Data from: Dearth of polymorphism associated with a sustained response to selection for flowering time in maize

Background: Long term selection experiments bring unique insights on the genetic architecture of quantitative traits and their evolvability. Indeed, they are utilized to (i) monitor changes in allele frequencies and assess the effects of genomic regions involved traits determinism; (ii) evaluate the role of standing variation versus new mutations during adaptation; (iii) investigate the contribution of non allelic interactions. Here we describe genetic and phenotypic evolution of two independent Divergent Selection Experiments (DSEs) for flowering time conducted during 16 years from two early maize inbred lines. Results: Our experimental design uses selfing as the mating system and small population sizes, so that two independent families evolved within each population, Late and Early. Observed patterns are strikingly similar between the two DSEs. We observed a significant response to selection in both directions during the first 7 generations of selection. Within Early families, the response is linear through 16 generations, consistent with the maintenance of genetic variance. Within Late families and despite maintenance of significant genetic variation across 17 generations, the response to selection reached a plateau after 7 generations. This plateau is likely caused by physiological limits. Residual heterozygosity in the initial inbreds can partly explain the observed responses as evidenced by 42 markers derived from both Methyl-Sensitive Amplification- and Amplified Fragment Length- Polymorphisms. Among the 42, a subset of 13 markers most of which are in high linkage disequilibrium, display a strong association with flowering time variation. Their fast fixation throughout DSEs’ pedigrees results in strong genetic differentiation between populations and families. Conclusions: Our results reveal a paradox between the sustainability of the response to selection and the associated dearth of polymorphisms. Among other hypotheses, we discuss the maintenance of heritable variation by few mutations with strong epistatic interactions whose effects are modified by continuous changes of the genetic background through time.

【背景】长期选择实验为解析数量性状的遗传结构及其演化潜力提供了独特视角。此类实验主要用于：(i) 监测等位基因频率变化，评估参与性状决定的基因组区域的效应；(ii) 评估适应过程中现存遗传变异与新发突变的相对作用；(iii) 探究非等位基因互作的贡献。本研究针对两个早期玉米自交系，开展了两项独立的开花期双向选择实验（Divergent Selection Experiments, DSEs），实验时长共计16年，下文将阐述该实验的遗传与表型演化特征。
【结果】本实验以自交作为交配系统，并采用小型种群规模，使得每个种群内分化出两个独立的家系——晚花（Late）与早花（Early）家系。两项DSE的观测结果呈现出惊人的相似性。在选择实验的前7个世代中，双向均观测到了显著的选择响应。早花家系的选择响应在16个世代内保持线性，这与遗传方差的维持相一致。晚花家系虽在17个世代中均保留了显著的遗传变异，但其选择响应在7个世代后便趋于平台期，该平台期大概率由生理极限所导致。初始自交系中的残留杂合性可部分解释观测到的选择响应，这一点可通过42个来自甲基敏感性扩增多态性（Methyl-Sensitive Amplification Polymorphism, MSAP）与扩增片段长度多态性（Amplified Fragment Length Polymorphism, AFLP）的标记得到验证。在这42个标记中，有13个标记的子集（其中多数处于高度连锁不平衡状态）与开花期变异呈现强关联。这些标记在DSEs的谱系中快速固定，导致了种群与家系间强烈的遗传分化。
【结论】本研究结果揭示了一个矛盾现象：选择响应可长期维持，但与之伴随的却是多态性的匮乏。在诸多假说中，我们探讨了由少数具有强上位互作的突变所维持的可遗传变异——这些突变的效应会随时间推移因遗传背景的持续改变而发生调控。