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ARS Home » Northeast Area » Beltsville, Maryland (BARC) » Beltsville Agricultural Research Center » Animal Genomics and Improvement Laboratory » Research » Publications at this Location » Publication #374707
Research Project: Enhancing Genetic Merit of Ruminants Through Improved Genome Assembly, Annotation, and Selection

Location: Animal Genomics and Improvement Laboratory

Title: A LINE-1 derived promoter driving over-expression of the ASIP gene is responsible for white color in swamp buffalo

Author
item LIANG, DONG - China Agricultural University
item ZHAO, PENGJU - China Agricultural University
item SI, JINGFANG - China Agricultural University
item FANG, LINGZHAO - University Of Edinburgh
item XU, QING - Beijing Jiaotong University
item HOU, YALI - Chinese Academy Of Sciences
item HU, XIAOXIANG - China Agricultural University
item GONG, YU - Collaborator
item LIANG, ZHENGWEN - Collaborator
item TIAN, BING - Collaborator
item MAO, HUAMING - Yunnan Agricultural University
item YINDEE, MARNOCH - Mahidol University
item FARUQUE, MD - Bangladesh Agricultural Research Institute
item Liu, Ge - George
item WU, DONGDONG - Chinese Academy Of Sciences
item BARKER, J - University Of New England
item HAN, JIANLIN - International Livestock Research Institute (ILRI) - Kenya
item ZHANG, YI - China Agricultural University

Submitted to: Molecular Biology and Evolution
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/3/2020
Publication Date: 11/3/2020
Citation: Liang, D., Zhao, P., Si, J., Fang, L., Xu, Q., Hou, Y., Hu, X., Gong, Y., Liang, Z., Tian, B., Mao, H., Yindee, M., Faruque, M.O., Liu, G., Wu, D., Barker, J.S., Han, J., Zhang, Y. 2020. A LINE-1 derived promoter driving over-expression of the ASIP gene is responsible for white color in swamp buffalo. Molecular Biology and Evolution. 38(3):1122-1136. https://doi.org/10.1093/molbev/msaa279.
DOI: https://doi.org/10.1093/molbev/msaa279

Interpretive Summary: Animal skin color is a visible and variable traits. Using multiple methods, we discovered that a transposable element LINE-1 insertion in the ASIP gene is the causative mutation for the white color skin in swamp buffalo. These results fill our knowledge gaps and provide the first trait example in swamp buffalo with its underline molecular mechanism uncovered. Farmers, scientist, and policy planners who need improve animal health and production, as well as human health based on genomic data will benefit from this study.

Technical Abstract: Transposable elements (TEs) are a key source of genomic structural variation that have been shown to regulate gene functions responsible for some important phenotypes. Pigmentation provides visible phenotypes to explore the regulation of gene expression and the evolution of color patterns in animals. We have integrated sequence-based genome-wide association study (GWAS), long-read sequencing, whole-genome transcription sequencing (RNA-Seq) and gene function analyses to demonstrate that a 2,809-bp LINE-1 insertion in the ASIP gene is the causative mutation for the white color phenotype in swamp buffalo. The 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 and hairs. The 165-bp of 5’ UTR transcribed from the LINE-1 is spliced to coding exons and results in a chimeric transcript. The increased expression of ASIP completely prevents melanocyte maturation, leading to an absence of pigment in white buffalo skin and hairs. Phylogenetic analyses indicate that the white buffalo-specific ASIP allele originated by a recent transposition event in swamp buffalo.