Whole genome resequencing analysis elucidate genetic features and signature of selection in binhu buffaloes

• Published in: Livestock science 2024-11, Vol.289, p.105587, Article 105587
• Main Authors: Zhang, Kunyu, Duan, Hongfeng, Li, Jianbo, Xu, Xiaoyu, Huan, Cheng, Ahmed, Zulfiqar, He, Fang, Luo, Yang, Zhang, Baizhong, Lei, Chuzhao, Yi, Kangle
• Format: Article
• Language: English
• Subjects: Binhu buffalo; fecundity; Genetic diversity; genetic variation; Genome; genomics; heat tolerance; immunity; labor; livestock; metabolism; nervous system; population structure; riparian areas; rivers; roughage; Selection traits; sequence analysis; swamps; vigor; weight gain
• ISSN: 1871-1413
• DOI: 10.1016/j.livsci.2024.105587

•Whole genome sequencing data revealed the population structure, genetic diversity, and selection characteristics of binhu buffaloes.•Binhu buffaloes was a swamp buffalo with relatively high genetic diversity.•Five methods for exploring candidate genes of binhu buffaloes.•ERCC3 and RAD51 are candidate genes for solving low reproductive of binhu buffaloes. : swamp buffaloes and riverine buffaloes. Binhu buffaloes (BB) are Chinese indigenous swamp buffaloes, characterized as strong body vigor, fit for durable work with docile nature. However, there is literature void regarding genomic architecture and selective sweeps analysis for this breed. Herein we utilized 20 newly whole genome sequences (WGS) of BB together with published WGS data of seventy-four buffaloes [Upper Yangtze (UY) buffaloes; n = 30, Middle-Lower Yangtze (MLY) buffaloes; (n = 30) and River buffaloes (RB); (n = 14)] to elucidate population structure, genetic diversity and selection characteristics of the BB. The results showed that the BB originated from swamp buffalos. The genetic diversity of the BB was lower than that of the RB and higher than that of the UY and the MLY buffaloes. In addition, employing five selective sweep detection methods numerous genes related to immunity (RELT, TP73, C5, CHMP1A, CDK10, ANKRD17), heat tolerance (DNAJB4, DNAJA1, HSF4, HELB, DNAJC28), growth (LYN, DYNC1I2, PLAG1, ADAMTSL3, CHKB, PDE1A, RXFP2), carcass and metabolism (SIRT6, LYPLA1, FADS1), nervous system (KIRREL3, AUTS2), and reproduction (SMG6, TSNAXIP1, CACNB2, ERCC3, RAD51, GDF9, CAMK4, KALRN, FANCA, SPIRE2, ATP2B1, AREG, EREG) were found to be under selection. Taken together, current investigation provides a genetic basis for the characteristics specific to the BB, such as high body strength; tolerance to roughage and easy to gain weight; docile nature; ability to endure labor; strong adaptability; and low fecundity and offers new ideas for the conservation, development and utilization of this breed.