1
|
Zhang D, Zhang X, Li F, Liu T, Hu Z, Gao N, Yuan L, Li X, Zhao Y, Zhao L, Zhang Y, Xu D, Song Q, Cheng J, Wang W. Whole-genome resequencing identified candidate genes associated with the number of ribs in Hu sheep. Genomics 2021; 113:2077-2084. [PMID: 33965549 DOI: 10.1016/j.ygeno.2021.05.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 04/12/2021] [Accepted: 05/04/2021] [Indexed: 10/21/2022]
Abstract
The number of ribs is an important economic trait in the sheep industry when the sheep are raised for mutton. However, in sheep, the genetic mechanisms regulating rib number are poorly understood. In the present study, we aimed to identify important candidate genes that affect the increase in rib number in sheep. Whole-genome resequencing of 36 Hu sheep with an increased number of ribs (R14) and 36 sheep with normal (R13) rib numbers was carried out. Analysis using three methods (fixation index (FST), Fisher's exact test, and Chi-squared test) showed that 219 single nucleotide polymorphism sites overlapped among the results of the three methods, which represented 206 genes. Gene ontology and Kyoto Encyclopedia of Genes and Genomes analyses indicated that the genes were mainly associated with regulation of developmental process, inorganic anion transport, cellular biosynthetic process, tight junction, the oxytocin signaling pathway, and arrhythmogenic right ventricular cardiomyopathy. Four mutations were selected according to the significantly selected genomic regions and important pathways for genotyping and association analysis. The result demonstrated that three synonymous mutations correlated significantly with the rib number. Importantly, we revealed that the CPOX (encoding coproporphyrinogen oxidase), KCNH1 (encoding potassium voltage-gated channel subfamily H member 1), and CPQ (encoding carboxypeptidase Q) genes have a combined effect on rib number in Hu sheep. Our results identified candidate molecular markers for rib number in sheep breeding.
Collapse
Affiliation(s)
- Deyin Zhang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Xiaoxue Zhang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Fadi Li
- Engineering Laboratory of Sheep Breeding and Reproduction Biotechnology in Gansu Province, Minqin 733300, China; The State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China
| | - Teng Liu
- Suzhou Zelgen Biopharmaceuticals Co., Ltd., Kunshan, Jiangsu 215300, China
| | - Zhihong Hu
- Changxing Yongsheng Animal Husbandry Co. Ltd., Huzhou, Zhejiang 313100, China
| | - Ning Gao
- Changxing Yongsheng Animal Husbandry Co. Ltd., Huzhou, Zhejiang 313100, China
| | - Lvfeng Yuan
- Engineering Laboratory of Sheep Breeding and Reproduction Biotechnology in Gansu Province, Minqin 733300, China
| | - Xiaolong Li
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Yuan Zhao
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Liming Zhao
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Yukun Zhang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Dan Xu
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Qizhi Song
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Jiangbo Cheng
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Weimin Wang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China.
| |
Collapse
|