Microsatellite based genetic variation among the buffalo breed populations in Pakistan

Abstract

IntroductionEight microsatellite loci were used to define genetic diversity among five native water buffalo breeds in Pakistan.Material and MethodsBlood samples (10 mL) from 25 buffaloes of each of the Nili, Ravi, Nili-Ravi, Kundhi, and Azi-Kheli breeds were collected aseptically from the jugular vein into 50 ml Falcon tubes containing 200 µl of 0.5 M EDTA. The phenol-chloroform method was used to extract DNA and the regions were amplified for microsatellite analysis. The eight microsatellite markers ETH10, INRA005, ILSTS029, ILSTS033, ILSTS049, ILSTS052, ETH225, and CSSM66 were analysed.ResultsThe effective number of alleles across all loci was as usual lower than the observed values with a mean value of 2.52 alleles per locus. The overall allele frequency varied from 0.0041 for alleles B, I, and J over respective loci ILSTS052, INRA005, and ILSTS029 to 0.80 for allele H over locus ILSTS029. The average observed and expected heterozygosity values across all polymorphic loci in all studied buffalo breeds were 0.43 and 0.53, respectively. The overall value for polymorphic information content of considered microsatellite markers was 0.53, suggesting their appropriateness for genetic diversity analysis in buffalo. The mean Fis value was 0.13 and all loci except ILSTS049 were found significantly deviated from HWE, most likely due to non-random breeding. The five buffalo populations were genetically less diverse as indicated by a small mean Fst value (0.07). The average gene flow (Nm) indicative for population migration was calculated as 3.31. Nei’s original measures of genetic distance (Ds) revealed ancient divergence of the Nili and Azi-Kheli breeds (Ds = 0.1747) and recent divergence of the Nili and Ravi breeds (Ds = 0.0374).ConclusionThese estimates of genetic diversity were seen to coincide with phenotypic differentiation among the studied buffalo breeds. The present study reports the first microsatellite marker-based genetic diversity analysis in Pakistani buffalo breeds, and might facilitate similar studies in other livestock breeds of Pakistan.

Determination and phylogenetic analysis of the complete mitochondrial genome of Bubalus bubalis Linnaeus, 1758 breed Nili-Ravi (Artiodactyla: Bovidae)

“…In addition, our work confirmed that NRB has a close genetic relationship with B. bubalis isolate India 4 which is consistent with those reported previously (Hussain et al. 2017 ).…”

Evaluation of Genetic Diversity and Structure of Turkish Water Buffalo Population by Using 20 Microsatellite Markers

“…All measures of genetic diversity: the mean number of alleles (N a ), the number of effective alleles (N e ), allelic richness (R s ), Shannon’s Information Index (I) and polymorphic information content values (PIC) showed that most of the studied loci were highly informative, indicating high polymorphism across the loci, thus suggesting the suitability of these microsatellite markers for genetic diversity studies in Turkish water buffalo populations. The values of genetic diversity parameters were higher compared with a similar study of Asian water buffalo population (Pakistan, Thai, Indonesia, Egypt and China) [ 42 , 52 , 53 , 54 , 55 ], South American buffalo populations (Brazil and Colombia) [ 10 , 38 , 56 ], North American buffalo populations (Cuba) [ 36 , 56 , 57 ], southeast of Central Europe (Romania) [ 58 ] and Southern Europe water buffalo populations (Italia and Greece) [ 41 ]. Molecular genetic parameters (N a , N e , PIC and HO) obtained from this study were higher than previous research in Turkish water buffalo [ 12 , 17 , 18 ].…”

“…The allele diversity for Turkish water buffalo populations was lower than that of the Colombian buffalo population studied with 10 microsatellite loci [ 10 ] but much higher than that reported for Cuban, Pakistan, Romanian, Egyptian, Iranian and Brazilian water buffalo populations [ 52 , 56 , 58 , 59 , 60 ]. Turkish water buffalo populations showed a drastic low number of the effective number of alleles (even lower than half) than the observed mean number of alleles.…”

“…Another measure of genetic variability is expected heterozygosity where the maximum expected heterozygosity (0.7280) was showed in the MUS population and the minimum (0.5833) was shown in the BUR population. This study results indicate the 17 tested Turkish water buffalo population have substantial amount of genetic diversity, when compared to some other water buffalo breeds around the world where, Pakistan water buffalo breeds such as, Nili (H E = 0.53), Ravi(H E = 0.55), Nili-Ravi (H E = 0.54), Kundhi (H E = 0.45), Azi-Kheli (H E = 0.44) [ 52 ], Romanian buffalo (H E = 0.4048; Popa et al [ 58 ]), Egyptian buffalo (H E = 0.527; Rushdi et al [ 60 ]); Cuban and Brazilian buffaloes such as, Brazilian Murrah (H E = 0.649), Brazilian Jaffarabadi (H E = 0.643), Cuban Buffalypso/Carabao hybrid (H E = 0.599) [ 56 ], Indonesian swamp buffalo (H E = 0.44; Saputra et al [ 53 ]), Thai swamp buffalo (H E = 0.61, Sraphet et al [ 54 ]), Cuban water buffalo population (H E = 0.54, Acosta et al [ 57 ]; H E = 0.509, Uffo et al [ 36 ]), Italian and Greek buffalo populations (H E respectively; 0.57 and 0.59; Moioli et al [ 41 ]), Brazilian buffaloes (H E = 0.558; Marques et al [ 38 ]), Colombian buffalo (H E = 0.70; Ángel-Marín et al [ 10 ]), Guilan buffalo populations (H E = 0.67; Aminafshar et al [ 14 ]), some of Turkish water buffalo populations (H E = 0.5359; Özkan Ünal et al [ 12 ]), Asian swamp buffalo (H E = 0.50; Barker et al [ 42 ]) and Chinese buffalo (H E = 0.53, Zhang et al [ 55 ]). On the other hand, the buffalo populations tested in our study showed less genetic diversity when compared to Iranian indigenous buffalo populations (H E = 0.75; Darestani et al [ 59 ]) and Iraqi buffalo populations (H E = 0.86; Jaayid and Dragh, [ 61 ]), Indian river buffalo breeds (H E = 0.71–0.78; Kumar et al [ 39 ]), and African buffalo (H E = 0.759; Van Hooft et al [ 62 ]).…”

Identification of novel single nucleotide polymorphisms in the growth hormone ( GH ) gene in Anatolian water buffalo ( Bubalus bubalis ) populations in Turkey

“…Water buffaloes have been reported to be of great importance to the lives of farmers and thus to the economies of many countries worldwide (Hussain et al, 2017). The number of water buffaloes in the world has increased rapidly over the past few decades, and according to FAO statistics, there are about 201 million buffaloes in the world (FAO, 2017).…”