Genetic patterns and genome-wide association analysis of eggshell quality traits of egg-type chicken across an extended laying period
ABSTRACT: The industry of egg-type chicken has shown a trend of extending the rearing period, with the goal of breeding chicken breeds capable of producing 500 qualified eggs by 700 d of age. However, the rapid decline in eggshell quality during the late laying period is one of the major challenges....
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| Format: | Article |
| Language: | English |
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Elsevier
2024-04-01
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| Series: | Poultry Science |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S0032579124000373 |
| _version_ | 1797256525759119360 |
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| author | Xiaoman Chen Xiaochang Li Conghao Zhong Xinwei Jiang Guiqin Wu Guangqi Li Yiyuan Yan Ning Yang Congjiao Sun |
| author_facet | Xiaoman Chen Xiaochang Li Conghao Zhong Xinwei Jiang Guiqin Wu Guangqi Li Yiyuan Yan Ning Yang Congjiao Sun |
| author_sort | Xiaoman Chen |
| collection | DOAJ |
| description | ABSTRACT: The industry of egg-type chicken has shown a trend of extending the rearing period, with the goal of breeding chicken breeds capable of producing 500 qualified eggs by 700 d of age. However, the rapid decline in eggshell quality during the late laying period is one of the major challenges. In this study, a total of 3,261 Rhode Island Red chickens were used to measure eggshell quality traits including eggshell strength (ESS), eggshell thickness (EST), eggshell color (ESC) and eggshell gloss (ESG) at seven age points ranging from 36 to 90 wk of age. Phenotypic variations increased with the aging process, especially during the late laying period (> 55 wk), and the heritability during this period decreased by 22.7 to 81.4% compared to the initial and peak laying periods. Then we performed genome-wide association study (GWAS) to identify the genomic variants that associated with eggshell quality, with a custom Illumina 50K BeadChip, named PhenoixChip-I. The results indicated that 2 genomic regions on GGA1(23.24-25.15Mb; 175.95-176.05 Mb) were significantly (P < 4.48E-06) or suggestively (P < 8.97E-05) associated with ESS, which can explain 9.59% and 0.48% of the phenotypic variations of ESS46 and ESS36, respectively. Three genes, FRY, PCNX2, and ENSGALG00000052468, were considered to be the candidate genes for ESS. For other traits, the genome-wide suggestive SNPs were identified at each age point, exhibiting a certain trend with aging process. Additionally, SNP enrichment analysis and functional annotation of cross-tissue regulatory elements to ESS36 revealed a high concentration of enhancer elements specific to shell gland and kidney tissues. This study, deepened our knowledge of eggshells and laying a valued scientific foundation for chicken molecular breeding. |
| first_indexed | 2024-03-08T02:03:20Z |
| format | Article |
| id | doaj.art-ff526a91f59f4ed8b4583ef966ef0f0c |
| institution | Directory Open Access Journal |
| issn | 0032-5791 |
| language | English |
| last_indexed | 2024-04-24T22:23:08Z |
| publishDate | 2024-04-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Poultry Science |
| spelling | doaj.art-ff526a91f59f4ed8b4583ef966ef0f0c2024-03-20T06:07:36ZengElsevierPoultry Science0032-57912024-04-011034103458Genetic patterns and genome-wide association analysis of eggshell quality traits of egg-type chicken across an extended laying periodXiaoman Chen0Xiaochang Li1Conghao Zhong2Xinwei Jiang3Guiqin Wu4Guangqi Li5Yiyuan Yan6Ning Yang7Congjiao Sun8State Key Laboratory of Animal Biotech Breeding, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing 100193, ChinaState Key Laboratory of Animal Biotech Breeding, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing 100193, ChinaState Key Laboratory of Animal Biotech Breeding, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing 100193, ChinaState Key Laboratory of Animal Biotech Breeding, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing 100193, ChinaBeijing Engineering Research Center of Layer, Beijing, 101206, ChinaBeijing Engineering Research Center of Layer, Beijing, 101206, ChinaBeijing Engineering Research Center of Layer, Beijing, 101206, ChinaState Key Laboratory of Animal Biotech Breeding, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing 100193, ChinaState Key Laboratory of Animal Biotech Breeding, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing 100193, China; Corresponding author:ABSTRACT: The industry of egg-type chicken has shown a trend of extending the rearing period, with the goal of breeding chicken breeds capable of producing 500 qualified eggs by 700 d of age. However, the rapid decline in eggshell quality during the late laying period is one of the major challenges. In this study, a total of 3,261 Rhode Island Red chickens were used to measure eggshell quality traits including eggshell strength (ESS), eggshell thickness (EST), eggshell color (ESC) and eggshell gloss (ESG) at seven age points ranging from 36 to 90 wk of age. Phenotypic variations increased with the aging process, especially during the late laying period (> 55 wk), and the heritability during this period decreased by 22.7 to 81.4% compared to the initial and peak laying periods. Then we performed genome-wide association study (GWAS) to identify the genomic variants that associated with eggshell quality, with a custom Illumina 50K BeadChip, named PhenoixChip-I. The results indicated that 2 genomic regions on GGA1(23.24-25.15Mb; 175.95-176.05 Mb) were significantly (P < 4.48E-06) or suggestively (P < 8.97E-05) associated with ESS, which can explain 9.59% and 0.48% of the phenotypic variations of ESS46 and ESS36, respectively. Three genes, FRY, PCNX2, and ENSGALG00000052468, were considered to be the candidate genes for ESS. For other traits, the genome-wide suggestive SNPs were identified at each age point, exhibiting a certain trend with aging process. Additionally, SNP enrichment analysis and functional annotation of cross-tissue regulatory elements to ESS36 revealed a high concentration of enhancer elements specific to shell gland and kidney tissues. This study, deepened our knowledge of eggshells and laying a valued scientific foundation for chicken molecular breeding.http://www.sciencedirect.com/science/article/pii/S0032579124000373chickeneggshell qualityGWASSNPfunctional annotation |
| spellingShingle | Xiaoman Chen Xiaochang Li Conghao Zhong Xinwei Jiang Guiqin Wu Guangqi Li Yiyuan Yan Ning Yang Congjiao Sun Genetic patterns and genome-wide association analysis of eggshell quality traits of egg-type chicken across an extended laying period Poultry Science chicken eggshell quality GWAS SNP functional annotation |
| title | Genetic patterns and genome-wide association analysis of eggshell quality traits of egg-type chicken across an extended laying period |
| title_full | Genetic patterns and genome-wide association analysis of eggshell quality traits of egg-type chicken across an extended laying period |
| title_fullStr | Genetic patterns and genome-wide association analysis of eggshell quality traits of egg-type chicken across an extended laying period |
| title_full_unstemmed | Genetic patterns and genome-wide association analysis of eggshell quality traits of egg-type chicken across an extended laying period |
| title_short | Genetic patterns and genome-wide association analysis of eggshell quality traits of egg-type chicken across an extended laying period |
| title_sort | genetic patterns and genome wide association analysis of eggshell quality traits of egg type chicken across an extended laying period |
| topic | chicken eggshell quality GWAS SNP functional annotation |
| url | http://www.sciencedirect.com/science/article/pii/S0032579124000373 |
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