Genome-wide diversity analysis for signatures of selection of Bos indicus adaptability under extreme agro-climatic conditions of temperate and tropical ecosystems

Q4 Biochemistry, Genetics and Molecular Biology

Animal Gene Pub Date : 2021-06-01 DOI:10.1016/j.angen.2021.200115

Shivam Bhardwaj , Sanjeev Singh , Indrajit Ganguly , A.K. Bhatia , Vijay K. Bharti , S.P. Dixit

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引用次数: 7

Abstract

Indigenous cattle breeds (Bos indicus) inhabited under diverse agroclimatic conditions may serve as a broad reservoir of genetic pool for identifying genes selected for local adaptation. The present study aimed at deciphering genomic diversity and identifying adaptation signatures of cattle breeds belonging to contrasting agro-climatic conditions: Siri and Ladakhi from cold hilly region; and Kankrej and Hallikar from hot arid and semi-arid regions, respectively. A total of 46 samples were genotyped using 777 K Illumina BovineHD BeadChip. The Principal Component Analysis brought together Hallikar and Kankrej, while Siri and Ladakhi formed a separate cluster. In contrast to the tropical cattle breeds, genetic variation was higher for temperate type. Linkage disequilibrium decay (r² < 0.2) in hot semi-arid/arid adapted (71–103 kb) and temperate-adapted (218–222 kb) breeds revealed that BovineHD BeadChip can be used in predicting their genomic breeding values. Runs of homozygosity and F_ST based selection signatures were also identified in these cattle breeds. Novel hypoxia-related genes viz. egl-9 family hypoxia inducible factor, hypoxia inducible factor 1 subunit alpha inhibitor and heme oxygenase 1 were detected in temperate adapted breeds, while heat stress (heat shock protein family H (Hsp110) member 1 and BAG cochaperone 2 and immunity (TANK binding kinase 1) related genes were identified in selection sweeps of tropical breeds. Gene ontology analysis identified several enriched terms for the genes in both hot semi-arid/arid and temperate adapted cattle breeds in ROH islands. The relevant adaptation signals found in the present study will help to establish new breeding opportunities with recognition of core genes.

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温带和热带极端农业气候条件下籼稻适应性选择特征的全基因组多样性分析

居住在不同农业气候条件下的土着牛品种(Bos indicus)可以作为一个广泛的基因库，用于识别为适应当地而选择的基因。本研究旨在解读不同农业气候条件下牛品种的基因组多样性和适应特征:来自寒冷丘陵地区的Siri和Ladakhi;Kankrej和Hallikar分别来自炎热干旱和半干旱地区。使用777 K Illumina BovineHD BeadChip对46份样本进行基因分型。主成分分析将Hallikar和Kankrej放在一起，而Siri和Ladakhi则形成了一个单独的集群。与热带品种相比，温带品种的遗传变异更高。热半干旱/干旱适应品种(71-103 kb)和温适应品种(218-222 kb)的连锁不平衡衰减(r2 < 0.2)表明，BovineHD BeadChip可用于预测其基因组育种价值。在这些牛品种中也发现了纯合子和基于FST的选择特征。在温带适应品种中发现了新的缺氧相关基因，即egl-9家族缺氧诱导因子、缺氧诱导因子1亚单位α抑制剂和血红素加氧酶1，而在热带品种的选择扫描中发现了热应激(热休克蛋白家族H (Hsp110)成员1和BAG合作蛋白2和免疫(TANK结合激酶1)相关基因。基因本体论分析发现了卢岛热半干旱/干旱和温带适应牛品种的几个基因富集项。本研究发现的相关适应信号将有助于建立新的育种机会，并识别核心基因。

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Animal Gene Agricultural and Biological Sciences-Insect Science

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期刊介绍： Gene Reports publishes papers that focus on the regulation, expression, function and evolution of genes in all biological contexts, including all prokaryotic and eukaryotic organisms, as well as viruses. Gene Reports strives to be a very diverse journal and topics in all fields will be considered for publication. Although not limited to the following, some general topics include: DNA Organization, Replication & Evolution -Focus on genomic DNA (chromosomal organization, comparative genomics, DNA replication, DNA repair, mobile DNA, mitochondrial DNA, chloroplast DNA). Expression & Function - Focus on functional RNAs (microRNAs, tRNAs, rRNAs, mRNA splicing, alternative polyadenylation) Regulation - Focus on processes that mediate gene-read out (epigenetics, chromatin, histone code, transcription, translation, protein degradation). Cell Signaling - Focus on mechanisms that control information flow into the nucleus to control gene expression (kinase and phosphatase pathways controlled by extra-cellular ligands, Wnt, Notch, TGFbeta/BMPs, FGFs, IGFs etc.) Profiling of gene expression and genetic variation - Focus on high throughput approaches (e.g., DeepSeq, ChIP-Seq, Affymetrix microarrays, proteomics) that define gene regulatory circuitry, molecular pathways and protein/protein networks. Genetics - Focus on development in model organisms (e.g., mouse, frog, fruit fly, worm), human genetic variation, population genetics, as well as agricultural and veterinary genetics. Molecular Pathology & Regenerative Medicine - Focus on the deregulation of molecular processes in human diseases and mechanisms supporting regeneration of tissues through pluripotent or multipotent stem cells.