Whole-genome resequencing identified candidate genes associated with the number of ribs in Hu sheep

Deyin Zhang; Xiaoxue Zhang; Fadi Li; Teng Liu; Zhihong Hu; Ning Gao; Lvfeng Yuan; Xiaolong Li; Yuan Zhao; Liming Zhao; Yukun Zhang; Dan Xu; Qizhi Song; Jiangbo Cheng; Weimin Wang

doi:10.1016/j.ygeno.2021.05.004

Whole-genome resequencing identified candidate genes associated with the number of ribs in Hu sheep

Genomics. 2021 Jul;113(4):2077-2084. doi: 10.1016/j.ygeno.2021.05.004. Epub 2021 May 11.

Authors

Deyin Zhang¹, Xiaoxue Zhang¹, Fadi Li², Teng Liu³, Zhihong Hu⁴, Ning Gao⁴, Lvfeng Yuan⁵, Xiaolong Li¹, Yuan Zhao¹, Liming Zhao¹, Yukun Zhang¹, Dan Xu¹, Qizhi Song¹, Jiangbo Cheng¹, Weimin Wang⁶

Affiliations

¹ College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China.
² 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.
³ Suzhou Zelgen Biopharmaceuticals Co., Ltd., Kunshan, Jiangsu 215300, China.
⁴ Changxing Yongsheng Animal Husbandry Co. Ltd., Huzhou, Zhejiang 313100, China.
⁵ Engineering Laboratory of Sheep Breeding and Reproduction Biotechnology in Gansu Province, Minqin 733300, China.
⁶ College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China. Electronic address: wangwm@gsau.edu.cn.

PMID: 33965549
DOI: 10.1016/j.ygeno.2021.05.004

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 (F_ST), 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.

Keywords: Association analysis; CPOX; CPQ; Genomic analysis; KCNH1; Rib number.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Animals
Genome*
Genome-Wide Association Study
Phenotype
Polymorphism, Single Nucleotide*
Ribs
Sheep / genetics