Assessment of genetic diversity and genetic characterization of Nili Ravi buffalo breed utilizing microsatellite markers

Atia Bukhari, Naveed Ahmed, Fizza Khan, Muhammad Shafique, Asif Suleman Sahi


Background: Livestock contribution to Pakistan’s GDP is 11.2% and it engages 8 million of rural families for their livelihood. Estimated population of buffalo is 40.00 million heads in Pakistan mostly consisting of low genetic worth population resulting in low productivity and pressure on natural resources. Assessment of genetic diversity and genetic characterization of indigenous livestock resources is an essential step towards conservation and to gauge effects of various breed improvement efforts on population genetics.

Methods: In present study genetic diversity of Nili Ravi buffalo population was assessed. A total of 196 unrelated Nili Ravi buffaloes from Punjab, Pakistan were sampled in this study. Genomic DNA was extracted and subjected to amplification using FAO recommended 12 Short Tandem Repeats (STRs) microsatellite markers. Among 12 microsatellite loci, 11 were successfully amplified (TGLA227, BM2113, ETH10, SPS115, TGLA126, TGLA122, INRA23, BM1818, ETH3, ETH225 and BM1824) whereas microsatellite locus TGLA53 was not amplified. Amplicons were resolved by genetic analyzer instrument and gene mapper software. Allele count, frequencies, gene diversity, heterozygosity, polymorphic information content (PIC) and linkage disequilibrium values were calculated by using Microsatellite toolkit v3 and Power Marker version 3.25.

Results: A total of 96 alleles were detected in 196 samples with average of 8.73 alleles per locus and range of 5 alleles (ETH 3) to 18 alleles (ETH 225) per locus. Gene diversity ranged from 0.198 (BM1824) to 0.841 (ETH225), observed heterozygosity values ranged from 0.081 (ETH10) to 0.831 (BM2113) and PIC values ranged from 0.191 (BM1824) to 0.825 (ETH225).

Conclusion: This study which will serve as a baseline to understand genetic dynamics of Nili Ravi buffalo breed. Highly polymorphic nature of STR markers will help in understanding effects of various breed improvements efforts on genetic diversity of Nili Ravi breed in future studies.

Keywords: Microsatellite; STR; Nili Ravi Buffalo; Genetic Characterization; Punjab

Full Text:



Pakistan Go (2019) Economic Survey of Pakistan. Islamabad.

Hussain T, Ellahi Babar M, Ali A, Nadeem A, Rehman ZU, et al. Microsatellite based Genetic Variation among the Buffalo Breed Populations in Pakistan. Journal of veterinary research, (2017); 61(4): 535-542.

FAO (2011) Molecular genetic characterization of animal genetic resources.

Hoffman I. New MoDAD marker sets to be used in diversity studies for the major farm animal species : recommendations of a joint ISAG/FAO working group. Proceedings of the 29th International Conference on Animal Genetics, September 11-16th 2004, Meiji University, Tokyo, Japan, (2004).

Liu K, Muse SV. PowerMarker: an integrated analysis environment for genetic marker analysis. Bioinformatics, (2005); 21(9): 2128-2129.

Harris AM, DeGiorgio M. An Unbiased Estimator of Gene Diversity with Improved Variance for Samples Containing Related and Inbred Individuals of any Ploidy. G3: Genes|Genomes|Genetics, (2017); 7(2): 671-691.


  • There are currently no refbacks.