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Title
Genomic Analysis Revealed a Convergent Evolution of LINE-1 in Coat Color: A Case Study in Water Buffaloes (Bubalus bubalis)
Fields of Research (FoR) 2008:
Author(s)
Liang, Dong
Zhao, Pengju
Si, Jingfang
Fang, Lingzhao
Pairo-Castineira, Erola
Hu, Xiaoxiang
Xu, Qing
Hou, Yali
Gong, Yu
Liang, Zhengwen
Tian, Bing
Mao, Huaming
Yindee, Marnoch
Faruque, Md Omar
Kongvongxay, Siton
Khamphoumee, Souksamlane
Liu, George E
Wu, Dong-Dong
Han, Jianlin
Zhang, Yi
Publication Date
2021-03
Socio-Economic Objective (SEO) 2008
Early Online Version
Open Access
Yes
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 <i>ASIP</i> (agouti signaling protein) gene is the causative mutation for the white coat phenotype in swamp buffalo (<i>Bubalus bubalis</i>). 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 <i>ASIP</i> in white buffalo skin. The 165 bp of 5' UTR transcribed from the LINE-1 is spliced into the first coding exon of <i>ASIP</i>, resulting in a chimeric transcript. The increased expression of <i>ASIP</i> prevents melanocyte maturation, leading to the absence of pigment in white buffalo skin and hairs. Phylogenetic analyses indicate that the white buffalo-specific <i>ASIP</i> allele originated from a recent genetic transposition event in swamp buffalo. Interestingly, as a similar LINE-1 insertion has been identified in the cattle <i>ASIP</i> gene, we discuss the convergent mechanism of coat color evolution in the Bovini tribe.
Publication Type
Journal Article
Source of Publication
Molecular Biology and Evolution, 38(3), p. 1122-1136
Publisher
Oxford University Press
Socio-Economic Objective (SEO) 2020
2020-11-03
Place of Publication
United States of America
ISSN
1537-1719
0737-4038
File(s) openpublished/GenomicBarker2021JournalArticle.pdf (1.13 MB)
Published version
Fields of Research (FoR) 2020
Socio-Economic Objective (SEO) 2020
Peer Reviewed
Yes
HERDC Category Description
Peer Reviewed
Yes
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