Genome-wide association studies uncover genes associated with litter traits in the pig
Litter traits are critical economic variables in the pig industry as they represent a production indicator that can serve to determine sow fertility. In this study, a genome-wide association study on litter traits, including total number born (TNB), number born alive (NBA), litter birth weight (LBW)...
| Main Authors: | , , , , , , |
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| Format: | Article |
| Language: | English |
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Elsevier
2022-12-01
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| Series: | Animal |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S1751731122002294 |
| _version_ | 1798004545120370688 |
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| author | Y.X. Zhao G.X. Gao Y. Zhou C.X. Guo B. Li S. El-Ashram Z.L. Li |
| author_facet | Y.X. Zhao G.X. Gao Y. Zhou C.X. Guo B. Li S. El-Ashram Z.L. Li |
| author_sort | Y.X. Zhao |
| collection | DOAJ |
| description | Litter traits are critical economic variables in the pig industry as they represent a production indicator that can serve to determine sow fertility. In this study, a genome-wide association study on litter traits, including total number born (TNB), number born alive (NBA), litter birth weight (LBW), average birth weight (ABW), and piglet uniformity (PU), was carried out on two pig breeds (Yorkshire and Landrace). A total of 3 637 pigs of both breeds were genotyped using the GeneSeek GGP Porcine 50K SNP BeadChip. A mixed linear model (MLM) and fixed and random model circulating probability unification (FarmCPU) were employed in the genome-wide association studies for litter traits using combined data from the two pig breeds and data from each breed separately. Additionally, the heritability of traits was estimated using three methods—pedigree-based best linear unbiased prediction (PBLUP), genomic best linear unbiased prediction (GBLUP), and single-step best linear unbiased prediction (ssGBLUP)—and was found to lie between 0.065 and 0.1289, 0.0478 and 0.0938, 0.0793 and 0.0935, 0.1862 and 0.2163, and 0.0327 and 0.0419 for TNB, NBA, LBW, ABW, and PU, respectively. We also compared the genomic prediction accuracies and unbiasedness for litter traits of the three BLUP models. Our results indicated that the ssGBLUP method provided higher predictive accuracies and more rational unbiasedness compared with the PBLUP and GBLUP methodologies. Furthermore, based on their possible roles, eight candidate genes (INHBA, LEPR, HDHD2, CTNND2, RNF216, HMX1, PAPPA2, and NTN1) were identified as being linked with litter traits. In the middle of the test, these genes were found to be connected with pig metabolism and ovulation rate. Our results provide the insights into the genetic architecture of litter traits in pigs, and the potential single nucleotide polymorphisms (SNPs) and candidate genes identified may benefit economic profits in pig-breeding industry and contribute to improve litter traits. |
| first_indexed | 2024-04-11T12:25:24Z |
| format | Article |
| id | doaj.art-060d65ffab2c436e8fbde4ce5f4fdffb |
| institution | Directory Open Access Journal |
| issn | 1751-7311 |
| language | English |
| last_indexed | 2024-04-11T12:25:24Z |
| publishDate | 2022-12-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Animal |
| spelling | doaj.art-060d65ffab2c436e8fbde4ce5f4fdffb2022-12-22T04:23:57ZengElsevierAnimal1751-73112022-12-011612100672Genome-wide association studies uncover genes associated with litter traits in the pigY.X. Zhao0G.X. Gao1Y. Zhou2C.X. Guo3B. Li4S. El-Ashram5Z.L. Li6School of Life Science and Engineering, Foshan University, Foshan, Guangdong 528000, China; Guangxi Yangxiang Agricultural and Animal Husbandry Co, Ltd, Guigang, Guangxi 537100, ChinaSchool of Life Science and Engineering, Foshan University, Foshan, Guangdong 528000, ChinaGuangxi Yangxiang Agricultural and Animal Husbandry Co, Ltd, Guigang, Guangxi 537100, ChinaGuangxi Yangxiang Agricultural and Animal Husbandry Co, Ltd, Guigang, Guangxi 537100, ChinaGuangxi Yangxiang Agricultural and Animal Husbandry Co, Ltd, Guigang, Guangxi 537100, ChinaFaculty of Science, Kafrelsheikh University, Kafr El-Sheikh 33516, EgyptSchool of Life Science and Engineering, Foshan University, Foshan, Guangdong 528000, China; Corresponding author.Litter traits are critical economic variables in the pig industry as they represent a production indicator that can serve to determine sow fertility. In this study, a genome-wide association study on litter traits, including total number born (TNB), number born alive (NBA), litter birth weight (LBW), average birth weight (ABW), and piglet uniformity (PU), was carried out on two pig breeds (Yorkshire and Landrace). A total of 3 637 pigs of both breeds were genotyped using the GeneSeek GGP Porcine 50K SNP BeadChip. A mixed linear model (MLM) and fixed and random model circulating probability unification (FarmCPU) were employed in the genome-wide association studies for litter traits using combined data from the two pig breeds and data from each breed separately. Additionally, the heritability of traits was estimated using three methods—pedigree-based best linear unbiased prediction (PBLUP), genomic best linear unbiased prediction (GBLUP), and single-step best linear unbiased prediction (ssGBLUP)—and was found to lie between 0.065 and 0.1289, 0.0478 and 0.0938, 0.0793 and 0.0935, 0.1862 and 0.2163, and 0.0327 and 0.0419 for TNB, NBA, LBW, ABW, and PU, respectively. We also compared the genomic prediction accuracies and unbiasedness for litter traits of the three BLUP models. Our results indicated that the ssGBLUP method provided higher predictive accuracies and more rational unbiasedness compared with the PBLUP and GBLUP methodologies. Furthermore, based on their possible roles, eight candidate genes (INHBA, LEPR, HDHD2, CTNND2, RNF216, HMX1, PAPPA2, and NTN1) were identified as being linked with litter traits. In the middle of the test, these genes were found to be connected with pig metabolism and ovulation rate. Our results provide the insights into the genetic architecture of litter traits in pigs, and the potential single nucleotide polymorphisms (SNPs) and candidate genes identified may benefit economic profits in pig-breeding industry and contribute to improve litter traits.http://www.sciencedirect.com/science/article/pii/S1751731122002294BreedingCandidate genesGenomic selectionProduction efficiencySwine |
| spellingShingle | Y.X. Zhao G.X. Gao Y. Zhou C.X. Guo B. Li S. El-Ashram Z.L. Li Genome-wide association studies uncover genes associated with litter traits in the pig Animal Breeding Candidate genes Genomic selection Production efficiency Swine |
| title | Genome-wide association studies uncover genes associated with litter traits in the pig |
| title_full | Genome-wide association studies uncover genes associated with litter traits in the pig |
| title_fullStr | Genome-wide association studies uncover genes associated with litter traits in the pig |
| title_full_unstemmed | Genome-wide association studies uncover genes associated with litter traits in the pig |
| title_short | Genome-wide association studies uncover genes associated with litter traits in the pig |
| title_sort | genome wide association studies uncover genes associated with litter traits in the pig |
| topic | Breeding Candidate genes Genomic selection Production efficiency Swine |
| url | http://www.sciencedirect.com/science/article/pii/S1751731122002294 |
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