Selection signatures in livestock genome: A review of concepts, approaches and applications

Saravanan, K.A.; Panigrahi, Manjit; Kumar, Harshit; Bhushan, Bharat; Dutt, Triveni; Mishra, Bishnu Prasad

doi:10.1016/j.livsci.2020.104257

Cited by 87 publications

(68 citation statements)

References 137 publications

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“…In general, the various approaches each detect different panels of genes with only little overlap, indicating for all methods a high frequency of false negatives. At the same time, all methods are prone to delivering false positives, further complicating the interpretation ( Utsunomiya et al 2015 ; Saravanan et al 2020 ). On the other hand, our large WGS data set allows to identify candidate causative mutations, at least in coding sequences but also in plausible miRNA binding sites, and to test their correlation with the breed-dependent phenotypes.…”

Section: Discussionmentioning

confidence: 99%

Whole-Genome Resequencing of Worldwide Wild and Domestic Sheep Elucidates Genetic Diversity, Introgression, and Agronomically Important Loci

Cao

Liu

et al. 2021

Molecular Biology and Evolution

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Domestic sheep and their wild relatives harbor substantial genetic variants that can form the backbone of molecular breeding, but their genome landscapes remain understudied. Here, we present a comprehensive genome resource for wild ovine species, landraces and improved breeds of domestic sheep, comprising high-coverage (∼16.10×) whole-genomes of 810 samples from 7 wild species and 158 diverse domestic populations. We detected, in total, ∼121.2 million single nucleotide polymorphisms (SNPs), ∼61 million of which are novel. Some display significant (P < 0.001) differences in frequency between wild and domestic species, or are private to continent-wide or individual sheep populations. Retained or introgressed wild gene variants in domestic populations have contributed to local adaptation, such as the variation in the HBB associated with plateau adaptation. We identified novel and previously reported targets of selection on morphological and agronomic traits such as stature, horn, tail configuration and wool fineness. We explored the genetic basis of wool fineness and unveiled a novel mutation (chr25: T7068586C) in the 3’-UTR of IRF2BP2 as plausible causal variant for fleece fiber diameter. We reconstructed pre-historical migrations from the Near Eastern domestication center to South-and-Southeast Asia, and found two main waves of migrations across the Eurasian Steppe and the Iranian Plateau in the Early and Late Bronze Ages. Our findings refine our understanding of genome variation as shaped by continental migrations, introgression, adaptation and selection of sheep.

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Section: Discussionmentioning

confidence: 99%

Whole-Genome Resequencing of Worldwide Wild and Domestic Sheep Elucidates Genetic Diversity, Introgression, and Agronomically Important Loci

Cao

Liu

et al. 2021

Molecular Biology and Evolution

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“…Fay and Wu statistics [177], in contrast, assess the relationship between ancestral and derived alleles, which enables both positive and negative recent selection occurring in medium-to high-frequency alleles to be detected. However, knowledge of ancestral alleles is necessary to apply the method [178]. Various approaches have been used to assess positive and negative selection in populations.…”

Section: Selection Signaturesmentioning

confidence: 99%

The Quest for Genes Involved in Adaptation to Climate Change in Ruminant Livestock

Passamonti

Somenzi

Barbato

et al. 2021

Animals

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Livestock radiated out from domestication centres to most regions of the world, gradually adapting to diverse environments, from very hot to sub-zero temperatures and from wet and humid conditions to deserts. The climate is changing; generally global temperature is increasing, although there are also more extreme cold periods, storms, and higher solar radiation. These changes impact livestock welfare and productivity. This review describes advances in the methodology for studying livestock genomes and the impact of the environment on animal production, giving examples of discoveries made. Sequencing livestock genomes has facilitated genome-wide association studies to localize genes controlling many traits, and population genetics has identified genomic regions under selection or introgressed from one breed into another to improve production or facilitate adaptation. Landscape genomics, which combines global positioning and genomics, has identified genomic features that enable animals to adapt to local environments. Combining the advances in genomics and methods for predicting changes in climate is generating an explosion of data which calls for innovations in the way big data sets are treated. Artificial intelligence and machine learning are now being used to study the interactions between the genome and the environment to identify historic effects on the genome and to model future scenarios.

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“…The increased LD within parts of the genome indicates a reduced recombination rate, likely because of an occurrence of a beneficial mutation. The LD-based selection signature detection methods are especially useful to detect variants under partial or soft selective sweep (Saravanan et al, 2020). The two most important LD based methods used in this context are the EHH (Sabeti et al, 2002) and its derived method of iHS (Voight et al, 2006).…”

Section: Linkage Disequilibriummentioning

confidence: 99%

Linkage disequilibrium, genomic inbreeding and effective populations size to unravel population history

Mészárosová

Mészáros

Moravčíková

et al. 2021

Acta fytotechn zootechn

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Licensed under a Creative Commons Attribution 4.0 International LicenseThe use of single nucleotide polymorphism (SNP) data had become commonplace in animal breeding activities and management of livestock populations. The cost-effective genotyping allowed us to assess entire populations and learn about their history on the genomic level. This paper reviews several approaches that are commonly used in the context of genomic diversity in livestock, such as the linkage disequilibrium (LD) and assessment of autozygosity via runs of homozygosity (ROH). Both methods, however, are being used to assess the impact of natural or artificial selection on the livestock genome. Apart from these selection signatures, both the LD and ROH are used to assess the effective population size (Ne), which likewise, serves as a diversity management tool and describes the historical events in populations.

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Selection signatures in livestock genome: A review of concepts, approaches and applications

Cited by 87 publications

References 137 publications

Whole-Genome Resequencing of Worldwide Wild and Domestic Sheep Elucidates Genetic Diversity, Introgression, and Agronomically Important Loci

Whole-Genome Resequencing of Worldwide Wild and Domestic Sheep Elucidates Genetic Diversity, Introgression, and Agronomically Important Loci

The Quest for Genes Involved in Adaptation to Climate Change in Ruminant Livestock

Linkage disequilibrium, genomic inbreeding and effective populations size to unravel population history

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