Robert W. Holley Center for Agriculture and Health, US Department of Agriculture-Agricultural Research Service, Cornell University, Ithaca, NY 14853, USA.
Proc Natl Acad Sci U S A. 2013 Mar 26;110(13):5241-6. doi: 10.1073/pnas.1220766110. Epub 2013 Mar 11.
Genome structure variation, including copy number variation and presence/absence variation, comprises a large extent of maize genetic diversity; however, its effect on phenotypes remains largely unexplored. Here, we describe how copy number variation underlies a rare allele that contributes to maize aluminum (Al) tolerance. Al toxicity is the primary limitation for crop production on acid soils, which make up 50% of the world's potentially arable lands. In a recombinant inbred line mapping population, copy number variation of the Al tolerance gene multidrug and toxic compound extrusion 1 (MATE1) is the basis for the quantitative trait locus of largest effect on phenotypic variation. This expansion in MATE1 copy number is associated with higher MATE1 expression, which in turn results in superior Al tolerance. The three MATE1 copies are identical and are part of a tandem triplication. Only three maize inbred lines carrying the three-copy allele were identified from maize and teosinte diversity panels, indicating that copy number variation for MATE1 is a rare, and quite likely recent, event. These maize lines with higher MATE1 copy number are also Al-tolerant, have high MATE1 expression, and originate from regions of highly acidic soils. Our findings show a role for copy number variation in the adaptation of maize to acidic soils in the tropics and suggest that genome structural changes may be a rapid evolutionary response to new environments.
基因组结构变异，包括拷贝数变异和存在/缺失变异，构成了玉米遗传多样性的很大一部分；然而，其对表型的影响在很大程度上仍未得到探索。在这里，我们描述了拷贝数变异如何导致一个稀有等位基因，从而有助于玉米对铝（Al）的耐受性。Al 毒性是酸性土壤上作物生产的主要限制因素，酸性土壤占世界潜在可耕地的 50%。在重组自交系作图群体中，Al 耐受性基因多药和毒性化合物外排 1（MATE1）的拷贝数变异是对表型变异影响最大的数量性状位点的基础。MATE1 拷贝数的这种扩增与更高的 MATE1 表达相关，这反过来又导致了更好的 Al 耐受性。这三个 MATE1 拷贝是相同的，是串联三重复的一部分。从玉米和墨西哥玉米多样性面板中仅鉴定出三个携带三拷贝等位基因的玉米自交系，表明 MATE1 的拷贝数变异是罕见的，而且很可能是最近发生的事件。这些具有更高 MATE1 拷贝数的玉米系也具有 Al 耐受性、高 MATE1 表达，并且起源于高度酸性土壤的地区。我们的研究结果表明，拷贝数变异在玉米适应热带酸性土壤方面发挥了作用，并表明基因组结构变化可能是对新环境的快速进化反应。
