Qian Lunwen, Qian Wei, Snowdon Rod J
Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Giessen, Germany.
College of Agronomy and Biotechnology, Southwest University, Chongqing, China.
Plant Biotechnol J. 2016 Jul;14(7):1578-88. doi: 10.1111/pbi.12521. Epub 2016 Jan 23.
Local haplotype patterns surrounding densely spaced DNA markers with significant trait associations can reveal information on selective sweeps and genome diversity associated with important crop traits. Relationships between haplotype and phenotype diversity, coupled with analysis of gene content in conserved haplotype blocks, can provide insight into coselection for nonrelated traits. We performed genome-wide analysis of haplotypes associated with the important physiological and agronomic traits leaf chlorophyll and seed glucosinolate content, respectively, in the major oilseed crop species Brassica napus. A locus on chromosome A01 showed opposite effects on leaf chlorophyll content and seed glucosinolate content, attributed to strong linkage disequilibrium (LD) between orthologues of the chlorophyll biosynthesis genes EARLY LIGHT-INDUCED PROTEIN and CHLOROPHYLL SYNTHASE, and the glucosinolate synthesis gene ATP SULFURYLASE 1. Another conserved haplotype block, on chromosome A02, contained a number of chlorophyll-related genes in LD with orthologues of the key glucosinolate biosynthesis genes METHYLTHIOALKYMALATE SYNTHASE-LIKE 1 and 3. Multigene haplogroups were found to have a significantly greater contribution to variation for chlorophyll content than haplotypes for any single gene, suggesting positive effects of additive locus accumulation. Detailed reanalysis of population substructure revealed a clade of ten related accessions exhibiting high leaf chlorophyll and low seed glucosinolate content. These accessions each carried one of the above-mentioned haplotypes from A01 or A02, generally in combination with further chlorophyll-associated haplotypes from chromosomes A05 and/or C05. The phenotypic rather than pleiotropic correlations between leaf chlorophyll content index and seed GSL suggest that LD may have led to inadvertent coselection for these two traits.
围绕与重要性状显著关联的紧密间隔DNA标记的局部单倍型模式，能够揭示与重要作物性状相关的选择性清除和基因组多样性信息。单倍型与表型多样性之间的关系，再结合对保守单倍型块中基因含量的分析，可以深入了解非相关性状的共选择情况。我们分别对主要油料作物甘蓝型油菜中与重要生理和农艺性状——叶片叶绿素和种子硫代葡萄糖苷含量相关的单倍型进行了全基因组分析。A01染色体上的一个位点对叶片叶绿素含量和种子硫代葡萄糖苷含量具有相反的影响，这归因于叶绿素生物合成基因早期光诱导蛋白和叶绿素合成酶的直系同源基因，与硫代葡萄糖苷合成基因ATP硫酸化酶1之间存在强烈的连锁不平衡（LD）。另一个位于A02染色体上的保守单倍型块，包含许多与叶绿素相关的基因，这些基因与硫代葡萄糖苷生物合成关键基因甲硫基烷基苹果酸合成酶样1和3的直系同源基因处于LD状态。发现多基因单倍型组对叶绿素含量变异的贡献显著大于任何单个基因的单倍型，这表明加性位点积累具有积极作用。对群体亚结构的详细重新分析揭示了一个由十个相关种质组成的分支，其表现出高叶片叶绿素含量和低种子硫代葡萄糖苷含量。这些种质各自携带上述来自A01或A02的单倍型之一，通常还与来自A05和/或C05染色体的其他与叶绿素相关的单倍型组合。叶片叶绿素含量指数与种子硫代葡萄糖苷之间的表型而非多效性相关性表明，LD可能导致了这两个性状的无意共选择。
