Research Article: Meta-analysis of genome-wide association studies for loin muscle area and loin muscle depth in two Duroc pig populations

Date Published: June 12, 2019

Publisher: Public Library of Science

Author(s): Zhanwei Zhuang, Shaoyun Li, Rongrong Ding, Ming Yang, Enqin Zheng, Huaqiang Yang, Ting Gu, Zheng Xu, Gengyuan Cai, Zhenfang Wu, Jie Yang, Roberta Davoli.

http://doi.org/10.1371/journal.pone.0218263

Abstract

Loin muscle area (LMA) and loin muscle depth (LMD) are important traits influencing the production performance of breeding pigs. However, the genetic architecture of these two traits is still poorly understood. To discern the genetic architecture of LMA and LMD, a material consisting of 6043 Duroc pigs belonging to two populations with different genetic backgrounds was collected and applied in genome-wide association studies (GWAS) with a genome-wide distributed panel of 50K single nucleotide polymorphisms (SNPs). To improve the power of detection for common SNPs, we conducted a meta-analysis in these two pig populations and uncovered additional significant SNPs. As a result, we identified 75 significant SNPs for LMA and LMD on SSC6, 7, 12, 16, and 18. Among them, 25 common SNPs were associated with LMA and LMD. One pleiotropic quantitative trait locus (QTL), which was located on SSC7 with a 283 kb interval, was identified to affect LMA and LMD. Marker ALGA0040260 is a key SNP for this QTL, explained 1.77% and 2.48% of the phenotypic variance for LMA and LMD, respectively. Another genetic region on SSC16 (709 kb) was detected and displayed prominent association with LMA and the peak SNP, WU_10.2_16_35829257, contributed 1.83% of the phenotypic variance for LMA. Further bioinformatics analysis determined eight promising candidate genes (GCLC, GPX8, DAXX, FGF21, TAF11, SPDEF, NUDT3, and PACSIN1) with functions in glutathione metabolism, adipose and muscle tissues development and lipid metabolism. This study provides the first GWAS for the LMA and LMD of Duroc breed to analyze the underlying genetic variants through a large sample size. The findings further advance our understanding and help elucidate the genetic architecture of LMA, LMD and growth-related traits in pigs.

Partial Text

The pig, which has abundant phenotypes, is a model animal that not only intimately resembles man in physiology, anatomy, and genetic architecture[1] but also contributes to meat consumption[2]. In the past decades, lean pigs account for a large share of the pork consumption market, and the traits that affect swine growth have been important breeding targets in the pig industry[2]. Loin muscle area (LMA) and loin muscle depth (LMD) play important roles in the determination of growth traits (e.g., back fat and carcass lean rate)[3]. Thus, prediction of growth traits by investigating LMA and LMD is important. It is generally accepted that both of nutrition and growth environment of the pig can affect the growth and development of loin muscle[4, 5], and muscle growth may be subject to number of muscle fibers in swine muscle composition[6]. However, genetics is widely considered to be the most important factor for the loin muscle development. Hence, it is the primary means to achieve this goal in terms of genetics, such as finding causal genes or mutations that affect muscle development[7, 8]. LMA and LMD are heritable and moderate-heritability above traits, where the estimated heritabilities range from 0.35 to 0.47[9–11], showing that these two traits can be improved via genetic approach.

In sum, we detected a set of significant SNPs for LMA and LMD in 6043 Duroc pigs from two populations with different genetic contexts. One pleiotropic QTL located on SSC7 with a 283 kb interval was identified to affect multiple traits. Another genetic region on SSC16 (709 kb) was also discovered to play an important role in LMA. A series of bioinformatics analysis strategies revealed many functional genes for LMA and LMD. For instance, GCLC, GPX8, DAXX, FGF21, TAF11, SPDEF, NUDT3, and PACSIN1 with biological functions such as increasing available amino acids in skeletal muscle, mammalian growth, fat deposition, and body size of pig were selected as promising candidates for swine carcass and growth-related traits. This study provides the first GWAS for the LMA and LMD of Duroc breed to analyze the underlying genetic variants through a large sample size. These findings revealed the complexity of the genetic mechanism that forms the phenotypic diversity and provide essential insights into the future production of pigs in the context of marker-assisted selection.

 

Source:

http://doi.org/10.1371/journal.pone.0218263

 

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