Elucidation of the genetic determination of body weight and size in Chinese local chicken breeds by large-scale genomic analyses
Abstract Background Body weight and size are important economic traits in chickens. While many growth-related quantitative trait loci (QTLs) and candidate genes have been identified, further research is needed to confirm and characterize these findings. In this study, we investigate genetic and geno...
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| Format: | Article |
| Language: | English |
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BMC
2024-03-01
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| Series: | BMC Genomics |
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| Online Access: | https://doi.org/10.1186/s12864-024-10185-6 |
| _version_ | 1797247470635319296 |
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| author | Jie Wang Jie Liu Qiuxia Lei Zhihe Liu Haixia Han Shuer Zhang Chao Qi Wei Liu Dapeng Li Fuwei Li Dingguo Cao Yan Zhou |
| author_facet | Jie Wang Jie Liu Qiuxia Lei Zhihe Liu Haixia Han Shuer Zhang Chao Qi Wei Liu Dapeng Li Fuwei Li Dingguo Cao Yan Zhou |
| author_sort | Jie Wang |
| collection | DOAJ |
| description | Abstract Background Body weight and size are important economic traits in chickens. While many growth-related quantitative trait loci (QTLs) and candidate genes have been identified, further research is needed to confirm and characterize these findings. In this study, we investigate genetic and genomic markers associated with chicken body weight and size. This study provides new insights into potential markers for genomic selection and breeding strategies to improve meat production in chickens. Methods We performed whole-genome resequencing of and Wenshang Barred (WB) chickens (n = 596) and three additional breeds with varying body sizes (Recessive White (RW), WB, and Luxi Mini (LM) chickens; (n = 50)). We then used selective sweeps of mutations coupled with genome-wide association study (GWAS) to identify genomic markers associated with body weight and size. Results We identified over 9.4 million high-quality single nucleotide polymorphisms (SNPs) among three chicken breeds/lines. Among these breeds, 287 protein-coding genes exhibited positive selection in the RW and WB populations, while 241 protein-coding genes showed positive selection in the LM and WB populations. Genomic heritability estimates were calculated for 26 body weight and size traits, including body weight, chest breadth, chest depth, thoracic horn, body oblique length, keel length, pelvic width, shank length, and shank circumference in the WB breed. The estimates ranged from 0.04 to 0.67. Our analysis also identified a total of 2,522 genome-wide significant SNPs, with 2,474 SNPs clustered around two genomic regions. The first region, located on chromosome 4 (7.41-7.64 Mb), was linked to body weight after ten weeks and body size traits. LCORL, LDB2, and PPARGC1A were identified as candidate genes in this region. The other region, located on chromosome 1 (170.46-171.53 Mb), was associated with body weight from four to eighteen weeks and body size traits. This region contained CAB39L and WDFY2 as candidate genes. Notably, LCORL, LDB2, and PPARGC1A showed highly selective signatures among the three breeds of chicken with varying body sizes. Conclusion Overall this study provides a comprehensive map of genomic variants associated with body weight and size in chickens. We propose two genomic regions, one on chromosome 1 and the other on chromosome 4, that could helpful for developing genome selection breeding strategies to enhance meat yield in chickens. |
| first_indexed | 2024-04-24T19:59:12Z |
| format | Article |
| id | doaj.art-61e4f479b6bf40ed9b1d026af0edd303 |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-04-24T19:59:12Z |
| publishDate | 2024-03-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-61e4f479b6bf40ed9b1d026af0edd3032024-03-24T12:11:22ZengBMCBMC Genomics1471-21642024-03-0125111510.1186/s12864-024-10185-6Elucidation of the genetic determination of body weight and size in Chinese local chicken breeds by large-scale genomic analysesJie Wang0Jie Liu1Qiuxia Lei2Zhihe Liu3Haixia Han4Shuer Zhang5Chao Qi6Wei Liu7Dapeng Li8Fuwei Li9Dingguo Cao10Yan Zhou11Poultry Breeding Engineering Technology Center of Shandong Province, Poultry Institute, Shandong Academy of Agricultural SciencesPoultry Breeding Engineering Technology Center of Shandong Province, Poultry Institute, Shandong Academy of Agricultural SciencesPoultry Breeding Engineering Technology Center of Shandong Province, Poultry Institute, Shandong Academy of Agricultural SciencesSichuan agricultural university college of animal science and technologyPoultry Breeding Engineering Technology Center of Shandong Province, Poultry Institute, Shandong Academy of Agricultural SciencesShandong Animal Husbandry General StationShandong Animal Husbandry General StationPoultry Breeding Engineering Technology Center of Shandong Province, Poultry Institute, Shandong Academy of Agricultural SciencesPoultry Breeding Engineering Technology Center of Shandong Province, Poultry Institute, Shandong Academy of Agricultural SciencesPoultry Breeding Engineering Technology Center of Shandong Province, Poultry Institute, Shandong Academy of Agricultural SciencesPoultry Breeding Engineering Technology Center of Shandong Province, Poultry Institute, Shandong Academy of Agricultural SciencesPoultry Breeding Engineering Technology Center of Shandong Province, Poultry Institute, Shandong Academy of Agricultural SciencesAbstract Background Body weight and size are important economic traits in chickens. While many growth-related quantitative trait loci (QTLs) and candidate genes have been identified, further research is needed to confirm and characterize these findings. In this study, we investigate genetic and genomic markers associated with chicken body weight and size. This study provides new insights into potential markers for genomic selection and breeding strategies to improve meat production in chickens. Methods We performed whole-genome resequencing of and Wenshang Barred (WB) chickens (n = 596) and three additional breeds with varying body sizes (Recessive White (RW), WB, and Luxi Mini (LM) chickens; (n = 50)). We then used selective sweeps of mutations coupled with genome-wide association study (GWAS) to identify genomic markers associated with body weight and size. Results We identified over 9.4 million high-quality single nucleotide polymorphisms (SNPs) among three chicken breeds/lines. Among these breeds, 287 protein-coding genes exhibited positive selection in the RW and WB populations, while 241 protein-coding genes showed positive selection in the LM and WB populations. Genomic heritability estimates were calculated for 26 body weight and size traits, including body weight, chest breadth, chest depth, thoracic horn, body oblique length, keel length, pelvic width, shank length, and shank circumference in the WB breed. The estimates ranged from 0.04 to 0.67. Our analysis also identified a total of 2,522 genome-wide significant SNPs, with 2,474 SNPs clustered around two genomic regions. The first region, located on chromosome 4 (7.41-7.64 Mb), was linked to body weight after ten weeks and body size traits. LCORL, LDB2, and PPARGC1A were identified as candidate genes in this region. The other region, located on chromosome 1 (170.46-171.53 Mb), was associated with body weight from four to eighteen weeks and body size traits. This region contained CAB39L and WDFY2 as candidate genes. Notably, LCORL, LDB2, and PPARGC1A showed highly selective signatures among the three breeds of chicken with varying body sizes. Conclusion Overall this study provides a comprehensive map of genomic variants associated with body weight and size in chickens. We propose two genomic regions, one on chromosome 1 and the other on chromosome 4, that could helpful for developing genome selection breeding strategies to enhance meat yield in chickens.https://doi.org/10.1186/s12864-024-10185-6ChickenGWASBody weightBody size |
| spellingShingle | Jie Wang Jie Liu Qiuxia Lei Zhihe Liu Haixia Han Shuer Zhang Chao Qi Wei Liu Dapeng Li Fuwei Li Dingguo Cao Yan Zhou Elucidation of the genetic determination of body weight and size in Chinese local chicken breeds by large-scale genomic analyses BMC Genomics Chicken GWAS Body weight Body size |
| title | Elucidation of the genetic determination of body weight and size in Chinese local chicken breeds by large-scale genomic analyses |
| title_full | Elucidation of the genetic determination of body weight and size in Chinese local chicken breeds by large-scale genomic analyses |
| title_fullStr | Elucidation of the genetic determination of body weight and size in Chinese local chicken breeds by large-scale genomic analyses |
| title_full_unstemmed | Elucidation of the genetic determination of body weight and size in Chinese local chicken breeds by large-scale genomic analyses |
| title_short | Elucidation of the genetic determination of body weight and size in Chinese local chicken breeds by large-scale genomic analyses |
| title_sort | elucidation of the genetic determination of body weight and size in chinese local chicken breeds by large scale genomic analyses |
| topic | Chicken GWAS Body weight Body size |
| url | https://doi.org/10.1186/s12864-024-10185-6 |
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