Microsatellite-based phylogeny of Indian domestic goats

Centre for cellular and Molecular biology, Uppal Road, Hyderabad-500007, India.
BMC Genetics (Impact Factor: 2.4). 02/2008; 9(1):11. DOI: 10.1186/1471-2156-9-11
Source: PubMed


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,
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    • "For instance, Zimbabwe chickens seem to form a unique genetic pool (Muchadeyi et al. 2007). Rout et al. (2008) showed that Indian goat breeds could be classified in two major genetic clusters. Zhang et al. (2007) studied 27 indigenous Chinese cattle breeds. "
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    ABSTRACT: The expansion of intensive livestock production systems in developing countries has increased the introduction of highly productive exotic breeds facilitating indiscriminate crossbreeding with local breeds. In this study, we set out to investigate the genetic status of the Vietnamese Black H'mong pig breed by evaluating (1) genetic diversity and (2) introgression from exotic breeds. Two exotic breeds, namely Landrace and Yorkshire used for crossbreeding, and the H'mong pig population from Ha Giang (HG) province were investigated using microsatellite markers. Within the province, three phenotypes were observed: a White, a Spotted and a Black phenotype. Genetic differentiation between phenotypes was low (0.5-6.1%). The White phenotypes showed intermediate admixture values between exotic breeds and the Black HG population (0.53), indicating a crossbreed status. Management practices were used to predict the rate of private diversity loss due to exotic gene introgressions. After 60 generations, 100% of Black private alleles will be lost. This loss is accelerated if the admixture rate is increased but can be slowed down if the mortality rate (e.g., recruitment rate) is decreased. Our study showed that a large number of markers are needed for accurately identifying hybrid classes for closely related populations. While our estimate of admixture still seems underestimated, genetic erosion can occur very fast even through indiscriminate crossbreeding.
    Ecology and Evolution 05/2012; 2(5):962-75. DOI:10.1002/ece3.229 · 2.32 Impact Factor
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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(6):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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    ABSTRACT: To better understand natural genetic variation in indigenous livestock resources, as well as formulate conservation policies, better genetic characterization is required to balance the competing needs of genetic improvement and conservation of native germplasm, primarily in rural agricultural systems in developing countries. Genetic diversity of goats in southern Nigeria was assessed using 295 indigenous goats with ten microsatellite DNA markers. The breeds are West African Dwarf (WAD), Red Sokoto (RS) and Sahel (SA) sampled from farms, market places and rural homesteads. The mean expected heterozygosity (HE) ranged from 0.608 to 0.784 in two sub-populations of WAD goats. Deviations from Hardy–Weinberg equilibrium (HWE) were statistically significant (p < 0.05) indicating that these populations are under various forces stemming from the management choices of rural dwellers. Polymorphic information content of these markers averaged 0.803 and mean GST index was 0.176. The measure of genetic distance between pairs of breeds indicated that the lowest distance was between WAD and RS (0.268) and the highest distance was between WAD and SA (0.662) goats, respectively. The estimated dendogram clustered these Nigerian goats into nine sub-populations and two major genetic groups. The study suggests that indigenous goat populations in southern Nigeria may be collapsed from three breeds into two distinct genetic groups, possibly due to extensive cross-breeding and gene flow between them, which are symptomatic of uncontrolled crossing across much of the country.
    11/2011; 49:33 - 41. DOI:10.1017/S207863361100035X
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