Article

Genomic Analysis Revealed a Convergent Evolution of LINE-1 in Coat Color: A Case Study in Water Buffaloes (<i>Bubalus bubalis</i>)

Dong LiangNational Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics and Breeding and Reproduction of MOAR, College of Animal Science and Technology, China Agricultural University, Beijing, ChinaPengju ZhaoNational Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics and Breeding and Reproduction of MOAR, College of Animal Science and Technology, China Agricultural University, Beijing, ChinaJingfang SiNational Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics and Breeding and Reproduction of MOAR, College of Animal Science and Technology, China Agricultural University, Beijing, ChinaLingzhao FangMedical Research Council Human Genetics Unit at the Medical Research Council Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United KingdomErola Pairo‐CastineiraMedical Research Council Human Genetics Unit at the Medical Research Council Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United KingdomXiaoxiang HuState Key Laboratory of AgroBiotechnology, College of Biological Sciences, China Agricultural University, Beijing, ChinaQing XuCollege of Life Sciences and Bioengineering, Beijing Jiaotong University, Beijing, ChinaYali HouBeijing Institute of Genomics, Chinese Academy of Sciences, Beijing, ChinaYu GongZhengwen LiangBin TianHuaming MaoCollege of Animal Science and Technology, Yunnan Agricultural University, Kunming, ChinaMarnoch YindeeAkkhararatchakumari Veterinary College (AVC), Walailak University, Nakorn Si Thammarat, ThailandMd. Omar FaruqueDepartment of Animal Breeding and Genetics, Bangladesh Agricultural University, Mymensingh, BangladeshSiton KongvongxayLivestock Research Center, National Agriculture and Forestry Research Institute, Ministry of Agriculture and Forestry, Vientiane, Lao PDRSouksamlane KhamphoumeeLivestock Research Center, National Agriculture and Forestry Research Institute, Ministry of Agriculture and Forestry, Vientiane, Lao PDRGeorge E. LiuAnimal Genomics and Improvement Laboratory, Henry A. Wallace Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, MDDong‐Dong WuKunming Institute of Zoology, Chinese Academy of Sciences, Kunming, ChinaJ. S. F. BarkerSchool of Environmental and Rural Science, University of New England, Armidale, NSW, AustraliaJianlin HanCAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, ChinaYi ZhangNational Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics and Breeding and Reproduction of MOAR, College of Animal Science and Technology, China Agricultural University, Beijing, China

Molecular Biology and Evolutionjournal2020en

ABI

Abstract

Visible pigmentation phenotypes can be used to explore the regulation of gene expression and the evolution of coat color patterns in animals. Here, we performed whole-genome and RNA sequencing and applied genome-wide association study, comparative population genomics and biological experiments to show that the 2,809-bp-long LINE-1 insertion in the ASIP (agouti signaling protein) gene is the causative mutation for the white coat phenotype in swamp buffalo (Bubalus bubalis). This LINE-1 insertion (3' truncated and containing only 5' UTR) functions as a strong proximal promoter that leads to a 10-fold increase in the transcription of ASIP in white buffalo skin. The 165 bp of 5' UTR transcribed from the LINE-1 is spliced into the first coding exon of ASIP, resulting in a chimeric transcript. The increased expression of ASIP prevents melanocyte maturation, leading to the absence of pigment in white buffalo skin and hairs. Phylogenetic analyses indicate that the white buffalo-specific ASIP allele originated from a recent genetic transposition event in swamp buffalo. Interestingly, as a similar LINE-1 insertion has been identified in the cattle ASIP gene, we discuss the convergent mechanism of coat color evolution in the Bovini tribe.

Topics

melanin and skin pigmentation Animal Genetics and Reproduction Genetic and phenotypic traits in livestock

Identifiers

DOI: 10.1093/molbev/msaa279

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