Maize HapMap2 identifies extant variation from a genome in flux
Maize HapMap2 identifies extant variation from a genome in flux
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DOI：
10.1038/ng.2313
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发表时间：
2012-07-01
期刊：
影响因子：
30.8
通讯作者：
Ware, Doreen
中科院分区：
文献类型：
--
作者：
Chia, Jer-Ming;Song, Chi;Ware, Doreen
尽管育种者已经利用玉米的多样性来提高产量，但在未驯化品种中使用有益等位基因的进展有限。在这个复杂的基因组中表征常设变异一直是具有挑战性的，迄今为止只描述了其中的一小部分。使用群体遗传学评分模型，我们确定了55万个SNPs在103行在驯化前和驯化的玉米品种，包括一个代表的姐妹属Tripsacum。我们发现，结构变化是普遍的Z。玉米基因组中，并在与重要性状相关的基因座上富集。通过研究基因组大小变异的驱动因素，我们发现，较大的Tripsacum基因组可以解释转座因子丰度，而不是异源多倍体的起源。相反，种内基因组大小的变化似乎是由染色体球内容控制。在玉米和Tripsacum中的关键基因内容有巨大的重叠，这表明Tripsacum的适应性（例如，多年生植物和抗冻性和耐旱性）可能会整合到玉米中。
Whereas breeders have exploited diversity in maize for yield improvements, there has been limited progress in using beneficial alleles in undomesticated varieties. Characterizing standing variation in this complex genome has been challenging, with only a small fraction of it described to date. Using a population genetics scoring model, we identified 55 million SNPs in 103 lines across pre-domestication and domesticated Zea mays varieties, including a representative from the sister genus Tripsacum. We find that structural variations are pervasive in the Z. mays genome and are enriched at loci associated with important traits. By investigating the drivers of genome size variation, we find that the larger Tripsacum genome can be explained by transposable element abundance rather than an allopolyploid origin. In contrast, intraspecies genome size variation seems to be controlled by chromosomal knob content. There is tremendous overlap in key gene content in maize and Tripsacum, suggesting that adaptations from Tripsacum (for example, perennialism and frost and drought tolerance) can likely be integrated into maize.