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首页> 外文期刊>Heredity: An International Journal of Genetics >Genome wide linkage disequilibrium in Chinese asparagus bean (Vigna. unguiculata ssp. sesquipedialis) germplasm: Implications for domestication history and genome wide association studies
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Genome wide linkage disequilibrium in Chinese asparagus bean (Vigna. unguiculata ssp. sesquipedialis) germplasm: Implications for domestication history and genome wide association studies

机译：中国芦笋种质资源的全基因组连锁不平衡：对驯化史和全基因组关联研究的启示

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摘要

Association mapping of important traits of crop plants relies on first understanding the extent and patterns of linkage disequilibrium (LD) in the particular germplasm being investigated. We characterize here the genetic diversity, population structure and genome wide LD patterns in a set of asparagus bean (Vigna. unguiculata ssp. sesquipedialis) germplasm from China. A diverse collection of 99 asparagus bean and normal cowpea accessions were genotyped with 1127 expressed sequence tag-derived single nucleotide polymorphism markers (SNPs). The proportion of polymorphic SNPs across the collection was relatively low (39%), with an average number of SNPs per locus of 1.33. Bayesian population structure analysis indicated two subdivisions within the collection sampled that generally represented the standard vegetable type (subgroup SV) and the non-standard vegetable type (subgroup NSV), respectively. Level of LD (r 2) was higher and extent of LD persisted longer in subgroup SV than in subgroup NSV, whereas LD decayed rapidly (0-2 cM) in both subgroups. LD decay distance varied among chromosomes, with the longest (≈5 cM) five times longer than the shortest (≈1 cM). Partitioning of LD variance into within- and between-subgroup components coupled with comparative LD decay analysis suggested that linkage group 5, 7 and 10 may have undergone the most intensive epistatic selection toward traits favorable for vegetable use. This work provides a first population genetic insight into domestication history of asparagus bean and demonstrates the feasibility of mapping complex traits by genome wide association study in asparagus bean using a currently available cowpea SNPs marker platform.
机译：作物重要性状的关联图谱依赖于首先了解所研究的特定种质中连锁不平衡（LD）的程度和模式。我们在这里表征了一组来自中国的芦笋豆（Vigna。unguiculata ssp。sesquipedialis）种质的遗传多样性，种群结构和全基因组LD模式。使用1127个表达的序列标签衍生的单核苷酸多态性标记（SNP）对99个芦笋豆和正常cow豆的不同品种进行基因分型。整个集合中多态性SNP的比例相对较低（39％），每个基因座的平均SNP数为1.33。贝叶斯种群结构分析表明，样本集合中的两个细分通常分别代表标准蔬菜类型（SV亚组）和非标准蔬菜类型（NSV亚组）。 SV组的LD水平（r 2）较高，并且LD的持续时间长于NSV组，而两个亚组的LD迅速衰减（0-2 cM）。 LD衰减距离在染色体之间变化，最长（≈5cM）比最短（≈1cM）长五倍。将LD方差分为亚组内和亚组间，再加上比较的LD衰减分析表明，连锁组5、7和10可能经历了对蔬菜有利性状的最强烈的上位选择。这项工作为芦笋豆的驯化历史提供了第一个群体遗传学见解，并证明了通过使用目前可用的cow豆SNPs标记平台在芦笋豆中进行全基因组关联研究来绘制复杂性状的可行性。

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