Implementing meta-analysis from genome-wide association studies for pork quality traits
Implementing meta-analysis from genome-wide association studies for pork quality traits
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DOI：
10.2527/jas.2015-9502
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发表时间：
2015-12-01
影响因子：
3.3
通讯作者：
Steibel, J. P.
中科院分区：
文献类型：
--
作者：
Bernal Rubio, Y. L.;Gualdron Duarte, J. L.;Steibel, J. P.
猪肉质量在肉类加工业中起着重要的作用。因此，采用不同的方法来阐明影响肉质性状的遗传结构。最常见和广泛使用的方法之一是进行全基因组关联（GWA）研究。然而，许多GWA在动物育种中的局限性是由于动物种群的小样本量而导致的有限功率。另一种选择是结合独立关联研究的结果对GWA （MA-GWA）进行meta分析。本研究的目的是通过对3个独立猪群的8个不同性状进行MA-GWA，确定与肉质性状相关的重要基因组区域。利用MA-GWA的结果搜索可能与所评价性状集相关的基因。数据来自3个猪数据集（美国肉类动物研究中心、商业猪和密歇根州立大学猪资源种群）。通过结合每个群体中每个SNP的z分数，然后使用SNP效应估计方差的倒数对其进行加权，实现MA。对注释基因的搜索检索了先前报道的剪切力候选基因（calpain-1催化亚基[CAPN1]和calpastatin [CAST]），以及最终pH值，清洗损失和烹饪损失（蛋白激酶，amp激活，蛋白质激酶）。3非催化亚基[PRKAG3])此外，我们还发现了肌内脂肪和脂肪损失的新候选基因（酰基辅酶a合成酶家族成员3线粒体[ACSF3]）和肌肉发红的客观测量基因CIEa*（肌肉糖原合成酶1 [GYS1]和铁蛋白轻多肽[FTL]）。因此，实施MA-GWA可以整合经济相关性状的结果，并确定新基因作为猪群肉质性状的候选基因进行测试。
Pork quality plays an important role in the meat processing industry. Thus, different methodologies have been implemented to elucidate the genetic architecture of traits affecting meat quality. One of the most common and widely used approaches is to perform genome-wide association (GWA) studies. However, a limitation of many GWA in animal breeding is the limited power due to small sample sizes in animal populations. One alternative is to implement a meta-analysis of GWA (MA-GWA) combining results from independent association studies. The objective of this study was to identify significant genomic regions associated with meat quality traits by performing MA-GWA for 8 different traits in 3 independent pig populations. Results from MA-GWA were used to search for genes possibly associated with the set of evaluated traits. Data from 3 pig data sets (U.S. Meat Animal Research Center, commercial, and Michigan State University Pig Resource Population) were used. A MA was implemented by combining z-scores derived for each SNP in every population and then weighting them using the inverse of estimated variance of SNP effects. A search for annotated genes retrieved genes previously reported as candidates for shear force (calpain-1 catalytic subunit [CAPN1] and calpastatin [CAST]), as well as for ultimate pH, purge loss, and cook loss (protein kinase, AMP-activated,. 3 noncatalytic subunit [PRKAG3]). In addition, novel candidate genes were identified for intramuscular fat and cook loss (acyl-CoA synthetase family member 3 mitochondrial [ACSF3]) and for the objective measure of muscle redness, CIEa* (glycogen synthase 1, muscle [GYS1] and ferritin, light polypeptide [FTL]). Thus, implementation of MA-GWA allowed integration of results for economically relevant traits and identified novel genes to be tested as candidates for meat quality traits in pig populations.