School of Agriculture and Food Sciences, The University of Queensland, St Lucia, Queensland, Australia.
PLoS One. 2011;6(8):e23041. doi: 10.1371/journal.pone.0023041. Epub 2011 Aug 10.
Detecting artificial selection in the genome of domesticated species can not only shed light on human history but can also be beneficial to future breeding strategies. Evidence for selection has been documented in domesticated species including maize and rice, but few studies have to date detected signals of artificial selection in the Sorghum bicolor genome. Based on evidence that domesticated S. bicolor and its wild relatives show significant differences in endosperm structure and quality, we sequenced three candidate seed storage protein (kafirin) loci and three candidate starch biosynthesis loci to test whether these genes show non-neutral evolution resulting from the domestication process. We found strong evidence of non-neutral selection at the starch synthase IIa gene, while both starch branching enzyme I and the beta kafirin gene showed weaker evidence of non-neutral selection. We argue that the power to detect consistent signals of non-neutral selection in our dataset is confounded by the absence of low frequency variants at four of the six candidate genes. A future challenge in the detection of positive selection associated with domestication in sorghum is to develop models that can accommodate for skewed frequency spectrums.
检测驯化物种基因组中的人工选择不仅可以揭示人类历史，还有助于未来的育种策略。在玉米和水稻等驯化物种中已经记录到了选择的证据，但迄今为止，在高粱基因组中很少有研究检测到人工选择的信号。基于驯化高粱及其野生近缘种在胚乳结构和质量上存在显著差异的证据，我们对三个候选种子贮藏蛋白（kafirin）基因座和三个候选淀粉生物合成基因座进行了测序，以检验这些基因是否因驯化过程而表现出非中性进化。我们发现淀粉合酶 IIa 基因存在强烈的非中性选择证据，而淀粉分支酶 I 和βkafirin 基因则表现出较弱的非中性选择证据。我们认为，在我们的数据集检测到非中性选择的一致信号的能力受到六个候选基因中的四个基因缺乏低频变异的影响。高粱驯化过程中与阳性选择相关的检测的未来挑战是开发能够适应偏态频率谱的模型。
