全基因组比较分析凸显了 Chilika 水牛适应盐碱环境的选择特征。

IF 2.5 4区 生物学 Q3 CELL BIOLOGY
Physiological genomics Pub Date : 2024-09-01 Epub Date: 2024-07-01 DOI:10.1152/physiolgenomics.00028.2024
Utsav Surati, Saket K Niranjan, Rakesh Kumar Pundir, Ymberzal Koul, Vikas Vohra, Ravi Kumar Gandham, Amod Kumar
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引用次数: 0

摘要

奇利卡水牛是印度东海岸的土生水牛品种,主要分布在与孟加拉湾相连的奇利卡咸水湖周围。该品种水牛具有一种独特的能力,能深入咸水湖中,并在那里以当地的盐碱植被为食。对盐度的适应是一种遗传现象,然而,动物(尤其是家畜)耐盐性的遗传基础仍然有限。本研究探讨了奇利卡水牛适应严酷盐碱环境(水和食物系统)的遗传进化过程。本研究收集了 18 头 Chilika 水牛和 10 头正常栖息地 Murrah 水牛的全基因组重测序数据。为了识别选择扫描,采用了种群内和种群间统计方法。利用核苷酸多样性(θπ)、Tajima's D、核苷酸多样性比(θπ-ratio)和 FST 方法,在 Chilika 水牛中分别检测到 709、309、468 和 354 个基因存在选择横扫。进一步的分析表明,在所有方法中,共有包括 EXOC6B、VPS8、LYPD1、VPS35、CAMKMT、NCKAP5、COMMD1、MYLK3、B3GNT2 在内的 23 个基因被发现具有共性。此外,对已鉴定基因的功能注释研究提供了一些通路,如 MAPK 信号、肾素分泌、内吞、催产素信号通路等。基因网络分析列出了枢纽基因,为了解这些基因之间的相互作用提供了线索。总之,本研究强调了盐碱环境下 Chilika 水牛局部适应功能的遗传基础。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
Genome-wide comparative analyses highlight selection signatures underlying saline adaptation in Chilika buffalo.

Chilika, a native buffalo breed of the Eastern coast of India, is mainly distributed around the Chilika brackish water lake connected with the Bay of Bengal Sea. This breed possesses a unique ability to delve deep into the salty water of the lake and stay there to feed on local vegetation of saline nature. Adaptation to salinity is a genetic phenomenon; however, the genetic basis underlying salinity tolerance is still limited in animals, specifically in livestock. The present study explores the genetic evolution that unveils the Chilika buffalo's adaptation to the harsh saline habitat, including both water and food systems. For this study, whole genome resequencing data on 18 Chilika buffalo and for comparison 10 Murrah buffalo of normal habitat were generated. For identification of selection sweeps, intrapopulation and interpopulation statistics were used. A total of 709, 309, 468, and 354 genes were detected to possess selection sweeps in Chilika buffalo using the nucleotide diversity (θπ), Tajima's D, nucleotide diversity ratio (θπ-ratio), and FST methods, respectively. Further analysis revealed a total of 23 genes including EXOC6B, VPS8, LYPD1, VPS35, CAMKMT, NCKAP5, COMMD1, myosin light chain kinase 3 (MYLK3), and B3GNT2 were found to be common by all the methods. Furthermore, functional annotation study of identified genes provided pathways such as MAPK signaling, renin secretion, endocytosis, oxytocin signaling pathway, etc. Gene network analysis enlists that hub genes provide insights into their interactions with each other. In conclusion, this study has highlighted the genetic basis underlying the local adaptive function of Chilika buffalo under saline environment.NEW & NOTEWORTHY Indian Chilika buffaloes are being maintained on extensive grazing system and have a unique ability to convert local salty vegetation into valuable human food. However, adaptability to saline habitat of Chilika buffalo has not been explored to date. Here, we identified genes and biological pathways involved, such as MAPK signaling, renin secretion, endocytosis, and oxytocin signaling pathway, underlying adaptability of Chilika buffalo to saline environment. This investigation shed light on the mechanisms underlying the buffalo's resilience in its native surroundings.

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来源期刊
Physiological genomics
Physiological genomics 生物-生理学
CiteScore
6.10
自引率
0.00%
发文量
46
审稿时长
4-8 weeks
期刊介绍: The Physiological Genomics publishes original papers, reviews and rapid reports in a wide area of research focused on uncovering the links between genes and physiology at all levels of biological organization. Articles on topics ranging from single genes to the whole genome and their links to the physiology of humans, any model organism, organ, tissue or cell are welcome. Areas of interest include complex polygenic traits preferably of importance to human health and gene-function relationships of disease processes. Specifically, the Journal has dedicated Sections focused on genome-wide association studies (GWAS) to function, cardiovascular, renal, metabolic and neurological systems, exercise physiology, pharmacogenomics, clinical, translational and genomics for precision medicine, comparative and statistical genomics and databases. For further details on research themes covered within these Sections, please refer to the descriptions given under each Section.
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