Genetic diversity and relationship of cattle populations of East India: distinguishing lesser known cattle populations and established breeds based on STR markers

Abstract

India has 34 recognized breeds of cattle in addition to many more not characterized and accredited so far. It is imperative to characterize all the cattle germplasm of the country so as to have better breeding and conservation options. Thus, present study was planned for assessing genetic diversity and relationship between three local cattle populations (Gangatiri, Shahabadi and Purnea) and two established cattle breeds (Bachaur and Siri) of eastern India by using 21 FAO and ISAG recommended microsatellite markers. A total of 243 unrelated DNA samples of five cattle populations were collected from respective habitats. A total of 304 microsatellite alleles were identified with number of alleles at one locus ranging from 5 to 29. The average observed heterozygosity lie within the narrow range of 0.681 ± 0.04 in Purnea to 0.721 ± 0.03 in Siri. Mean estimates of observed and expected heterozygosity over all loci and breeds were 0.704 ± 0.02 and 0.720 ± 0.01, respectively. In the overall population, the homozygote excess (FIT) of 0.073 ± 0.02, was partly due to the homozygote excess within breeds (FIS = 0.026 ± 0.02) and to a larger extent due to genetic differentiation among breeds (FST = 0.048 ± 0.01). The genetic distance, STRUCTURE and Principal Component Analyses concluded that the Siri cattle are most distinct among the investigated cattle populations. Furthermore the analysis of genetic structure indicated that the most probable number of clusters is four. All analysis showed that a significant amount of genetic variation is maintained in local cattle populations of which Shahabadi and Purnea are distinct from the recognized breeds of the area and needs recognition as breeds.

Genetic diversity in Zimbabwean Sanga cattle breeds using microsatellite markers

“…The current study revealed higher heterozygosity values compared with50-63%, 70%, 71%, 68%, and 70% reported in indigenous cattle from Mozambique (Bessa et al, 2009), South Africa (Sanarana et al, 2016), Senegal (Ndiaye et al, 2015), Cameroon (Ngono-Ema et al, 2014), and India (Sharma et al, 2013), respectively. Higher Ho compared with He and fixation indices suggested that breeds were in HWE.…”

“…Edea et al (2013) and Zerabruk et al (2012) reported very low levels of differentiation among Ethiopian cattle populations (F ST = 1% and 1.1%) using single nucleotide polymorphisms (SNPs) and microsatellites, respectively. However, higher F ST values of 13.3% were reported for Indian cattle breeds (Sharma et al, 2013). The moderate value of genetic differentiation may be attributed to recent divergence of the breeds from a common ancestry, reproductive isolation, or moderate selection pressure in the populations from which samples were collected (Felius et al, 2014).…”

“…In Mozambique, Bessa et al (2009) found allelic diversity of 5.9-6.4 alleles per locus. However, Ndiaye et al (2015) reported 10.5 alleles per locus among Senegalese cattle, and Sharma et al (2013) reported 9.0 alleles per locus in Indian cattle breeds. Although comparable with other studies, genetic variability in this study was moderate and similar between breeds.…”

“…This signifies low gene flow between breeds, resulting in moderately high measures of genetic differentiation. Ngono-Ema et al (2014) Kugonza et al (2011) and Sharma et al (2013) found considerably higher Nm values among Ankole and Indian cattle populations.…”

“…Since these deviations were not consistent across breeds, they were considered to be caused by a Type I error sampling effect (FAO, 2011). The level of variation depicted by number and size of alleles at each microsatellite locus is a useful measure of genetic variability and differentiation among breeds within a species (Sharma et al, 2013). All markers except RM067 exceeded FAO's recommended minimum threshold of five alleles per locus, which is required for estimation of genetic differences among animal breeds (FAO, 2011;Sanarana et al, 2016).…”