RESEARCH ARTICLES

Linkage disequilibrium over short physical genomic distances measured using medium density snp beadchip in native goat breeds of Kerala
Marykutty Thomas, G. Radhika, T.V. Aravindakshan, R. Thirupathy, K. Raji. and M. Shynu.

doi: https://doi.org/10.51966/jvas.2021.52.1.14-18

Journal of Veterinary and Animal Sciences.2021. 52(1):14-18.

Author Details

Marykutty Thomas: Assistant Professor and PhD Scholar, Centre for Advanced Studies in Animal Genetics and Breeding, College of Veterinary and Animal Sciences, Mannuthy, Kerala Veterinary and Animal Sciences University, Kerala, India.

G. Radhika: Associate Professor, Centre for Advanced studies in Animal Genetics and Breeding,College of Veterinary and Animal Sciences, Mannuthy, Kerala Veterinary and Animal Sciences University, Kerala, India.

T. V. Aravindakshan: Director, Centre for Advanced studies in Animal Genetics and Breeding, College of Veterinary and Animal Sciences, Mannuthy, Kerala Veterinary and Animal Sciences University, Kerala, India.

R. Thirupathy: Professor and Head, University Goat and Sheep Farm, Mannuthy, Kerala Veterinary and Animal Sciences University, Kerala, India.

K. Raji: Associate Professor, Department of Veterinary Physiology, College of Veterinary and Animal Sciences, Mannuthy, Kerala Veterinary and Animal Sciences University, Kerala, India.

M. Shynu: Associate Professor, Department of Veterinary Biochemistry, College of Veterinary and Animal Sciences, Pookode, Kerala Veterinary and Animal Sciences University, Kerala, India.

Article History

Received: 13.06.2020, Accepted: 20.07.2020, Published online: 01.01.2021

Corrersponding author: Marykutty Thomas

e-mail: marykutty@kvasu.ac.in

Citation: Marykutty, T., Radhika, G., Aravindakshan, T.V., Thirupathy, R., Raji, K. and Shynu, M. 2021. Linkage disequilibrium over short physical genomic distances measured using medium density SNP beadchip in native goat breeds of Kerala.J. Vet. Anim. Sci.52(1): 14-18.



Abstract


The extent of linkage disequilibrium (LD) at genome wide level is crucial in determining the effectiveness of genomics tools in livestock breeding. The present population genomic study was conducted in native goat breeds of Kerala namely; Attapady Black goats (n=24) and Malabari goats (n=24) to characterise extent of LD within 40kbp marker interval using genome wide single nucleotide polymorphism (SNP) marker data obtained by SNP50 BeadChip genotyping. Extent of LD between bi allelic markers was measured using correlation coefficient (r2). Mean r2 between adjacent SNP pairs across all autosomes within 40Kbp marker interval was low (Attapady Black: 0.1336; Malabari: 0.1284). The LD varied across autosomes in native goats. It was the highest for SNP pairs on Capra hircus autosome 6 (CHI 6) and the lowest for SNP pairs harboured in CHI 28 in Attapady Black goats and for SNP pairs in CHI 29 in Malabari goats. The low LD estimates indicate the genetically diverse nature of native goats. Current results also imply that denser SNP beadchip array with inter marker interval of below 40kbp would be desirable for effective genome wide association study (GWAS) and genomic selection in native goats.

Keywords: Linkage disequilibrium, goat, SNP BeadChip