Detection of genome-wide copy number variation in Murrah buffaloes

Kumar, Harshit; Panigrahi, Manjit; Strillacci, M.G.; Nayak, Sonali Sonejita; Rajawat, Divya; Ghildiyal, Kanika; Bhushan, Bharat; Dutt, Triveni

doi:10.1080/10495398.2023.2227670

Cited by 6 publications

(3 citation statements)

References 75 publications

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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(Chhotaray et al, , 2021Haasl & Payseur, 2016;Kumar, Panigrahi, Saravanan, Rajawat, et al, 2021;Kumar et al, 2023;Saravanan et al, 2020). 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).…”

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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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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“…CNV is widely used in livestock. On the one hand, the analysis of CNV differences between different individuals can identify CNV regions associated with traits and use them as selective markers for genome selection and for genetic improvement [18][19][20]. On the other hand, comparing the differences in CNV between infected and uninfected individuals allows for the identification of regions of CNV associated with disease resistance [21].…”

Section: Introductionmentioning

confidence: 99%

Effects of Copy Number Variations in the Plectin (PLEC) Gene on the Growth Traits and Meat Quality of Leizhou Black Goats

Wang,

Zhang,

Han

et al. 2023

Animals

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The plectin (PLEC) gene is crucial in regulating muscle development and maintaining the cytoskeleton. An abnormal expression of PLEC can lead to muscle atrophy and muscular dystrophy. In a previous study, we found that Leizhou black goats exhibit abundant structural variations in the PLEC gene. However, the genetic effects of these variations on growth traits and meat quality in goats are not fully understood. In this study, three PLEC copy number variations (CNVs) were identified in a population of 417 Leizhou black goats, using quantitative polymerase chain reaction (qPCR) technology. Population distribution analysis revealed a high abundance of various types of these three CNVs. PLEC mRNA was found to be highly expressed in muscle tissue and remained consistently high from 1 month to 24 months after birth. Specifically, the gain type of CNV-1 (chr14: 81056401-81064800) showed a significant association with PLEC mRNA expression in muscle tissue (p < 0.01). The sequence of CNV-1 in PLEC shares similarities with three domain superfamilies associated with muscle development and skin disease. Furthermore, there were significant differences in chest circumference, body weight, carcass weight, the cross-sectional area of the longissimus dorsi lumbar muscle, and shear stress between different types of CNV-1 (p < 0.05). Notably, goats with the CNV-1 gain type demonstrated better phenotypic values compared to those with loss and normal types. These findings suggest that PLEC CNV-1 could play a crucial role in the growth and muscle development of Leizhou black goats, making it a potential marker for assisted selection in goat breeding.

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“…A population's genetic makeup evolves as a result of the process of evolution. The adaptations made by organisms to their altering environments are reflected in evolution, which can produce altered genes, unique features, and new species (Kumar et al, 2021;Pal et al, 2022;Kumar et al, 2023;. It is anticipated that selection will leave behind signatures, which can be recognized in the genome.…”

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Deciphering climate resilience in Indian cattle breeds by selection signature analyses

Nayak,

Panigrahi,

Rajawat

et al. 2023

Preprint

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The signature of selection is a crucial concept in evolutionary biology that refers to the pattern of genetic variation that arises in a population as a result of natural selection. In the context of climate adaptation, the signature of selection can reveal the genetic basis of adaptive traits that enable organisms to survive and thrive in changing environmental conditions. Breeds cultivated in diverse agroecological zones exhibit genetic "footprints" within their genomes that mirror the influence of climate-induced selective pressures, subsequently impacting phenotypic variance. We examined genotypic data from eight different cattle groups (Gir, Hariana, Kankrej, Nelore, Ongole, Red Sindhi, Sahiwal, and Tharparkar) that are adapted to diverse regional climates in India. It is assumed that the genomes of animals residing in these regions have been altered through selection for various climatic adaptations. In this study, we utilized bovine 50k chip data and four genome scan techniques to assess the genetic regions of positive selection for high temperature adaptation in eight distinct cattle populations. We have also investigated the population stratification i.e. PCA, genome-wide investigation of genetic diversity, inbreeding, effective population size in our target dataset. To identify selection signature regions in this work, we used four intra-population statistics: Tajima's D, CLR, iHS, and ROH. We identified potential regions for selection that is likely to be caused by climate. We have identified many adaption genes as several potential selection signature areas. These include genes like HSPB2, HSPB3, HSP20, HSP90AB1, HSF4, HSPA1B, CLPB, GAP43, MITF, and MCHR1 that have been previously identified in the cattle population that lives in high- and low-temperature regions.

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Detection of genome-wide copy number variation in Murrah buffaloes

Cited by 6 publications

References 75 publications

Landmarks in the history of selective sweeps

Landmarks in the history of selective sweeps

Effects of Copy Number Variations in the Plectin (PLEC) Gene on the Growth Traits and Meat Quality of Leizhou Black Goats

Deciphering climate resilience in Indian cattle breeds by selection signature analyses

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