Linkage disequilibrium in Angus, Charolais, and Crossbred beef cattle.
Linkage disequilibrium in Angus, Charolais, and Crossbred beef cattle.
复制标题
DOI：
10.3389/fgene.2012.00152
复制
发表时间：
2012
影响因子：
3.7
通讯作者：
Miller SP
中科院分区：
文献类型：
--
作者：
Lu D;Sargolzaei M;Kelly M;Li C;Vander Voort G;Wang Z;Plastow G;Moore S;Miller SP
连锁不平衡 (LD) 及其在群体中的持续性对于基因组选择以及数量性状基因座 (QTL) 的精细定位非常重要。然而，对肉牛 LD 以及杂交种 (C) 和纯种牛之间 LD 阶段持续性的了解有限。本研究的目的是根据每个群体中分别 31,073、32,088 和 33,286 个 SNP 来了解安格斯 (AN)、夏洛莱 (CH) 和 C 肉牛的 LD 模式。当标记之间的距离范围分别从0-30 kb变为30-70 kb，然后变为70-100 kb时，LD量迅速减少，AN中为0.29至0.23至0.19，CH中为0.22至0.16至0.12，C中为0.21至0.15至0.11。品种和染色体对 LD 衰减有显着影响（P < 0.001）。品种和染色体之间存在显着的相互作用（P < 0.001）。对于距离小于或等于 70 kb，C 和 AN (0.84)、C 和 CH (0.81) 以及 AN 和 CH (0.77) 之间的 LD 相位相关性较高。当距离增加时，这些会下降。估计 10 代以前 AN 和 CH 的有效种群规模分别为 207 和 285。鉴于 SNP 对之间的有用 LD 至少为 0.3，三个品种组中任何一对之间的 LD 阶段都具有高度持久性。目前的 SNP 密度将允许在 AN 中捕获 SNP 和标记 QTL 之间大约 49% 的有用 LD，在 CH 中捕获 38%。需要更高密度的 SNP panel 或重新设计当前的 panel，以实现更多有用的 LD，用于基因组选择肉牛。
Linkage disequilibrium (LD) and the persistence of its phase across populations are important for genomic selection as well as fine scale mapping of quantitative trait loci (QTL). However, knowledge of LD in beef cattle, as well as the persistence of LD phase between crossbreds (C) and purebreds, is limited. The objective of this study was to understand the patterns of LD in Angus (AN), Charolais (CH), and C beef cattle based on 31,073, 32,088, and 33,286 SNP in each population, respectively. Amount of LD decreased rapidly from 0.29 to 0.23 to 0.19 in AN, 0.22 to 0.16 to 0.12 in CH, 0.21 to 0.15 to 0.11 in C, when the distance range between markers changed from 0–30 kb to 30–70 kb and then to 70–100 kb, respectively. Breeds and chromosomes had significant effects (P < 0.001) on LD decay. There was significant interaction between breeds and chromosomes (P < 0.001). Correlations of LD phase were high between C and AN (0.84), C and CH (0.81), as well as between AN and CH (0.77) for distances less than or equal to 70 kb. These dropped when the distance increased. Estimated effective population sizes for AN and CH were 207 and 285, respectively, for 10 generations ago. Given a useful LD of at least 0.3 between pairs of SNPs, the LD phase between any pair of the three breed groups was highly persistent. The current SNP density would allow the capture of approximately 49% of useful LD between SNP and marker QTL in AN, and 38% in CH. A higher density SNP panel or redesign of the current panel is needed to achieve more of useful LD for the purpose of genomic selection beef cattle.