Identification of important genomic footprints using eight different selection signature statistics in domestic cattle breeds

Rajawat, Divya; Panigrahi, Manjit; Kumar, Harshit; Nayak, Sonali Sonejita; Parida, Subhashree; Bhushan, Bharat; Gaur, Gyanendra Kumar; Dutt, Triveni; Mishra, Bishnu Prasad

doi:10.1016/j.gene.2021.146165

Cited by 35 publications

(16 citation statements)

References 104 publications

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“…This gene produces a protein found in melanocytes and neurons related to melanin-producing cells from the neural crest in the epidermis of the skin ( Zhang et al, 2021 ). Several SNPs within the MYO5A gene have been linked to heat tolerance in cattle ( Jia et al, 2019 ; Rajawat et al, 2022 ). The link between MYO5A and heat tolerance may be due to its role in pigmentation.…”

Section: Discussionmentioning

confidence: 99%

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Genome-wide analysis identified candidate variants and genes associated with heat stress adaptation in Egyptian sheep breeds

Aboul-Naga¹,

Alsamman

Allali

et al. 2022

Front. Genet.

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Heat stress caused by climatic changes is one of the most significant stresses on livestock in hot and dry areas. It has particularly adverse effects on the ability of the breed to maintain homeothermy. Developing countries are advised to protect and prepare their animal resources in the face of potential threats such as climate change. The current study was conducted in Egypt’s three hot and dry agro-ecological zones. Three local sheep breeds (Saidi, Wahati, and Barki) were studied with a total of 206 ewes. The animals were exercised under natural heat stress. The heat tolerance index of the animals was calculated to identify animals with high and low heat tolerance based on their response to meteorological and physiological parameters. Genomic variation in these breeds was assessed using 64,756 single nucleotide polymorphic markers (SNPs). From the perspective of comparative adaptability to harsh conditions, our objective was to investigate the genomic structure that might control the adaptability of local sheep breeds to environmental stress under hot and dry conditions. In addition, indices of population structure and diversity of local breeds were examined. Measures of genetic diversity showed a significant influence of breed and location on populations. The standardized index of association (rbarD) ranged from 0.0012 (Dakhla) to 0.026 (Assuit), while for the breed, they ranged from 0.004 (Wahati) to 0.0103 (Saidi). The index of association analysis (Ia) ranged from 1.42 (Dakhla) to 35.88 (Assuit) by location and from 6.58 (Wahati) to 15.36 (Saidi) by breed. The most significant SNPs associated with heat tolerance were found in the MYO5A, PRKG1, GSTCD, and RTN1 genes (p ≤ 0.0001). MYO5A produces a protein widely distributed in the melanin-producing neural crest of the skin. Genetic association between genetic and phenotypic variations showed that OAR1_18300122.1, located in ST3GAL3, had the greatest positive effect on heat tolerance. Genome-wide association analysis identified SNPs associated with heat tolerance in the PLCB1, STEAP3, KSR2, UNC13C, PEBP4, and GPAT2 genes.

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Section: Discussionmentioning

confidence: 99%

“…Frontiers in Genetics frontiersin.org Frontiers in Genetics frontiersin.org (Zhang et al, 2021). Several SNPs within the MYO5A gene have been linked to heat tolerance in cattle (Jia et al, 2019;Rajawat et al, 2022). The link between MYO5A and heat tolerance may be due to its role in pigmentation.…”

Section: Figurementioning

confidence: 99%

Genome-wide analysis identified candidate variants and genes associated with heat stress adaptation in Egyptian sheep breeds

Aboul-Naga¹,

Alsamman

Allali

et al. 2022

Front. Genet.

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“…Runs of homozygosity (ROH) were detected across autosomes for each sample, using PLINK v.1.9 ( Purcell et al, 2007 ) with the following settings: 1) required minimum density (-homozyg-density 50); 2) number of heterozygotes allowed in a window (-homozyg-window-het 3); and 3) number of missing calls allowed in a window (-homozyg-window-missing 5). The numbers and lengths of ROH in each breed were calculated, and the lengths of ROH were divided into three categories: 0.5–1 Mb, 1–2 Mb and 2–4 Mb ( Zimin et al, 2009 ; Saravanan et al, 2021 ; Rajawat et al, 2022a ; Rajawat et al, 2022b ).…”

Section: Methodsmentioning

confidence: 99%

Genome-wide analysis emancipates genomic diversity and signature of selection in Altay white-headed cattle of Xinjiang, China

Wang¹,

Qi²,

Cheng³

et al. 2023

Front. Genet.

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Altay white-headed cattle have not received enough attention for several reasons. Due to irrational breeding and selection practices, the number of pure Altay white-headed cattle has decreased significantly and the breed is now on the eve of extinction. The genomic characterization will be a crucial step towards understanding the genetic basis of productivity and adaptability to survival under native Chinese agropastoral systems; nevertheless, no attempt has been made in Altay white-headed cattle. In the current study, we compared the genomes of 20 Altay white-headed cattle to the genomes of 144 individuals in representative breeds. Population genetic diversity revealed that the nucleotide diversity of Altay white-headed cattle was less than that of indicine breeds and comparable to that of Chinese taurus cattle. Using population structure analysis, we also found that Altay white-headed cattle carried the ancestry of the European and East Asian cattle lineage. In addition, we used three different methods (FST, θπ ratio and XP-EHH) to investigate the adaptability and white-headed phenotype of Altay white-headed cattle and compared it with Bohai black cattle. We found EPB41L5, SCG5 and KIT genes on the list of the top one percent genes, these genes might have an association with environmental adaptability and the white-headed phenotype for this breed. Our research reveals the distinctive genomic features of Altay white-headed cattle at the genome-wide level.

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“…The analyses and understanding of the molecular underpinnings of phenotypic diversity are one of the major challenges of population genetics and comparative genomics (Nielsen et al, 2007; Rajawat, Panigrahi, Kumar, Nayak, Parida, et al, 2022; Rajawat, Panigrahi, Kumar, Nayak, Saravanan, et al, 2022; Vitti et al, 2013). It is essential for a wide range of fundamental and applied fields, including human diseases and adaptation, genetic improvement of crops and livestock breeds, and genetic resource conservation, in addition to evolutionary biology (Chhotaray et al, 2020, 2021; Haasl & Payseur, 2016; Kumar, Panigrahi, Saravanan, Parida, et al, 2021; Kumar, Panigrahi, Saravanan, Rajawat, et al, 2021; Kumar et al, 2023; Saravanan et al, 2020).…”

Section: Challenges and Prospectsmentioning

confidence: 99%

“…High‐throughput sequencing technologies and cutting‐edge bioinformatics tools have recently created a lot of new opportunities to understand the genomic footprints of selection (Saravanan, Panigrahi, Kumar, Bhushan, et al, 2021; Saravanan, Panigrahi, Kumar, Parida, et al, 2021). For several plant and animal species, fully sequenced genomes and high‐density SNP chips have been made available (Rajawat, Panigrahi, Kumar, Nayak, Parida, et al, 2022; Rajawat, Panigrahi, Kumar, Nayak, Saravanan, et al, 2022). These discoveries have unavoidably sped up the development of new computational techniques that fully exploit the data.…”

Section: Introductionmentioning

confidence: 99%

Landmarks in the history of selective sweeps

Panigrahi,

Rajawat,

Nayak

et al. 2023

Animal Genetics

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Half a century ago, a seminal article on the hitchhiking effect by Smith and Haigh inaugurated the concept of the selection signature. Selective sweeps are characterised by the rapid spread of an advantageous genetic variant through a population and hence play an important role in shaping evolution and research on genetic diversity. The process by which a beneficial allele arises and becomes fixed in a population, leading to a increase in the frequency of other linked alleles, is known as genetic hitchhiking or genetic draft. Kimura's neutral theory and hitchhiking theory are complementary, with Kimura's neutral evolution as the ‘null model’ and positive selection as the ‘signal’. Both are widely accepted in evolution, especially with genomics enabling precise measurements. Significant advances in genomic technologies, such as next‐generation sequencing, high‐density SNP arrays and powerful bioinformatics tools, have made it possible to systematically investigate selection signatures in a variety of species. Although the history of selection signatures is relatively recent, progress has been made in the last two decades, owing to the increasing availability of large‐scale genomic data and the development of computational methods. In this review, we embark on a journey through the history of research on selective sweeps, ranging from early theoretical work to recent empirical studies that utilise genomic data.

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Identification of important genomic footprints using eight different selection signature statistics in domestic cattle breeds

Cited by 35 publications

References 104 publications

Genome-wide analysis identified candidate variants and genes associated with heat stress adaptation in Egyptian sheep breeds

Genome-wide analysis identified candidate variants and genes associated with heat stress adaptation in Egyptian sheep breeds

Genome-wide analysis emancipates genomic diversity and signature of selection in Altay white-headed cattle of Xinjiang, China

Landmarks in the history of selective sweeps

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