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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] [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.
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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.
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Li C, Li M, Li X, Ni W, Xu Y, Yao R, Wei B, Zhang M, Li H, Zhao Y, Liu L, Ullah Y, Jiang Y, Hu S. Whole-Genome Resequencing Reveals Loci Associated With Thoracic Vertebrae Number in Sheep. Front Genet 2019; 10:674. [PMID: 31379930 PMCID: PMC6657399 DOI: 10.3389/fgene.2019.00674] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Accepted: 06/27/2019] [Indexed: 12/31/2022] Open
Abstract
The number of vertebrae, especially thoracic vertebrae, is an important economic trait that may influence carcass length and meat production in animals. However, the genetic basis of vertebrae number in sheep is still poorly understood. To detect the candidate genes, 400 increased number of thoracic vertebrae (T14L6) and 200 normal (T13L6) Kazakh sheep were collected. We generated and sequenced 60 pools of genomic DNA (each pool prepared by mixing genomic DNA from 10 sheep with the same thoracic traits), with an average depth of coverage of 25.65×. We identified a total of 42,075,402 SNPs and 11 putatively selected genomic regions, including the VRTN gene and the HoxA gene family that regulate vertebral development. The most prominent areas of selective elimination were located in a region of chromosome 7, including VRTN, which regulates spinal development and morphology. Further investigation indicated that the expression level of the VRTN gene during fetal development was significantly higher in sheep with more thoracic vertebrae than in those with a normal number of thoracic vertebrae. A genome-wide comparison between sheep with increased and normal numbers of thoracic vertebrae showed that the VRTN gene is the major selection locus for the number of thoracic vertebrae in sheep and has the potential to be utilized in sheep breeding in the future.
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Affiliation(s)
- Cunyuan Li
- College of Life Sciences, Shihezi University, Shihezi, China.,College of Animal Science and Technology, Shihezi University, Shihezi, China
| | - Ming Li
- College of Animal Science and Technology, Northwest A&F University, Xianyang, China
| | - Xiaoyue Li
- College of Life Sciences, Shihezi University, Shihezi, China
| | - Wei Ni
- College of Life Sciences, Shihezi University, Shihezi, China
| | - Yueren Xu
- College of Life Sciences, Shihezi University, Shihezi, China
| | - Rui Yao
- College of Life Sciences, Shihezi University, Shihezi, China
| | - Bin Wei
- College of Animal Science and Technology, Northwest A&F University, Xianyang, China
| | - Mengdan Zhang
- College of Life Sciences, Shihezi University, Shihezi, China
| | - Huixiang Li
- College of Life Sciences, Shihezi University, Shihezi, China
| | - Yue Zhao
- College of Animal Science and Technology, Northwest A&F University, Xianyang, China
| | - Li Liu
- College of Life Sciences, Shihezi University, Shihezi, China
| | - Yaseen Ullah
- College of Life Sciences, Shihezi University, Shihezi, China
| | - Yu Jiang
- College of Animal Science and Technology, Northwest A&F University, Xianyang, China
| | - Shengwei Hu
- College of Life Sciences, Shihezi University, Shihezi, China
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Abstract
The main goal of this chapter was to review the state of the art in the recent advances in sheep and goat meat products research. Research and innovation have been playing an important role in sheep and goat meat production and meat processing as well as food safety. Special emphasis will be placed on the imaging and spectroscopic methods for predicting body composition, carcass and meat quality. The physicochemical and sensory quality as well as food safety will be referenced to the new sheep and goat meat products. Finally, the future trends in sheep and goat meat products research will be pointed out.
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