A haplotype map of allohexaploid wheat reveals distinct patterns of selection on homoeologous genomes.
A haplotype map of allohexaploid wheat reveals distinct patterns of selection on homoeologous genomes.
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DOI：
10.1186/s13059-015-0606-4
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发表时间：
2015-02-26
期刊：
影响因子：
12.3
通讯作者：
Akhunov E
中科院分区：
文献类型：
--
作者：
Jordan KW;Wang S;Lun Y;Gardiner LJ;MacLachlan R;Hucl P;Wiebe K;Wong D;Forrest KL;IWGS Consortium;Sharpe AG;Sidebottom CH;Hall N;Toomajian C;Close T;Dubcovsky J;Akhunova A;Talbert L;Bansal UK;Bariana HS;Hayden MJ;Pozniak C;Jeddeloh JA;Hall A;Akhunov E
面包小麦是一种异源多倍体物种，具有大的、高度重复的基因组。为了研究选择对分布在同源异型小麦基因组中的变体的影响，并为理解基因型-表型关系奠定基础，我们对一组不同的小麦品系进行了群体规模的重新测序。使用全外显子组捕获和测序基因分型方法对62个不同品系的样品进行重新测序。我们描述了157万个单核苷酸多态性和161，719个小插入缺失的等位基因频率，功能意义和染色体分布。我们的研究结果表明，重复的同源异型基因是在纯化选择。我们发现小麦基因组之间的变异和变异间关联的对比模式，这，除了人口因素，可以解释重复homoeologs的定向选择的效果的差异。在任何给定的小麦品系中，只有一小部分携带所选变体的同源异型区域在小麦基因组之间重叠。这些选择的区域富集与全基因组关联研究中检测到的农艺性状相关的基因座。有证据表明，异源多倍体中的定向选择很少作用于跨同源同源区域的多个平行有利突变，这可能表明可以通过在任何一个同源物处的突变获得适应性益处。其他homoelogs中的其他有利变体可能要么贡献不大，要么在定向选择的群体中不可用。我们假设异源多倍体可能通过扩大可能的选择靶点来增加有益等位基因恢复的可能性。本文的在线版本（doi：10.1186/s13059-015-0606-4）包含补充材料，可供授权用户使用。
Bread wheat is an allopolyploid species with a large, highly repetitive genome. To investigate the impact of selection on variants distributed among homoeologous wheat genomes and to build a foundation for understanding genotype-phenotype relationships, we performed population-scale re-sequencing of a diverse panel of wheat lines. A sample of 62 diverse lines was re-sequenced using the whole exome capture and genotyping-by-sequencing approaches. We describe the allele frequency, functional significance, and chromosomal distribution of 1.57 million single nucleotide polymorphisms and 161,719 small indels. Our results suggest that duplicated homoeologous genes are under purifying selection. We find contrasting patterns of variation and inter-variant associations among wheat genomes; this, in addition to demographic factors, could be explained by differences in the effect of directional selection on duplicated homoeologs. Only a small fraction of the homoeologous regions harboring selected variants overlapped among the wheat genomes in any given wheat line. These selected regions are enriched for loci associated with agronomic traits detected in genome-wide association studies. Evidence suggests that directional selection in allopolyploids rarely acted on multiple parallel advantageous mutations across homoeologous regions, likely indicating that a fitness benefit could be obtained by a mutation at any one of the homoeologs. Additional advantageous variants in other homoelogs probably either contributed little benefit, or were unavailable in populations subjected to directional selection. We hypothesize that allopolyploidy may have increased the likelihood of beneficial allele recovery by broadening the set of possible selection targets. The online version of this article (doi:10.1186/s13059-015-0606-4) contains supplementary material, which is available to authorized users.
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影响因子：
4.4
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Akhunov ED;Akhunova AR;Anderson OD;Anderson JA;Blake N;Clegg MT;Coleman-Derr D;Conley EJ;Crossman CC;Deal KR;Dubcovsky J;Gill BS;Gu YQ;Hadam J;Heo H;Huo N;Lazo GR;Luo MC;Ma YQ;Matthews DE;McGuire PE;Morrell PL;Qualset CO;Renfro J;Tabanao D;Talbert LE;Tian C;Toleno DM;Warburton ML;You FM;Zhang W;Dvorak J
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