Dataset Information

Whole-genome resequencing reveals signature of local adaptation and divergence in wild soybean.

ABSTRACT: Global climate change has threatened world crop production and food security. Decoding the adaptive genetic basis of wild relatives provides an invaluable genomic resource for climate-smart crop breedinG. Here, we performed whole-genome sequencing of 185 diverse wild soybean (Glycine soja) accessions collected from three major agro-ecological zones in China to parse the genomic basis of local adaptation in wild soybean. The population genomic diversity pattern exhibited clear agro-ecological zone-based population structure, and multiple environmental factors were observed to contribute to the genetic divergence. Demographic analysis shows that wild soybeans from the three ecological zones diverged about 1 × 10⁵ years ago, and then the effective population sizes have undergone different degrees of expansions. Genome-environment association identified multiple genes involved in the local adaptation, such as flowering time and temperature-related genes. A locus containing two adjacent MADS-box transcription factors on chromosome 19 was identified for multiple environmental factors, and it experienced positive selection that enables the adaptation to high-latitude environment. This study provides insights into the genetic mechanism of ecological adaptation in wild soybean that may facilitate climate-resilient soybean breeding.

SUBMITTER: Wang J

PROVIDER: S-EPMC9679240 | biostudies-literature | 2022 Nov

REPOSITORIES: biostudies-literature

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Whole-genome resequencing reveals signature of local adaptation and divergence in wild soybean.

Wang Jiao J Hu Zhenbin Z Liao Xiliang X Wang Zhiyu Z Li Wei W Zhang Peipei P Cheng Hao H Wang Qing Q Bhat Javaid Akhter JA Wang Hui H Liu Biao B Zhang Hengyou H Huang Fang F Yu Deyue D

Evolutionary applications 20220920 11

Global climate change has threatened world crop production and food security. Decoding the adaptive genetic basis of wild relatives provides an invaluable genomic resource for climate-smart crop breedinG. Here, we performed whole-genome sequencing of 185 diverse wild soybean (<i>Glycine soja</i>) accessions collected from three major agro-ecological zones in China to parse the genomic basis of local adaptation in wild soybean. The population genomic diversity pattern exhibited clear agro-ecologi ...[more]

PMID: 36426120

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Project description:Glycine soja is the wild relative species of cultivated soybean. In this study, we investigated the population divergence and genetic basis of the local adaptation of wild soybean in China using genome-wide single-nucleotide polymorphisms (SNPs) of a population of 72 G. soja accessions. Using phylogenetic analysis, we observed that G. soja accessions clustered into three distinct groups, each corresponding to a specific geographic region, the northeastern region (NER), central region (CR), and southern region (SR), consistent with previous studies. Notably, we found a significant positive correlation between genetic and geographic distances. Further population structure analysis revealed each group was associated with an ancestral population and a specific geographic area. By utilizing the genome sequencing data of accessions from 16 different locations, we inferred the population history of these wild soybean groups. Our results indicate that the three groups diverged ~25,000 years ago, coinciding with the time of the last glacial maximum. The effective population size of the SR group expanded first, and subsequently, the NER and CR groups expanded approximately 5000 and 2500 years ago, respectively. Moreover, 83, 104, and 101 significant associated loci (SALs) were identified using genome-wide association analysis for annual mean temperature, annual precipitation, and latitude, respectively. Functional analysis of genes located in SALs highlighted candidate genes related to local adaptation. This study highlights the significant role of geographic isolation and environmental factors in shaping the genetic structure and adaptability of wild soybean populations. Furthermore, it emphasizes the value of wild soybean as a crucial genetic resource for enhancing the adaptability of cultivated soybeans, which have experienced a loss of genetic diversity due to domestication and intensive breeding practices. The insights gained from our research provide valuable information for the protection, conservation, and utilization of this important genetic resource.

Dataset Information

Whole-genome resequencing reveals signature of local adaptation and divergence in wild soybean.

Publications

Whole-genome resequencing reveals signature of local adaptation and divergence in wild soybean.

Similar Datasets

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