Thépot Stéphanie, Restoux Gwendal, Goldringer Isabelle, Hospital Frédéric, Gouache David, Mackay Ian, Enjalbert Jérôme
Université Paris-Sud, Unité Mixte de Recherche 0320/Unité Mixte de Recherche 8120, Génétique Végétale, F-91190 Gif-sur-Yvette, France Institut National de la Recherche Agronomique, Unité Mixte de Recherche 0320/Unité Mixte de Recherche 8120, Génétique Végétale, F-91190 Gif-sur-Yvette, France
Unité d'Ecologie, Systématique et Evolution, Centre National de la Recherche Scientifique Unité Mixte de Recherche 8079, Université Paris-Sud, Orsay, France.
Genetics. 2015 Feb;199(2):609-23. doi: 10.1534/genetics.114.169995. Epub 2014 Nov 17.
Multiparental populations are innovative tools for fine mapping large numbers of loci. Here we explored the application of a wheat Multiparent Advanced Generation Inter-Cross (MAGIC) population for QTL mapping. This population was created by 12 generations of free recombination among 60 founder lines, following modification of the mating system from strict selfing to strict outcrossing using the ms1b nuclear male sterility gene. Available parents and a subset of 380 SSD lines of the resulting MAGIC population were phenotyped for earliness and genotyped with the 9K i-Select SNP array and additional markers in candidate genes controlling heading date. We demonstrated that 12 generations of strict outcrossing rapidly and drastically reduced linkage disequilibrium to very low levels even at short map distances and also greatly reduced the population structure exhibited among the parents. We developed a Bayesian method, based on allelic frequency, to estimate the contribution of each parent in the evolved population. To detect loci under selection and estimate selective pressure, we also developed a new method comparing shifts in allelic frequency between the initial and the evolved populations due to both selection and genetic drift with expectations under drift only. This evolutionary approach allowed us to identify 26 genomic areas under selection. Using association tests between flowering time and polymorphisms, 6 of these genomic areas appeared to carry flowering time QTL, 1 of which corresponds to Ppd-D1, a major gene involved in the photoperiod sensitivity. Frequency shifts at 4 of 6 areas were consistent with earlier flowering of the evolved population relative to the initial population. The use of this new outcrossing wheat population, mixing numerous initial parental lines through multiple generations of panmixia, is discussed in terms of power to detect genes under selection and association mapping. Furthermore we provide new statistical methods for use in future analyses of multiparental populations.
多亲本群体是精细定位大量基因座的创新工具。在此，我们探索了小麦多亲本高级世代互交（MAGIC）群体在数量性状基因座（QTL）定位中的应用。该群体由60个创始系经过12代自由重组创建而成，随后利用ms1b核雄性不育基因将交配系统从严格自交修改为严格异交。对现有的亲本以及由此产生的MAGIC群体的380个单粒传（SSD）株系的一个子集进行了早熟表型分析，并使用9K i-Select SNP芯片以及控制抽穗期的候选基因中的其他标记进行了基因分型。我们证明，即使在短的图谱距离下，12代严格异交也能迅速且大幅地将连锁不平衡降低到非常低的水平，同时也大大减少了亲本之间呈现的群体结构。我们基于等位基因频率开发了一种贝叶斯方法，以估计每个亲本在进化群体中的贡献。为了检测受选择的基因座并估计选择压力，我们还开发了一种新方法，该方法比较由于选择和遗传漂变导致的初始群体和进化群体之间等位基因频率的变化与仅在漂变情况下的预期。这种进化方法使我们能够识别出26个受选择的基因组区域。通过开花时间与多态性之间的关联测试，这些基因组区域中有6个似乎携带开花时间QTL，其中1个对应于Ppd-D1，这是一个参与光周期敏感性的主要基因。6个区域中有4个的频率变化与进化群体相对于初始群体更早开花一致。本文讨论了这种新的异交小麦群体通过多代随机交配混合众多初始亲本系在检测受选择基因和关联作图方面的能力。此外，我们提供了新的统计方法，供未来多亲本群体分析使用。
