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Johnsson M, Jungnickel MK. Evidence for and localization of proposed causative variants in cattle and pig genomes. Genet Sel Evol 2021; 53:67. [PMID: 34461824 PMCID: PMC8404348 DOI: 10.1186/s12711-021-00662-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 08/20/2021] [Indexed: 12/18/2022] Open
Abstract
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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Affiliation(s)
- Martin Johnsson
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Box 7023, 750 07 Uppsala, Sweden
| | - Melissa K. Jungnickel
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Midlothian, EH25 9RG Scotland, UK
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Accelerated discovery of functional genomic variation in pigs. Genomics 2021; 113:2229-2239. [PMID: 34022350 DOI: 10.1016/j.ygeno.2021.05.017] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 03/30/2021] [Accepted: 05/17/2021] [Indexed: 11/21/2022]
Abstract
The genotype-phenotype link is a major research topic in the life sciences but remains highly complex to disentangle. Part of the complexity arises from the number of genes contributing to the observed phenotype. Despite the vast increase of molecular data, pinpointing the causal variant underlying a phenotype of interest is still challenging. In this study, we present an approach to map causal variation and molecular pathways underlying important phenotypes in pigs. We prioritize variation by utilizing and integrating predicted variant impact scores (pCADD), functional genomic information, and associated phenotypes in other mammalian species. We demonstrate the efficacy of our approach by reporting known and novel causal variants, of which many affect non-coding sequences. Our approach allows the disentangling of the biology behind important phenotypes by accelerating the discovery of novel causal variants and molecular mechanisms affecting important phenotypes in pigs. This information on molecular mechanisms could be applicable in other mammalian species, including humans.
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miRNA-mRNA network regulation in the skeletal muscle fiber phenotype of chickens revealed by integrated analysis of miRNAome and transcriptome. Sci Rep 2020; 10:10619. [PMID: 32606372 PMCID: PMC7326969 DOI: 10.1038/s41598-020-67482-9] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Accepted: 06/08/2020] [Indexed: 12/23/2022] Open
Abstract
Skeletal muscle fibers are primarily categorized into oxidative and glycolytic fibers, and the ratios of different myofiber types are important factors in determining livestock meat quality. However, the molecular mechanism for determining muscle fiber types in chickens was hardly understood. In this study, we used RNA sequencing to systematically compare mRNA and microRNA transcriptomes of the oxidative muscle sartorius (SART) and glycolytic muscle pectoralis major (PMM) of Chinese Qingyuan partridge chickens. Among the 44,705 identified mRNAs in the two types of muscles, 3,457 exhibited significantly different expression patterns, including 2,364 up-regulated and 1,093 down-regulated mRNAs in the SART. A total of 698 chicken miRNAs were identified, including 189 novel miRNAs, among which 67 differentially expressed miRNAs containing 42 up-regulated and 25 down-regulated miRNAs in the SART were identified. Furthermore, function enrichment showed that the differentially expressed mRNAs and miRNAs were involved in energy metabolism, muscle contraction, and calcium, peroxisome proliferator-activated receptor (PPAR), insulin and adipocytokine signaling. Using miRNA-mRNA integrated analysis, we identified several candidate miRNA-gene pairs that might affect muscle fiber performance, viz, gga-miR-499-5p/SOX6 and gga-miR-196-5p/CALM1, which were supported by target validation using the dual-luciferase reporter system. This study revealed a mass of candidate genes and miRNAs involved in muscle fiber type determination, which might help understand the molecular mechanism underlying meat quality traits in chickens.
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Liu X, Zhou L, Xie X, Wu Z, Xiong X, Zhang Z, Yang J, Xiao S, Zhou M, Ma J, Huang L. Muscle glycogen level and occurrence of acid meat in commercial hybrid pigs are regulated by two low-frequency causal variants with large effects and multiple common variants with small effects. Genet Sel Evol 2019; 51:46. [PMID: 31443641 PMCID: PMC6708195 DOI: 10.1186/s12711-019-0488-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Accepted: 08/08/2019] [Indexed: 11/10/2022] Open
Abstract
Background Meat production from the commercial crossbred Duroc × (Landrace × Yorkshire) (DLY) pig is predominant in the pork industry, but its meat quality is often impaired by low ultimate pH (pHu). Muscle glycogen level at slaughter is closely associated with pHu and meat technological quality, but its genetic basis remains elusive. The aim of this study was to identify genes and/or causative mutations associated with muscle glycogen level and other meat quality traits by performing a genome-wide association study (GWAS) and additional analyses in a population of 610 DLY pigs. Results Our initial GWAS identified a genome-wide significant (P = 2.54e−11) quantitative trait locus (QTL) on SSC15 (SSC for Sus scrofa chromosome) for the level of residual glycogen and glucose (RG) in the longissimus muscle at 45 min post-mortem. Then, we demonstrated that a low-frequency (minor allele frequency = 0.014) R200Q missense mutation in the PRKAG3 (RN) gene caused this major QTL effect on RG. Moreover, we showed that the 200Q (RN–) allele was introgressed from the Hampshire breed into more than one of the parental breeds of the DLY pigs. After conditioning on R200Q, re-association analysis revealed three additional QTL for RG on SSC3 and 4, and on an unmapped scaffold (AEMK02000452.1). The SSC3 QTL was most likely caused by a splice mutation (g.8283C>A) in the PHKG1 gene that we had previously identified. Based on functional annotation, the genes TMCO1 on SSC4 and CKB on the scaffold represent promising candidate genes for the other two QTL. There were significant interaction effects of the GWAS tag SNPs at those two loci with PRKAG3 R200Q on RG. In addition, a number of common variants with potentially smaller effects on RG (P < 10−4) were uncovered by a second conditional GWAS after adjusting for the two causal SNPs, R200Q and g.8283C>A. Conclusions We found that the RN– allele segregates in the parental lines of our DLY population and strongly influences its meat quality. Our findings also indicate that the genetic basis of RG in DLY can be mainly attributed to two major genes (PRKAG3 and PHKG1), along with many minor genes. Electronic supplementary material The online version of this article (10.1186/s12711-019-0488-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xianxian Liu
- State Key Laboratory for Swine Genetics, Breeding and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Lisheng Zhou
- State Key Laboratory for Swine Genetics, Breeding and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Xianhua Xie
- State Key Laboratory for Swine Genetics, Breeding and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Zhongzi Wu
- State Key Laboratory for Swine Genetics, Breeding and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Xinwei Xiong
- State Key Laboratory for Swine Genetics, Breeding and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Zhiyan Zhang
- State Key Laboratory for Swine Genetics, Breeding and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Jie Yang
- State Key Laboratory for Swine Genetics, Breeding and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Shijun Xiao
- State Key Laboratory for Swine Genetics, Breeding and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Mengqing Zhou
- State Key Laboratory for Swine Genetics, Breeding and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Junwu Ma
- State Key Laboratory for Swine Genetics, Breeding and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China.
| | - Lusheng Huang
- State Key Laboratory for Swine Genetics, Breeding and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China.
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Dall'Olio S, Scotti E, Costa LN, Fontanesi L. Effects of single nucleotide polymorphisms and haplotypes of the protein kinase AMP-activated non-catalytic subunit gamma 3 (PRKAG3) gene on production, meat quality and carcass traits in Italian Large White pigs. Meat Sci 2017; 136:44-49. [PMID: 29096286 DOI: 10.1016/j.meatsci.2017.09.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Revised: 09/15/2017] [Accepted: 09/22/2017] [Indexed: 10/18/2022]
Abstract
PRKAG3 is a major gene for meat quality and production in pigs. In this study, we investigated two single nucleotide polymorphisms (SNPs) of the PRKAG3 promoter region (g.-995A>G and g.-311A>G) in 381 pigs of different breeds. Association between these SNPs and three major haplotypes, constructed including other three substitutions (c.89C>A, c.154A>G and c.595G>A) and different traits (meat quality parameters: pH2h, pHu, glycogen and lactate content, glycolytic potential and cathepsin B activity of Semimembranosus muscle; estimated breeding values and random residuals for growth performances and carcass traits) were analysed in 271 Italian Large White performance tested pigs. A significant effect (P=0.043) of the g.-995A>G SNP on cathepsin B activity and a suggestive effect (P=0.067) of the g.-311A>G SNP on pHu were found. The haplotype [g.-995G:g.-311G:c.89A:c.154G:c.595G] was associated with pHu (P=0.024), glycolytic potential (P=0.040) and cathepsin B activity (P=0.086). This study on haplotypes, including promoter region SNPs, contribute to explain the effect of this gene on meat quality traits in pigs.
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Affiliation(s)
- Stefania Dall'Olio
- Department of Agricultural and Food Sciences (DISTAL), Division of Animal Sciences, University of Bologna, Viale Fanin 46, 40127 Bologna, Italy.
| | - Emilio Scotti
- Department of Agricultural and Food Sciences (DISTAL), Division of Animal Sciences, University of Bologna, Viale Fanin 46, 40127 Bologna, Italy
| | - Leonardo Nanni Costa
- Department of Agricultural and Food Sciences (DISTAL), Division of Animal Sciences, University of Bologna, Viale Fanin 46, 40127 Bologna, Italy
| | - Luca Fontanesi
- Department of Agricultural and Food Sciences (DISTAL), Division of Animal Sciences, University of Bologna, Viale Fanin 46, 40127 Bologna, Italy
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Casiró S, Velez-Irizarry D, Ernst CW, Raney NE, Bates RO, Charles MG, Steibel JP. Genome-wide association study in an F2 Duroc x Pietrain resource population for economically important meat quality and carcass traits. J Anim Sci 2017; 95:545-558. [PMID: 28380601 DOI: 10.2527/jas.2016.1003] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Meat quality is essential for consumer acceptance, it ultimately impacts pork production profitability and it is subject to genetic control. The objective of this study was to map genomic regions associated with economically important meat quality and carcass traits. We performed a genome-wide association (GWA) analysis to map regions associated with 38 meat quality and carcass traits recorded for 948 F2 pigs from the Michigan State University Duroc × Pietrain resource population. The F0, F1, and 336 F2 pigs were genotyped with the Illumina Porcine SNP60 BeadChip, while the remaining F2 pigs were genotyped with the GeneSeek Genomic Profiler for Porcine Low Desnisty (LD) chip, and imputed with high accuracy ( = 0.97). Altogether the genomic dataset comprised 1,019 animals and 44,911 SNP. A Gaussian linear mixed model was fitted to estimate the breeding values and the variance components. A linear transformation was performed to estimate the marker effects and variances. Type I error rate was controlled at a False Discovery Rate of 5%. Seven putative QTL found in this study were previously reported in other studies. Two novel QTL associated with tenderness (TEN) were located on SSC3 [135.6:137.5Mb; False Discovery rate (FDR) < 0.03] and SSC5 (67.3:69.1Mb; FDR < 0.02). The QTL region identified on SSC15 includes Protein Kinase AMP-activated ɣ 3-subunit gene (), which has been associated with 24-h pH (pH24), drip loss (DL) and cook yield (CY). Also, novel candidate genes were identified for TEN in the region on SSC5 [A Kinase (PRKA) Anchor Protein 3 (], and for tenth rib backfat thickness (BF10) [Carnitine O-Acetyltransferase ()] on SSC1. The association of gene polymorphisms with pork quality traits has been reported for several pig populations. However, there are no SNP for this gene on the chip used, thus we genotyped the animals for 2 non-synonymous variants ( and ). We then performed a GWA conditioning on the genotype of both SNP and was associated with pH24, DL, protein content (PRO) and CY ( < 0.004) and T30N with Juiciness, TEN, shear force, pH24, PRO, and CY < 0.04). Finally, we performed a GWA conditioning on the genotype of the SNP peak detected in this study, and T30N remained associated only with PRO ( < 0.02). Therefore, in this study we identified 2 novel QTL regions, suggest 2 novel candidate genes, and conclude that other SNP in PRKAG3 or nearby gene(s) explain the observed associations on SSC15 in this population.
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Verardo LL, Sevón-Aimonen ML, Serenius T, Hietakangas V, Uimari P. Whole-genome association analysis of pork meat pH revealed three significant regions and several potential genes in Finnish Yorkshire pigs. BMC Genet 2017; 18:13. [PMID: 28193157 PMCID: PMC5307873 DOI: 10.1186/s12863-017-0482-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Accepted: 02/07/2017] [Indexed: 12/11/2022] Open
Abstract
Background One of the most commonly used quality measurements of pork is pH measured 24 h after slaughter. The most probable mode of inheritance for this trait is oligogenic with several known major genes, such as PRKAG3. In this study, we used whole-genome SNP genotypes of over 700 AI boars; after a quality check, 42,385 SNPs remained for association analysis. All the boars were purebred Finnish Yorkshire. To account for relatedness of the animals, a pedigree-based relationship matrix was used in a mixed linear model to test the effect of SNPs on pH measured from loin. A bioinformatics analysis was performed to identify the most promising genes in the significant regions related to meat quality. Results Genome-wide association study (GWAS) revealed three significant chromosomal regions: one on chromosome 3 (39.9 Mb–40.1 Mb) and two on chromosome 15 (58.5 Mb–60.5 Mb and 132 Mb–135 Mb including PRKAG3). A conditional analysis with a significant SNP in the PRKAG3 region, MARC0083357, as a covariate in the model retained the significant SNPs on chromosome 3. Even though linkage disequilibrium was relatively high over a long distance between MARC0083357 and other significant SNPs on chromosome 15, some SNPs retained their significance in the conditional analysis, even in the vicinity of PRKAG3. The significant regions harbored several genes, including two genes involved in cyclic AMP (cAMP) signaling: ADCY9 and CREBBP. Based on functional and transcription factor-gene networks, the most promising candidate genes for meat pH are ADCY9, CREBBP, TRAP1, NRG1, PRKAG3, VIL1, TNS1, and IGFBP5, and the key transcription factors related to these genes are HNF4A, PPARG, and Nkx2-5. Conclusions Based on SNP association, pathway, and transcription factor analysis, we were able to identify several genes with potential to control muscle cell homeostasis and meat quality. The associated SNPs can be used in selection for better pork. We also showed that post-GWAS analysis reveals important information about the genes’ potential role on meat quality. The gained information can be used in later functional studies.
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Affiliation(s)
- Lucas L Verardo
- Department of Animal Science/Animal Breeding, Federal University of Viçosa, Viçosa, Brazil
| | | | | | - Ville Hietakangas
- Department of Biosciences, University of Helsinki, Helsinki, Finland.,Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Pekka Uimari
- Department of Agricultural Sciences, University of Helsinki, Helsinki, Finland.
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Braud M, Magee DA, Park SDE, Sonstegard TS, Waters SM, MacHugh DE, Spillane C. Genome-Wide microRNA Binding Site Variation between Extinct Wild Aurochs and Modern Cattle Identifies Candidate microRNA-Regulated Domestication Genes. Front Genet 2017; 8:3. [PMID: 28197171 PMCID: PMC5281612 DOI: 10.3389/fgene.2017.00003] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2016] [Accepted: 01/09/2017] [Indexed: 12/21/2022] Open
Abstract
The domestication of cattle from the now-extinct wild aurochs (Bos primigenius) involved selection for physiological and behavioral traits, with underlying genetic factors that remain largely unknown. Non-coding microRNAs have emerged as key regulators of the spatio-temporal expression of target genes controlling mammalian growth and development, including in livestock species. During the domestication process, selection of mutational changes in miRNAs and/or miRNA binding sites could have provided a mechanism to generate some of the traits that differentiate domesticated cattle from wild aurochs. To investigate this, we analyzed the open reading frame DNA sequence of 19,994 orthologous protein-coding gene pairs from extant Bos taurus genomes and a single extinct B. primigenius genome. We identified miRNA binding site polymorphisms in the 3′ UTRs of 1,620 of these orthologous genes. These 1,620 genes with altered miRNA binding sites between the B. taurus and B. primigenius lineages represent candidate domestication genes. Using a novel Score Site ratio metric we have ranked these miRNA-regulated genes according to the extent of divergence between miRNA binding site presence, frequency and copy number between the orthologous genes from B. taurus and B. primigenius. This provides an unbiased approach to identify cattle genes that have undergone the most changes in miRNA binding (i.e., regulation) between the wild aurochs and modern-day cattle breeds. In addition, we demonstrate that these 1,620 candidate domestication genes are enriched for roles in pigmentation, fertility, neurobiology, metabolism, immunity and production traits (including milk quality and feed efficiency). Our findings suggest that directional selection of miRNA regulatory variants was important in the domestication and subsequent artificial selection that gave rise to modern taurine cattle.
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Affiliation(s)
- Martin Braud
- Genetics and Biotechnology Lab, Plant and AgriBiosciences Research Centre, School of Natural Sciences, National University of Ireland Galway, University Road Galway, Ireland
| | - David A Magee
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin Dublin, Ireland
| | - Stephen D E Park
- IdentiGEN Ltd, Unit 2, Trinity Enterprise Centre Dublin, Ireland
| | | | - Sinead M Waters
- Animal and Bioscience Research Department, Animal and Grassland Research and Innovation Centre, Teagasc Dunsany, Ireland
| | - David E MacHugh
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College DublinDublin, Ireland; UCD Conway Institute of Biomolecular and Biomedical Research, University College DublinDublin, Ireland
| | - Charles Spillane
- Genetics and Biotechnology Lab, Plant and AgriBiosciences Research Centre, School of Natural Sciences, National University of Ireland Galway, University Road Galway, Ireland
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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. Genome-wide association analyses for meat quality traits in Chinese Erhualian pigs and a Western Duroc × (Landrace × Yorkshire) commercial population. Genet Sel Evol 2015; 47:44. [PMID: 25962760 PMCID: PMC4427942 DOI: 10.1186/s12711-015-0120-x] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2014] [Accepted: 04/09/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND 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. METHODS 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. RESULTS 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. CONCLUSIONS 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.
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Affiliation(s)
- Xianxian Liu
- Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, Nanchang, 330045, China.
| | - Xinwei Xiong
- Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, Nanchang, 330045, China.
| | - Jie Yang
- Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, Nanchang, 330045, China.
| | - Lisheng Zhou
- Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, Nanchang, 330045, China.
| | - Bin Yang
- Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, Nanchang, 330045, China.
| | - Huashui Ai
- Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, Nanchang, 330045, China.
| | - Huanban Ma
- Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, Nanchang, 330045, China.
| | - Xianhua Xie
- Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, Nanchang, 330045, China.
| | - Yixuan Huang
- Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, Nanchang, 330045, China.
| | - Shaoming Fang
- Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, Nanchang, 330045, China.
| | - Shijun Xiao
- Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, Nanchang, 330045, China.
| | - Jun Ren
- Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, Nanchang, 330045, China.
| | - Junwu Ma
- Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, Nanchang, 330045, China.
| | - Lusheng Huang
- Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, Nanchang, 330045, China.
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Yang G, Zhou H, Wang R, Hickford J. Variation in the ovine PRKAG3 gene. Gene 2015; 567:251-4. [PMID: 25967386 DOI: 10.1016/j.gene.2015.05.021] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2014] [Revised: 04/08/2015] [Accepted: 05/02/2015] [Indexed: 10/23/2022]
Abstract
The 5'AMP-activated protein kinase (AMPK) is a heterotrimeric enzyme that controls cellular energy homeostasis in response to environmental or nutritional stress. The PRKAG3 gene (PRKAG3) encodes the γ3 subunit of the AMPK. Variation in this gene has been found to be associated with meat quality traits in pigs. In this study, we used polymerase chain reaction-single stranded conformational polymorphism (PCR-SSCP) to investigate variation in exon 3 and exons 4-6 of ovine PRKAG3. In 160 New Zealand Suffolk sheep, two variant sequences (named a and b) were identified in the exon 3 region of the gene and three variant sequences (named A, B and C) were identified in the exon 4-6 region of the gene, respectively. A total of three nucleotide substitutions were revealed and these were located in intron 4, exon 4 and intron 5, respectively. The nucleotide substitution identified in the exon 4 (g.2656 C>T) could nominally lead to an amino acid substitution of tryptophan to arginine at position 230 (R230W) in ovine PRKAG3. In comparison with the PRKAG3 amino acid sequences in other species, this R230W substitution appeared to occur only in sheep. This is the first report of genetic variation in ovine PRKAG3, and the variation found in this study could be functionally important for AMPK activity, which in turn may affect meat quality traits in sheep.
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Affiliation(s)
- Guo Yang
- Cold and Arid Regions Environmental and Engineering Research Institute, Chinese Academy of Sciences, Lanzhou 730000, China; Gene-Marker Laboratory, Faculty of Agriculture and Life Sciences, P.O. Box 84, Lincoln University, Lincoln 7647, New Zealand
| | - Huitong Zhou
- Gene-Marker Laboratory, Faculty of Agriculture and Life Sciences, P.O. Box 84, Lincoln University, Lincoln 7647, New Zealand
| | - Ruoyu Wang
- Cold and Arid Regions Environmental and Engineering Research Institute, Chinese Academy of Sciences, Lanzhou 730000, China.
| | - Jon Hickford
- Gene-Marker Laboratory, Faculty of Agriculture and Life Sciences, P.O. Box 84, Lincoln University, Lincoln 7647, New Zealand.
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Zhang C, Wang Z, Bruce H, Kemp RA, Charagu P, Miar Y, Yang T, Plastow G. Genome-wide association studies (GWAS) identify a QTL close to PRKAG3 affecting meat pH and colour in crossbred commercial pigs. BMC Genet 2015; 16:33. [PMID: 25887635 PMCID: PMC4393631 DOI: 10.1186/s12863-015-0192-1] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2014] [Accepted: 03/23/2015] [Indexed: 12/29/2022] Open
Abstract
Background Improving meat quality is a high priority for the pork industry to satisfy consumers’ preferences. GWAS have become a state-of-the-art approach to genetically improve economically important traits. However, GWAS focused on pork quality are still relatively rare. Results Six genomic regions were shown to affect loin pH and Minolta colour a* and b* on both loin and ham through GWAS in 1943 crossbred commercial pigs. Five of them, located on Sus scrofa chromosome (SSC) 1, SSC5, SSC9, SSC16 and SSCX, were associated with meat colour. However, the most promising region was detected on SSC15 spanning 133–134 Mb which explained 3.51% - 17.06% of genetic variance for five measurements of pH and colour. Three SNPs (ASGA0070625, MARC0083357 and MARC0039273) in very strong LD were considered most likely to account for the effects in this region. ASGA0070625 is located in intron 2 of ZNF142, and the other two markers are close to PRKAG3, STK36, TTLL7 and CDK5R2. After fitting MARC0083357 (the closest SNP to PRKAG3) as a fixed factor, six SNPs still remained significant for at least one trait. Four of them are intragenic with ARPC2, TMBIM1, NRAMP1 and VIL1, while the remaining two are close to RUFY4 and CDK5R2. The gene network constructed demonstrated strong connections of these genes with two major hubs of PRKAG3 and UBC in the super-pathways of cell-to-cell signaling and interaction, cellular function and maintenance. All these pathways play important roles in maintaining the integral architecture and functionality of muscle cells facing the dramatic changes that occur after exsanguination, which is in agreement with the GWAS results found in this study. Conclusions There may be other markers and/or genes in this region besides PRKAG3 that have an important effect on pH and colour. The potential markers and their interactions with PRKAG3 require further investigation Electronic supplementary material The online version of this article (doi:10.1186/s12863-015-0192-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Chunyan Zhang
- Department of Agricultural, Food & Nutritional Sciences, University of Alberta, Edmonton, AB, T6G 2P5, Canada.
| | - Zhiquan Wang
- Department of Agricultural, Food & Nutritional Sciences, University of Alberta, Edmonton, AB, T6G 2P5, Canada.
| | - Heather Bruce
- Department of Agricultural, Food & Nutritional Sciences, University of Alberta, Edmonton, AB, T6G 2P5, Canada.
| | | | | | - Younes Miar
- Department of Agricultural, Food & Nutritional Sciences, University of Alberta, Edmonton, AB, T6G 2P5, Canada.
| | - Tianfu Yang
- Department of Agricultural, Food & Nutritional Sciences, University of Alberta, Edmonton, AB, T6G 2P5, Canada.
| | - Graham Plastow
- Department of Agricultural, Food & Nutritional Sciences, University of Alberta, Edmonton, AB, T6G 2P5, Canada.
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Xiong X, Liu X, Zhou L, Yang J, Yang B, Ma H, Xie X, Huang Y, Fang S, Xiao S, Ren J, Chen C, Ma J, Huang L. Genome-wide association analysis reveals genetic loci and candidate genes for meat quality traits in Chinese Laiwu pigs. Mamm Genome 2015; 26:181-90. [PMID: 25678226 DOI: 10.1007/s00335-015-9558-y] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Accepted: 01/29/2015] [Indexed: 12/29/2022]
Abstract
Meat quality traits have economically significant impacts on the pig industry, and can be improved using molecular approaches in pig breeding. Since 1994 when the first genome-wide scan for quantitative trait loci (QTLs) in pig was reported, over the past two decades, numerous QTLs have been identified for meat quality traits by family based linkage analyses. However, little is known about the genetic variants for meat quality traits in Chinese purebred or outbred populations. To unveil it, we performed a genome-wide association study for 10 meat quality traits in Chinese purebred Laiwu pigs. In total, 75 significant SNPs (P < 1.01 × 10(-6)) and 33 suggestive SNPs (P < 2.03 × 10(-5)) were identified. On SSC12, a region between 56.22 and 61.49 Mb harbored a cluster of SNPs that were associated with meat color parameters (L*, lightness; a*, redness; b*, yellowness) and moisture content of longissimus muscle (LM) and semimembranosus muscle at the genome-wide significance level. A region on SSC4 also has pleiotropic effects on moisture content and drip loss of LM. In addition, this study revealed at least five novel QTLs and several candidate genes including 4-linked MYH genes (MYH1, MYH2, MYH3, and MYH13), MAL2, LPAR1, and PRKAG3 at four significant loci. Except for the SSC12 QTL, other QTLs are likely tissue-specific. These results provide new insights into the genetic basis of meat quality traits in Chinese Laiwu pigs and some significant SNPs reported here could be incorporated into the selection programs involving this breed.
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Affiliation(s)
- Xinwei Xiong
- Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, Nanchang, 330045, China
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