Bio-Evaluation Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju, Chungbuk, 28116, Korea.
Plant Immunity Research Center, Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Korea.
Nat Commun. 2021 Jan 4;12(1):97. doi: 10.1038/s41467-020-20337-3.
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.
全球范围内，大豆是一种主要的蛋白质和油料作物。深入了解大豆的驯化和改良过程有助于推动基于基因组学的育种工作。在这里，我们展示了 781 个大豆个体的全基因组变异图谱，包括 418 个驯化种（Glycine max）、345 个野生种（Glycine soja）和 18 个自然杂种（G. max/G. soja）。我们描述了 183 个驯化选择的增强检测以及在驯化和改良过程中假定有害突变的模式。在这个主要自交的物种中，与野生大豆相比，驯化大豆的整体有害突变减少了 7.1%，而从地方品种到改良品种又减少了 1.4%。检测到的驯化选择也显示出有害等位基因水平的降低。重要的是，利用这一资源进行基因型推断，提高了大豆多样性群体中种子蛋白和油性状全基因组关联研究的作图分辨率。
