Evaluating efficiency of customized medium density INDUSCHIP for genotyping of Indicine cattle breeds

SUJIT SAHA; NILESH NAYEE; A SUDHAKAR; SWAPNIL GAJJAR; K R TRIVEDI; R O GUPTA; G KISHORE

doi:10.56093/ijans.v90i11.111492

Authors

SUJIT SAHA National Dairy Development Board, Anand, Gujarat 388 001 India
NILESH NAYEE National Dairy Development Board, Anand, Gujarat 388 001 India
A SUDHAKAR National Dairy Development Board, Anand, Gujarat 388 001 India
SWAPNIL GAJJAR National Dairy Development Board, Anand, Gujarat 388 001 India
K R TRIVEDI National Dairy Development Board, Anand, Gujarat 388 001 India
R O GUPTA National Dairy Development Board, Anand, Gujarat 388 001 India
G KISHORE National Dairy Development Board, Anand, Gujarat 388 001 India

https://doi.org/10.56093/ijans.v90i11.111492

Keywords:

HWE, INDUSCHIP, LD, MAF, SNP

Abstract

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.

Downloads

Download data is not yet available.

References

Bejarano D, Martinez R, Manrique C, Parra L M, Rocha J F, Gomez Y, Abuabara Y and Gallego J. 2018. Linkage disequilibrium levels and allele frequency distribution in Blanco Orejinegro and Romosinuano Creole cattle using medium density SNP chip data. Genetics and Molecular Biology 41(2): 426–33. DOI: https://doi.org/10.1590/1678-4685-gmb-2016-0310

Espigolan R, Fernando B, Arione A B, Fabio R P S, Daniel G M G, Rafael L T, Diércles F C, Henrique N O, Humberto T and Mehdi S. 2013. Study of whole genome linkage disequilibrium in Nellore cattle. BMC Genomics 14: 305. DOI: https://doi.org/10.1186/1471-2164-14-305

Mustafa H, Ahmad N, Heather H J, Eui-soo K, Khan W A, Ajmal A, Javed K, Pasha T N, Ali A, Kim J J and Sonstegard T S. 2018. Whole genome study of linkage disequilibrium in Sahiwal cattle. South African Journal of Animal Science 48: 353–60. DOI: https://doi.org/10.4314/sajas.v48i2.16

Mrode R, Ojango J M K, Okeyo A M and Mwacharo M. 2019. Genomic Selection and use of Molecular tools in Breeding Programs for Indigenous and Crossbred Cattle in Developing Countries: Current Status and Future Prospects. Frontiers in Genetics. 9: 694. DOI: https://doi.org/10.3389/fgene.2018.00694

Nayee N, Sahana G, Gajjar S, Sudhakar A, Trivedi K R, Lund M S and Guldbrandtsen B. 2018. Suitability of existing commercial single nucleotide polymorphism chips for genomic studies in Bos indicus cattle breeds and their Bos taurus crosses. Journal of Animal Breeding and Genetics. doi: 10.1111/jbg.12356 DOI: https://doi.org/10.1111/jbg.12356

Price A L, Patterson N J, Plenge R M, Weinblatt M E, Shadick N A and Reich D. 2006. Principal components analysis corrects for stratification in genome-wide association studies. Nature Genetics 38: 904–09. DOI: https://doi.org/10.1038/ng1847

Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira M A, Bender D, Maller J, Sklar P, de Bakker P I, Daly M J and Sham P C. 2007. PLINK: A tool set for whole–genome association and population based linkage analysis. American Journal of Human Genetics 81: 559–75. DOI: https://doi.org/10.1086/519795

Xu L, Zhu B, Wang Z, Xu L, Liu Y, Chen Y, Zhang L, Gao X, Gao H, Zhang S, Xu L and Li J. 2019. Evaluation of linkage disequilibrium, effective population size and haplotype block structure in Chinese cattle. Animals 83: 1–14. DOI: https://doi.org/10.3390/ani9030083