Data from: Polymorphism pattern at a Miniature Inverted-repeat Transposable Element locus downstream of the domestication gene Teosinte-branched1 in wild and domesticated pearl millet

Unraveling the mechanisms involved in adaptation to understand plant morphological evolution is a challenging goal. For crop species, identification of molecular causal polymorphisms involved in domestication traits are central to this issue. Pearl millet, a domesticated grass mostly found in semi-arid areas of Africa and India, is an interesting model to address this topic: the domesticated form shares common derived phenotypes with some other cereals such as a decreased ability to develop basal and axillary branches in comparison with the wild phenotype. Two recent studies have shown that the orthologue of the maize gene Teosinte-Branched1 in pearl millet (PgTb1) was likely involved in branching evolution during domestication and that a Miniature Inverted-repeat Transposable Element (MITE) of the Tuareg family was inserted in the 3'-untranslated region of PgTb1. For a set of 35 wild and domesticated populations, we compared the polymorphism patterns at this MITE and at microsatellite loci. The Tuareg insertion was nearly absent in the wild populations, whereas a strong longitudinal frequency cline was observed in the domesticated populations. The geographic pattern revealed by neutral microsatellite loci clearly demonstrated that isolation by distance does not account for the existence of this cline. However, comparison of population differentiation at the microsatellite and the MITE loci and analyses of the nucleotide polymorphism pattern in the downstream region of PgTb1 did not show evidence that the cline at the MITE locus has been shaped by selection, suggesting the implication of a neutral process. Alternative hypotheses are discussed.解析适应相关机制以阐释植物形态演化的内在逻辑，是一项极具挑战性的研究目标。对于作物物种而言，鉴定与驯化性状相关的分子因果多态性，是该研究方向的核心议题。珍珠粟（Pearl millet）是一种主要分布于非洲与印度半干旱地区的驯化禾本科作物，亦是阐释该主题的理想模式研究体系：与野生型相比，其驯化型与部分其他谷类作物共享部分衍生表型，例如基部分枝与腋生分枝能力减弱。两项近期研究表明，珍珠粟中玉米Teosinte-Branched1基因的直系同源基因（PgTb1）很可能在驯化过程中参与了分枝演化，且图阿雷格（Tuareg）家族的微型反向重复转座元件（Miniature Inverted-repeat Transposable Element, MITE）插入了PgTb1的3'-非翻译区。针对35份野生与驯化种群材料，本研究对比了该MITE位点以及微卫星（microsatellite）位点的多态性分布模式。图阿雷格家族MITE的插入事件在野生种群中几乎不存在，而在驯化种群中则呈现出显著的经度频率梯度。中性微卫星位点所揭示的地理分布模式明确表明，距离隔离效应无法解释该频率梯度的存在。然而，对微卫星与MITE位点的种群分化程度对比，以及对PgTb1下游区域的核苷酸多态性模式分析，均未发现该MITE位点的频率梯度由选择作用塑造的证据，这提示该梯度可能由中性过程主导。本研究还对其他替代假说进行了探讨。