Genome-wide association analyses for meat quality traits in Chinese Erhualian pigs and a Western Duroc × (Landrace × Yorkshire) commercial population.
Genome-wide association analyses for meat quality traits in Chinese Erhualian pigs and a Western Duroc × (Landrace × Yorkshire) commercial population.
复制标题
中国二花猪和西部杜洛克×（长白×约克夏）商业猪群肉品质性状的全基因组关联分析
DOI：
10.1186/s12711-015-0120-x
复制
发表时间：
2015-05-12
期刊：
影响因子：
--
通讯作者：
Huang L
中科院分区：
文献类型：
--
作者：
Liu X;Xiong X;Yang J;Zhou L;Yang B;Ai H;Ma H;Xie X;Huang Y;Fang S;Xiao S;Ren J;Ma J;Huang L
了解肉质性状背后的遗传机制对于提高猪肉品质至关重要。迄今为止，大多数数量性状基因座 (QTL) 分析都是在远交猪品系之间的 F2 杂交中进行的，并导致了许多 QTL 的鉴定。然而，由于此类杂交中连锁不平衡程度较高，QTL作图精度并不令人满意，并且仅发现少数QTL在远交品系中分离，这限制了它们在提高动物生产性能方面的应用。为了检测中国和西方起源的近交猪群体中的QTL，我们对中国纯种二花莲猪和西方杜洛克 × （长白×约克夏）（DLY）商业群体的肉品质性状进行了全基因组关联研究（GWAS）。使用 Illumina PorcineSNP60K Beadchip 对 336 头中国二花莲猪和 610 头 DLY 猪进行了基因分型，并评估了 20 种肉质性状。经过质量控制，中国儿花脸和 DLY 数据集分别有 35 985 个和 56 216 个单核苷酸多态性 (SNP)，并用于执行两个单独的 GWAS。我们还进行了一项荟萃分析，结合了二花莲、DLY、F2 和苏泰猪群体常见的 29 516 个 SNP 的 P 值和效应。我们在二花莲猪和 DLY 猪中分别检测到 28 个和 9 个超过肉质显着性水平的提示性 SNP。其中，猪4号染色体（SSC4）上的ss131261254最为显着（P = 7.97E-09），并且与二花莲猪的滴水损失相关。我们的结果表明，SSC12 和 SSC15 上至少有两个 QTL 可能对几个相关性状具有多效性效应。 GWAS检测到的所有QTL都是群体特异性的，包括12个新区域。然而，荟萃分析揭示了肉类特征的七个新QTL，这表明存在常见的潜在变异，这些变异在不同人群中的频率可能不同。这些QTL区域包含几个相关的候选基因。这些发现为了解表现出不同表型的中国和西方品种肉质性状趋同进化的分子基础提供了有价值的见解。它们可能有助于纯种马的杂交性能的遗传改良。本文的在线版本 (doi:10.1186/s12711-015-0120-x) 包含补充材料，可供授权用户使用。
Understanding the genetic mechanisms that underlie meat quality traits is essential to improve pork quality. To date, most quantitative trait loci (QTL) analyses have been performed on F2 crosses between outbred pig strains and have led to the identification of numerous QTL. However, because linkage disequilibrium is high in such crosses, QTL mapping precision is unsatisfactory and only a few QTL have been found to segregate within outbred strains, which limits their use to improve animal performance. To detect QTL in outbred pig populations of Chinese and Western origins, we performed genome-wide association studies (GWAS) for meat quality traits in Chinese purebred Erhualian pigs and a Western Duroc × (Landrace × Yorkshire) (DLY) commercial population. Three hundred and thirty six Chinese Erhualian and 610 DLY pigs were genotyped using the Illumina PorcineSNP60K Beadchip and evaluated for 20 meat quality traits. After quality control, 35 985 and 56 216 single nucleotide polymorphisms (SNPs) were available for the Chinese Erhualian and DLY datasets, respectively, and were used to perform two separate GWAS. We also performed a meta-analysis that combined P-values and effects of 29 516 SNPs that were common to Erhualian, DLY, F2 and Sutai pig populations. We detected 28 and nine suggestive SNPs that surpassed the significance level for meat quality in Erhualian and DLY pigs, respectively. Among these SNPs, ss131261254 on pig chromosome 4 (SSC4) was the most significant (P = 7.97E-09) and was associated with drip loss in Erhualian pigs. Our results suggested that at least two QTL on SSC12 and on SSC15 may have pleiotropic effects on several related traits. All the QTL that were detected by GWAS were population-specific, including 12 novel regions. However, the meta-analysis revealed seven novel QTL for meat characteristics, which suggests the existence of common underlying variants that may differ in frequency across populations. These QTL regions contain several relevant candidate genes. These findings provide valuable insights into the molecular basis of convergent evolution of meat quality traits in Chinese and Western breeds that show divergent phenotypes. They may contribute to genetic improvement of purebreds for crossbred performance. The online version of this article (doi:10.1186/s12711-015-0120-x) contains supplementary material, which is available to authorized users.
登录
查看更多内容
DOI：
10.1038/nrg2544
发表时间：
2009-05
期刊：
Nature reviews. Genetics
影响因子：
--
作者：
Ioannidis JP;Thomas G;Daly MJ
通讯作者：
Daly MJ
全基因组 SNP 标记揭示中国和西方猪的遗传多样性、连锁不平衡和选择特征
影响因子：
3.7
作者：
Ai H;Huang L;Ren J
通讯作者：
Ren J
影响因子：
2.6
作者：
Huff-Lonergan, E.;Lonergan, S. M.
通讯作者：
Lonergan, S. M.
影响因子：
3.3
作者：
Li, H. D.;Lund, M. S.;Bendixen, C.
通讯作者：
Bendixen, C.
影响因子：
5.3
作者：
Alvarado, David M.;Buchan, Jillian G.;Dobbs, Matthew B.
通讯作者：
Dobbs, Matthew B.