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Deng M, Qiu Z, Liu C, Zhong L, Fan X, Han Y, Wang R, Li P, Huang R, Zhao Q. Genome-wide association analysis revealed new QTL and candidate genes affecting the teat number in Dutch Large White pigs. Anim Genet 2024; 55:206-216. [PMID: 38191772 DOI: 10.1111/age.13397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 11/07/2023] [Accepted: 12/27/2023] [Indexed: 01/10/2024]
Abstract
Teat number (TNUM) is an important reproductive trait of sows, which affects the weaning survival rate of piglets. In this study, 1166 Dutch Large White pigs with TNUM phenotype were used as the research object. These pigs were genotyped by 50K SNP chip and the chip data were further imputed to the resequencing level. The estimated heritabilities of left teat number (LTN), right teat number (RTN) and total teat number (TTN) were 0.21, 0.19 and 0.3, respectively. Based on chip data, significant SNPs for RTN on SSC2, SSC5, SSC9 and SSC13 were identified using genome-wide association analysis (GWAS). Significant SNPs for TTN were identified on SSC2, SSC5 and SSC7. Based on imputed data, the GWAS identified a significant SNP (rs329158522) for LTN on SSC17, two significant SNPs (rs342855242 and rs80813115) for RTN on SSC2 and SSC9, and two significant SNPs (rs327003548 and rs326943811) for TTN on SSC5 and SSC6. Among them, four novel QTL were discovered. The Bayesian fine-mapping method was used to fine map the QTL identified in the GWAS of the imputed data, and the confidence intervals of QTL affecting LTN (SSC17: 45.22-46.20 Mb), RTN (SSC9: 122.18-122.80 Mb) and TTN (SSC5: 14.01-15.91 Mb, SSC6: 120.06-121.25 Mb) were detected. A total of 52 candidate genes were obtained. Furthermore, we identified five candidate genes, WNT10B, AQP5, FMNL3, NUAK1 and CKAP4, for the first time, which involved in breast development and other related functions by gene annotation. Overall, this study provides new molecular markers for the breeding of teat number in pigs.
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Affiliation(s)
- Michao Deng
- Key Laboratory in Nanjing for Evaluation and Utilization of Pigs Resources, Institute of Swine Science, Nanjing Agricultural University, Nanjing, China
| | - Zijian Qiu
- Key Laboratory in Nanjing for Evaluation and Utilization of Pigs Resources, Institute of Swine Science, Nanjing Agricultural University, Nanjing, China
| | - Chenxi Liu
- Key Laboratory in Nanjing for Evaluation and Utilization of Pigs Resources, Institute of Swine Science, Nanjing Agricultural University, Nanjing, China
| | - Lijing Zhong
- Jiangsu Lihua Animal Husbandry Co., Ltd, Changzhou, China
| | - Xinfeng Fan
- Jiangsu Lihua Animal Husbandry Co., Ltd, Changzhou, China
| | - Yuquan Han
- Key Laboratory in Nanjing for Evaluation and Utilization of Pigs Resources, Institute of Swine Science, Nanjing Agricultural University, Nanjing, China
| | - Ran Wang
- Key Laboratory in Nanjing for Evaluation and Utilization of Pigs Resources, Institute of Swine Science, Nanjing Agricultural University, Nanjing, China
| | - Pinghua Li
- Key Laboratory in Nanjing for Evaluation and Utilization of Pigs Resources, Institute of Swine Science, Nanjing Agricultural University, Nanjing, China
- Huaian Academy, Nanjing Agricultural University, Huaian, China
| | - Ruihua Huang
- Key Laboratory in Nanjing for Evaluation and Utilization of Pigs Resources, Institute of Swine Science, Nanjing Agricultural University, Nanjing, China
- Huaian Academy, Nanjing Agricultural University, Huaian, China
| | - Qingbo Zhao
- Key Laboratory in Nanjing for Evaluation and Utilization of Pigs Resources, Institute of Swine Science, Nanjing Agricultural University, Nanjing, China
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