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Globally, soybean is a major protein and oil crop. Enhancing our understanding of the soybean domestication and improvement process helps boost genomics-assisted breeding efforts. Here we present a genome-wide variation map of 10.6 million single-nucleotide polymorphisms and 1.4 million indels for 781 soybean individuals which includes 418 domesticated (Glycine max), 345 wild (Glycine soja), and 18 natural hybrid (G. max/G. soja) accessions. We describe the enhanced detection of 183 domestication-selective sweeps and the patterns of putative deleterious mutations during domestication and improvement. This predominantly selfing species shows 7.1% reduction of overall deleterious mutations in domesticated soybean relative to wild soybean and a further 1.4% reduction from landrace to improved accessions. The detected domestication-selective sweeps also show reduced levels of deleterious alleles. Importantly, genotype imputation with this resource increases the mapping resolution of genome-wide association studies for seed protein and oil traits in a soybean diversity panel. The accumulation of recombination events in selfing species may lead to a rapid fixation of both beneficial and deleterious mutations. Here, the authors resequence 781 soybean accessions, show purging of deleterious mutation during domestication, and report genome-wide associations for seed protein and oil traits. [ABSTRACT FROM AUTHOR]

The mutant allele of rice calmodulin-binding transcription activator OsCBT, oscbt-1, exhibits broad-spectrum resistance against rice pathogens. Previously, we reported that the strong resistance of the oscbt-1 mutant to pathogens was conferred by a constitutive upregulation of defense-related genes even under pathogen-free conditions. We also found strong induction of the hypersensitive response as a reaction to pathogen invasion. The results suggest that OsCBT acts as a negative regulator of basal resistance to pathogen attack. To identify the transcriptional network regulated by OsCBT, we compared global gene expression profiles between wild-type (WT) and oscbt-1 rice plants grown under pathogen-free conditions. The results of a 3′ tiling microarray revealed that in oscbt-1 plants, 81 genes are upregulated and 200 genes are downregulated when compared with the WT. A gene ontology analysis showed that differentially regulated genes in oscbt-1 were very closely associated with "death" GO term in a biological process category, and "catalytic activity" and "binding" GO terms in a molecular function category. A MapMan analysis indicated that the functions of these genes were associated with plant responses to biotic stress. Moreover, the results from quantitative real-time PCR in the oscbt-1 mutant showed a significant effect on the gene expression patterns of the fungal pathogen response. Our results suggested that the OsCBT regulates a rice defense response by modulating the expressions of various defense-related genes. [ABSTRACT FROM AUTHOR]

Key message: Genotyping data of a comprehensive Korean soybean collection obtained using a large SNP array were used to clarify global distribution patterns of soybean and address the evolutionary history of soybean. Understanding diversity and evolution of a crop is an essential step to implement a strategy to expand its germplasm base for crop improvement research. Accessions intensively collected from Korea, which is a small but central region in the distribution geography of soybean, were genotyped to provide sufficient data to underpin population genetic questions. After removing natural hybrids and duplicated or redundant accessions, we obtained a non-redundant set comprising 1957 domesticated and 1079 wild accessions to perform population structure analyses. Our analysis demonstrates that while wild soybean germplasm will require additional sampling from diverse indigenous areas to expand the germplasm base, the current domesticated soybean germplasm is saturated in terms of genetic diversity. We then showed that our genome-wide polymorphism map enabled us to detect genetic loci underlying flower color, seed-coat color, and domestication syndrome. A representative soybean set consisting of 194 accessions was divided into one domesticated subpopulation and four wild subpopulations that could be traced back to their geographic collection areas. Population genomics analyses suggested that the monophyletic group of domesticated soybeans was likely originated at a Japanese region. The results were further substantiated by a phylogenetic tree constructed from domestication-associated single nucleotide polymorphisms identified in this study. [ABSTRACT FROM AUTHOR]

Seed coat cracking (SCC), particularly the Type-I irregular cracking, is critical in determining the quality of appearance and commercial value of soybean seeds. The objective of this study was to identify the quantitative trait loci (QTLs) for SCC with high-density genetic map. One hundred sixty-seven recombinant inbred lines (RILs) developed from a cross between Uram (SCC-resistant) and Chamol (SCC-susceptible) were evaluated for SCC over 2 years (2016–2017). The QTL analysis identified 12 QTLs located on chromosomes 2 (D1b), 6 (C2), 8 (A2), 9 (K), 10 (O), 12 (H), 19 (L), and 20 (I). Out of the 12 QTLs, qSC2-1, qSC9, SC10-1, qSC10-2, and qSC12 were novel QTLs and the other seven QTLs (qSC2-2, qSC2-3, qSC6, qSC8, qSC19-1, qSC19-2, and qSC20) were found to co-localize with the previously identified QTLs. The mean SCC of the RILs of early maturity group was significantly higher than that of the late maturity group, suggesting an association between SCC and maturity loci. In addition, although 10 QTLs were distantly located from the maturity loci (E1, E3, E4, E7, and E10), qSC10-1 and qSC10-2 co-localized with the maturity loci E2. The results obtained in this study provide useful genetic information on SCC which could be used in the SCC breeding programs. [ABSTRACT FROM AUTHOR]