Liu Zhi, Shi Xiaolei, Yang Qing, Li Ying, Yang Chunyan, Zhang Mengchen, An Yong-Qiang Charles, Nguyen Henry T, Yan Long, Song Qijian
Hebei Key Laboratory of Crop Genetics and Breeding, National Soybean Improvement Center Shijiazhuang Sub-Center, Huang-Huai-Hai Key Laboratory of Biology and Genetic Improvement of Soybean, Ministry of Agriculture and Rural Affairs, Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, China.
USDA-ARS Midwest Area, Plant Genetics Research Unit, St. Louis, Missouri, USA.
Plant Genome. 2025 Jun;18(2):e70020. doi: 10.1002/tpg2.70020.
Rare-allele variants are important for crop improvement because they can be linked to important traits. However, genome-wide distribution and annotation of rare-allele variants have not been reported. We analyzed sequencing data from 1556 soybean accessions and found 6,533,419 rare-allele variants in Glycine max and 941,274 in Glycine soja populations. Although the total number of variants was 20% less in G. max than G. soja, the number of rare-allele variants in G. max was six times that in G. soja. Among the rare-allele variants in G. max, 19.16% were novel mutations that did not exist in G. soja. Domestication and artificial selection have not only reduced overall genetic diversity but also the frequency of variants of cultivated soybean. Rare-allele variants were mainly located in intergenic and noncoding regions rather than coding regions, and in heterochromatin regions rather than euchromatic regions. There were 121,450 rare-allele variations in 36,213 G. max genes and 20,645 in 12,332 G. soja genes, resulting in nonsynonymous, stop gain or stop loss mutations. This study provided the first comprehensive understanding of rare-allele variants in wild and cultivated soybean genomes and its potential impact on gene functions. This information will be valuable for future studies aimed at improving soybean varieties, as these variants may help reveal the underlying mechanisms controlling traits and have the potential to improve stress resistance, yield, and adaptability to environments.
稀有等位基因变异对于作物改良很重要，因为它们可能与重要性状相关联。然而，尚未有关于稀有等位基因变异的全基因组分布和注释的报道。我们分析了1556份大豆种质的测序数据，在栽培大豆（Glycine max）群体中发现了6,533,419个稀有等位基因变异，在野生大豆（Glycine soja）群体中发现了941,274个。尽管栽培大豆中的变异总数比野生大豆少20%，但其稀有等位基因变异的数量却是野生大豆的六倍。在栽培大豆的稀有等位基因变异中，19.16%是野生大豆中不存在的新突变。驯化和人工选择不仅降低了栽培大豆的总体遗传多样性，也降低了其变异频率。稀有等位基因变异主要位于基因间和非编码区域，而非编码区，并且位于异染色质区域而非常染色质区域。在36,213个栽培大豆基因中有121,450个稀有等位基因变异，在12,332个野生大豆基因中有20,645个，导致非同义、终止密码子获得或终止密码子丢失突变。本研究首次全面了解了野生和栽培大豆基因组中的稀有等位基因变异及其对基因功能的潜在影响。这些信息对于未来旨在改良大豆品种的研究将是有价值的，因为这些变异可能有助于揭示控制性状的潜在机制，并有可能提高抗逆性、产量和环境适应性。
