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The improvement in imputation accuracy diminished across different methods of selecting SNPs with increased panel density. 5 O'Brien, A.C., Judge, M.M., Fair, S. & Berry, D.P. (2019) High imputation accuracy from informative low-to-medium density single nucleotide polymorphism genotypes is achievable in sheep1. Genomic technologies have not penetrated enough in livestock, especially in developing nations where animals from a particular breed/population cannot be concurrently genotyped mainly due to financial constraints. [Extracted from the article]

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 (F ST). 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. [ABSTRACT FROM AUTHOR]

In present study, association of five single nucleotide polymorphisms (SNPs) of database rs109421300, rs43691049, rs109727821, rs109047657 and rs135678421 was investigated with milk minerals including calcium (Ca), phosphorus (P), copper (Cu), zinc (Zn), manganese (Mn), iron (Fe), sodium (Na), potassium (K) and constituents (fat and protein percentage) after adjusting the records with various significant non-genetic factors in crossbred (Vrindavani) cattle. The effect of rs109421300 pertaining to Diacylglycerol Acyltransferase (DGAT) gene located on BTA 14, was highly significant on fat percentage and significant on test day milk yield and non-significant on Ca, Cu, Mn, Zn, Fe, Na, K, test day milk yield and protein percentage. The AA genotypes of rs109421300 locus had significantly lower (2.96±0.17%) fat percentage than AG (4.64±0.22%), GG (4.62±0.27%) genotypes but simultaneously cows with AA genotypes had significantly highest (11.59±0.51 kg) test day milk yield than other two genotypes. At locus rs109727821, the manganese concentration was significantly highest (1.64±0.16 mg/l) for AG followed by AA (0.98±0.15 mg/l) and GG (0.77±0.24 mg/l) genotypes. The other SNPs had no significant association with traits under investigation. The existing association suggested possibilities to select animals for specific minerals and constituent traits in crossbred population. [ABSTRACT FROM AUTHOR]

The present investigation was conducted to compare milk minerals and constituents in different bovine species and breeds. The genetic and non-genetic factors affecting milk fat, protein and milk mineral composition in crossbred cattle were investigated. The effect of breeds was highly significant on copper (Cu), zinc (Zn), manganese (Mn), sodium (Na), potassium (K), fat and protein, significant (p≤0.05) on calcium (Ca) and non-significant on phosphorus (P) and iron (Fe) content. The Ca, Cu, fat and protein were significantly higher in Murrah buffalo followed by Tharparkar cattle and crossbred cattle. However, Mn and Zn were higher in Tharparkar cattle followed by Murrah buffalo and crossbred cattle. Tharparkar milk was also rich in Na and K followed by crossbred cattle and Murrah buffalo. The effect of parity was highly significant only on Mn, whereas, effect of lactation stage (LS) was significant on Fe and Cu in milk of crossbred cattle. The effect of Test Day Milk Yield (TDMY) was significant on Fe and Cu. The product moment correlation was highest (0.414) between Zn and Fe and lowest (-0.347) between Cu and Zn. Among milk minerals, the estimates of heritability for Fe, Ca and Mn were moderate, whereas it was low for other minerals in crossbred cattle. [ABSTRACT FROM AUTHOR]

• We elucidated putative CNVs and CNV regions in Vrindavani cattle using Bovine SNP50 genotyping data. • 252 putative CNVs were detected which further concatenated into 69 CNVRs. • Five CNVRs were significantly associated with 10 (re)production traits in Vrindavani population. • The study provides useful insights to establish the comprehensive CNV map of Vrindavani population for association studies. The present study was aimed to analyze the genome-wide copy number variations (CNVs) in Vrindavani composite cattle and concatenate them into CNV regions (CNVRs), and finally test the association of CNVRs with different production and reproduction traits. Genotypic data, generated on BovineSNP50 Beadchip (v3) array for 96 Vrindavani animals, was used to elucidate the CNVs at the genome level. Intensity data covering over 53,218 SNP genotypes on bovine genome was used. Algorithm based on Hidden Markov Model was employed in PennCNV program to detect, normalize and filter CNVs across the genome. 252 putative CNVs, detected via PennCNV program, in different individuals were concatenated into 71 CNV regions (CNVRs) using CNVRuler program. Association of CNVRs with important (re)production traits in Vrindavani animals was assessed using linear regression. Five CNVRs were found to be significantly associated with ten important (re)production traits. The genes harbored in these regions provided useful insights into the association of CNVRs with genes and ultimately the variation at phenotype level. Important genes that overlapped with CNVRs included WASHC4, HS6ST3, MBNL2, TOLLIP, PIDD1 and TSPAN4. Furthermore, the CNVRs were found to overlap with important QTLs available in AnimalQTL database which affect milk yield and composition along with reproduction and immune function traits. The copy number states of three enes were validated using digital droplet PCR technique. The results from the present study significantly enhance the understanding about CNVs in Vrindavani cattle and should help establish its CNV map. The study will also enable further investigation on association of these variants with important traits of economic interest including disease incidence. [ABSTRACT FROM AUTHOR]