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Yang L, Li X, Zhuang Z, Zhou S, Wu J, Xu C, Ruan D, Qiu Y, Zhao H, Zheng E, Cai G, Wu Z, Yang J. Genome-Wide Association Study Identifies the Crucial Candidate Genes for Teat Number in Crossbred Commercial Pigs. Animals (Basel) 2023; 13:1880. [PMID: 37889833 PMCID: PMC10251818 DOI: 10.3390/ani13111880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 05/27/2023] [Accepted: 06/03/2023] [Indexed: 10/29/2023] Open
Abstract
The number of teats is a crucial reproductive trait with significant economic implications on maternal capacity and litter size. Consequently, improving this trait is essential to facilitate genetic selection for increased litter size. In this study, we performed a genome-wide association study (GWAS) of the number of teats in a three-way crossbred commercial Duroc × (Landrace × Yorkshire) (DLY) pig population comprising 1518 animals genotyped with the 50K BeadChip. Our analysis identified crucial quantitative trait loci (QTL) for the number of teats, containing the ABCD4 and VRTN genes on porcine chromosome 7. Our results establish SNP variants of ABCD4 and VRTN as new molecular markers for improving the number of teats in DLY pigs. Furthermore, the most significant noteworthy single nucleotide polymorphism (SNP) (7_97568284) was identified within the ABCD4 gene, exhibiting a significant association with the total teat number traits. This SNP accounted for a substantial proportion of the genetic variance, explaining 6.64% of the observed variation. These findings reveal a novel gene on SSC7 for the number of teats and provide a deeper understanding of the genetic mechanisms underlying reproductive traits.
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Affiliation(s)
- Lijuan Yang
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China; (L.Y.); (X.L.); (Z.Z.); (S.Z.); (J.W.); (C.X.); (D.R.); (Y.Q.); (E.Z.); (G.C.)
| | - Xuehua Li
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China; (L.Y.); (X.L.); (Z.Z.); (S.Z.); (J.W.); (C.X.); (D.R.); (Y.Q.); (E.Z.); (G.C.)
| | - Zhanwei Zhuang
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China; (L.Y.); (X.L.); (Z.Z.); (S.Z.); (J.W.); (C.X.); (D.R.); (Y.Q.); (E.Z.); (G.C.)
| | - Shenping Zhou
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China; (L.Y.); (X.L.); (Z.Z.); (S.Z.); (J.W.); (C.X.); (D.R.); (Y.Q.); (E.Z.); (G.C.)
| | - Jie Wu
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China; (L.Y.); (X.L.); (Z.Z.); (S.Z.); (J.W.); (C.X.); (D.R.); (Y.Q.); (E.Z.); (G.C.)
| | - Cineng Xu
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China; (L.Y.); (X.L.); (Z.Z.); (S.Z.); (J.W.); (C.X.); (D.R.); (Y.Q.); (E.Z.); (G.C.)
| | - Donglin Ruan
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China; (L.Y.); (X.L.); (Z.Z.); (S.Z.); (J.W.); (C.X.); (D.R.); (Y.Q.); (E.Z.); (G.C.)
| | - Yibin Qiu
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China; (L.Y.); (X.L.); (Z.Z.); (S.Z.); (J.W.); (C.X.); (D.R.); (Y.Q.); (E.Z.); (G.C.)
| | - Hua Zhao
- National S&T Innovation Center for Modern Agricultural Industry, Guangzhou 510642, China;
- Key Laboratory of South China Modern Biological Seed Industry, Ministry of Agriculture and Rural Affairs, Guangzhou 510642, China
| | - Enqin Zheng
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China; (L.Y.); (X.L.); (Z.Z.); (S.Z.); (J.W.); (C.X.); (D.R.); (Y.Q.); (E.Z.); (G.C.)
| | - Gengyuan Cai
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China; (L.Y.); (X.L.); (Z.Z.); (S.Z.); (J.W.); (C.X.); (D.R.); (Y.Q.); (E.Z.); (G.C.)
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou 510642, China
| | - Zhenfang Wu
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China; (L.Y.); (X.L.); (Z.Z.); (S.Z.); (J.W.); (C.X.); (D.R.); (Y.Q.); (E.Z.); (G.C.)
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou 510642, China
- Yunfu Subcenter of Guangdong Laboratory for Lingnan Modern Agriculture, Yunfu 527400, China
| | - Jie Yang
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China; (L.Y.); (X.L.); (Z.Z.); (S.Z.); (J.W.); (C.X.); (D.R.); (Y.Q.); (E.Z.); (G.C.)
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou 510642, China
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van den Berg I, Hayes BJ, Chamberlain AJ, Goddard ME. Overlap between eQTL and QTL associated with production traits and fertility in dairy cattle. BMC Genomics 2019; 20:291. [PMID: 30987590 PMCID: PMC6466667 DOI: 10.1186/s12864-019-5656-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Accepted: 03/29/2019] [Indexed: 01/26/2023] Open
Abstract
Background Identifying causative mutations or genes through which quantitative trait loci (QTL) act has proven very difficult. Using information such as gene expression may help to identify genes and mutations underlying QTL. Our objective was to identify regions associated both with production traits or fertility and with gene expression, in dairy cattle. We used three different approaches to discover QTL that are also expression QTL (eQTL): 1) estimate the correlation between local genomic estimated breeding values (GEBV) and gene expression, 2) investigate whether the 300 intervals explaining most genetic variance for a trait contain more eQTL than 300 randomly selected intervals, and 3) a colocalisation analysis. Phenotypes and genotypes up to sequence level of 35,775 dairy bulls and cows were used for QTL mapping, and gene expression and genotypes of 131 cows were used to identify eQTL. Results With all three approaches, we identified some overlap between eQTL and QTL, though the majority of QTL in our dataset did not seem to be eQTL. The most significant associations between QTL and eQTL were found for intervals on chromosome 18, where local GEBV for all traits showed a strong association with the expression of the FUK and DDX19B. Intervals whose local GEBV for a trait correlated highly significantly with the expression of a nearby gene explained only a very small part of the genetic variance for that trait. It is likely that part of these correlations were due to linkage disequilibrium (LD) in the interval. While the 300 intervals explaining most genetic variance explained most of the GEBV variance, they contained only slightly more eQTL than 300 randomly selected intervals that explained a minimal portion of the GEBV variance. Furthermore, some variants showed a high colocalisation probability, but this was only the case for few variants. Conclusions Several reasons may have contributed to the low level of overlap between QTL and eQTL detected in our study, including a lack of power in the eQTL study and long-range LD making it difficult to separate QTL and eQTL. Furthermore, it may be that eQTL explain only a small fraction of QTL. Electronic supplementary material The online version of this article (10.1186/s12864-019-5656-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- I van den Berg
- Faculty of Veterinary & Agricultural Science, University of Melbourne, Parkville, Victoria, Australia. .,Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, Victoria, Australia.
| | - B J Hayes
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, Victoria, Australia.,Queensland Alliance for Agriculture and Food Innovation, Centre for Animal Science, University of Queensland, St Lucia, Queensland, 4067, Australia
| | - A J Chamberlain
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, Victoria, Australia
| | - M E Goddard
- Faculty of Veterinary & Agricultural Science, University of Melbourne, Parkville, Victoria, Australia.,Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, Victoria, Australia
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Chalkias H, Jonas E, Andersson LS, Jacobson M, de Koning DJ, Lundeheim N, Lindgren G. Identification of novel candidate genes for the inverted teat defect in sows using a genome-wide marker panel. J Appl Genet 2017; 58:249-259. [PMID: 28050760 PMCID: PMC5391382 DOI: 10.1007/s13353-016-0382-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Accepted: 11/24/2016] [Indexed: 11/29/2022]
Abstract
The number of functional teats is an important selection criterion in pig breeding. Inherited defects of the udder, such as the inverted teat, do have a considerable negative impact on the nursing ability of the sow. To investigate the genetic background of this defect and the number of functional teats in Swedish maternal lines, samples from 230 Yorkshire pigs were selected for genotyping using the PorcineSNP60K BeadChip (Illumina Inc.), each pig with at least one inverted teat was matched with one non-affected pig (fullsib or pairs with matching herd and gender). A genome-wide association study on these 230 pigs was performed using the two-step approach implemented in GenABEL using 46,652 single nucleotide polymorphisms across all autosomes and the X chromosome. A number of significant regions were identified for the inverted teat defect on chromosomes 2, 10, and 18. Many of the regions associated with the number of functional teats were located in the same or close regions, except two associated markers on the X chromosome and one on chromosome 3. We identified some of the regions on chromosomes previously reported in one linkage and one gene expression study. We conclude, despite being able to suggest new candidate genes, that further studies are needed to better understand the biologic background of the teat development. Despite the in-depth comparison of identified regions for the inverted teat defect done here, more studies are required to allow a clear identification of genetic regions relevant for this defect across many pig populations.
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Affiliation(s)
- Helena Chalkias
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Box 7023, SE-750 07, Uppsala, Sweden
| | - Elisabeth Jonas
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Box 7023, SE-750 07, Uppsala, Sweden.
| | - Lisa S Andersson
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Box 7023, SE-750 07, Uppsala, Sweden
| | - Magdalena Jacobson
- Department of Clinical Sciences, Swedish University of Agricultural Sciences, Box 7054, SE-750 07, Uppsala, Sweden
| | - Dirk Jan de Koning
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Box 7023, SE-750 07, Uppsala, Sweden
| | - Nils Lundeheim
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Box 7023, SE-750 07, Uppsala, Sweden
| | - Gabriella Lindgren
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Box 7023, SE-750 07, Uppsala, Sweden.,Capilet Genetics AB, SE-725 93, Västerås, Sweden
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Verardo LL, Silva FF, Varona L, Resende MDV, Bastiaansen JWM, Lopes PS, Guimarães SEF. Bayesian GWAS and network analysis revealed new candidate genes for number of teats in pigs. J Appl Genet 2014; 56:123-32. [DOI: 10.1007/s13353-014-0240-y] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Revised: 05/27/2014] [Accepted: 07/23/2014] [Indexed: 01/01/2023]
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