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Wang H, Wang X, Li M, Sun H, Chen Q, Yan D, Dong X, Pan Y, Lu S. Genome-wide association study reveals genetic loci and candidate genes for meat quality traits in a four-way crossbred pig population. Front Genet 2023; 14:1001352. [PMID: 36814900 PMCID: PMC9939654 DOI: 10.3389/fgene.2023.1001352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Accepted: 01/24/2023] [Indexed: 02/08/2023] Open
Abstract
Meat quality traits (MQTs) have gained more attention from breeders due to their increasing economic value in the commercial pig industry. In this genome-wide association study (GWAS), 223 four-way intercross pigs were genotyped using the specific-locus amplified fragment sequencing (SLAF-seq) and phenotyped for PH at 45 min post mortem (PH45), meat color score (MC), marbling score (MA), water loss rate (WL), drip loss (DL) in the longissimus muscle, and cooking loss (CL) in the psoas major muscle. A total of 227, 921 filtered single nucleotide polymorphisms (SNPs) evenly distributed across the entire genome were detected to perform GWAS. A total of 64 SNPs were identified for six meat quality traits using the mixed linear model (MLM), of which 24 SNPs were located in previously reported QTL regions. The phenotypic variation explained (PVE) by the significant SNPs was from 2.43% to 16.32%. The genomic heritability estimates based on SNP for six meat-quality traits were low to moderate (0.07-0.47) being the lowest for CL and the highest for DL. A total of 30 genes located within 10 kb upstream or downstream of these significant SNPs were found. Furthermore, several candidate genes for MQTs were detected, including pH45 (GRM8), MC (ANKRD6), MA (MACROD2 and ABCG1), WL (TMEM50A), CL (PIP4K2A) and DL (CDYL2, CHL1, ABCA4, ZAG and SLC1A2). This study provided substantial new evidence for several candidate genes to participate in different pork quality traits. The identification of these SNPs and candidate genes provided a basis for molecular marker-assisted breeding and improvement of pork quality traits.
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Affiliation(s)
- Huiyu Wang
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, Yunnan, China,Faculty of Animal Science, Xichang University, Xichang, Sichuan, China
| | - Xiaoyi Wang
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Mingli Li
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Hao Sun
- Faculty of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Qiang Chen
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Dawei Yan
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Xinxing Dong
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Yuchun Pan
- Faculty of Animal Science, Zhejiang University, Hangzhou, Zhejiang, China,*Correspondence: Yuchun Pan, ; Shaoxiong Lu,
| | - Shaoxiong Lu
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, Yunnan, China,*Correspondence: Yuchun Pan, ; Shaoxiong Lu,
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Ncube KT, Dzomba EF, Hadebe K, Soma P, Frylinck L, Muchadeyi FC. Carcass Quality Profiles and Associated Genomic Regions of South African Goat Populations Investigated Using Goat SNP50K Genotypes. Animals (Basel) 2022; 12:ani12030364. [PMID: 35158687 PMCID: PMC8833661 DOI: 10.3390/ani12030364] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Revised: 11/05/2021] [Accepted: 11/17/2021] [Indexed: 11/16/2022] Open
Abstract
Simple Summary South Africa is one of the major goat producing countries on the African continent. However, despite a large number of goats being produced, there is still a growing demand for chevon, which leads to producers being unable to reach demand, resulting in an absence of chevon in retail markets. Carcass quality is an important economic trait that plays a major role in influencing consumer preferences and high nutrient provision. Even though chevon is an easily accessible meat for smallholder farmers and has health benefits, it is still less preferred due to perceptions of low meat quality attributes such as toughness, off-odours and flavour, and unappealing colour. The majority of goat populations are village ecotypes whose genetic potential for meat and carcass quality is unknown. Abstract Carcass quality includes a battery of essential economic meat traits that play a significant role in influencing farmer breed preferences. A preliminary study was undertaken to investigate the carcass quality and the associated genomic regions in a small nucleus of animals that are representative of South African goat genetic resources. Samples of the South African Boer (n = 14), Northern Cape Speckled (n = 14), Eastern Cape Xhosa Lob ear (n = 12), Nguni/Mbuzi (n = 13), and Village (n = 20) were genotyped using the Illumina goat SNP50K and were phenotyped for carcass quality traits. SA Boer goats had heavier warm and cold carcass weights (17.2 ± 2.3 kg and 16.3 ± 2.3 kg). Pella village goats raised under an intensive system had significantly (p < 0.05) heavier warm and cold carcass weights (9.9 ± 1.1 kg and 9.2 ± 1.2 kg) compared to the village goats that are raised extensively (9.1 ± 2.0 kg and 8.4 ± 1.9). A total of 40 SNPs located on chromosomes 6, 10, 12, 13, 19, and 21 were significantly associated with carcass traits at (−log10 [p < 0.05]). Candidate genes that were associated with carcass characteristics (GADD45G, IGF2R, GAS1, VAV3, CAPN8, CAPN7, CAPN2, GHSR, COLQ, MRAS, and POU1F1) were also observed. Results from this study will inform larger future studies that will ultimately find use in breed improvement programs.
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Affiliation(s)
- Keabetswe Tebogo Ncube
- Agricultural Research Council, Biotechnology Platform, Private Bag X5, Onderstepoort, Pretoria 0110, South Africa; (K.T.N.); (K.H.)
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Private Bag X01, Scottsville, Pietermaritzburg 3209, South Africa;
| | - Edgar Farai Dzomba
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Private Bag X01, Scottsville, Pietermaritzburg 3209, South Africa;
| | - Khanyisile Hadebe
- Agricultural Research Council, Biotechnology Platform, Private Bag X5, Onderstepoort, Pretoria 0110, South Africa; (K.T.N.); (K.H.)
| | - Pranisha Soma
- Agricultural Research Council, Animal Production, Private Bag X2, Irene 0062, South Africa; (P.S.); (L.F.)
| | - Lorinda Frylinck
- Agricultural Research Council, Animal Production, Private Bag X2, Irene 0062, South Africa; (P.S.); (L.F.)
| | - Farai Catherine Muchadeyi
- Agricultural Research Council, Biotechnology Platform, Private Bag X5, Onderstepoort, Pretoria 0110, South Africa; (K.T.N.); (K.H.)
- Correspondence:
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Lee J, Park N, Lee D, Kim J. Evolutionary and Functional Analysis of Korean Native Pig Using Single Nucleotide Polymorphisms. Mol Cells 2020; 43:728-738. [PMID: 32868490 PMCID: PMC7468586 DOI: 10.14348/molcells.2020.0040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 07/21/2020] [Accepted: 07/24/2020] [Indexed: 11/27/2022] Open
Abstract
Time and cost-effective production of next-generation sequencing data has enabled the performance of population-scale comparative and evolutionary studies for various species, which are essential for obtaining the comprehensive insight into molecular mechanisms underlying species- or breed-specific traits. In this study, the evolutionary and functional analysis of Korean native pig (KNP) was performed using single nucleotide polymorphism (SNP) data by comparative and population genomic approaches with six different mammalian species and five pig breeds. We examined the evolutionary history of KNP SNPs, and the specific genes of KNP based on the uniqueness of non-synonymous SNPs among the used species and pig breeds. We discovered the evolutionary trajectory of KNP SNPs within the used mammalian species as well as pig breeds. We also found olfaction-associated functions that have been characterized and diversified during evolution, and quantitative trait loci associated with the unique traits of KNP. Our study provides new insight into the evolution of KNP and serves as a good example for a better understanding of domestic animals in terms of evolution and domestication using the combined approaches of comparative and population genomics.
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Affiliation(s)
- Jongin Lee
- Department of Biomedical Science and Engineering, Konkuk University, Seoul 05029, Korea
- These authors contributed equally to this work.
| | - Nayoung Park
- Department of Biomedical Science and Engineering, Konkuk University, Seoul 05029, Korea
- These authors contributed equally to this work.
| | - Daehwan Lee
- Department of Biomedical Science and Engineering, Konkuk University, Seoul 05029, Korea
| | - Jaebum Kim
- Department of Biomedical Science and Engineering, Konkuk University, Seoul 05029, Korea
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Taweechaipaisankul A, Kim GA, Jin JX, Yeom SC, Lee BC. Establishment and identification of cell lines from type O blood Korean native pigs and their efficiency in supporting embryonic development via somatic cell nuclear transfer. J Vet Sci 2018; 19:492-499. [PMID: 29486531 PMCID: PMC6070591 DOI: 10.4142/jvs.2018.19.4.492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Revised: 07/28/2017] [Accepted: 02/02/2018] [Indexed: 11/20/2022] Open
Abstract
Due to their similarities with humans in anatomy, physiology, and genetics miniature pigs are becoming an attractive model for biomedical research. We aim to establish and evaluate blood type O cells derived from Korean native pig (KNP), a typical miniature pig breed in Korea. Ten cell lines derived from 8 KNP piglets and one adult female KNP (kidney and ear tissues) were established. To confirm the presence of blood type O, genomic DNA, fucosyltransferase (FUT) expression, and immunofluorescence staining were examined. Additionally, fluorescence-activated cell sorting and somatic cell nuclear transfer were performed to investigate the normality of the cell lines and to evaluate their effectiveness in embryo development. We found no significant bands corresponding to specific blood group A, and no increase in FUT expression in cell lines derived from piglets No. 1, No. 4, No. 5, No. 8, and the adult female KNP; moreover, they showed normal levels of expression of α 1,3-galactosyltransferase and cytidine monophosphate-N-acetylneuraminic acid hydroxylase. There was no significant difference in embryo development between skin and kidney fibroblasts derived from the blood type O KNPs. In conclusion, we successfully established blood type O KNP cell lines, which may serve as a useful model in xenotransplantation research.
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Affiliation(s)
- Anukul Taweechaipaisankul
- Department of Theriogenology and Biotechnology, College of Veterinary Medicine, Seoul National University, Seoul 08826, Korea
| | - Geon A Kim
- Department of Theriogenology and Biotechnology, College of Veterinary Medicine, Seoul National University, Seoul 08826, Korea
| | - Jun-Xue Jin
- Department of Theriogenology and Biotechnology, College of Veterinary Medicine, Seoul National University, Seoul 08826, Korea
| | - Su Cheong Yeom
- Institutes of Green Bio Science and Technology, Seoul National University, Pyeongchang 25354, Korea
| | - Byeong Chun Lee
- Department of Theriogenology and Biotechnology, College of Veterinary Medicine, Seoul National University, Seoul 08826, Korea.,Institutes of Green Bio Science and Technology, Seoul National University, Pyeongchang 25354, Korea
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Cho IC, Yoo CK, Lee JB, Jung EJ, Han SH, Lee SS, Ko MS, Lim HT, Park HB. Genome-wide QTL analysis of meat quality-related traits in a large F2 intercross between Landrace and Korean native pigs. Genet Sel Evol 2015; 47:7. [PMID: 25888076 PMCID: PMC4336478 DOI: 10.1186/s12711-014-0080-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2013] [Accepted: 11/20/2014] [Indexed: 11/21/2022] Open
Abstract
Background We conducted a genome-wide linkage analysis to identify quantitative trait loci (QTL) that influence meat quality-related traits in a large F2 intercross between Landrace and Korean native pigs. Thirteen meat quality-related traits of the m. longissimus lumborum et thoracis were measured in more than 830 F2 progeny. All these animals were genotyped with 173 microsatellite markers located throughout the pig genome, and the GridQTL program based on the least squares regression model was used to perform the QTL analysis. Results We identified 23 genome-wide significant QTL in eight chromosome regions (SSC1, 2, 6, 7, 9, 12, 13, and 16) (SSC for Sus Scrofa) and detected 51 suggestive QTL in the 17 chromosome regions. QTL that affect 10 meat quality traits were detected on SSC12 and were highly significant at the genome-wide level. In particular, the QTL with the largest effect affected crude fat percentage and explained 22.5% of the phenotypic variance (F-ratio = 278.0 under the additive model, nominal P = 5.5 × 10−55). Interestingly, the QTL on SSC12 that influenced meat quality traits showed an obvious trend for co-localization. Conclusions Our results confirm several previously reported QTL. In addition, we identified novel QTL for meat quality traits, which together with the associated positional candidate genes improve the knowledge on the genetic structure that underlies genetic variation for meat quality traits in pigs. Electronic supplementary material The online version of this article (doi:10.1186/s12711-014-0080-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- In-Cheol Cho
- Subtropical Animal Experiment Station, National Institute of Animal Science, Rural Development Administration, Jeju, 690-150, Korea.
| | - Chae-Kyoung Yoo
- Department of Animal Science, College of Agriculture and Life Sciences, Gyeongsang National University, Jinju, 660-701, Korea. .,Institute of Agriculture and Life Science, Gyeongsang National University, Jinju, 660-701, Korea.
| | - Jae-Bong Lee
- Department of Animal Science, College of Agriculture and Life Sciences, Gyeongsang National University, Jinju, 660-701, Korea. .,Institute of Agriculture and Life Science, Gyeongsang National University, Jinju, 660-701, Korea.
| | - Eun-Ji Jung
- Department of Animal Science, College of Agriculture and Life Sciences, Gyeongsang National University, Jinju, 660-701, Korea. .,Institute of Agriculture and Life Science, Gyeongsang National University, Jinju, 660-701, Korea.
| | - Sang-Hyun Han
- Subtropical Animal Experiment Station, National Institute of Animal Science, Rural Development Administration, Jeju, 690-150, Korea.
| | - Sung-Soo Lee
- Subtropical Animal Experiment Station, National Institute of Animal Science, Rural Development Administration, Jeju, 690-150, Korea.
| | - Moon-Suck Ko
- Subtropical Animal Experiment Station, National Institute of Animal Science, Rural Development Administration, Jeju, 690-150, Korea.
| | - Hyun-Tae Lim
- Department of Animal Science, College of Agriculture and Life Sciences, Gyeongsang National University, Jinju, 660-701, Korea. .,Institute of Agriculture and Life Science, Gyeongsang National University, Jinju, 660-701, Korea.
| | - Hee-Bok Park
- Department of Animal Science, College of Agriculture and Life Sciences, Gyeongsang National University, Jinju, 660-701, Korea. .,Institute of Agriculture and Life Science, Gyeongsang National University, Jinju, 660-701, Korea. .,Department of Animal Science and Biotechnology (BK21 plus program), College of Agriculture and Life Sciences, Chungnam National University, Daejeon, 305-764, Korea.
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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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Kim JJ, Dekkers JCM. A least squares regression model to detect quantitative trait Loci with polar overdominance in a cross of outbred breeds: simulation. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2014; 26:1536-44. [PMID: 25049739 PMCID: PMC4093823 DOI: 10.5713/ajas.2013.13356] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Revised: 08/28/2013] [Accepted: 08/19/2013] [Indexed: 12/02/2022]
Abstract
A least squares regression interval mapping model was derived to detect quantitative trait loci (QTL) with a unique mode of genomic imprinting, polar overdominance (POD), under a breed cross design model in outbred mammals. Tests to differentiate POD QTL from Mendelian, paternal or maternal expression QTL were also developed. To evaluate the power of the POD models and to determine the ability to differentiate POD from non-POD QTL, phenotypic data, marker data and a biallelic QTL were simulated on 512 F2 offspring. When tests for Mendelian versus parent-of-origin expression were performed, most POD QTL were classified as partially imprinted QTL. The application of the series of POD tests showed that more than 90% and 80% of medium and small POD QTL were declared as POD type. However, when breed-origin alleles were segregating in the grand parental breeds, the proportion of declared POD QTL decreased, which was more pronounced in a mating design with a small number of parents (F0 and F1). Non-POD QTL, i.e. with Mendelian or parent-of-origin expression (complete imprinting) inheritance, were well classified (>90%) as non-POD QTL, except for QTL with small effects and paternal or maternal expression in the design with a small number of parents, for which spurious POD QTL were declared.
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Affiliation(s)
- Jong-Joo Kim
- School of Biotechnology, Yeungnam University, Gyeongsan, Gyeongbuk, Korea
| | - Jack C M Dekkers
- School of Biotechnology, Yeungnam University, Gyeongsan, Gyeongbuk, Korea
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