Genomic analysis of GBS data reveals genes associated with facial pigmentation in Xinyang blue-shelled layers

Haobin Hou; Xiaoliang Wang; Caiyun Zhang; Yingying Tu; Wenwei Lv; Xia Cai; Zhigang Xu; Junfeng Yao; Changsuo Yang

doi:10.5194/aab-63-483-2020

Genomic analysis of GBS data reveals genes associated with facial pigmentation in Xinyang blue-shelled layers

Arch Anim Breed. 2020 Dec 18;63(2):483-491. doi: 10.5194/aab-63-483-2020. eCollection 2020.

Authors

Haobin Hou^#^{1

2}, Xiaoliang Wang^#^{1

2}, Caiyun Zhang², Yingying Tu², Wenwei Lv², Xia Cai^{1

2}, Zhigang Xu³, Junfeng Yao^{1

2}, Changsuo Yang^{1

2}

Affiliations

¹ Shanghai Academy of Agricultural Sciences, Shanghai 201106, China.
² National Poultry Engineer Research Center, Shanghai 201106, China.
³ Shanghai Poultry Breeding Co., Ltd., Shanghai 201100, China.

^# Contributed equally.

Abstract

Facial pigmentation is an important economic trait of chickens, especially for laying hens, which will affect the carcass appearance of eliminated layers. Therefore, identifying the genomic regions and exploring the function of this region that contributes to understanding the variation of skin color traits is significant for breeding. In the study, 291 pure-line Xinyang blue-shelled laying hens were selected, of which 75 were dark-faced chickens and 216 were white-faced chickens. The population was sequenced and typed by GBS genotyping technology. The obtained high-quality SNPs and pigmentation phenotypes were analyzed by a genome-wide association study (GWAS) and a $F_{ST}$ scan. Based on the two analytical methods, we identified a same genomic region (10.70-11.60 Mb) on chromosome 20 with 68 significant SNPs ( $- log⁡ 10 (P) > 6$ ), mapped to 10 known genes, including NPEPL1, EDN3, GNAS, C20orf85, VAPB, BMP7, TUBB1, ELMO2, DDX27, and NCOA5, which are associated with dermal hyperpigmentation.