Key Laboratory of Crop Germplasm Resources and Utilization, Ministry of Agriculture, The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China.
PLoS One. 2011 Feb 18;6(2):e17279. doi: 10.1371/journal.pone.0017279.
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 r(2)>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.
两百五十个小麦品种，主要是中国微型核心品种，基于代表平均标记密度为 5.1cM 的 512 个全基因组微卫星位点，对其多态性和连锁不平衡（LD）进行了检测。在所有的品种中，共鉴定出 6724 个等位基因，每个位点的范围从 1 到 49 个。平均 PIC 值为 0.650，范围从 0 到 0.965。种群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。就总等位基因数和等位基因丰富度而言，地方品种的基因组和染色体上的等位基因多样性均高于现代品种。在地方品种和现代品种的基因库中，分别发现了 3833（57.0%）和 2788（41.5%）个频率<5%的稀有等位基因，表明地方品种中有更多的稀有变异体，或可能有新的等位基因。分子方差分析（AMOVA）表明，A 基因组的遗传分化最大，D 基因组的遗传分化最小。与遗传多样性相反，现代品种在整个基因组上，对于 r(2)>0.05（P<0.001）的位点对，表现出更宽的平均 LD 衰减。地方品种在全基因组水平上的平均 LD 衰减距离<5cM，而现代品种的 LD 衰减距离为 5-10cM。21 条染色体中的每一条染色体的 LD 衰减距离也有所不同，现代品种的大多数染色体（<5-25cM）比地方品种（<5-15cM）的 LD 衰减距离更高，这可能表明了驯化和选育的影响。本研究有助于预测在中国小麦遗传资源中，有效关联基因型与性状所需的标记密度。
