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ARS Home » Northeast Area » Ithaca, New York » Robert W. Holley Center for Agriculture & Health » Plant, Soil and Nutrition Research » Research » Publications at this Location » Publication #321908
Title: Population genetics and structure of a global foxtail millet germplasm collection

Author
item UPADHYAYA, HARI - International Crops Research Institute For Semi-Arid Tropics (ICRISAT) - India
item VETRIVENTHAN, MANI - International Crops Research Institute For Semi-Arid Tropics (ICRISAT) - India
item DESHPANDE, SANTOSH - International Crops Research Institute For Semi-Arid Tropics (ICRISAT) - India
item SIVASUBRAMANI, SELVANAYAGAM - International Crops Research Institute For Semi-Arid Tropics (ICRISAT) - India
item WALLACE, JASON - University Of Georgia
item Buckler, Edward - Ed
item HASH, TOM - International Crops Research Institute For Semi-Arid Tropics (ICRISAT) - India
item RAMU, PUNNA - Cornell University

Submitted to: The Plant Genome
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/24/2015
Publication Date: 9/2/2015
Citation: Upadhyaya, H.D., Vetriventhan, M., Deshpande, S.P., Sivasubramani, S., Wallace, J.G., Buckler IV, E.S., Hash, T.C., Ramu, P. 2015. Population genetics and structure of a global foxtail millet germplasm collection. The Plant Genome. DOI: 10.385/plantgenome2015.07.0054.

Interpretive Summary: Foxtail millet is one of the most ancient crops of dryland agriculture. It is the second most important crop among millets, grown for grains or forage. Foxtail millet is valued for its drought tolerance and short duration, and its grains are nutritionally superior to other cereals such as rice and wheat. Foxtail millet germplasm resources provide reservoirs of novel alleles and genes for crop improvement that have remained mostly unexplored. This study applied genomic approaches to profile the genomes of nearly 200 diverse accessions. The race of foxtail millet were clearly differentiated, and the ability to conduct genetic mapping with these populations was demonstrated with the identification of genes controlling flowering and pigmentation. Overall, this study provides a launch point for conducting larger and more comprehensive studies to tap this tremendous genetic reservoir.

Technical Abstract: Foxtail millet is one among the most ancient crops of dryland agriculture. It is the second most important crop among millets, grown for grains or forage. Foxtail millet germplasm resources provide reservoirs of novel alleles and genes for crop improvement that have remained mostly unexplored. We genotyped a set of 190 foxtail millet germplasm accessions (including 155 accessions of the foxtail millet core collection) using genotyping-by-sequencing (GBS) for rapid single nucleotide polymorphisms (SNP) characterization to study population genetics and structure, which enable allele mining through association mapping approaches. After filtering a total 350,000 raw SNPs identified across 190 germplasm accessions for Minor Allele Frequency (MAF), coverage for samples and coverage for sites, we retained 181 accessions with 17,714 high quality SNPs with >/- 5% MAF. Genetic structure analyses revealed that foxtail millet germplasm accessions are structured along both on the basis of races and geographic origin, and the maximum proportion of variation was due to among individuals within populations. Accessions of race indica were less diverse and are highly differentiated from those of maxima and moharia. Genome-wide linkage disequilibrium (LD) analysis showed on an average LD extends up to ~150 kbp, and varied with individual chromosomes. The utility of these data for performing genome-wide association studies was tested with plant pigmentation and days to flowering, and identified significant marker-trait associations. This SNP data provides a foundation for exploration of foxtail millet diversity and for mining novel alleles and mapping genes for economically important traits.