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Sci Rep. 2017 Nov 9;7(1):15142. doi: 10.1038/s41598-017-15516-0.

Identification of selection signals by large-scale whole-genome resequencing of cashmere goats.

Li X1, Su R1,2,3,4,5, Wan W6, Zhang W1, Jiang H7, Qiao X1, Fan Y1, Zhang Y1,2,3,4, Wang R1,2,3,4, Liu Z1,2,3,4, Wang Z1,2,3,4, Liu B8, Ma Y9, Zhang H10, Zhao Q9, Zhong T10, Di R9, Jiang Y11, Chen W12,13, Wang W14, Dong Y15,16,17, Li J18,19,20,21.

Author information

1
College of Animal Science, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, 010018, China.
2
Key Laboratory of Animal Genetics, Breeding and Reproduction - Inner Mongolia Autonomous Region, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, 010018, China.
3
Key Laboratory of Mutton Sheep Genetics and Breeding, Ministry of Agriculture, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, 010018, China.
4
Engineering Research Center for Goat Genetics and Breeding - Inner Mongolia Autonomous Region, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, 010018, China.
5
State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China.
6
Center for Ecological and Environmental Sciences, Key Laboratory for Space Bioscience & Biotechnology, Northwestern Polytechnical University, Xi'an, Shaanxi, 710072, China.
7
College of Animal Science and Technology, Jilin Agricultural University, Changchun, Jilin, 130118, China.
8
Institute of Animal Husbandry, Academy of Agriculture and Stockbreeding Sciences, Hohhot, Inner Mongolia, 010030, China.
9
The Key Laboratory for Farm Animal Genetic Resources and Utilization of Ministry of Agriculture of China, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
10
Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China.
11
College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China.
12
College of Biological Big Data, Yunnan Agriculture University, Kunming, Yunnan, 650504, China.
13
Yunnan Research Institute for Local Plateau Agriculture and Industry, Kunming, Yunnan, 650201, China.
14
State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China. wwang@mail.kiz.ac.cn.
15
College of Biological Big Data, Yunnan Agriculture University, Kunming, Yunnan, 650504, China. loyalyang@163.com.
16
BGI-Shenzhen, Shenzhen, Guangdong, 518083, China. loyalyang@163.com.
17
Yunnan Research Institute for Local Plateau Agriculture and Industry, Kunming, Yunnan, 650201, China. loyalyang@163.com.
18
College of Animal Science, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, 010018, China. lijinquan_nd@126.com.
19
Key Laboratory of Animal Genetics, Breeding and Reproduction - Inner Mongolia Autonomous Region, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, 010018, China. lijinquan_nd@126.com.
20
Key Laboratory of Mutton Sheep Genetics and Breeding, Ministry of Agriculture, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, 010018, China. lijinquan_nd@126.com.
21
Engineering Research Center for Goat Genetics and Breeding - Inner Mongolia Autonomous Region, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, 010018, China. lijinquan_nd@126.com.

Abstract

Inner Mongolia and Liaoning cashmere goats are two outstanding Chinese multipurpose breeds that adapt well to the semi-arid temperate grassland. These two breeds are characterized by their soft cashmere fibers, thus making them great models to identify genomic regions that are associated with cashmere fiber traits. Whole-genome sequencing of 70 cashmere goats produced more than 5.52 million single-nucleotide polymorphisms and 710,600 short insertions and deletions. Further analysis of these genetic variants showed some population-specific molecular markers for the two cashmere goat breeds that are otherwise phenotypically similar. By analyzing F ST and θπ outlier values, we identified 135 genomic regions that were associated with cashmere fiber traits within the cashmere goat populations. These selected genomic regions contained genes, which are potential involved in the production of cashmere fiber, such as FGF5, SGK3, IGFBP7, OXTR, and ROCK1. Gene ontology enrichment analysis of identified short insertions and deletions also showed enrichment in keratinocyte differentiation and epidermal cell differentiation. These findings demonstrate that this genomic resource will facilitate the breeding of cashmere goat and other Capra species in future.

PMID:
29123196
PMCID:
PMC5680388
DOI:
10.1038/s41598-017-15516-0
[Indexed for MEDLINE]
Free PMC Article

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