwide. Understanding the genetic
complexity and genomic distribution of cotton genes is necessary for improving the fiber yield and quality of the cotton crop. Scientists in the Crop Germplasm Research Unit at the Southern Plains Agricultural Research Center, College Station, Texas, conducted a genome-wide survey of the cotton transcriptome profile that consists of 39,384 fiber development EST unigenes and 19,160 non-fiber EST unigenes; the work revealed cotton gene islands and revised two of 13 pairs of the cotton homoeologous chromosomes. This accomplishment is important because it represents the first survey ever accomplished on the tetraploid genome of Upland cotton, it provides important information on the structural and functional genomics of cotton, and it contributes useful knowledge and tools that can be applied to the development of improved cotton cultivars for U.S. farmers. (NP 301; Component 2, Genomic Characterization and Genetic Improvement; ARS Strategic Plan Performance Measure 1.2.8) 5. Describe
the major accomplishments to date and their predicted or actual impact. Work under this project substantially advanced the integrated mapping of the cotton genome to include a 76,800-clone cotton BAC library and a 76, 800-clone cotton BIBAC library, nearly 100,000 BAC fingerprints, about 5, 000 contigs, and over 750 SSR markers that are physically isolated from the cotton genome. The SSR-containing BACs streamline identification of new genes and QTLs in cotton, and the eventual integration of cotton genetic maps with BAC-based physical maps. Under this project, approximately 4,000 pairs of SSR primers were developed and/or evaluated; approximately 1,300 pairs of SSR primers showing an interspecific polymorphism were used to genotype the TM-1 x 3-79 mapping populations. A multinational investigation of cotton germplasm collections (China, Uzbekistan and USA) was initiated by use of a common set of SSR markers to characterize 288 cotton accessions selected from each collection. Under
this project, a genome-wide survey of the cotton transcriptome profile was accomplished that consists of about 40,000 fiber development EST unigenes and about 20,000 non-fiber EST unigenes; this work represents the first survey on the tetraploid genome of Upland cotton. Additional accomplishments under this project include the production and characterization of more than 1,000 sequences of TM-1 BAC ends with 1,000 conserved ortholog genes of Arabidopsis to develop syntenic relationships between cultivated cotton and the model plant Arabidopsis. Project work accomplished the first complete assignment of 26 cotton chromosomes by use of TM-1 BAC-FISH and translocation analyses. All accomplishments made under this project are fully consistent with relevant milestones listed in the Project Plan, and with the relevant research components as defined in the National Program 301 Action Plan. Accomplishments under this project contribute to the achievement of ARS Strategic Plan Goal 1,
Objective 2, Performance Measure 8, in that project accomplishments contribute substantially to the attainment of the Agency FY 2007 target of expanding the diversity of important germplasm collections and using genetic resources from these collections to produce new and improved crops for U.S. farmers. 6. What science and/or technologies have been transferred and to whom? When is the science and/or technology likely to become available to the end- user (industry, farmer, other scientists)? What are the constraints, if known, to the adoption and durability of the technology products? Science and technologies developed by this project have been effectively transferred to appropriate users. Technology transfer is primarily directed to the research community rather than end-users. Submittals to GenBank included 2,896 sequences of TM-1 BAC and BIBAC clones that contained a SSR locus, and 750 pairs of TMB primers that were characterized. The GenBank accession numbers along with the
sequence information were posted to the Plant Genome Database, CottonDB, and to the Cotton Microsatellite Database (CMD), which are publicly accessible. Genetic and genomic materials characterized by project work were made available to other researchers upon request. An integrated cotton genome map of SSR markers and BAC contigs, and a core set of molecular reference descriptors will be made available to the cotton community, within the next 2-3 years, for enhanced cotton research. Although progress in improving cotton through genetic manipulation is inevitably a complex and difficult process, which makes it time consuming and expensive, we see no technical constraints to our work continuing to facilitate the development of new cotton varieties for use by U.S. farmers and that have significantly improved productivity, fiber quality, and seed quality traits.
Impacts
(N/A)
Publications
- Gao, W., Chen, Z.J., Yu, J., Kohel, R.J., Womack, J.E., Stelly, D.M. 2005. Wide-cross whole-genome radiation hybrid mapping of the cotton (Gossypium barbadense L.) genome. Molecular Genetics and Genomics. 275:105-113.
- Wang, K., Song, X., Han, Z., Guo, W., Yu, J., Sun, J., Pan, J., Kohel, R.J. , Zhang, T. 2006. Complete assignment of the G. hirsutum L. chromosomes by BAC-FISH and translocation analyses. Journal of Theoretical and Applied Genetics. 113:73-80.
- Xu, Z., Song, G., Cho, J., Jianmin, D., Koo, P., Kohel, R.J., Yu, J. 2006. Distribution of fiber elongation genes in the upland cotton genome [abstract]. Proceedings of Plant and Animal Genome XIV Conference. Paper No. P684.
- Hoffman, S., Kohel, R.J., Ulloa, M., Cho, J., Xu, Z., Smith, W., Pepper, A. , Cantrell, R., Yu, J. 2006. Association analysis of morphological characters with molecular markers in a TM-1 x 3-79 RIL population grown in three diverse environments [abstract]. In: Proceedings of the Beltwide Cotton Conferences, January 3-6, 2006, San Antonio, Texas. 2006 CDROM.
- Hoffman, S., Yu, J., Kohel, R.J., Cantrell, R.G., Xiao, J., Pepper, A. 2006. Characterization of 656 new SSR markers developed from Gossypium hirsutum sequences [abstract]. Proceedings of Plant and Animal Genome XIV Conference. Paper No. P157.
- Abdurakhmonov, I.Y., Kohel, R.J., Saha, S., Pepper, A.E., Yu, J., Buriev, T.Z., Shermatov, S., Abdullaev, A., Jenkins, J.N., Abdukarimov, A. 2006. Molecular genetic diversity of G. hirsutum cotton accession from Uzbek cotton germplasm revealed by a core set and chromosome specific microsatellite markers [abstract]. Proceedings of Plant and Animal Genome XIV Conference. Paper No. P131.
- Frelichowski, J.E., Palmer, M., Main, D., Tomkins, J.P., Cantrell, R.G., Stelly, D., Yu, J., Kohel, R.J., Ulloa, M. 2006. Genetic mapping of microsatellites derived from BAC-end sequences of Gossypium hirsutum Acala 'Maxxa'. Molecular Genetics and Genomics. Mol. Genet. Genom. 275 (5) 479- 491. Online DOI: 10.1007/s00438-006-0106-z.
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