Multi-breed genome-wide association study reveals heterogeneous loci associated with loin eye area in pigs

He, Yanqun; Ma, Junwu; Zhang, Feng; Hou, Lijuan; Chen, Hao; Guo, Yuanmei; Zhang, Zhiyan

doi:10.1007/s13353-016-0351-8

Cited by 10 publications

(9 citation statements)

References 31 publications

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“…These studies successfully identified causal mutation and verified the causal genes[29]. For LMA and LMD, GWAS have also been performed to detect the underlying genetic mechanisms[4, 30], but the sample size of these studies is smaller compared with that of the current study. Although GWAS have obtained remarkable findings[31], the use of association studies in the genetics of human and other species is bound by population structure and limited sample size[32].…”

Section: Introductionmentioning

confidence: 97%

“…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.…”

Section: Introductionmentioning

confidence: 99%

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

Zhuang

Ding

et al. 2019

PLoS ONE

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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.

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Section: Introductionmentioning

confidence: 97%

Section: Introductionmentioning

confidence: 99%

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

Zhuang

Ding

et al. 2019

PLoS ONE

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“…A previous study demonstrated that the FUBP3 gene was associated with the skeletal formation in Duroc population [ 29 ]. Furthermore, the FUBP3 gene was identified as a candidate gene associated with the loin eye area in pigs [ 30 ]. The PAPPA2 gene encodes pregnancy-associated plasma protein A2 (PAPPA2) which plays an important role in the regulation of IGF-I bioavailability [ 31 ].…”

Section: Discussionmentioning

confidence: 99%

Genome-wide DNA methylation analysis in Chinese Chenghua and Yorkshire pigs

Wang

et al. 2021

BMC Genom Data

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Background The Chinese Chenghua pig (CHP) is a typical Chinese domestic fatty pig breed with superior meat quality characteristics, while the Yorkshire pig (YP) has the characteristics of fast growth and a high rate of lean meat. Long term natural selection and artificial selection resulted in great phenotypic differences between the two breeds, including growth, development, production performance, meat quality, and coat color. However, genome-wide DNA methylation differences between CHP and YP remain unclear. Results DNA methylation data were generated for muscle tissues of CHP and YP using reduced representation bisulfite sequencing (RRBS). In this study, a total of 2,416,211 CpG sites were identified. Besides, the genome-wide DNA methylation analysis revealed 722 differentially methylated regions (DMRs) and 466 differentially methylated genes (DMGs) in pairwise CHP vs. YP comparison. Six key genomic regions (Sus scrofa chromosome (SSC)1:253.47–274.23 Mb, SSC6:148.71–169.49 Mb, SSC7:0.25–9.86 Mb, SSC12:43.06–61.49 Mb, SSC14:126.43–140.95 Mb, and SSC18:49.17–54.54 Mb) containing multiple DMRs were identified, and differences of methylation patterns in these regions may be related to phenotypic differences between CHP and YP. Based on the functional analysis of DMGs, 8 DMGs (ADCY1, AGBL4, EXOC2, FUBP3, PAPPA2, PIK3R1, MGMT and MYH8) were considered as important candidate genes associated with muscle development and meat quality traits in pigs. Conclusions This study explored the difference in meat quality between CHP and YP from the epigenetic point of view, which has important reference significance for the local pork industry and pork food processing.

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“…Further evidence from genome scans Genome-wide association studies reported growth-related associations on a distal region of pig chromosome 2 [ 76 , 77 ]. However, the original locus showed evidence of genomic imprinting, and one of these associations did not.…”

Section: Main Textmentioning

confidence: 99%

Evidence for and localization of proposed causative variants in cattle and pig genomes

Johnsson

Jungnickel

2021

Genet Sel Evol

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Background This paper reviews the localization of published potential causative variants in contemporary pig and cattle reference genomes, and the evidence for their causality. In spite of the difficulties inherent to the identification of causative variants from genetic mapping and genome-wide association studies, researchers in animal genetics have proposed putative causative variants for several traits relevant to livestock breeding. Results For this review, we read the literature that supports potential causative variants in 13 genes (ABCG2, DGAT1, GHR, IGF2, MC4R, MSTN, NR6A1, PHGK1, PRKAG3, PLRL, RYR1, SYNGR2 and VRTN) in cattle and pigs, and localized them in contemporary reference genomes. We review the evidence for their causality, by aiming to separate the evidence for the locus, the proposed causative gene and the proposed causative variant, and report the bioinformatic searches and tactics needed to localize the sequence variants in the cattle or pig genome. Conclusions Taken together, there is usually good evidence for the association at the locus level, some evidence for a specific causative gene at eight of the loci, and some experimental evidence for a specific causative variant at six of the loci. We recommend that researchers who report new potential causative variants use referenced coordinate systems, show local sequence context, and submit variants to repositories.

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Multi-breed genome-wide association study reveals heterogeneous loci associated with loin eye area in pigs

Cited by 10 publications

References 31 publications

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

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

Genome-wide DNA methylation analysis in Chinese Chenghua and Yorkshire pigs

Evidence for and localization of proposed causative variants in cattle and pig genomes

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