Genetic diversity and bottleneck analysis of Konkan Kanyal goats

Mishra, Prachi; Ali, A.S.; Aggarwal, R. A. K.; Dixit, S. P.; Kawitkar, V.S.; Dangi, P.S.; Verma, Naresh K.

doi:10.1017/s2078633612000082

Cited by 8 publications

(4 citation statements)

References 6 publications

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“…The allelic polymorphism ranged between 4 (ETH10, ILSTS008) and 17 (BM64444) with a mean number of alleles of 10.14±0.83. The mean observed number of allele recorded in this study was higher than the values reported in Barbari and Kanni Adu goats [5,12] and comparable to the value of 10.20 reported for Konkan Kanyal goats [13]. The high allelic diversity observed is probably due to no selection pressure and choice of samples based on random sampling.…”

Section: Resultssupporting

confidence: 61%

“…In general, few studies have reported on the possible occurrence of the genetic bottleneck based on microsatellite data, viz., Dexter, Bargur and African cattle breeds and Valais Blackneck goat [19][20][21][22]. Earlier studies on different Indian and Iranian goat breeds did not reveal any indication of recent occurrence of the genetic bottleneck [1,5,12,13,[23][24][25].…”

Section: Resultsmentioning

confidence: 99%

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Genetic architecture and bottleneck analyses of Salem Black goat breed based on microsatellite markers

Thiruvenkadan¹,

Jayakumar²,

Kathiravan³

et al. 2014

Vet World

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Aim: The present study was undertaken in Salem Black goat population for genetic analysis at molecular level to exploit the breed for planning sustainable improvement, conservation and utilization, which subsequently can improve the livelihood of its stakeholders. Materials and Methods:Genomic DNA was isolated from blood samples of 50 unrelated Salem Black goats with typical phenotypic features in several villages in the breeding tract and the genetic characterization and bottleneck analysis in Salem Black goat was done using 25 microsatellite markers as recommended by the Food and Agricultural Organization, Rome, Italy. The basic measures of genetic variation were computed using bioinformatic software. To evaluate the Salem Black goats for mutation drift equilibrium, three tests were performed under three different mutation models, viz., infinite allele model (IAM), stepwise mutation model (SMM) and two-phase model (TPM) and the observed gene diversity (He) and expected equilibrium gene diversity (Heq) were estimated under different models of microsatellite evolution. Results:The study revealed that the observed number of alleles ranged from 4 (ETH10, ILSTS008) to 17 (BM64444) with a total of 213 alleles and mean of 10.14±0.83 alleles across loci. The overall observed heterozygosity, expected heterozygosity, inbreeding estimate and polymorphism information content values were 0.631±0.041, 0.820±0.024, 0.233±0.044 and 0.786±0.023 respectively indicating high genetic diversity. The average observed gene diversities (He) pooled over different markers was 0.829±0.024 and the average expected gene diversities under IAM, TPM and SMM models were 0.769±0.026, 0.808±0.024 and 0.837±0.020 respectively. The number of loci found to exhibit gene diversity excess under IAM, TPM and SMM models were 18, 17 and 12 respectively. Conclusion:All the three statistical tests, viz., sign test, standardized differences test and Wilcoxon sign rank test, revealed significant deviation of Salem Black goats from mutation-drift equilibrium under IAM and TPM models, however, nonsignificant deviation under SMM model. The qualitative test of mode shift analysis supported the results under SMM indicating the absence of the genetic bottleneck in the recent past in Salem Black goats.

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Section: Resultssupporting

confidence: 61%

Section: Resultsmentioning

confidence: 99%

Genetic architecture and bottleneck analyses of Salem Black goat breed based on microsatellite markers

Thiruvenkadan¹,

Jayakumar²,

Kathiravan³

et al. 2014

Vet World

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“…Matrix of NEI's (1978) showed that all of the studied loci were highly informative, indicating high polymorphism across the loci, thus suggesting suitability of these markers for the study of genetic diversity in buffalos. Suitability of these markers was further supported by the fact that the number of alleles for each marker was higher than the minimum number of alleles (four) recommended for microsatellite markers to be used in the estimation of genetic distance in order to reduce the standard error (MISHRA et al, 2012).…”

Section: Resultsmentioning

confidence: 99%

Study of genetic diversity of Iranian indigenous buffalo populations using microsatellite markers

2019

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Indigenous buffalo breeds represent a unique genetic resource, and understanding their variability, population structure and breeding units is important for their sustainable conservation. In the present study the genetic structure of Iranian buffalo populations was analyzed using ten microsatellite markers. Two hundred hair samples were collected and DNA was extracted using modified salting out method. After Polymerase Chain Reaction (PCR), the PCR products were electrophoresed using 9% polyacrylamide gel. Fifty-nine alleles were observed for all the loci. The average number of alleles was 5.90 and the effective average number of alleles was 4.86. The high level of mean heterozygosity index between three populations indicate that the genetic diversity is high in within and between populations. The mean of polymorphism information content (PIC) value for all loci was 0.70. The FST value for the total loci was 0.01, indicating a very low level of genetic structure among populations. The genetic structure AMOVA analysis showed that about 3% of the total genetic variation was explained by population differences and 97 percent was corresponded to differences among individuals. The obtained results at the present study indicated that characterization of genetic diversity by employing molecular tools is a prerequisite in developing strategies for conservation and utilization of buffalo genetic resources.

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“…In the present investigation, the markers used are neutral and are widely distributed in the genome, their chromosomal locations are given somewhere else (Verma et al, 2007a). 2010), Changthangi (Mishra et al, 2010) and Konkan Kanyal (Mishra et al, 2012). of alleles; Ne, effective no.…”

Section: Microsatellite Markersmentioning

confidence: 99%

Microsatellite-based genetic evaluation of Ghumusar goats of Orissa, India

Mishra¹,

Ali²,

Dixit

et al. 2013

Anim. Genet. Resour.

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Ghumusar is an inadequately studied goat population of western region of Ganjam district of Orissa state. Sporadic information is available on its morphological traits but no information is found on its genetic variability. Therefore, an attempt was made to measure the genetic diversity in Ghumusar goat population using 25 microsatellite markers. Genomic DNA isolated from blood samples drawn at random from 50 individuals were utilized for this study. The average number of observed allele was 9.80 and the effective average number of allele was 4.28. The polymorphic information contents ranged from 0.53 to 0.91. The average observed and expected heterozygosity was 0.73 and 0.71, respectively. The values of Nei's gene diversity in Ghumusar goat population ranged from 0.11 to 0.87 with a mean of 0.69. The overall Fis value was observed to be 0.002, which is not significantly different from zero; hence indicating no global deficit of heterozygotes. Under sign test, expected number of loci with heterozygosity excess (Hee) was 14.88, 14.79 and 14.74 for the infinite allele model (IAM), stepwise mutation model (SMM) and two-phased model (TPM) of mutation, respectively. The observed number of loci with heterozygotic excess (He) was 14, 8 and 2 under these three models, respectively. Under all the three models, He was less than Hee and this deviation was significant under SMM and TPM models. There was no serious genetic reduction in effective population size as indicated by L-shaped curve in Ghumusar goat population. RésuméLes chèvres Ghumusar constituent une population caprine de l'ouest du district de Ganjam, dans l'état d'Orissa, à peine étudiée. On ne dispose que de l'information sporadique sur ses traits morphologiques sans qu'il ait été trouvé de l'information sur sa variabilité génétique. C'est ainsi que l'on a cherché à mesurer la diversité génétique chez la population des chèvres Ghumusar au moyen de 25 marqueurs microsatellites. Pour mener cette étude, l'ADN génomique isolé dans les échantillons de sang prélevés sur 50 individus choisis au hasard a été utilisé. Le nombre moyen d'allèles observés a été de 9,80 alors que le nombre moyen effectif a été de 4,28. Les contenus d'information polymorphique ont varié entre 0,53 et 0,91. L'hétérozygotie moyenne observée et attendue a été respectivement de 0,73 et 0,71. Les valeurs de la diversité génétique de Nei ont varié de 0,11 à 0,87, avec une moyenne de 0,69, au sein de la population de chèvres Ghumusar. Il a été observé que la valeur globale pour le paramètre F IS était de 0,002, ce qui n'est pas statistiquement différent de zéro et indique donc une absence de déficit en hétérozygotes. Pour ce qui est du test des signes, le nombre attendu de loci avec excès d'hétérozygotie (Ha) a été respectivement de 14,88, 14,79 et 14,74 pour le modèle d'allèles infinis, le modèle de mutation par étape et le modèle de mutation en deux phases. Le nombre de loci observé avec excès d'hétérozygotie (Ho) a été de 14, 8 et 2 pour ces trois modèles, respectivement. Pour les trois modèles,...

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Genetic diversity and bottleneck analysis of Konkan Kanyal goats

Cited by 8 publications

References 6 publications

Genetic architecture and bottleneck analyses of Salem Black goat breed based on microsatellite markers

Genetic architecture and bottleneck analyses of Salem Black goat breed based on microsatellite markers

Study of genetic diversity of Iranian indigenous buffalo populations using microsatellite markers

Microsatellite-based genetic evaluation of Ghumusar goats of Orissa, India

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