Identification of Polymorphisms Associated with Drought Adaptation QTL in Brassica napus by Resequencing.
Identification of Polymorphisms Associated with Drought Adaptation QTL in Brassica napus by Resequencing.
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DOI：
10.1534/g3.115.021279
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发表时间：
2016-04-07
期刊：
影响因子：
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通讯作者：
McKay JK
中科院分区：
文献类型：
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作者：
Fletcher RS;Herrmann D;Mullen JL;Li Q;Schrider DR;Price N;Lin J;Grogan K;Kern A;McKay JK
甘蓝型油菜（Brassica napus）是一种全球重要的油籽，对其干旱适应基因知之甚少。我们之前在一个由冬春油菜品种杂交创建的双亲本定位群体中定位了12个干旱相关性状的数量性状位点（QTL）。在这里，我们对作图群体亲本的基因组进行重排序，以确定整个基因组和QTL区域内的遗传多样性。我们在Illumina HiSeq平台上对每个亲本栽培进行了最小深度23 ×的测序，并进行了基于参考的组装，以描述在基因组、QTL和基因尺度上区分它们的分子变异。全基因组变异模式的特点是，A基因组的单核苷酸多态性（SNP）密度总体较高，C基因组的非同义置换与同义置换比例较高。使用非同义替换对基因本体术语进行分类，以区分亲本基因组以及每个QTL中包含的假定功能变体列表。对A10染色体上一个多效性QTL中发现的多态性进行了标记分析。QTL分析显示，最相关的标记来自候选基因Bna.FLC的插入/删除多态性。A10，是QTL区间内唯一存在多态性的候选QTL。总之，这些结果提供了区分一年生和二年生甘蓝型的全基因组变异的一瞥，以及更好地理解根和干旱表型的遗传基础。
Brassica napus is a globally important oilseed for which little is known about the genetics of drought adaptation. We previously mapped twelve quantitative trait loci (QTL) underlying drought-related traits in a biparental mapping population created from a cross between winter and spring B. napus cultivars. Here we resequence the genomes of the mapping population parents to identify genetic diversity across the genome and within QTL regions. We sequenced each parental cultivar on the Illumina HiSeq platform to a minimum depth of 23 × and performed a reference based assembly in order to describe the molecular variation differentiating them at the scale of the genome, QTL and gene. Genome-wide patterns of variation were characterized by an overall higher single nucleotide polymorphism (SNP) density in the A genome and a higher ratio of nonsynonymous to synonymous substitutions in the C genome. Nonsynonymous substitutions were used to categorize gene ontology terms differentiating the parent genomes along with a list of putative functional variants contained within each QTL. Marker assays were developed for several of the discovered polymorphisms within a pleiotropic QTL on chromosome A10. QTL analysis with the new, denser map showed the most associated marker to be that developed from an insertion/deletion polymorphism located in the candidate gene Bna.FLC.A10, and it was the only candidate within the QTL interval with observed polymorphism. Together, these results provide a glimpse of genome-wide variation differentiating annual and biennial B. napus ecotypes as well as a better understanding of the genetic basis of root and drought phenotypes.