Bos indicus cattle breeds are genetically distinct from Bos taurus breeds. We examined the performance of three SNP arrays, the Illumina BovineHD BeadChip (777k; Illumina Inc.), the Illumina BovineSNP50 BeadChip (50k) and the GeneSeek 70k Indicus chip (75Ki; GeneSeek) in four B. indicus breeds (Gir, Kankrej, Sahiwal and Red Sindhi) and their B. taurus crosses, along with two B. taurus breeds, Holstein and Jersey. More SNPs on both Illumina SNP chips were monomorphic in B. indicus breeds (average 20.3%-29.3% on the 777k chip, 35.5%-45.5% on the 50k chip) than in Holstein (19.7% on the 777k chip, 17.1% on the 50k chip). The proportion of monomorphic SNPs on the 75Ki chip was much lower, 4% (2.8%-7%) in B. indicus breeds, while it was 33.5% in Holstein. With on average 164,357 heterozygous loci in B. indicus breeds, the 777k SNP chip has sufficient heterozygous loci to design a chip customized for B. indicus breeds. Principal component analysis clearly differentiated B. indicus from B. taurus breeds. Differentiation among B. indicus breeds was only achieved by plotting the third and fifth principal components using 777k genotype data. Admixture analysis showed that many B. indicus animals, previously believed to be of pure origin, are in fact had mixed ancestry. The extent of linkage disequilibrium showed comparatively higher effective population sizes in four B. indicus breeds compared to two B. taurus breeds. The results of admixture analyses show that it is important to assess the genomic composition of a bull before using it in a breeding programme.
The objective of this study was to investigate the effect of composition and size of the reference population in imputation efficiency of INDUSCHIP v2 in Indian HF crossbred cattle. Data set consisted of a total of 869 cattle from 14 Indicine breeds, 2 crossbreds (HF and Jersey crossbreds) and 2 exotic breeds (HF, Jersey) genotyped with Illumina BovineHD (Illumina, San Diego, CA) panel. Post QC, 846 animals and 449955 SNPs remained for imputation study. 3 test groups each with randomly selected 25 HFCB animals with subset genotype of INDUSCHIP v2 were created, whereas with HD genotyping data of remaining animals, 3 different categories of reference groups were created namely reference 1 (HF, Jersey, all 14 Indicine breeds, HF and Jersey crossbreds), reference 2 (HF, HF crossbred, Sahiwal, Gir and Kankrej) and reference 3 (pure HF, Sahiwal, Gir and Kankrej). Imputation efficiency of INDUSCHIP v2 was expressed in terms of concordance rate and Dosage R2 (DR2). Reference groups 1 and 2 were found to be better than Reference group 3. Further, the size of the reference population had an impact on imputation efficiency. The concordance rate and DR2 decreased with decline about population size. However, a reference population with 280 animals was found to be sufficient to obtain a concordance rate of around 95% or more and DR2 around 0.93. More number of HF, HF crossbred, Sahiwal, Gir and Kankrej animals need to be HD genotyped and incorporated in the reference population to improve the imputation efficiency of INDUSCHIP v2.
The present study was conducted to compare the estimated breeding values of progeny tested sires and pedigree selected sires for test day milk yield of crossbred Holstein Friesian cattle. First lactation milk yield records (1,20,198) of 12,971 daughters sired by 267 sires were collected from INAPH database maintained by NDDB. Variance and covariance components for test-day milk yield (TDMY) were estimated by different random regression test day models (RRTDM), viz. Cubic B- Spline function, Quadratic B-Spline function, Legendre polynomial (LP) function and Wilmink function using Average Information Restricted Maximum Likelihood (AIREML). Considering various criteria for comparison of different orders of TDMs, LP of 6th order for TDMY was the best fitted model for further estimation of breeding values. The heritability estimates ranged from 0.15 to 0.39 for TDMY using Leg_2 model. The additive genetic correlations were higher than the phenotypic correlations among different TDs. The additive genetic correlations between test day yields varied from 0.73 to 0.99. The expected progeny difference (EPD) for TDMYcalculated based on dam’s yield for the top ten and bottom ten PS bulls was 2,662.5 kg; whereas, the actual progeny difference (APD) for these bulls was -28.47 kg. While, EPD for top 10 and bottom 10 PT bulls selected based on EBVs was 2,820.52 kg whereas the APD for PT bulls was 890.48 kg. The difference in expected and actual MY of progeny was higher in PS bulls as compared to PT bulls indicating that the pedigree information for EPDs had a poor association with APDs and sire superiority is not reflected in progeny’s actual performance. The rank correlation between ranks of all PS and PT bulls were very poor and non-significant. The bulls selected based on estimated breeding values will give faster genetic progress and decision to select replacement bulls based on breeding values instead of dam’s yield will have positive effect on genetic progress.
To initiate genomic selection programme for indicine cattle breeds and their crosses in India, National Dairy Development Board designed a medium-density (52K) customized chip on Illumina platform named as “INDUSCHIP”. The present study was conducted to examine the efficiency of INDUSCHIP SNP panel for genotyping indicine cattle breeds. Total of 500 animals belonging to 14 different indicine breeds were genotyped with Illumina Bovine HD chip. A subset of SNPs was taken for evaluating the performance of selected SNPs in different indicine breeds. The average minor allele frequency (MAF) was found to vary between 0.20–0.29 for different indicine breeds. However, for important milk breeds like Sahiwal, Gir, Red Sindhi and Kankrej the average MAF was found to be 0.27 and above. Mean Linkage Disequilibrium (LD) at 50–60 kbp distance was found to be around 0.21. There was considerable LD decay with increasing distance between SNPs. Around 0.06% SNPs were found to be significantly deviating from Hardy-Weinberg equilibrium. From the Principal component analysis (PCA) it was found that the first three Principal Components i.e. PC1, PC2 and PC3) could separate different indicine breeds. The present study indicated that due to the presence of highly polymorphic SNPs for the breeds of indicine origin, INDUSCHIP panel was found to be effective and informative in genotyping indicine breeds.
The current study tested the suitability of Illumina® BovineHD BeadChip in genotyping three riverine breeds of buffalo viz. Jaffarabadi, Murrah and Mehsana. Of the 777962 SNPs, 670955 SNPs were called in all animals and only 13150 SNPs were found to be polymorphic at a call rate of 90%, and had Minor Allele Frequency (MAF) greater than 0.05. The average Minor Allele Frequency (MAF) of polymorphic SNPs was 0.23 and average expected heterozygosity (HE) of 0.321. Principal Component Analysis (PCA) revealed 2 different clusters where Murrah and Mehsana breeds clustered together, while Jaffarabadi breed formed a distinct cluster. Result obtained in this study indicated that the SNPs available in Illumina BovineHD BeadChip may not be good enough for studying population structure and genetic analyses in Indian buffalo breeds. Hence it might be necessary to develop a custom SNP marker panel for Indian riverine buffaloes.
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