Trajectory of livestock genomics in South Asia: A comprehensive review

Panigrahi, Manjit; Kumar, Harshit; Saravanan, K.A.; Rajawat, Divya; Nayak, Sonali Sonejita; Ghildiyal, Kanika; Kaisa, Kaiho; Parida, Subhashree; Bhushan, Bharat; Dutt, Triveni

doi:10.1016/j.gene.2022.146808

Cited by 20 publications

(12 citation statements)

References 228 publications

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“…Sheep (Ovis aries) were among the earliest livestock species to be domesticated (Ryder, 1981). They were originally bred primarily for meat; however, archaeological evidence suggests that the rearing of sheep for secondary utility items such as wool and milk began some millennia later (Debono Spiteri et al, 2016;Rajawat et al, 2022). Sheep populations specialized in wool production were first developed in south-west Asia, then spread over Europe, eventually displacing primitive sheep breeds (Chessa et al, 2009).…”

Section: Sheepmentioning

confidence: 99%

“…Most of these limits, however, can be overcome by using high sample sizes, restricting the analysis to SNPs with evolutionary signatures, performing gene and pathway‐based association studies, and transitioning from SNP arrays to whole genome sequencing techniques. Detection of the selection signatures in the genome harboring candidate genes for fiber production and quality traits is achievable with the current technical advances, such as next‐generation sequencing technologies, high‐density SNP arrays, and strong statistical and bioinformatics tools (Panigrahi et al, 2022; Saravanan et al, 2021). For the identification of selection signatures, statistical approaches based on linkage disequilibrium (LD), allele frequency spectrum, reduced local variability, and haplotype features have all been developed (Qanbari & Simianer, 2014).…”

Section: Introductionmentioning

confidence: 99%

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Selection signatures for fiber production in commercial species: A review

et al. 2022

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Natural fibers derived from diverse animal species have gained increased attention in recent years due to their favorable environmental effects, long-term sustainability benefits, and remarkable physical and mechanical properties that make them valuable raw materials used for textile and non-textile production. Domestication and selective breeding for the economically significant fiber traits play an imperative role in shaping the genomes and, thus, positively impact the overall productivity of the various fiber-producing species. These selection pressures leave unique footprints on the genome due to alteration in the allelic frequencies at specific loci, characterizing selective sweeps. Recent advances in genomics have enabled the discovery of selection signatures across the genome using a variety of methods. The increased demand for 'green products' manufactured from natural fibers necessitates a detailed investigation of the genomes of the various fiber-producing plant and animal species to identify the candidate genes associated with important fiber attributes such as fiber diameter/fineness, color, length, and strength, among others. The objective of this review is to present a comprehensive overview of the concept of selection signature and selective sweeps, discuss the main methods used for its detection, and address the selection signature studies conducted so far in the diverse fiberproducing animal species.

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Section: Sheepmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Selection signatures for fiber production in commercial species: A review

et al. 2022

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“…The genomics revolution has sparked genome-wide analyses in a wide range of species, enabling population geneticists to better understand how selection modifies a species' genome and phenotype through its interactions with other evolutionary forces (Horscroft et al, 2019). We are now able to process massive amounts of genomic data owing to technological advances like high-throughput sequencing combined with rapidly growing computational methods and data management (Panigrahi et al, 2022;Saravanan, Panigrahi, et al, 2022). These advances resulted in the development T A B L E 1 Studies related to selective sweeps using different summary statistics and machine learning tools.…”

Section: H a Llenge S A N D Prospectsmentioning

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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“…“Selection signatures” are the distinctive genetic traces or prints left in the areas of the genome that were exposed to selection ( Nielsen, 2005 ; Jensen et al, 2016 ; Saravanan et al, 2020 ; Panigrahi et al, 2022 ). Identification of the selection features, such as disease, pests, drought, high temperature and high-altitude tolerance ( Yang et al, 2016 ; Kim et al, 2017 ; Taye et al, 2017 ) can offer various livestock populations a selective advantage.…”

Section: Introductionmentioning

confidence: 99%

“…Identification of the selection features, such as disease, pests, drought, high temperature and high-altitude tolerance ( Yang et al, 2016 ; Kim et al, 2017 ; Taye et al, 2017 ) can offer various livestock populations a selective advantage. Whole-genome sequencing (WGS) has dramatically improved our ability to detect the genomic regions under selection in livestock species ( Panigrahi et al, 2022 ; Saravanan et al, 2022 ). We can now more easily identify the genomic areas being selected in livestock animals thanks to WGS.…”

Section: Introductionmentioning

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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Trajectory of livestock genomics in South Asia: A comprehensive review

Cited by 20 publications

References 228 publications

Selection signatures for fiber production in commercial species: A review

Selection signatures for fiber production in commercial species: A review

Landmarks in the history of selective sweeps

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

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