ALBERT

Description: The United States Department of Agriculture, Soybean Germplasm Collection includes 18,480 domesticated soybean and 1168 wild soybean accessions introduced from 84 countries or developed in the United States. This collection was genotyped with the SoySNP50K BeadChip containing greater than 50K single-nucleotide polymorphisms. Redundant accessions were identified in the collection, and distinct genetic backgrounds of soybean from different geographic origins were observed that could be a unique resource for soybean genetic improvement. We detected a dramatic reduction of genetic diversity based on linkage disequilibrium and haplotype structure analyses of the wild, landrace, and North American cultivar populations and identified candidate regions associated with domestication and selection imposed by North American breeding. We constructed the first soybean haplotype block maps in the wild, landrace, and North American cultivar populations and observed that most recombination events occurred in the regions between haplotype blocks. These haplotype maps are crucial for association mapping aimed at the identification of genes controlling traits of economic importance. A case-control association test delimited potential genomic regions along seven chromosomes that most likely contain genes controlling seed weight in domesticated soybean. The resulting dataset will facilitate germplasm utilization, identification of genes controlling important traits, and will accelerate the creation of soybean varieties with improved seed yield and quality.

Description: As an ancient cereal of great importance for dryland agriculture even today, foxtail millet ( Setaria italica ) is fast becoming a new plant genomic model crop. A genotypic analysis of 250 foxtail millet landraces, which represent 1% of foxtail millet germplasm kept in the Chinese National Gene Bank (CNGB), was conducted with 77 SSRs covering the foxtail millet genome. A high degree of molecular diversity among the landraces was found, with an average of 20.9 alleles per locus detected. STRUCTURE, neighbor-jointing, and principal components analyses classify the accessions into three clusters (topmost hierarchy) and, ultimately, four conservative subgroups (substructuring within the topmost clusters) in total, which are in good accordance with eco-geographical distribution in China. The highest subpopulation diversity was identified in the accessions of Pop3 from the middle regions of the Yellow River, followed by accessions in Pop1 from the downstream regions of the Yellow River, suggesting that foxtail millet was domesticated in the Yellow River drainage area first and then spread to other parts of the country. Linkage disequilibrium (LD) decay of less than 20 cM of genetic distance in the foxtail millet landrace genome was observed, which suggests that it could be possible to achieve resolution down to the 20 cM level for association mapping.

Description: A total of 992,682 single-nucleotide polymorphisms (SNPs) was identified as ideal for Illumina Infinium II BeadChip design after sequencing a diverse set of 17 common bean ( Phaseolus vulgaris L) varieties with the aid of next-generation sequencing technology. From these, two BeadChips each with 〉5000 SNPs were designed. The BARCBean6K_1 BeadChip was selected for the purpose of optimizing polymorphism among market classes and, when possible, SNPs were targeted to sequence scaffolds in the Phaseolus vulgaris 14 x genome assembly with sequence lengths 〉10 kb. The BARCBean6K_2 BeadChip was designed with the objective of anchoring additional scaffolds and to facilitate orientation of large scaffolds. Analysis of 267 F 2 plants from a cross of varieties Stampede x Red Hawk with the two BeadChips resulted in linkage maps with a total of 7040 markers including 7015 SNPs. With the linkage map, a total of 432.3 Mb of sequence from 2766 scaffolds was anchored to create the Phaseolus vulgaris v1.0 assembly, which accounted for approximately 89% of the 487 Mb of available sequence scaffolds of the Phaseolus vulgaris v0.9 assembly. A core set of 6000 SNPs (BARCBean6K_3 BeadChip) with high genotyping quality and polymorphism was selected based on the genotyping of 365 dry bean and 134 snap bean accessions with the BARCBean6K_1 and BARCBean6K_2 BeadChips. The BARCBean6K_3 BeadChip is a useful tool for genetics and genomics research and it is widely used by breeders and geneticists in the United States and abroad.