Abstract
Population structure and genetic architecture of phenotypic traits in oat (Avena sativa L.) remain relatively under-researched compared to other small grain species. This study explores the historic context of current elite germplasm, including phenotypic and genetic characterization, with a particular focus on identifying under-utilized areas. A diverse panel of cultivated oat accessions was assembled from the USDA National Small Grains Collection to represent a gene pool relatively unaffected by twentieth century breeding activity and unlikely to have been included in recent molecular studies. The panel was genotyped using an oat iSelect 6K beadchip SNP array. The final dataset included 759 unique individuals and 2,715 polymorphic markers. Some population structure was apparent, with the first three principal components accounting for 38.8% of variation and 73% of individuals belonging to one of three clusters. One cluster with high genetic distinctness appears to have been largely overlooked in twentieth century breeding. Classification and phenotype data provided by the Germplasm Resources Information Network were evaluated for their relationship to population structure. Of the structuring variables evaluated, improvement status (cultivar or landrace) was relatively unimportant, indicating that landraces and cultivars included in the panel were all sampled from a similar underlying population. Instead, lemma color and region of origin showed the strongest explanatory power. An exploratory association mapping study of the panel using a subset of 2,588 mapped markers generated novel indications of genomic regions associated with awn frequency, kernels per spikelet, lemma color, and panicle type. Further results supported previous findings of loci associated with barley yellow dwarf virus tolerance, crown rust (caused by Puccinia coronata f. sp. avenae) resistance, days to anthesis, and growth habit (winter/spring). In addition, two novel loci were identified for crown rust resistance.
Highlights
Oat (Avena sativa L., 2n = 6x = 42) has played an important role in the development of agriculture around the world, but received less investment from the plant and agricultural research sectors during the twentieth century than other small grain crops such as wheat and barley (Frey, 1996)
In a study of 83 North American oat cultivars using restriction fragment length polymorphisms (RFLPs), polymorphism was found to be 54.8% in oat as compared to 5% in wheat and 28% in barley (O’Donoughue et al, 1994), supporting an earlier finding based on pedigree analysis that diversity in North American oat germplasm was greater than that in wheat (Souza and Sorrells, 1989)
Compared with the National Small Grains Collection (NSGC) A. sativa collection, the panel compiled for this study had proportionally fewer cultivars and accessions of uncertain improvement status compared with landraces
Summary
In a study of 83 North American oat cultivars using restriction fragment length polymorphisms (RFLPs), polymorphism was found to be 54.8% in oat as compared to 5% in wheat and 28% in barley (O’Donoughue et al, 1994), supporting an earlier finding based on pedigree analysis that diversity in North American oat germplasm was greater than that in wheat (Souza and Sorrells, 1989). This diversity is a valuable resource for agriculture because it enables oats to be adapted to a wide range of environments and end-uses
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