Whole genome resequencing reveals genomic regions related to red plumage in ducks

Xinye Zhang; Fangxi Yang; Tao Zhu; Xiurong Zhao; Jinxin Zhang; Junhui Wen; Yalan Zhang; Gang Wang; Xufang Ren; Anqi Chen; Xue Wang; Liang Wang; Xueze Lv; Weifang Yang; Changqing Qu; Huie Wang; Zhonghua Ning; Lujiang Qu

Poultry Science (Jun 2024)

Whole genome resequencing reveals genomic regions related to red plumage in ducks

Xinye Zhang,
Fangxi Yang,
Tao Zhu,
Xiurong Zhao,
Jinxin Zhang,
Junhui Wen,
Yalan Zhang,
Gang Wang,
Xufang Ren,
Anqi Chen,
Xue Wang,
Liang Wang,
Xueze Lv,
Weifang Yang,
Changqing Qu,
Huie Wang,
Zhonghua Ning,
Lujiang Qu

Affiliations

Xinye Zhang: Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
Fangxi Yang: Beijing Nankou Duck Breeding Technology Co., Ltd., Beijing, China
Tao Zhu: Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
Xiurong Zhao: Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
Jinxin Zhang: Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
Junhui Wen: Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
Yalan Zhang: Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
Gang Wang: Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
Xufang Ren: Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
Anqi Chen: Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
Xue Wang: VVBK Animal Medical Diagnostic Technology (Beijing) Co., Ltd, Daxing District, Beijing, China
Liang Wang: Beijing Municipal General Station of Animal Science, Beijing, China
Xueze Lv: Beijing Municipal General Station of Animal Science, Beijing, China
Weifang Yang: Beijing Municipal General Station of Animal Science, Beijing, China
Changqing Qu: Engineering Technology Research Center of Anti-aging Chinese Herbal Medicine of Anhui Province, Fuyang Normal University, Fuyang, China
Huie Wang: College of Animal Science, Tarim University, Xinjiang, China
Zhonghua Ning: Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
Lujiang Qu: Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; Corresponding author:

Journal volume & issue: Vol. 103, no. 6
p. 103694

Abstract

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ABSTRACT: Plumage color is a characteristic trait of ducks that originates as a result of natural and artificial selection. As a conspicuous phenotypic feature, it is a breed characteristic. Previous studies have identified some genes associated with the formation of black and white plumage in ducks. However, studies on the genetic basis underlying the red plumage phenotype in ducks are limited. Here, genome-wide association analysis (GWAS) and selection signal detection (Fst, θπ ratio, and cross-population composite likelihood ratio [XP-CLR]) were conducted to identify candidate regions and genes underlying duck plumage color phenotype. Selection signal detection revealed 29 overlapping genes (including ENPP1 and ULK1) significantly associated with red plumage color in Ji'an Red ducks. ENSAPLG00000012679, ESRRG, and SPATA5 were identified as candidate genes associated with red plumage using GWAS. Selection signal detection revealed that 19 overlapping genes (including GMDS, PDIA6, and ODC1) significantly correlated with light brown plumage in Brown Tsaiya ducks. GWAS to narrow down the significant regions further revealed nine candidate genes (AKT1, ATP6V1C2, GMDS, LRP4, MAML3, PDIA6, PLD5, TMEM63B, and TSPAN8). Notably, in Brown Tsaiya ducks, GMDS, ODC1, and PDIA6 exhibit significantly differentiated allele frequencies among other feather-colored ducks, while in Ji'an Red ducks, ENSAPLG00000012679 has different allele frequency distributions compared with that in other feather-colored ducks. This study offers new insights into the variation and selection of the red plumage phenotype using GWAS and selective signals.

Published in Poultry Science

ISSN: 0032-5791 (Print); 1525-3171 (Online)
Publisher: Elsevier
Country of publisher: United States
LCC subjects: Agriculture: Animal culture
Website: https://www.journals.elsevier.com/poultry-science

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