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

Published online by Cambridge University Press:  10 April 2013

Priyanka Mishra
Affiliation:
Department of Biotechnology, Saifia Science College, Bhopal, Madhya Pradesh, India National Bureau of Animal Genetic Resources, Karnal 132001, Haryana, India
Ayesha S. Ali
Affiliation:
Department of Biotechnology, Saifia Science College, Bhopal, Madhya Pradesh, India
S.P. Dixit
Affiliation:
National Bureau of Animal Genetic Resources, Karnal 132001, Haryana, India
R.A.K. Aggarwal
Affiliation:
National Bureau of Animal Genetic Resources, Karnal 132001, Haryana, India
P.S. Dangi
Affiliation:
National Bureau of Animal Genetic Resources, Karnal 132001, Haryana, India
Neha Tyagi
Affiliation:
National Bureau of Animal Genetic Resources, Karnal 132001, Haryana, India
S.K. Dash
Affiliation:
Orissa University of Agriculture and Technology, Bhubaneshwar, Orrisa, India
N.K. Verma*
Affiliation:
National Bureau of Animal Genetic Resources, Karnal 132001, Haryana, India
*
Correspondence to: N.K. Verma, Principal Scientist, National Bureau of Animal Genetic Resources, Karnal-132 001, Haryana, India. email: [email protected]
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Summary

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.

Résumé

Les 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 FIS 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, Ho a été plus bas que Ha et cette déviation a été significative dans le cas des modèles à mutation par étape et à mutation en deux phases. Comme indiqué sur la courbe en forme de L, il n'y a pas eu de réduction génétique sévère dans la taille effective de la population des chèvres Ghumusar.

Resumen

Las cabras Ghumusar constituyen una población caprina del oeste del distrito de Ganjam en el estado de Orissa escasamente estudiada. Se dispone de información esporádica sobre sus rasgos morfológicos pero no se encuentra ninguna información sobre su variabilidad genética. Es por ello que se ha intentado medir la diversidad genética en la población de cabras Ghumusar usando 25 marcadores microsatélites. Para este estudio se utilizó el ADN genómico aislado en las muestras de sangre de 50 individuos seleccionados aleatoriamente. El número medio de alelos observados fue de 9,80 mientras que el número medio efectivo ascendió a 4,28. Los contenidos de información polimórfica variaron entre 0,53 y 0,91. La heterocigosis media observada y esperada fue respectivamente de 0,73 y 0,71. Los valores de diversidad genética de Nei en la población caprina Ghumusar oscilaron entre 0,11 y 0,87 con una media de 0,69. Se observó que el valor global para el estadístico FIS era de 0,002, el cual no difiere significativamente de cero con lo que esto indica que globalmente no hubo déficit de heterocigotos. En el caso de la prueba de signos, el número esperado de loci con exceso de heterocigosis fue de 14,88, 14,79 y 14,74 para el modelo de alelos infinitos, el modelo de mutación por pasos y el modelo de mutación en dos fases, respectivamente. El número de loci con exceso de heterocigosis observado fue, respectivamente, de 14, 8 y 2 para estos tres modelos. Bajo los tres modelos, el número observado de loci con exceso de heterocigosis fue menor que el esperado y esta desviación fue significativa bajo los modelos de mutación por pasos y de mutación en dos fases. Tal y como indica la curva en forma de L, no se ha dado una reducción genética grave en el tamaño efectivo de población para las cabras Ghumusar.

Type
Research Article
Copyright
Copyright © Food and Agriculture Organization of the United Nations 2013 

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References

Aggarwal, R.A.K., Dixit, S.P., Verma, N.K., Ahlawat, S.P.S., Kumar, Y., Kumar, S., Chander, R. & Singh, K.P. 2007. Population genetics analysis of Mehsana goat based on microsatellite markers. Current Science, 92: 11331137.Google Scholar
Barker, J.S.F. 1994. A global protocol for determining genetic distances among domestic livestock breeds. In Proceedings of 5th World Congress of Genetics Applied to Livestock Production held at Guelph, Ontario, Canada, vol. 21, pp. 501508.Google Scholar
Botstein, D., White, R.L., Skolnick, M. & Davis, R.W. 1980. Construction of a genetic linkage map in man using restriction fragment length polymorphism. American Journal of Human Genetics, 32: 3948.Google Scholar
Cornuet, J.M. & Luikart, G. 1996. Description and power analysis of two tests for checking recent population bottle necks from allele frequency data. Genetics, 144: 20012014.CrossRefGoogle Scholar
Dixit, S.P., Verma, N.K., Ahlawat, S.P.S., Aggarwal, R.A.K., Kumar, S. & Singh, K.P. 2008. Molecular genetic characterization of Kutchi breed of goat. Current Science, 95: 946952.Google Scholar
Dixit, S.P., Verma, N.K., Aggarwal, R.A.K., Vyas, M.K., Rana, J., Sharma, A., Tyagi, P., Arya, P. & Ulmek, B.R. 2010. Genetic diversity and relationship among southern Indian goat breeds based on microsatellite markers. Small Ruminant Research, 91: 153159.Google Scholar
Dixit, S.P., Verma, N.K., Aggarwal, R.A.K., Vyas, M.K., Rana, J., Sharma, A., Chander, R. 2011. Genetic variability and bottleneck analyses of Kanniadu goat breed based on microsatellite markers. Indian Journal of Animal Science, 81: 4043.Google Scholar
Goudet, J. 2002. FSTAT ( version 2.9.3.2): a program to estimate and test gene diversities and fixation indices. F- statistics. Journal of Heredity, 86, 485486.Google Scholar
Kumar, D., Dixit, S.P., Sharma, R., Pandey, A.K. & Sirohi, G. 2005. Population structure, genetic variation and management of Marwari goats. Small Ruminant Research, 59: 4148.Google Scholar
Kumar, S., Dixit, S.P., Verma, N.K., Singh, D.K., Pande, A., Chander, R. & Singh, L.B. 2009. Genetic diversity analysis of the Gohilwari breed of Indian goat (Capra hircus) using microsatellite markers. American Journal of Animal and Veterinary Science, 4: 4957.Google Scholar
Li, J.Y., Chen, J., Lan, X.Y., Kong, X.J. & Min, L.J. 2008. Genetic diversity of five Chinese goat breeds assessed by microsatellite markers. Czechoslovakia Jornal of Animal Science, 53: 315319.Google Scholar
Luikart, G. & Cornuet, J.M. 1998. Empirical evaluation of a test for identifying recently bottlenecked populations from allelic frequency data. Conservation Biology, 12: 228237.Google Scholar
Mishra, P., Verma, N.K., Aggarwal, R.A.K. & Dixit, S.P. 2010. Breed characteristics and genetic variability in Changthangi goats. Indian Journal of Animal Science, 80(12): 4348.Google Scholar
Mishra, P., Ali, A.S., Aggarwal, R.A.K., Dixit, S.P., Kawitkar, V.S., Dangi, P.S. & Verma, N.K. 2012. Genetic diversity and bottleneck analysis of Konkan Kanyal goats. Animal Genetic Resources, 50: 4348.Google Scholar
Muema, E.K., Wakhungu, J.W., Hanotti, O. & Jianlin, H. 2009. Genetic diversity and relationship of Indian goats of sub-saharan Africa using microsatellite DNA markers. Livestock Research and Rural Development, 21, Article # 28.Google Scholar
Patro, B.N., Nayak, S., Rao, P.K. & Panda, P. 2007. Genetic studies of Ghumusar goats of Orissa. Indian Journal of Animal Breeding and Genetics, 27: 1216.Google Scholar
Rao, P.K., Dash, S.K., Patro, B.N. & Nayak, S. 2002. Studies on Ganjam, Black Bengal goats and their crosses found in Orissa. Indian Journal of Animal Production and Management, 18: 135138.Google Scholar
Rout, P.K., Joshi, M.B., Mandal, A., Laloe, D., Singh, L. & Thangaraj, K. 2008. Microsatellite based phylogeny of Indian domestic goats. BMC Genetics, 9: 11.Google Scholar
Sambrook, J., Fritsch, E.F. & Maniatis, T. 1989. Molecular Cloning: A Laboratory Manual. New York, Cold Spring Harbor Press.Google Scholar
Serrano, M., Calvo, J.H., Martinej, M., Marcos-Carcavila, A., Cuevas, J., Gonzalez, C., Jurado, J.J. & Tejada, P.D. 2009. Microsatellite based genetic diversity and population structure of the endangered Spanish Guadarrama goat breed. BMC Genetics, 10: 61.Google Scholar
Verma, N.K., Dixit, S.P., Aggarwal, R.A.K., Chander, R., Kumar, S. & Ahlawat, S.P.S. 2007a. Genetic analysis of the Sirohi breed of Indian goat (Capra hircus). Korean Journal of Genetics, 29: 129136.Google Scholar
Verma, N.K., Dixit, S.P., Kumar, D., Aggarwal, R.A.K. & Ahlawat, S.P.S. 2007b. Physical characteristics, performance status and genetic variation in Jakhrana breed of goat in its native tract. Indian Journal of Animal Science, 77(5): 390394.Google Scholar
Yeh, F.C., Boyle, T., Rongcai, Y., Ye, Z. & Xian, J.M. 1999. POPGENE Version 1.31. A Microsoft Window Based Freeware for Population Genetic Analysis. Edmonton, University of Alberta.Google Scholar