Landscape of rare-allele variants in cultivated and wild soybean genomes

Authors: LIU, ZHI - Hebei Academy Of Agriculture & Forestry; SHI, XIAOLEI - Hebei Academy Of Agriculture & Forestry; YANG, QING - Hebei Academy Of Agriculture & Forestry; LI, YING - Hebei Academy Of Agriculture & Forestry; YANG, CHUNYAN - Hebei Academy Of Agriculture & Forestry; ZHANG, MENGCHEN - Hebei Academy Of Agriculture & Forestry; An, Yong Qiang; YAN, LONG - Hebei Academy Of Agriculture & Forestry; Song, Qijian; NGUYEN, HENRY - University Of Missouri

Submitted to: Plant Journal
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/27/2025
Publication Date: 3/27/2025
Citation: Liu, Z., Shi, X., Yang, Q., Li, Y., Yang, C., Menhchen, Z., An, Y., Yan, L., Song, Q. 2025. Landscape of rare-allele variants in cultivated and wild soybean genomes. Plant Journal. 18(2). Article e70020. https://doi.org/10.1002/tpg2.70020.
DOI: https://doi.org/10.1002/tpg2.70020

Interpretive Summary: Rare-allele variants, genetic variants that occur at low frequencies in a population, are important for crop improvement because some variants may be associated with important traits such as disease resistance, insect resistance, drought tolerance, and seed composition. However, their genome-wide distribution and their mutation effects on gene function and protein synthesis in soybeans have not been reported. USDA researchers and collaborators analyzed the sequences of 1,556 cultivated and wild soybean genomes, identified and functionally annotated all variants, especially rare allelic variations in cultivated and wild soybeans. They concluded that domestication and artificial selection have greatly reduced the genetic diversity of cultivated soybean by decreasing the total number of variants and variant allele frequencies compared to wild soybean. They found that rare-allele variants are prevalent in noncoding and heterochromatic regions, resulting in nonsynonymous or stop gain/stop loss mutations in 40-60% of genes. This is the first comprehensive study of rare allelic variation in wild and cultivated soybean genomes and its potential effects on gene function. This information is a source for future genetic and genomic research, as these rare alleles may have untapped potential to improve crop stress resistance, yield, and adaptability to changing environments.

Technical Abstract: 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 varaiants have not been reported. We analyzed sequencing data from 1,556 soybean accessions and found 6,533,419 rare-allele variants in G. max and 941,274 in G. 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 6 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 some variants in wild soybeans. Rare-allele variants were mainly located in intergenic and noncoding regions rather than coding regions, and in heterochromatin regions rather than euchromatic regions. Among all base substitutions, C-T and G-A were the most common types of the substitutions, while C-G and G-C were the least common substitutions. 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 mutations or stop gain/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 function. 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.