A combination of genome-wide association study and selection signature analysis dissects the genetic architecture underlying bone traits in chickens

Y.D. Li; X. Liu; Z.W. Li; W.J. Wang; Y.M. Li; Z.P. Cao; P. Luan; F. Xiao; H.H Gao; H.S. Guo; N. Wang; H. Li; S.Z. Wang

Animal (Aug 2021)

A combination of genome-wide association study and selection signature analysis dissects the genetic architecture underlying bone traits in chickens

Y.D. Li,
X. Liu,
Z.W. Li,
W.J. Wang,
Y.M. Li,
Z.P. Cao,
P. Luan,
F. Xiao,
H.H Gao,
H.S. Guo,
N. Wang,
H. Li,
S.Z. Wang

Affiliations

Y.D. Li: Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Harbin 150030, PR China; Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin 150030, PR China; College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, PR China
X. Liu: Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Harbin 150030, PR China; Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin 150030, PR China; College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, PR China
Z.W. Li: Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Harbin 150030, PR China; Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin 150030, PR China; College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, PR China
W.J. Wang: Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Harbin 150030, PR China; Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin 150030, PR China; College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, PR China
Y.M. Li: Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Harbin 150030, PR China; Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin 150030, PR China; College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, PR China
Z.P. Cao: Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Harbin 150030, PR China; Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin 150030, PR China; College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, PR China
P. Luan: Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Harbin 150030, PR China; Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin 150030, PR China; College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, PR China
F. Xiao: Fujian Sunnzer Biotechnology Development Co., Ltd, Guangze, Fujian Province 354100, PR China
H.H Gao: Fujian Sunnzer Biotechnology Development Co., Ltd, Guangze, Fujian Province 354100, PR China
H.S. Guo: Fujian Sunnzer Biotechnology Development Co., Ltd, Guangze, Fujian Province 354100, PR China
N. Wang: Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Harbin 150030, PR China; Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin 150030, PR China; College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, PR China
H. Li: Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Harbin 150030, PR China; Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin 150030, PR China; College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, PR China
S.Z. Wang: Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Harbin 150030, PR China; Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin 150030, PR China; College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, PR China; Corresponding author at: Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Harbin 150030, PR China.

Journal volume & issue: Vol. 15, no. 8
p. 100322

Abstract

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The bones of chicken play an important role in supporting and protecting the body. The growth and development of bones have a substantial influence on the health and production performance in chickens. However, genetic architecture underlying chicken bone traits is not well understood. The objectives of this study are to dissect the genetic basis of bone traits in chickens and to identify valuable genes and genetic markers for chicken breeding. We performed a combination of genome-wide association study (GWAS) and selection signature analysis (fixation index values and nucleotide diversity ratios) in an F2 crossbred experimental population with different genetic backgrounds (broiler × layer) to identify candidate genes and significant variants related to femur, shank, keel length, chest width, metatarsal claw weight, metatarsal length, and metatarsal circumference. A total of 545 individuals were genotyped based on the whole genome re-sequencing method (26 F0 individuals were re-sequenced at 10 × coverage; 519 F2 individuals were re-sequenced at 3 × coverage). A total of 2 028 112 single-nucleotide polymorphisms (SNPs) remained to carry out analysis after quality control and imputation. The integration of GWAS and selection signature analysis indicated that all significant SNPs responsible for bone traits were mainly localized on chicken chromosomes 1, 4, and 27. Finally, we identified 21 positional candidate genes that might regulate chicken bone growth and development, including LRCH1, RB1, FNDC3A, MLNR, CAB39L, FOXO1, LHFP, TRPC4, POSTN, SMAD9, RBPJ, PPARGC1A, SLIT2, NCAPG, NKX3-2, CPZ, SPOP, NGFR, SOST, ZNF652, and HOXB3. Additionally, an array of uncharacterized genes was identified. The findings provide an in-depth understanding of the genetic architecture of chicken bone traits and offer a molecular basis for applying genomics in practical chicken breeding.

Published in Animal

ISSN: 1751-7311 (Print); 1751-732X (Online)
Publisher: Elsevier
Country of publisher: Netherlands
LCC subjects: Agriculture: Animal culture
Website: https://www.journals.elsevier.com/animal/

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