Progress and future perspectives of livestock genomics in India: a mini review

Saravanan, K.A.; Panigrahi, Manjit; Kumar, Harshit; Nayak, Sonali Sonejita; Rajawat, Divya; Bhushan, Bharat; Dutt, Triveni

doi:10.1080/10495398.2022.2056046

Cited by 10 publications

(5 citation statements)

References 85 publications

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“…However, the study of goat genomes is still in its infancy compared to other livestock species. However, progress is being made in performing genome-wide studies, identifying genomic variants and QTL analysis [55,56].…”

Section: Discussionmentioning

confidence: 99%

Genome-Wide Association and Pathway Analysis of Carcass and Meat Quality Traits in Karachai Young Goats

Selionova,

Aibazov,

Sermyagin

et al. 2023

Animals

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Goats with diverse economic phenotypic traits play an important role in animal husbandry. However, the genetic mechanisms underlying complex phenotypic traits are unclear in goats. Genomic studies of variations provided a lens to identify functional genes. The work aimed to search for candidate genes related to body measurements and body weight of Karachai goats and develop an experimental PCR-RV test system for genotyping significant SNPs. Comparison of GWAS results for ages 4 and 8 months revealed 58 common SNPs for significant genotypes. 11 common SNPs were identified for body weight, 4 SNPs—for group of traits withers height, rump height, body length, 2 SNPs—for withers height and rump height, 1 SNP—for body length and chest depth. Structural annotation of genomic regions covering a window of ±0.20 Mb showed the presence of 288 genes; 52 of them had the described functions in accordance with gene ontology. The main molecular functions of proteins encoded by these genes are the regulation of transcription, cell proliferation, angiogenesis, body growth, fatty acid and lipid metabolism, nervous system development, and spermatogenesis. SNPs common to body weight and localized within a window of ±200 kb from the structural genes CRADD, HMGA2, MSRB3, FUT8, MAX, and RAB15 were selected to create a test system. The study of meat productivity after slaughter and chemical analysis of muscle tissue in Karachai goats at the age of 8 months of different genotypes according to the identified SNPs revealed that rs268269710 is the most promising for further research and use in breeding. The GG genotype is associated with a larger live weight of animals, a larger carcass yield, the content of the boneless part in it, and the ratio of protein and adipose tissue in meat preferred for dietary nutrition. These results will contribute to the genetic improvement of Karachai goats.

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Section: Discussionmentioning

confidence: 99%

Genome-Wide Association and Pathway Analysis of Carcass and Meat Quality Traits in Karachai Young Goats

Selionova,

Aibazov,

Sermyagin

et al. 2023

Animals

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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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“…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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Progress and future perspectives of livestock genomics in India: a mini review

Cited by 10 publications

References 85 publications

Genome-Wide Association and Pathway Analysis of Carcass and Meat Quality Traits in Karachai Young Goats

Genome-Wide Association and Pathway Analysis of Carcass and Meat Quality Traits in Karachai Young Goats

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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