A first insight into population structure and linkage disequilibrium in the US peanut minicore collection
A first insight into population structure and linkage disequilibrium in the US peanut minicore collection
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DOI：
10.1007/s10709-011-9556-2
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发表时间：
2011-04-01
期刊：
影响因子：
1.5
通讯作者：
Burow, Mark D.
中科院分区：
文献类型：
--
作者：
Belamkar, Vikas;Selvaraj, Michael Gomez;Burow, Mark D.
对目标群体的遗传多样性、群体结构和连锁不平衡度的了解是非常重要的，也是进行连锁不平衡定位的前提。本研究以美国花生微核种质、四倍体品种Florunner的组成系、二倍体祖系A。duranensis（AA）和A.利用32对多态性较高的SSR引物对392个SSR标记进行了扩增，分析了日本血吸虫（BB）和人工合成双二倍体TxAG-6的遗传多样性。距离和基于模型（贝叶斯）的聚类分析揭示了结构化多样性的存在。在一般情况下，野生种加入和合成双二倍体分组从大多数微核心加入除了COC 155，并从大多数随后的分析中消除。UPGMA分析将种群分为四个亚组，两个主要亚组代表fastigiata和hypogaea亚种，第三组包含来自每个亚种的个体或可能的混合祖先，第四组，如果排除野生物种，则由COC 155单独组成，或者由COC 155，二倍体物种和合成双二倍体组成。基于模型的聚类确定了四个亚组-fastigiata和hypogaea亚种各一个，第三组由主要来自非洲或亚洲的两个亚种或混合祖先的个体组成，第四组由主要来自南美洲的var fastigiata，peruviana和aequatoriana加入的个体组成，包括COC 155。分子方差分析（AMOVA）显示，亚组间的遗传变异为16.87%，差异极显著（P < 0.0001）。4.85%的SSR标记在r（2）>= 0.1时表现出显著的LD效应。在距离< 10 cM、11-20 cM、21-50 cM和> 50 cM的同线标记对中，强LD标记对的检出率分别为19.33%、5.19%、6.25%和5.29（P 0.035）在统计学上区分了连锁距离组的平均r（2）值和非连锁标记的平均r（2）值; LD被发现延伸到10厘米以上的整个微核心收集这个标准。然而，即使在紧密连锁的标记之间，标记对之间的r（2）值也存在很大差异。这些研究结果的可能性，使用关联映射检测全基因组SSR标记表型关联方面的影响进行了讨论。
Knowledge of genetic diversity, population structure, and degree of linkage disequilibrium (LD) in target association mapping populations is of great importance and is a prerequisite for LD-based mapping. In the present study, 96 genotypes comprising 92 accessions of the US peanut minicore collection, a component line of the tetraploid variety Florunner, diploid progenitors A. duranensis (AA) and A. ipaensis (BB), and synthetic amphidiploid accession TxAG-6 were investigated with 392 simple sequence repeat (SSR) marker bands amplified using 32 highly-polymorphic SSR primer pairs. Both distance-and model-based (Bayesian) cluster analysis revealed the presence of structured diversity. In general, the wild-species accessions and the synthetic amphidiploid grouped separately from most minicore accessions except for COC155, and were eliminated from most subsequent analyses. UPGMA analysis divided the population into four subgroups, two major subgroups representing subspecies fastigiata and hypogaea, a third group containing individuals from each subspecies or possibly of mixed ancestry, and a fourth group, either consisting of COC155 alone if wild species were excluded, or of COC155, the diploid species, and the synthetic amphidiploid. Model-based clustering identified four subgroups- one each for fastigiata and hypogaea subspecies, a third consisting of individuals of both subspecies or of mixed ancestry predominantly from Africa or Asia, and a fourth group, consisting of individuals predominantly of var fastigiata, peruviana, and aequatoriana accessions from South America, including COC155. Analysis of molecular variance (AMOVA) revealed statistically-significant (P < 0.0001) genetic variance of 16.87% among subgroups. A total of 4.85% of SSR marker pairs revealed significant LD (at r(2) >= 0.1). Of the syntenic marker pairs separated by distances < 10 cM, 11-20 cM, 21-50 cM, and > 50 cM, 19.33, 5.19, 6.25 and 5.29% of marker pairs were found in strong LD (P 0.035 was found to distinguish mean r(2) values of linkage distance groups statistically from the mean r(2) values of unlinked markers; LD was found to extend to 10 cM over the entire minicore collection by this criterion. However, there were large differences in r(2) values among marker pairs even among tightly-linked markers. The implications of these findings with regard to the possibility of using association mapping for detection of genome-wide SSR marker-phenotype association are discussed.