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      Assessment of genetic diversity of Mithun (Bos frontalis) population in Bhutan using microsatellite DNA markers

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          Summary

          Genetic diversity of Mithun population in Bhutan was studied using 14 microsatellite markers. Two sets of two-step polymerase chain reactions were performed with multiplex and individual markers for genotyping 105 hair samples collected from Arong in Samdrupjongkhar (AS, 36) and Wangdigang in Zhemgang (WZ, 69). Fifty-three alleles were detected with average of 3.89 alleles and polymorphism information content of 0.44 ± 0.03 per locus. A low level of genetic variability within population was present with observed heterozygosity at 0.50 ± 0.06 and expected heterozygosity at 0.48 ± 0.06. Analysis of molecular variance attributed 58 percent of total variation to within the individuals. Mean F IS and F IT were −0.056 and 0.005 respectively, indicated low level of population differentiation and limited out-breeding. The normal L-shaped distribution of allelic frequencies without any mode-shift revealed the absence of recent genetic bottleneck in Mithun populations. Therefore to manage inbreeding in the small Mithun population of Bhutan, periodic assessment of inbreeding levels and exchange of animals between farms is recommended to reduce frequency of introduction of animals from India.

          Résumé

          La diversité génétique de la population de gayals au Bhoutan a été étudiée en utilisant 14 marqueurs microsatellites. Deux séries de réactions en chaîne par polymérase (PCR selon ses sigles en anglais) en deux étapes ont été réalisées avec plusieurs marqueurs et avec des marqueurs individuels pour génotyper 105 échantillons de poils prélevés à Arong au Samdrup Jongkhar (AS, 36) et à Wangdigang au Zhemgang (WZ, 69). Cinquante-trois allèles ont été détectés pour une moyenne de 3.89 allèles et un contenu d'information sur le polymorphisme de 0.44 ± 0.03 par locus. Un faible niveau de variabilité génétique a été observé au sein de la population avec une hétérozygotie observée de 0.50 ± 0.06 et une hétérozygotie attendue de 0.48 ± 0.06. L'analyse de variance moléculaire (AMOVA) a attribué le 58 pour cent de la variation totale à la variabilité intra-individuelle. Les valeurs moyennes des coefficients F ST, F IS et F IT ont été de 0.054, −0.056 et 0.005 respectivement, ce qui est le reflet d'un faible niveau de différenciation dans la population et d'un manque de croisements exogames. La distribution habituelle des fréquences alléliques en L, sans aucune distorsion, a décelé l'absence de goulots d'étranglement génétique récents dans les populations de gayals. Ainsi, afin de gérer la consanguinité dans la petite population de gayals du Bhoutan, une évaluation périodique des niveaux de consanguinité et un échange d'animaux entre les fermes sont conseillés pour réduire la fréquence des importations depuis l'Inde.

          Resumen

          Se estudió la diversidad genética de la población de gayales en Bhután, utilizando para ello 14 marcadores microsatélites. Se llevaron a cabo dos tandas de reacciones en cadena de la polimerasa (PCR, por sus siglas en inglés) de dos pasos con múltiples marcadores y con marcadores individuales para genotipificar 105 muestras de pelo tomadas de Arong en Samdrupjongkhar (AS, 36) y de Wangdigang en Zhemgang (WZ, 69). Se detectaron 53 alelos, con una media de 3.89 alelos y un contenido de información polimórfica de 0.44 ± 0.03 por locus. Se constató un bajo nivel de variabilidad genética dentro de la población, con una heterocigosis observada de 0.50 ± 0.06 y una heterocigosis esperada de 0.48 ± 0.06. El análisis de varianza molecular (AMOVA) atribuyó el 58 por ciento de la variación total a la variabilidad intraindividual. Los valores medios para los coeficientes F ST, F IS y F IT fueron de 0.054, −0.056 y 0.005, respectivamente, lo cual refleja un bajo nivel de diferenciación en la población y una escasez de cruzamientos exogámicos. La distribución típica en forma de L de las frecuencias alélicas, sin ninguna distorsión, puso de manifiesto la ausencia de cuellos de botella genéticos recientes en las poblaciones de gayales. Por tanto, para gestionar la endogamia en la pequeña población de gayales de Bhután, se recomienda una evaluación periódica de los niveles de consanguinidad y el intercambio de animales entre las granjas con el fin de recudir la frecuencia de las importaciones desde la India.

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          Most cited references 6

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          Two-step multiplex polymerase chain reaction improves the speed and accuracy of genotyping using DNA from noninvasive and museum samples.

          Many studies in molecular ecology rely upon the genotyping of large numbers of low-quantity DNA extracts derived from noninvasive or museum specimens. To overcome low amplification success rates and avoid genotyping errors such as allelic dropout and false alleles, multiple polymerase chain reaction (PCR) replicates for each sample are typically used. Recently, two-step multiplex procedures have been introduced which drastically increase the success rate and efficiency of genotyping. However, controversy still exists concerning the amount of replication needed for suitable control of error. Here we describe the use of a two-step multiplex PCR procedure that allows rapid genotyping using at least 19 different microsatellite loci. We applied this approach to quantified amounts of noninvasive DNAs from western chimpanzee, western gorilla, mountain gorilla and black and white colobus faecal samples, as well as to DNA from ~100-year-old gorilla teeth from museums. Analysis of over 45 000 PCRs revealed average success rates of > 90% using faecal DNAs and 74% using museum specimen DNAs. Average allelic dropout rates were substantially reduced compared to those obtained using conventional singleplex PCR protocols, and reliable genotyping using low (< 25 pg) amounts of template DNA was possible. However, four to five replicates of apparently homozygous results are needed to avoid allelic dropout when using the lowest concentration DNAs (< 50 pg/reaction), suggesting that use of protocols allowing routine acceptance of homozygous genotypes after as few as three replicates may lead to unanticipated errors when applied to low-concentration DNAs. © 2008 The Authors. Journal compilation © 2008 Blackwell Publishing Ltd.
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            Genetic diversity of Indian native cattle breeds as analysed with 20 microsatellite loci

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              Genetic diversity in Swiss cattle breeds

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                Author and article information

                Journal
                applab
                Animal Genetic Resources/Ressources génétiques animales/Recursos genéticos animales
                Anim. Genet. Resour.
                Cambridge University Press (CUP)
                2078-6336
                2078-6344
                December 2016
                January 3 2017
                December 2016
                : 59
                : 1-6
                Article
                10.1017/S2078633616000072
                © 2016

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