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首页> 美国卫生研究院文献>PLoS Clinical Trials >Genetic Diversity and Linkage Disequilibrium in Chinese Bread Wheat (Triticum aestivum L.) Revealed by SSR Markers
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Genetic Diversity and Linkage Disequilibrium in Chinese Bread Wheat (Triticum aestivum L.) Revealed by SSR Markers

机译：利用SSR标记揭示中国面包小麦的遗传多样性和连锁不平衡

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Two hundred and fifty bread wheat lines, mainly Chinese mini core accessions, were assayed for polymorphism and linkage disequilibrium (LD) based on 512 whole-genome microsatellite loci representing a mean marker density of 5.1 cM. A total of 6,724 alleles ranging from 1 to 49 per locus were identified in all collections. The mean PIC value was 0.650, ranging from 0 to 0.965. Population structure and principal coordinate analysis revealed that landraces and modern varieties were two relatively independent genetic sub-groups. Landraces had a higher allelic diversity than modern varieties with respect to both genomes and chromosomes in terms of total number of alleles and allelic richness. 3,833 (57.0%) and 2,788 (41.5%) rare alleles with frequencies of <5% were found in the landrace and modern variety gene pools, respectively, indicating greater numbers of rare variants, or likely new alleles, in landraces. Analysis of molecular variance (AMOVA) showed that A genome had the largest genetic differentiation and D genome the lowest. In contrast to genetic diversity, modern varieties displayed a wider average LD decay across the whole genome for locus pairs with r2>0.05 (P<0.001) than the landraces. Mean LD decay distance for the landraces at the whole genome level was <5 cM, while a higher LD decay distance of 5–10 cM in modern varieties. LD decay distances were also somewhat different for each of the 21 chromosomes, being higher for most of the chromosomes in modern varieties (<5∼25 cM) compared to landraces (<5∼15 cM), presumably indicating the influences of domestication and breeding. This study facilitates predicting the marker density required to effectively associate genotypes with traits in Chinese wheat genetic resources.
机译：基于512个全基因组微卫星基因座，代表5.1 cM的平均标记密度，分析了250个面包小麦品系（主要是中国小型核心种质）的多态性和连锁不平衡（LD）。在所有集合中共鉴定了6,724个等位基因，每个位点的范围为1至49。 PIC平均值为0.650，范围为0至0.965。人口结构和主坐标分析表明，地方品种和现代品种是两个相对独立的遗传亚群。就等位基因总数和等位基因丰富度而言，就基因组和染色体而言，地方品种的等位基因多样性高于现代品种。在地方品种和现代品种基因库中分别发现了3,833个（57.0％）和2,788（41.5％）个频率小于5％的稀有等位基因，这表明在地方品种中稀有变体或可能的新等位基因数量更多。分子变异分析（AMOVA）显示，A基因组的遗传分化最大，而D基因组的遗传分化最低。与遗传多样性相反，现代品种对r 2 > 0.05（P <0.001）的基因座对在整个基因组中的平均LD衰减范围更大。在整个基因组水平上，地方品种的平均LD衰变距离<5 cM，而在现代品种中，LD衰变距离更高，为5–10 cM。 21条染色体中每条的LD衰变距离也有所不同，现代品种（<5〜25 cM）的大多数染色体的LD衰变距离高于地方品种（<5〜15 cM），这大概表明了驯化和繁殖的影响。这项研究有助于预测将中国小麦遗传资源中的基因型与性状有效关联所需的标记密度。

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