Extent of linkage disequilibrium in chicken
Extent of linkage disequilibrium in chicken
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DOI：
10.1159/000103196
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发表时间：
2007-01-01
影响因子：
1.7
通讯作者：
Groenen, M.
中科院分区：
文献类型：
--
作者：
Aerts, J.;Megens, H. J.;Groenen, M.
鸡的许多重要经济性状是多因子性状，由位于不同数量性状位点（qtl）的多个基因控制。在连锁和关联研究中，识别这些qtl的最佳标记密度在很大程度上取决于它们周围的连锁不平衡（LD）程度。在本研究中，我们研究了白蛋鸡和两个肉鸡品种的两条染色体上的LD程度。对10号和28号染色体上的33个和36个标记分别计算LD的成对水平。我们发现，在Nutreco鸡品种E5（自交系）中，有用LD（即r(2)值大于0.3）在第10和28染色体上可以延伸到约1 cM，尽管在第28染色体上的第二个区域可以延伸到约2.5 cM。Nutreco E3（外交种）在第10染色体上的程度很短（15kb），而在第28染色体上的程度很大，特别是在杂合性降低的一个区域。蛋鸡品种E2（自交系）在10号染色体上的有用LD最大可达4 cM；由于28号染色体上的LD模式不稳定，无法评估该染色体上的程度，尽管在一个区域LD似乎在0.8 cM左右。这表明不同鸡品种和不同基因组区域之间的LD模式可能存在很大差异。版权所有(C) 2007 S. Karger AG，巴塞尔
Many of the economically important traits in chicken are multifactorial and governed by multiple genes located at different quantitative trait loci (QTLs). The optimal marker density to identify these QTLs in linkage and association studies is largely determined by the extent of linkage disequilibrium (LD) around them. In this study, we investigated the extent of LD on two chromosomes in a white layer and two broiler chicken breeds. Pairwise levels of LD were calculated for 33 and 36 markers on chromosomes 10 and 28, respectively. We found that useful LD (i.e. an r(2) value higher than 0.3) in Nutreco chicken breed E5 (inbred) can extend to around 1 cM on chromosomes 10 and 28, although in a second region on chromosome 28 it extends to about 2.5 cM. The extent in breed Nutreco E3 (out-bred) was very short in chromosome 10 (15 kb) but very much larger on chromosome 28, particularly in one region of depressed heterozygosity. The layer breed E2 (inbred) showed an extent of useful LD up to 4 cM on chromosome 10; the extent on chromosome 28 could not be assessed due to an erratic pattern of LD on that chromosome, although in one region LD appears to be in the order of 0.8 cM. This indicates that there may be very large differences in patterns of LD between different chicken breeds and different genomic regions. Copyright (C) 2007 S. Karger AG, Basel.