Assessment of genetic diversity and bottleneck in Purnathadi buffaloes using short tandem repeat markers

Abstract

This study is the maiden attempt for genetic characterization of the Purnathadi, a phenotypically distinct buffalo population of the western Vidarbha region of Maharashtra and to explore genetic diversity using STR markers. A total of 48 unrelated Purnathadi buffaloes from the entire native tract were genotyped using a battery of 25 heterologous microsatellite markers. 5′ end of forward primer of each microsatellite marker was labeled with one of the fluorescent dyes, viz., FAM (Blue), VIC (Green), NED (Yellow) or PET (Red) to assess the fragment length of genotyped PCR product with automated DNA sequencer (ABI 3100). 23 microsatellite loci (except ETH003 and ILSTS030) amplified successfully and adequately high allelic diversity (observed: 0.615 ± 0.043 and expected: 0.655 ± 0.037) was reported with 162 distinct microsatellite alleles. Sufficiently high Shannon index and PIC indicated the suitability of markers to evaluate genetic diversity in Purnathadi buffaloes. Within-population inbreeding estimates (F_IS) for Purnathadi buffalo ranged between −0.171 and 0.495 with global F_IS average of 5.9%. The outcome for IAM, TPM and test for mode shift revealed the absence of any recent bottleneck in Purnathadi buffalo. Pairwise F_ST (genetic differentiation) and gene flow between Purnathadi, Nagpuri and Marathwadi buffaloes were estimated using genotype data of 19 microsatellite markers. Lowest F_ST (0.031) was observed between Nagpuri and Purnathadi buffaloes with highest gene flow of 7.91% and highest F_ST (0.094) was between Purnathadi and Marathwadi populations. Present findings will definitely support in designing breeding plan for genetic improvement, as well as for developing conservation strategies of Purnathadi buffalo population. The comparative molecular study with other breeds of the regions is needed.

Keywords:

• Buffalo
• microsatellite
• genetic characterization
• SSR markers

Acknowledgments

Authors wish to thank Director, NBAGR, Karnal to include Purnathadi buffalo under their project and to provide all necessary facilities to do the molecular work and the Associate Dean, PGIVAS, Akola to provide the necessary support to carry out this work. Sincere gratitude to the state animal husbandry officers and field veterinarians for rendering necessary help and to all the livestock keepers who allowed the collection of blood samples from their buffaloes.

Disclosure statement

No potential conflict of interest was reported by the author(s).