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

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.