3-Title: Genetic divergence in Kasaragod and Vilwadri cattle of Kerala detected using microsatellites

3-Title: Genetic divergence in Kasaragod and Vilwadri cattle of Kerala detected using microsatellites

Authors: Radhika G, Aravindakshan TV, Anilkumar K, Manoj M, Stephy Thomas and Jayaprakash G

Source: Ruminant Science (2021)-10(1):13-18.

How to cite this manuscript: Radhika G, Aravindakshan TV, Anilkumar K, Manoj M, Stephy Thomas and Jayaprakash G (2021). Genetic divergence in Kasaragod and Vilwadri cattle of Kerala detected using microsatellites. Ruminant Science 10(1):13-18.


Native cattle breeds are noted for their adaptability to local environments, resistance to local diseases and form an integral part of the culture and heritage of a geographical area. Kerala, the southernmost state of India, has only one recognized cattle breed, the legendary Vechur cattle, but other native cattle genetic groups like Kasaragod, Vadakara and Vilwadri also contribute to the cattle genetic biodiversity of the state. These animals are generally short in stature and have specific characteristics of their own, but are poor milk producers and hence the demand for milk production in the state is mainly met by the crossbred cattle. The native cattle genetic groups namely, Vechur, Kasaragod, Vadakara and Vilwadri along with high, medium and low milk producing crossbred cattle, were analysed for genetic diversity using microsatellites. Twenty-five microsatellite markers were chosen from the FAO-ISAG panel and these chosen loci were amplified from genomic DNA isolated from whole blood, by multiplex PCR with fluorescent-labelled primers. After genotyping, allelic microsatellite data obtained were analysed using different softwares. The Nei’s genetic distance and identity between the cattle populations studied revealed that the genetic distance was highest between Vilwadri and high yielding crossbred. Vilwadri remained distant from all other cattle populations studied, whereas Kasaragod was genetically distant from Vilwadri and all groups of crossbreds. The dendrogram depicted that Vechur, Vilwadri and Kasaragod cattle separated into distinct populations, diverging from the rest of the studied ones. The observed number of alleles, heterozygosity and the number of private alleles were more in Vilwadri and Kasaragod populations. The results of the present study thus supported the fact that Kasaragod and Vilwadri cattle were genetically divergent from the rest of the studied cattle populations in the state.


Anilkumar K and Reghunandanan KV (2003). Monograph on short cattle of Kerala. Thrissur, India: Kerala Agricultural University 2003.

Amos W, Hoffman JI, Frodsham A, Zhang L, Best S and Hill AVS (2007). Automated binning of microsatellite alleles: problems and solutions. Molecular Ecology Notes 7:10-14.

Azhar PM, Chakraborty D, Kumar D, Anamika, Sofi TA, Kumar N and Taggar RK (2017). Molecular characterization of Poonchi sheep. Ruminant Science 6(2):231-236.

Chacko CT (1993). Development of the Sunandini cattle breed in India. Rome, Italy: Development Support Communication Branch, FAO.http://www.fao.org/docrep/t4650t/t4650T0v.htm

Excoffier L and Lischer HEL (2010). Arlequin suite ver 3.5: A new series of programs to perform population genetics analyses under Linus and windows.  Molecular Ecology Resources 10:564-567.

FAO (2011). Molecular genetic characterization of animal genetic resources. FAO Animal Production and Health Guidelines. No. 9, Rome.

Gayathri SL and Asif M (2019). Vilwadri cattle – Natural elegance from the land of Nila. Veterinarian 1(2):26-27.

Glaubitz JC (2004). Convert: A user-friendly program to reformat diploid genotypic data for commonly used population genetic software packages. Molecular Ecology Notes 4:309-310.

Inamdar Basavraj, Nagaraja R, Yathish HM, Kumar Naveen S, Kumar Naveen GS, Prasanna SB and Prabhu TM (2020). Cytogenetic characterization of Bidri goats of Karnataka. Ruminant Science 9(1):131-136.

Joshi BK, Sodhi M, Mukesh M and Mishra BP (2012). Genetic characterization of farm animal genetic resources of India: A review. Indian Journal of Animal Science 82(3):1259-1275.

Lenstra JA and Bradley DG (1999). Systematics and phylogeny of cattle. In: The Genetics of Cattle. Eds: RFA Ruvinsky, Wallingford: CAB Int :1-14.

Levene H (1949). On a matching problem arising in genetics. Annals of Mathematical Statistics 20:91-94.

Mukesh M, Sodhi M, Bhatia S and Mishra BP (2004). Genetic diversity of Indian native cattle breeds as analyzed with 20 microsatellite loci. Journal of Animal Breeding and Genetics 121:416-424.

Nei M (1972).  Genetic distance between populations. American Naturalist 106:283-292.

Oosterhout CV, Hutchinson DW and Shipley P (2004).  Micro-Checker 2.2.3. Available http://www.microchecker.hull.ac.uk/.

Pandey AK, Sharma R, Singh Y, Prakash BB and Ahlawat SPS (2006). Genetic diversity studies of Kherigarh cattle breed based on microsatellite markers. Journal of Genetics 85(2):117-22.

Pritchard JK, Stephens M and Donnelly P (2000).  Inference of population structure using multilocus genotype data.  Genetics 155:945-959.

Radhika G, Aravindakshan TV, Jinty S and Ramya K (2017). Evaluation of genetic diversity, population structure, and relationship between legendary Vechur cattle and crossbred cattle of Kerala state, India. Animal Biotechnology DOI:10.1080/10495398.2017.1297719

Sambrook J and Russell DW (2001). Molecular Cloning: A Laboratory Manual. 3rd Ed, Cold Spring Harbor Laboratory Press, New York.

Shah TM, Patel JS and Bhong CD (2012). Evaluation of genetic diversity and population structure of west-central Indian cattle breeds. Anime Generator 44(4):442-445.

Sharma R, Kishore A and Mukesh M (2015). Genetic diversity and relationship of Indian cattle inferred from microsatellite and mitochondrial DNA markers. BMC Genetics 16:73.

Vani S and Sakunthala Devi K (2017). Genetic diversity and phylogenetic relationship between indigenous cattle breeds. International Journal of Current Microbiology and Applied Sciences 6(3):1650-1654.

Yeh FC, Yang RC, Boyle TBJ, Ye ZH and Mao JX (1999). POPGENE Version 1.32, the user-friendly shareware for population genetic analysis. Molecular Biology and Biotechnology Centre, University of Alberta, Canada. http://www.ualberta.ca/-fyeh/fyeh.