Revelation of genomic breed composition in a crossbred cattle of India with the help of Bovine50K BeadChip

Ahmad, Sheikh Firdous; Panigrahi, Manjit; Chhotaray, Supriya; Pal, D. K.; Parida, Subhashree; Bhushan, Bharat; Gaur, Gyanendra Kumar; Mishra, Bishnu Prasad; Singh, Rajendra

doi:10.1016/j.ygeno.2019.08.025

Cited by 32 publications

(18 citation statements)

References 19 publications

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“…They are however noticeably closer to the Holstein cluster than any of the other parental breeds. In concordance with Ahmad et al (2020), Admixture analysis with K = 4 showed that the average breed composition proportions for our population of Vrindavani was 42.5%, 26.0%, 17.1%, and 14.4% of HF, Hariana, Jersey and BSW, respectively ( Figure 1B).…”

Section: Descriptive Statistics and Population Structure Analysessupporting

confidence: 80%

“…Over the last decade, SNP microarrays and whole genome sequencing technology has enabled researchers to explore the genetic architecture and signatures of post-admixture selection in composite breeds (Decker et al, 2014;Kim and Rothschild, 2014;Cheruiyot et al, 2018). In Vrindavani cattle, the Bovine SNP50K array has recently been used to investigate the population structure of the breed (Chhotaray et al, 2019;Ahmad et al, 2020). Since the inception of the Vrindavani breeding program almost five decades ago, the breed has been under selection for milk production and adaptation to tropical conditions.…”

Section: Introductionmentioning

confidence: 99%

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Signatures of Selection in Composite Vrindavani Cattle of India

et al. 2020

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Vrindavani is an Indian composite cattle breed developed by crossbreeding taurine dairy breeds with native indicine cattle. The constituent breeds were selected for higher milk production and adaptation to the tropical climate. However, the selection response for production and adaptation traits in the Vrindavani genome is not explored. In this study, we provide the first overview of the selection signatures in the Vrindavani genome. A total of 96 Vrindavani cattle were genotyped using the BovineSNP50 BeadChip and the SNP genotype data of its constituent breeds were collected from a public database. Within-breed selection signatures in Vrindavani were investigated using the integrated haplotype score (iHS). The Vrindavani breed was also compared to each of its parental breeds to discover between-population signatures of selection using two approaches, cross-population extended haplotype homozygosity (XP-EHH) and fixation index (FST). We identified 11 common regions detected by more than one method harboring genes such as LRP1B, TNNI3K, APOB, CACNA2D1, FAM110B, and SPATA17 associated with production and adaptation. Overall, our results suggested stronger selective pressure on regions responsible for adaptation compared to milk yield.

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Section: Descriptive Statistics and Population Structure Analysessupporting

confidence: 80%

Section: Introductionmentioning

confidence: 99%

Signatures of Selection in Composite Vrindavani Cattle of India

et al. 2020

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show abstract

“…They are however noticeably closer to the Holstein cluster than any of the other parental breeds. In concordance with Ahmad et al (2020), Admixture analysis with K=4 showed that the average breed composition proportions for our population of Vrindavani was 42.5%, 26.0%, 17.1% and 14.4% of HF, Hariana, Jersey and BSW, respectively. (Figure S2).…”

Section: Resultssupporting

confidence: 81%

“…The Admixture analysis and PCA plot reflects the presence of both indicine and taurine ancestry in our Vrindavani population, with a higher proportion of taurine ancestry (Holstein). The dominance of the Holstein component in Vrindavani cattle has also been recently reported in a different set of Vrindavani population (Ahmad et al, 2020).…”

Section: Discussionsupporting

confidence: 53%

“…Over the last decade, SNP microarrays and whole genome sequencing technology has enabled researchers to explore the genetic architecture and signatures of post-admixture selection in synthetic breeds (Cheruiyot et al, 2018; Decker et al, 2014; Kim and Rothschild, 2014). In Vrindavani cattle, the Bovine SNP50K array has recently been used to investigate the population structure of the breed (Ahmad et al, 2020; Chhotaray et al, 2019).…”

Section: Introductionmentioning

confidence: 99%

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Signatures of Selection in Composite Vrindavani Cattle of India

Singh

Mehrotra

Gondro

et al. 2020

Preprint

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Vrindavani is an Indian composite cattle breed developed by crossbreeding taurine dairy breeds with native insicine cattle in the 1960s. About 190,000 semen doses of Vrindavni bulls have been distributed to the farmer till date. the animals are under artificial and natural selection for higher milk production and adaptation traits in the Vrindavani genome is not explored. In this study, we provide the first overview of the selection signatures in Vrindavani genome. 96 Vrindavani cattle were genotyped using BovineSNP BeadChip and the SNP genotype data of its constituent breeds were collected from a public database. Within-breed selection signatures in VRindavani were investigted using the integrated haplotype score. Vrindavani was also compared to each of its parental breeds to discover between-population signature of selection using two approaches, cross population extended haplotype homozygosity and fixation index. Signature of selection identifies 11 common region identified by more than one mthod harbouring gene such as LRP1B, TNN13K, APOB, CACNA2D1, FAM110B and SPATA17 associated with production and adaptation. Overall, our results suggest stronger selection pressure on regions responsible for adaptation compared to milk yield.

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Identification of genetic variants affecting reproduction traits in Vrindavani cattle

Gangwar,

Kumar,

Ahmad

et al. 2023

Mamm Genome

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Genome-wide association studies (GWAS) are one of the best ways to look into the connection between single nucleotide polymorphisms (SNPs) and phenotypic performance. This study aimed to identify the genetic variants that signi cantly affect the important reproduction traits in Vrindavani cattle using genome-wide SNP chip array data. In this study, 96 randomly chosen Vrindavani cows were genotyped using the Illumina Bovine50K BeadChip platform. A linear regression model of the genome-wide association study was tted in the PLINK program between genome-wide SNP markers and reproduction traits, including age at rst calving (AFC), inter calving period (ICP), dry days (DD), and service period (SP) in the rst three lactations. Information on different QTLs and genes, overlapping or adjacent to genomic coordinates of signi cant SNPs, was also mined from relevant databases in order to identify biological pathways associated with reproductive traits in bovine. The Bonferroni correction resulted in 39 SNP markers present on different chromosomes being identi ed that signi cantly affected the variation in AFC (6 SNPs), ICP (7 SNPs), DD (9 SNPs), and SP (17 SNPs), respectively. Novel potential candidate genes for reproductive traits identi ed using the GWAS methodology included UMPS,

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Revelation of genomic breed composition in a crossbred cattle of India with the help of Bovine50K BeadChip

Cited by 32 publications

References 19 publications

Signatures of Selection in Composite Vrindavani Cattle of India

Signatures of Selection in Composite Vrindavani Cattle of India

Signatures of Selection in Composite Vrindavani Cattle of India

Identification of genetic variants affecting reproduction traits in Vrindavani cattle

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