Microsatellite-based phylogeny of Indian domestic goats

Centre for cellular and Molecular biology, Uppal Road, Hyderabad-500007, India.
BMC Genetics (Impact Factor: 2.36). 02/2008; 9:11. DOI: 10.1186/1471-2156-9-11
Source: PubMed

ABSTRACT The domestic goat is one of the important livestock species of India. In the present study we assess genetic diversity of Indian goats using 17 microsatellite markers. Breeds were sampled from their natural habitat, covering different agroclimatic zones.
The mean number of alleles per locus (NA) ranged from 8.1 in Barbari to 9.7 in Jakhrana goats. The mean expected heterozygosity (He) ranged from 0.739 in Barbari to 0.783 in Jakhrana goats. Deviations from Hardy-Weinberg Equilibrium (HWE) were statistically significant (P < 0.05) for 5 loci breed combinations. The DA measure of genetic distance between pairs of breeds indicated that the lowest distance was between Marwari and Sirohi (0.135). The highest distance was between Pashmina and Black Bengal. An analysis of molecular variance indicated that 6.59% of variance exists among the Indian goat breeds. Both a phylogenetic tree and Principal Component Analysis showed the distribution of breeds in two major clusters with respect to their geographic distribution.
Our study concludes that Indian goat populations can be classified into distinct genetic groups or breeds based on the microsatellites as well as mtDNA information.

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Available from: Pramod Rout, Jul 31, 2015
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    • "Microsatellite analysis was carried out to test for signatures of recent population bottlenecks in Jamunapari goats. This analysis was carried out on 49 DNA samples with 17 microsatellite markers (Table 1) as reported by Rout et al. [11]. For these 17 loci, genetic variation was quantified using measures of the total number of alleles, number of polymorphic loci, observed and expected heterozygosity per locus, and allelic richness using GENEPOP (Version 3.4; [15]), FSTAT2.93 [16], and AGA rst [17]. "
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    ABSTRACT: Jamunapari, a dairy goat breed of India, has been gradually declining in numbers in its home tract over the years. We have analysed genetic variation and population history in Jamunapari goats based on 17 microsatellite loci, 2 milk protein loci, mitochondrial hypervariable region I (HVRI) sequencing, and three Y-chromosomal gene sequencing. We used the mitochondrial DNA (mtDNA) mismatch distribution, microsatellite data, and bottleneck tests to infer the population history and demography. The mean number of alleles per locus was 9.0 indicating that the allelic variation was high in all the loci and the mean heterozygosity was 0.769 at nuclear loci. Although the population size is smaller than 8,000 individuals, the amount of variability both in terms of allelic richness and gene diversity was high in all the microsatellite loci except ILST 005. The gene diversity and effective number of alleles at milk protein loci were higher than the 10 other Indian goat breeds that they were compared to. Mismatch analysis was carried out and the analysis revealed that the population curve was unimodal indicating the expansion of population. The genetic diversity of Y-chromosome genes was low in the present study. The observed mean M ratio in the population was above the critical significance value (Mc) and close to one indicating that it has maintained a slowly changing population size. The mode-shift test did not detect any distortion of allele frequency and the heterozygosity excess method showed that there was no significant departure from mutation-drift equilibrium detected in the population. However, the effects of genetic bottlenecks were observed in some loci due to decreased heterozygosity and lower level of M ratio. There were two observed genetic subdivisions in the population supporting the observations of farmers in different areas. This base line information on genetic diversity, bottleneck analysis, and mismatch analysis was obtained to assist the conservation decision and management of the breed.
    The Scientific World Journal 04/2012; 2012:618909. DOI:10.1100/2012/618909 · 1.73 Impact Factor
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    • "Increasing F IT values suggest some measure of homozygosity and heterozygote deficit resulting from relatedness of individuals which may be a consequence of the emergent population structure of Nigerian goats, not previously uncovered by protein polymorphisms based on haemoglobin and transferrin. The presence of negative F IS values at loci ETH225, TGLA40, ILSTS5, SRCRSP10 and IDVGA7 suggests heterozygote deficiencies which have also been reported in other studies on goats (Barker et al., 1997; Luikart et al., 1999; Agha et al., 2008; Rout et al., 2008; Dixit et al., 2009). This heterozygote deficiency may arise due to population sub-structure from pooling together different populations (admixture) in the analysis (Cerda-Flores et al., 2002; Muema et al., 2009). "
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    11/2011; 49:33 - 41. DOI:10.1017/S207863361100035X
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