Genome-wide single nucleotide polymorphism (SNP) data reveal potential candidate genes for litter traits in a Yorkshire pig population
<p>The litter trait is one of the most important economic traits, and increasing litter size is of great economic value in the pig industry. However, the molecular mechanisms underlying pig litter traits remain elusive. To identify molecular markers and candidate genes for pig litter traits, a...
| Main Authors: | , , , , , , |
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| Format: | Article |
| Language: | English |
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Copernicus Publications
2023-11-01
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| Series: | Archives Animal Breeding |
| Online Access: | https://aab.copernicus.org/articles/66/357/2023/aab-66-357-2023.pdf |
| _version_ | 1827667565974913024 |
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| author | Y. Zhang J. Lai X. Wang M. Li Y. Zhang C. Ji Q. Chen S. Lu |
| author_facet | Y. Zhang J. Lai X. Wang M. Li Y. Zhang C. Ji Q. Chen S. Lu |
| author_sort | Y. Zhang |
| collection | DOAJ |
| description | <p>The litter trait is one of the most important economic traits, and increasing litter size is of great economic value in the pig industry. However, the molecular mechanisms underlying pig litter traits remain elusive. To identify molecular markers and candidate genes for pig litter traits, a genome-wide association study (GWAS) and selection signature analysis were conducted in a Yorkshire pig population. A total of 518 producing sows were genotyped with Illumina Porcine SNP 50 BeadChip, and 1969 farrowing records for the total number born (TNB), the number born alive (NBA), piglets born dead (PBD), and litter weight born alive (LWB) were collected. Then, a GWAS was performed for the four litter traits using a repeatability model. Based on the estimated breeding values (EBVs) of TNB, 15 high- and 15 low-prolificacy individuals were selected from the 518 sows to implement selection signature analysis. Subsequently, the selection signatures affecting the litter traits of sows were detected by using two methods including the fixation index (FST) and <span class="inline-formula"><i>θ</i><i>π</i></span>. Combining the results of the GWAS and selection signature analysis, 20 promising candidate genes (<i>NKAIN2</i>, <i>IGF1R</i>, <i>KISS1R</i>, <i>TYRO3</i>, <i>SPINT1</i>, <i>ADGRF5</i>, <i>APC2</i>, <i>PTBP1</i>, <i>CLCN3</i>, <i>CBR4</i>, <i>HPF1</i>, <i>FAM174A</i>, <i>SCP2</i>, <i>CLIC1</i>, <i>ZFYVE9</i>, <i>SPATA33</i>, <i>KIF5C</i>, <i>EPC2</i>, <i>GABRA2</i>, and <i>GABRA4</i>) were identified. These findings provide novel insights into the genetic basis of pig litter traits and will be helpful for improving the reproductive performances of sows in pig breeding.</p> |
| first_indexed | 2024-03-10T03:20:06Z |
| format | Article |
| id | doaj.art-61389d839e6446ef9e8dfc160176bee3 |
| institution | Directory Open Access Journal |
| issn | 0003-9438 2363-9822 |
| language | English |
| last_indexed | 2024-03-10T03:20:06Z |
| publishDate | 2023-11-01 |
| publisher | Copernicus Publications |
| record_format | Article |
| series | Archives Animal Breeding |
| spelling | doaj.art-61389d839e6446ef9e8dfc160176bee32023-11-23T12:21:06ZengCopernicus PublicationsArchives Animal Breeding0003-94382363-98222023-11-016635736810.5194/aab-66-357-2023Genome-wide single nucleotide polymorphism (SNP) data reveal potential candidate genes for litter traits in a Yorkshire pig populationY. Zhang0J. Lai1X. Wang2M. Li3Y. Zhang4C. Ji5Q. Chen6S. Lu7Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, 650201, ChinaFaculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, 650201, ChinaFaculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, 650201, ChinaFaculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, 650201, ChinaYunnan Fuyuefa Livestock and Poultry Feeding Company Limited, Kunming, 650300, ChinaYunnan Fuyuefa Livestock and Poultry Feeding Company Limited, Kunming, 650300, ChinaFaculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, 650201, ChinaFaculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, 650201, China<p>The litter trait is one of the most important economic traits, and increasing litter size is of great economic value in the pig industry. However, the molecular mechanisms underlying pig litter traits remain elusive. To identify molecular markers and candidate genes for pig litter traits, a genome-wide association study (GWAS) and selection signature analysis were conducted in a Yorkshire pig population. A total of 518 producing sows were genotyped with Illumina Porcine SNP 50 BeadChip, and 1969 farrowing records for the total number born (TNB), the number born alive (NBA), piglets born dead (PBD), and litter weight born alive (LWB) were collected. Then, a GWAS was performed for the four litter traits using a repeatability model. Based on the estimated breeding values (EBVs) of TNB, 15 high- and 15 low-prolificacy individuals were selected from the 518 sows to implement selection signature analysis. Subsequently, the selection signatures affecting the litter traits of sows were detected by using two methods including the fixation index (FST) and <span class="inline-formula"><i>θ</i><i>π</i></span>. Combining the results of the GWAS and selection signature analysis, 20 promising candidate genes (<i>NKAIN2</i>, <i>IGF1R</i>, <i>KISS1R</i>, <i>TYRO3</i>, <i>SPINT1</i>, <i>ADGRF5</i>, <i>APC2</i>, <i>PTBP1</i>, <i>CLCN3</i>, <i>CBR4</i>, <i>HPF1</i>, <i>FAM174A</i>, <i>SCP2</i>, <i>CLIC1</i>, <i>ZFYVE9</i>, <i>SPATA33</i>, <i>KIF5C</i>, <i>EPC2</i>, <i>GABRA2</i>, and <i>GABRA4</i>) were identified. These findings provide novel insights into the genetic basis of pig litter traits and will be helpful for improving the reproductive performances of sows in pig breeding.</p>https://aab.copernicus.org/articles/66/357/2023/aab-66-357-2023.pdf |
| spellingShingle | Y. Zhang J. Lai X. Wang M. Li Y. Zhang C. Ji Q. Chen S. Lu Genome-wide single nucleotide polymorphism (SNP) data reveal potential candidate genes for litter traits in a Yorkshire pig population Archives Animal Breeding |
| title | Genome-wide single nucleotide polymorphism (SNP) data reveal potential candidate genes for litter traits in a Yorkshire pig population |
| title_full | Genome-wide single nucleotide polymorphism (SNP) data reveal potential candidate genes for litter traits in a Yorkshire pig population |
| title_fullStr | Genome-wide single nucleotide polymorphism (SNP) data reveal potential candidate genes for litter traits in a Yorkshire pig population |
| title_full_unstemmed | Genome-wide single nucleotide polymorphism (SNP) data reveal potential candidate genes for litter traits in a Yorkshire pig population |
| title_short | Genome-wide single nucleotide polymorphism (SNP) data reveal potential candidate genes for litter traits in a Yorkshire pig population |
| title_sort | genome wide single nucleotide polymorphism snp data reveal potential candidate genes for litter traits in a yorkshire pig population |
| url | https://aab.copernicus.org/articles/66/357/2023/aab-66-357-2023.pdf |
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