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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 #333561

Title: The genetic makeup of a global barnyard millet germplasm collection

item WALLACE, JASON - Cornell University
item UPADHYAYA, HARI - Cornell University
item VETRIVENTHAN, M - International Crops Research Institute For Semi-Arid Tropics (ICRISAT) - India
item Buckler, Edward - Ed
item HASH, TOM - International Crops Research Institute For Semi-Arid Tropics (ICRISAT) - Nigeria
item RAMU, PUNNA - Cornell University

Submitted to: The Plant Genome
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/9/2014
Publication Date: 3/13/2015
Citation: Wallace, J.G., Upadhyaya, H.D., Vetriventhan, M., Buckler IV, E.S., Hash, T.C., Ramu, P. 2015. The genetic makeup of a global barnyard millet germplasm collection. The Plant Genome. 8(1):1-39.

Interpretive Summary: Barnyard millet is an orphan/neglected tropical cereal crop and mostly grown as forage crop in USA. Because of highly nutritious and short generation time, barnyard millet has become a model species for forage crops. We have characterized the barnyard germplasm collection available at ICRISAT with Genotyping-by-sequencing (GBS) and identified the groups based on geographic distribution. The clusters information enables the breeders to select diverse accessions to make suitable crosses to study the genetic architecture of different traits and also helps to improve the production of forage. Improved production of this forage crop will help to enhance the food security of small holder farmers in Asia and Africa.

Technical Abstract: Barnyard millet (Echinochloa spp.) is an important crop for many smallholder farmers in southern and eastern Asia. It is valued for its drought tolerance, rapid maturation, and superior nutritional qualities. Despite these characteristics there are almost no genetic or genomic resources for this crop in either cultivated species (E. colona and E. crus-galli). Recently, a core collection of 89 barnyard millet accessions was developed at the genebank at the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT). To enhance the use of this germplasm and genomic research in barnyard millet improvement, we report the genetic characterization of this core collection using whole-genome genotyping-by-sequencing. We identified several thousand single-nucleotide polymorphisms segregating in the core collection, and we use them to show patterns of population structure and phylogenetic relationships among the accessions. We determine that there are probably four population clusters within the E. colona accessions and three such clusters within E. crus-galli. These clusters match phylogenetic relationships but by and large do not correspond to classification into individual races or clusters based on morphology. Geospatial data available for a subset of samples indicates that the clusters probably originate from geographic divisions. In all, these data will be useful to breeders working to improve this crop for smallholder farmers. This work also serves as a case study of how modern genomics can rapidly characterize crops, including ones with little to no prior genetic data.