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

IF 1.8 3区农林科学 Q2 AGRICULTURE, DAIRY & ANIMAL SCIENCE Livestock Science Pub Date : 2024-11-01 DOI:10.1016/j.livsci.2024.105587

Kunyu Zhang , Hongfeng Duan , Jianbo Li , Xiaoyu Xu , Cheng Huan , Zulfiqar Ahmed , Fang He , Yang Luo , Baizhong Zhang , Chuzhao Lei , Kangle Yi

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Abstract

The world's buffaloes are primarily divided into two main categories

: 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.

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全基因组重测序分析阐明了滨湖水牛的遗传特征和选择特征

世界上的水牛主要分为两大类：沼泽水牛和河流水牛。滨湖水牛（BB）是中国土生土长的沼泽水牛，具有体格健壮、耐劳、性情温顺的特点。然而，有关该品种的基因组结构和选择性扫描分析的文献尚属空白。在此，我们利用20个新的BB全基因组序列（WGS）和已发表的74头水牛的WGS数据[长江上游（UY）水牛；n = 30，长江中下游（MLY）水牛；（n = 30）和江河水牛（RB）；（n = 14）]来阐明BB的种群结构、遗传多样性和选择特征。结果表明，BB源于沼泽水牛。BB 的遗传多样性低于 RB，高于 UY 和 MLY 水牛。此外，采用五种选择性扫查方法检测了与免疫（RELT、TP73、C5、CHMP1A、CDK10、ANKRD17）、耐热（DNAJB4、DNAJA1、HSF4、HELB、DNAJC28）、生长（LYN、DYNC1I2、PLAG1、ADAMTSL3、CHKB、PDE1A、RXFP2）、胴体和新陈代谢（SIRT6、LYPLA1、FADS1）、神经系统（KIRREL3、AUTS2）和生殖（SMG6、TSNAXIP1、CACNB2、ERCC3、RAD51、GDF9、CAMK4、KALRN、FANCA、SPIRE2、ATP2B1、AREG、EREG）均在选择范围之内。综上所述，目前的研究为 BB 牛体力强、耐粗饲料、易增重、性情温顺、耐劳、适应性强、繁殖力低等特性提供了遗传学依据，为该品种的保护、开发和利用提供了新思路。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Livestock Science 农林科学-奶制品与动物科学

CiteScore

4.30

自引率

5.60%

发文量

237

审稿时长

3 months

期刊介绍： Livestock Science promotes the sound development of the livestock sector by publishing original, peer-reviewed research and review articles covering all aspects of this broad field. The journal welcomes submissions on the avant-garde areas of animal genetics, breeding, growth, reproduction, nutrition, physiology, and behaviour in addition to genetic resources, welfare, ethics, health, management and production systems. The high-quality content of this journal reflects the truly international nature of this broad area of research.