University of Hohenheim, Stuttgart, Germany.
Plant Sciences Institute, Agricultural Research Organization (ARO), The Volcani Center, Rishon LeZion, Israel.
Heredity (Edinb). 2022 Feb;128(2):107-119. doi: 10.1038/s41437-021-00494-x. Epub 2022 Jan 11.
Determining the extent of genetic variation that reflects local adaptation in crop-wild relatives is of interest for the purpose of identifying useful genetic diversity for plant breeding. We investigated the association of genomic variation with geographical and environmental factors in wild barley (Hordeum vulgare L. ssp. spontaneum) populations of the Southern Levant using genotyping by sequencing (GBS) of 244 accessions in the Barley 1K+ collection. The inference of population structure resulted in four genetic clusters that corresponded to eco-geographical habitats and a significant association between lower gene flow rates and geographical barriers, e.g. the Judaean Mountains and the Sea of Galilee. Redundancy analysis (RDA) revealed that spatial autocorrelation explained 45% and environmental variables explained 15% of total genomic variation. Only 4.5% of genomic variation was solely attributed to environmental variation if the component confounded with spatial autocorrelation was excluded. A synthetic environmental variable combining latitude, solar radiation, and accumulated precipitation explained the highest proportion of genomic variation (3.9%). When conditioned on population structure, soil water capacity was the most important environmental variable explaining 1.18% of genomic variation. Genome scans with outlier analysis and genome-environment association studies were conducted to identify adaptation signatures. RDA and outlier methods jointly detected selection signatures in the pericentromeric regions, which have reduced recombination, of the chromosomes 3H, 4H, and 5H. However, selection signatures mostly disappeared after correction for population structure. In conclusion, adaptation to the highly diverse environments of the Southern Levant over short geographical ranges had a limited effect on the genomic diversity of wild barley. This highlighted the importance of nonselective forces in genetic differentiation.
确定反映作物野生近缘种局部适应的遗传变异程度，对于鉴定植物育种中有用的遗传多样性具有重要意义。我们使用大麦 1K+ 集合中的 244 个样本的测序基因型 (GBS)，调查了南黎凡特野生大麦 (Hordeum vulgare L. ssp. spontaneum) 种群的基因组变异与地理和环境因素的关联。种群结构的推断导致了四个遗传聚类，它们与生态地理生境相对应，并且基因流率与地理屏障之间存在显著关联，例如朱迪亚山脉和加利利海。冗余分析 (RDA) 显示，空间自相关解释了总基因组变异的 45%，环境变量解释了 15%。如果排除与空间自相关混淆的组成部分，则仅 4.5%的基因组变异归因于环境变异。将纬度、太阳辐射和累积降水量相结合的综合环境变量解释了最高比例的基因组变异 (3.9%)。当条件为群体结构时，土壤水分容量是解释基因组变异的最重要环境变量 (1.18%)。进行了基于基因组扫描的外显子分析和基因组-环境关联研究，以鉴定适应特征。RDA 和外显子方法共同检测到染色体 3H、4H 和 5H 着丝粒区域的选择特征，这些区域的重组减少。然而，选择特征在经过群体结构校正后大多消失。总之，在短地理范围内对南黎凡特高度多样化环境的适应对野生大麦的基因组多样性影响有限。这强调了非选择性力量在遗传分化中的重要性。
