Zhong Limei, Zhu Youlin, Olsen Kenneth M
Key Laboratory of Molecular Biology and Gene Engineering in Jiangxi, School of Life Sciences, Nanchang University, Nanchang, China.
Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA.
Mol Ecol. 2022 Jun;31(11):3137-3153. doi: 10.1111/mec.16454. Epub 2022 Apr 12.
Genome scans for selection can provide an efficient way to dissect the genetic basis of domestication traits and understand mechanisms of adaptation during crop evolution. Selection involving soft sweeps (simultaneous selection for multiple alleles) is probably common in plant genomes but is under-studied, and few if any studies have systematically scanned for soft sweeps in the context of crop domestication. Using genome resequencing data from 302 wild and domesticated soybean accessions, we conducted selection scans using five widely employed statistics to identify selection candidates under classical (hard) and soft sweeps. Across the genome, inferred hard sweeps are predominant in domesticated soybean landraces and improved varieties, whereas soft sweeps are more prevalent in a representative subpopulation of the wild ancestor. Six domestication-related genes, representing both hard and soft sweeps and different stages of domestication, were used as positive controls to assess the detectability of domestication-associated sweeps. Performance of various test statistics suggests that differentiation-based (F ) methods are robust for detecting complete hard sweeps, and that LD-based strategies perform well for identifying recent/ongoing sweeps; however, none of the test statistics detected a known soft sweep we previously documented at the domestication gene Dt1. Genome scans yielded a set of 66 candidate loci that were identified by both differentiation-based and LD-based (iHH) methods; notably, this shared set overlaps with many previously identified QTLs for soybean domestication/improvement traits. Collectively, our results will help to advance genetic characterizations of soybean domestication traits and shed light on selection modes involved in adaptation in domesticated plant species.
用于选择的基因组扫描可以提供一种有效的方法来剖析驯化性状的遗传基础，并了解作物进化过程中的适应机制。涉及软清除（对多个等位基因进行同时选择）的选择在植物基因组中可能很常见，但研究较少，并且几乎没有研究在作物驯化背景下系统地扫描软清除。利用来自302份野生和驯化大豆种质的基因组重测序数据，我们使用五种广泛使用的统计方法进行选择扫描，以识别经典（硬）清除和软清除下的选择候选基因。在整个基因组中，推断出的硬清除在驯化大豆地方品种和改良品种中占主导地位，而软清除在野生祖先的一个代表性亚群中更为普遍。六个与驯化相关的基因，代表硬清除和软清除以及驯化的不同阶段，被用作阳性对照来评估驯化相关清除的可检测性。各种检验统计量的表现表明，基于分化的（F）方法对于检测完全硬清除是稳健的，基于连锁不平衡的策略对于识别近期/正在进行的清除表现良好；然而，没有一个检验统计量检测到我们之前记录在驯化基因Dt1处的已知软清除。基因组扫描产生了一组66个候选位点，这些位点通过基于分化和基于连锁不平衡（iHH）的方法都被识别出来；值得注意的是，这个共享集与许多先前鉴定的大豆驯化/改良性状的QTL重叠。总的来说，我们的结果将有助于推进大豆驯化性状的遗传特征分析，并揭示驯化植物物种适应过程中涉及的选择模式。
