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United States Department of Agriculture

Agricultural Research Service

Research Project: GENETIC ANALYSES AND TRAIT MAPPING TO EXPLOIT UNTAPPED GENETIC DIVERSITY IN SORGHUM

Location: Crop Germplasm Research

2013 Annual Report


1a.Objectives (from AD-416):
Objective 1: Refine the sorghum genome map to accelerate map-based gene discovery and comparative analyses of genes and gene networks in the Poaceae family. Completion of a genome map of sorghum will permit direct cross-referencing of the genomes of sorghum, rice, and maize, thereby permitting a unified Poaceae genome map to be assembled. This map and associated technology platforms will enhance gene discovery and expedite germplasm development via marker-assisted selection of key agronomic traits. Objective 2: Utilize the sorghum genome map and genetic resources to clone key genes, including those controlling pollen fertility and drought tolerance. As the products of Objective 1 are developed and released, positional cloning of genes will be simplified when complemented with high-quality linkage analyses. Sub-objective 2.A: Elucidate the genetic basis of drought tolerance by positional cloning of a major stay-green QTL in sorghum. Utilizing genetic stocks that are isogenic for a given stay-green QTL, high resolution maps have been constructed and continued refinement of each QTL will be achieved. The further refinement of the QTL, coupled with detailed genetic, physiological, and molecular analyses of gene candidates will ultimately permit the gene(s) conditioning the stay-green phenotype to be cloned. Sub-objective 2.B: Elucidate the genetic basis of pollen fertility restoration in sorghum by positional cloning of the Rf2 fertility gene. Armed with fine mapping populations, genomic technology platforms for sorghum, and having cloned the first major sorghum fertility gene, positional cloning of Rf2 fertility restoration gene is achievable. Objective 3: Map genome regions controlling photoperiodism and plant height in sorghum and identify robust molecular markers linked to these traits. Completion of the genome map flanking these trait loci will expedite high-resolution mapping by revealing sequences representing potential markers for additional fine mapping, while also revealing candidate genes conditioning photoperiodic-insensitivity and reduced plant height. Objective 4: Conduct proof-of-concept study, utilizing molecular markers, to expedite the conversion of tropical sorghum to temperate adaptation. We will utilize the genome map and molecular markers discovered under Objective 3 to evaluate the introgression of recessive alleles conditioning photoperiod insensitivity, plus reduced plant height, into tropical germplasm. This molecular evaluation will supplant the additional selfing generations and associated phenotypic evaluation normally required to track the introgression of recessive alleles into exotic germplasm during their conversion to photoperiod-insensitive, short-stature cultivars suitable for production in the U.S.


1b.Approach (from AD-416):
The long-term goal of this project is to develop and utilize appropriate approaches and techniques in genomics and biotechnology to discover genes that control key agronomic traits, and to utilize these to augment breeding strategies that will facilitate the development of improved sorghum cultivars. At present, positional cloning in sorghum is a daunting task, but the further refinement of a sequenced-based sorghum genome map will greatly simplify gene discovery. We have targeted several agronomically critical genes for positional cloning, including the stay-green gene(s) conditioning sorghum’s exceptional tolerance to post-anthesis drought. In ongoing collaboration with scientists at Texas A&M University and the Department of Primary Industries and Fisheries, Queensland, Australia, an integrated approach that includes the plant disciplines of physiology, breeding, molecular genetics, and genomics is being employed to clone stay-green genes. This information, and markers linked to these genes, will be exploited to introgress post-anthesis drought tolerance into elite sorghum cultivars. Additionally, the molecular tools developed under Objective 1 and Sub-objective 2.A will facilitate our ongoing efforts to clone pollen fertility restoration genes. Work with our Queensland collaborator will target cloning of Rf2 because of its importance in hybrid seed production, and the need for informative markers tightly linked to Rf2 for germplasm evaluation. We also seek to map, at high resolution, the height and photoperiod-insensitive genes required to convert tropical sorghums to photoperiod-insensitive, short-stature cultivars suitable for production in the U.S. Objectives 1-3 are complementary, and the knowledge gained under one objective will facilitate success in all. Continued map resolution of photoperiodic and height trait loci obtained under Objective 3 will provide the foundation for identification of additional robust molecular markers and potential candidate genes, which will positively impact achievement of Objective 4.


3.Progress Report:
Work under this project during FY 2013, in collaboration with university and industry partners, resulted in significant progress in sorghum germplasm breeding which included the release of 50 temperate-zone adapted sorghum lines derived from tropical sorghum germplasm. The discoveries made by this collaborative team will facilitate ongoing efforts focused on exploiting newly developed molecular technologies in developing improved sorghum hybrids for effective utilization by farmers in all production areas of the world. During the life of this project, significant accomplishments were made in functional comparison/analysis of the sorghum genome and in the mapping and cloning of genes controlling important traits in sorghum. Specific accomplishments include the development/utilization of NexGen nucleic acid sequencing technology for whole-genome genotyping and gene expression profiling. The development of these genomic resources facilitated the high-resolution mapping of important agronomic traits, including genes controlling pollen fertility restoration (rf2), plant height (dw2), and photoperiod sensitivity (ma1). Gene expression profiling of different plant organs provided a genome-wide description of entire networks of genes that are involved in plant defense against biotic and abiotic stresses. Fine mapping efforts culminated in the cloning of the photoperiod-responsive gene ma1, the key gene controlling flowering of sorghum in temperate zones worldwide. This project expired in FY 2013, but was replaced by 6202-21000-034-00D which is expanding upon the work of the precursor project.


4.Accomplishments
1. Temperate-zone adapted sorghum germplasm developed and released. Sorghum is an important grain crop in many areas of the world including the U.S.; ongoing efforts are needed to use molecular tools to genetically improve the crop. Much potentially valuable sorghum germplasm is tropical in origin and, because these accessions evolved under conditions where day-length is relatively constant, they do not successfully flower and produce seed in temperate environments (including U.S. growing areas) where day-length is much longer during the growing season. ARS scientists at College Station, Texas, working with an industry partner, used modern molecular tools in conjunction with classical plant breeding techniques to convert ARS tropical sorghums to short-stature, early flowering versions, with the objective of making a diverse range of germplasm available to the sorghum industry. Dozens of tropical-adapted sorghum germplasm types were released to breeders; the work represents major success in exploiting the wealth of previously unusable ARS sorghum germplasm in development of higher-producing sorghum varieties for farmers in the U.S. and worldwide.


Review Publications
Washburn, J.D., Murray, S.C., Burson, B.L., Klein, R.R., Jessup, R.W. 2013. Targeted mapping of quantitative trait locus regions for rhizomatousness in chromosome SBI-01 and analysis of overwintering in a Sorghum bicolor x S. propinquum population. Molecular Breeding. 31:153-162.

Klein, R.R., Miller, F.R., Klein, P.E., Burke, J.J. 2013. Registration of partially converted germplasm from 44 accessions of the USDA-ARS Ethiopian and Sudanese sorghum collections. Journal of Plant Registrations. 7(3):368-372.

Last Modified: 4/19/2014
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