Genome-wide detection of copy number variations in Tharparkar cattle

Kumar, Harshit; Panigrahi, Manjit; Saravanan, K.A.; Rajawat, Divya; Parida, Subhashree; Bhushan, Bharat; Gaur, Gyanendra Kumar; Dutt, Triveni; Mishra, Bina; Singh, Rajendra

doi:10.1080/10495398.2021.1942027

Cited by 30 publications

(11 citation statements)

References 44 publications

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“…Structural variants in the genome, such as insertions and deletions, as well as copy number variations (CNVs) and chromosomal rearrangements such as duplications, inversions, and translocations (Tattini et al, 2015), are targeted during selection events for traits related to morphology, production, and reproduction. Copy number variations are a significant source of genetic variation that aid in understanding prevalent phenotypic diversity, economic traits, and livestock species evolution (Kumar et al, 2021). Yuan et al (2021) used whole-genome resequencing to study CNVs in Chinese indigenous fine-wool sheep populations.…”

Section: Sheepmentioning

confidence: 99%

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%

Selection signatures for fiber production in commercial species: A review

et al. 2022

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“…Genetic variation lurked multifarious historical events, reflecting the historical selection and evolutionary pressures experienced as various cattle breeds developed ( Ahmad et al, 2020 ; Kumar et al, 2021a ; Kumar et al, 2021b ; Ghildiyal et al, 2023 ). ROH is a critical metric for evaluating inbreeding and recessive inheritance ( Curik et al, 2014 ; Nandolo et al, 2018 ).…”

Section: Discussionmentioning

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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“…We chose the CNV method by region approach for our investigation. Subsequently, we applied a recurrence value of 0.3, as advised by the CNVRuler manual and previous studies [ 25 ], to avoid overestimating the size and frequency of CNVRs. Finally, control raw data filtered for occurrence in at least three individuals were used as the last of our results.…”

Section: Methodsmentioning

confidence: 99%

Genome-Wide Detection and Analysis of Copy Number Variation in Anhui Indigenous and Western Commercial Pig Breeds Using Porcine 80K SNP BeadChip

Zhang

Jiang

et al. 2023

Genes

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Copy number variation (CNV) is an important class of genetic variations widely associated with the porcine genome, but little is known about the characteristics of CNVs in foreign and indigenous pig breeds. We performed a genome-wide comparison of CNVs between Anhui indigenous pig (AHIP) and Western commercial pig (WECP) breeds based on data from the Porcine 80K SNP BeadChip. After analysis using the PennCNV software, we detected 3863 and 7546 CNVs in the AHIP and WECP populations, respectively. We obtained 225 (loss: 178, gain: 47) and 379 (loss: 293, gain: 86) copy number variation regions (CNVRs) randomly distributed across the autosomes of the AHIP and WECP populations, accounting for 10.90% and 22.57% of the porcine autosomal genome, respectively. Functional enrichment analysis of genes in the CNVRs identified genes related to immunity (FOXJ1, FOXK2, MBL2, TNFRSF4, SIRT1, NCF1) and meat quality (DGAT1, NT5E) in the WECP population; these genes were a loss event in the WECP population. This study provides important information on CNV differences between foreign and indigenous pig breeds, making it possible to provide a reference for future improvement of these breeds and their production performance.

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Genome-wide detection of copy number variations in Tharparkar cattle

Cited by 30 publications

References 44 publications

Selection signatures for fiber production in commercial species: A review

Selection signatures for fiber production in commercial species: A review

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

Genome-Wide Detection and Analysis of Copy Number Variation in Anhui Indigenous and Western Commercial Pig Breeds Using Porcine 80K SNP BeadChip

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