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Location: Crop Germplasm Research

2010 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
Significant progress was made during FY 2010 on the fine mapping of sorghum genes that condition pollen fertility restoration (Rf) and photoperiodism (the responsiveness of flowering to day length). As a first step towards breeding sorghum lines adapted for the temperate climates associated with U.S. sorghum production areas, first-generation hybrids were created using photoperiod-sensitive sorghum germplasm and elite sorghum inbreds. The information obtained and methodologies developed by this work will be critical for the successful use of previously unusable photoperiod-sensitive sorghum germplasm in development of higher-producing sorghum hybrids for temperate climates. In collaboration with Australian scientists, a major gene that controls pollen fertility restoration in sorghum was fine mapped, and this mapping effort resulted in the identification of a candidate fertility restoration gene we have designated Rf5. The gene sequence of Rf5, and the markers linked to this gene, will be utilized by breeders to create new parental lines for hybrid seed production. As part of an effort to define the molecular mechanisms controlling sorghum's photoperiod response, project work focused on detailed examination of genes controlling the sorghum biological clock. Studies at the cellular level are underway to understand how mutations in specific clock genes lead to ability of mutant sorghum lines to flower in the long days of temperate climates. Newly established collaboration with geneticists of a major U.S. sorghum breeding company has as its goal the development of photoperiod-insensitive germplasm through a conversion breeding project. Crossing of photoperiod-sensitive germplasm to an elite inbred continues to transfer adapted genes into the ARS-maintained germplasm accessions. These new sorghums are being characterized with molecular markers to help track the movement of adapted genes from the donor line into the photoperiod-insensitive lines.

4. Accomplishments
1. Identifying and locating the Rf5 gene, a new source for pollen fertility restoration in sorghum. Sorghum is an important grain crop in many areas of the world including the U.S. Nearly all of the grain sorghum grown in the U.S. is from high yielding hybrid seed, whose production is dependent upon genetic components known as pollen fertility restoration genes. The development of new parental lines for hybrid sorghum is a laborious process that requires the breeding of both female and male parents, each with a very specific complement of fertility restoration genes. ARS researchers at College Station, Texas, in cooperation with scientists in Australia, genetically analyzed in great detail (fine mapped) the Rf5 gene, confirming that it is a distinct, major fertility restoration gene. Markers associated with Rf5 have been identified that will greatly facilitate locating and transferring this gene in breeding efforts. The development and application of these sophisticated molecular biology tools (molecular markers) are critical to the work by breeders in developing new male and female parental lines for production of hybrid seed. This work contributes foundational new molecular and breeding methodology that will allow rapid and efficient exploitation of the wealth of previously unusable sorghum germplasm in development of higher-producing sorghum hybrids for U.S. farmers.

Review Publications
Jordan, D.R., Mace, E.S., Henzell, R.G., Klein, P.E., Klein, R.R. 2010. Molecular mapping and candidate gene identification of the Rf2 gene for pollen fertility restoration in sorghum (Sorghum bicolor (L.) Moench). Theoretical and Applied Genetics. 120(7):1279-1287.