Genetic diversity of Albanian goat breeds based on microsatellite markers

Hoda, Anila; Hyka, G.; Dunner, S.; Obexer-Ruff, Gabriela

doi:10.4321/s0004-05922011000300049

Cited by 13 publications

(13 citation statements)

References 9 publications

(14 reference statements)

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“…It was suggested that less inbreeding values of less than 0.5 or closer to zero (Wang, 1996) might have happened due to the absence of mating between close relatives and/or within individuals. Similarly, such comparable inbreeding values were also reported for Asian (Barker et al, 2001), Indian goat populations (Kumar et al, 2005;Aggarwal et al, 2007;Dixit et al, 2008;Dixit et al, 2010) and local Albanian goat breeds (Hoda et al, 2011). The HWE test results revealed that most of the markers used to study Syrian goats were not in HWE, except one locus (that is, ETH10) did show adherence to HWE for Jabali goats (Table S1).…”

Section: Genetic Diversity and Differentiationsupporting

confidence: 74%

Morphological and molecular genetic diversity of Syrian indigenous goat populations

Hassen¹,

Rischkowsky²,

Termanini³

et al. 2016

Afr. J. Biotechnol.

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Domestic goats in Syria may provide an interesting source of genetic variability due to its proximity to the centers of domestication. This study aimed to assess the morphological variation, genetic diversity and population substructure of the Syrian goat populations. Commonly, three goat genotypes are distinguished in Syria, namely Jabali or mountain goat, Baladi or local goat and Shami or Damascus (a well-known dairy goat). A pre-tested semi-structured questionnaire was used in recording both qualitative (coat color, eye color, horn length, horn orientation, nose profile) and quantitative (height at wither, chest girth, cannon length, body length, ear length and ear width) morphological data. Data from a total of 5,730 individual goats of the three goat populations reared in ten representative provinces of Syria were collected and analyzed using GenStat version 14 statistical packages. Results of the morphological analysis confirmed that there were clear morphological variations among the three goat populations. The three goat populations are mainly distinguished by their straight (Baladi, 71.1% and Jabali, 82.8%) and curved (Shami, 89.5%) nose profiles. Substantial phenotypic variability was found among and within the breeds suggesting that these goat breeds have not yet undergone an organized breeding program. The genetic variability and population substructures from 398 individual animals of the three breeds were genotyped using 12 DNA microsatellite markers from Food and Agricultural Organization (FAO) panel. All microsatellites typed were found to be polymorphic and a total of 41 distinct alleles were detected on Baladi, Jabali and Shami goat populations. The Syrian goat populations had observed and expected heterozygosity values that ranged from 0.50 to 0.62 and 0.74 to 0.85, respectively, and an average of 13.97 alleles per locus across breeds. For all loci, an average inbreeding values (F IS ) of low to moderate level was obtained across the three goat breeds, which ranged from 0.29 (Shami goats) to 0.34 (Baladi goats) indicating the absence of mating between close relatives within these populations. The observed positive F IS coefficients among the studied goat breeds also suggested heterozygote deficiencies. The analyses of the molecular data using STRUCURE program indicated there were two primary populations, which did support the results based on morphological data of the same goat populations that clustered these goat populations into two main groups and confirmed the admixture nature of the Baladi and Jabali goat populations, while the Shami goat breed was well differentiated and grouped into a separate cluster that suggests its evolutionary and genetic uniqueness. The analysis of molecular variance (AMOVA) results detected genetic variations within individuals in a population (96%). The high genetic variability within individuals in a population provides a good base for designing genetic improvement programs under the existing goat management systems.

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Section: Genetic Diversity and Differentiationsupporting

confidence: 74%

Morphological and molecular genetic diversity of Syrian indigenous goat populations

Hassen¹,

Rischkowsky²,

Termanini³

et al. 2016

Afr. J. Biotechnol.

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“…The F ST analysis indicated that 98.7% of the variation was found within the goat breeds and only 1.3% ( P = 0.039) among them. These results show a low level of breed differentiation and are in concordance with the results obtained previously for the same goat breeds, using microsatellites,[ 19 ] SNP [ 20 ] and AFLP. [ 21 ] Table 2 represents the pairwise F ST values among breeds with their significance levels.…”

Section: Resultssupporting

confidence: 91%

Genetic diversity of Albanian goat breeds revealed by mtDNA sequence variation

Hoda¹,

Biçoku²,

Dobi³

2014

Biotechnology & Biotechnological Equipment

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Albanian farmers have a long tradition in goat farming. Recently, several studies were carried out to determine genetic diversity of local goat populations, using molecular markers such as SNP (Single Nucleotide Polymorphisms), microsatellites and AFLP (Amplified Fragment Length Polymorphism). In the present study 77 mtDNA D-loop sequences from six different goat breeds were analysed. The results revealed 67 different haplotypes, with haplotype diversity ranging from 0.864 to 1 and nucleotide diversity values ranging from 0.016 to 0.106. The results showed that the studied breed grouped only in lineage A. The F ST analysis indicated that 98.7% of the variation was found within the goat breeds and only 1.3% among them.

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“…; Hoda et al . ), pig (Fan et al . ), horse (Bjornstad & Roed ), dog (Toskinen & Bredbadka ), poultry and rabbit (Gotz & Thaller ).…”

Section: Training and Testing Performances Of Various Modelsmentioning

confidence: 99%

Locus minimization in breed prediction using artificial neural network approach

et al. 2014

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Molecular markers, viz. microsatellites and single nucleotide polymorphisms, have revolutionized breed identification through the use of small samples of biological tissue or germplasm, such as blood, carcass samples, embryos, ova and semen, that show no evident phenotype. Classical tools of molecular data analysis for breed identification have limitations, such as the unavailability of referral breed data, causing increased cost of collection each time, compromised computational accuracy and complexity of the methodology used. We report here the successful use of an artificial neural network (ANN) in background to decrease the cost of genotyping by locus minimization. The webserver is freely accessible (http://nabg.iasri.res.in/bisgoat) to the research community. We demonstrate that the machine learning (ANN) approach for breed identification is capable of multifold advantages such as locus minimization, leading to a drastic reduction in cost, and web availability of reference breed data, alleviating the need for repeated genotyping each time one investigates the identity of an unknown breed. To develop this model web implementation based on ANN, we used 51,850 samples of allelic data of microsatellite-marker-based DNA fingerprinting on 25 loci covering 22 registered goat breeds of India for training. Minimizing loci to up to nine loci through the use of a multilayer perceptron model, we achieved 96.63% training accuracy. This server can be an indispensable tool for identification of existing breeds and new synthetic commercial breeds, leading to protection of intellectual property in case of sovereignty and bio-piracy disputes. This server can be widely used as a model for cost reduction by locus minimization for various other flora and fauna in terms of variety, breed and/or line identification, especially in conservation and improvement programs.

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Genetic diversity of Albanian goat breeds based on microsatellite markers

Cited by 13 publications

References 9 publications

Morphological and molecular genetic diversity of Syrian indigenous goat populations

Morphological and molecular genetic diversity of Syrian indigenous goat populations

Genetic diversity of Albanian goat breeds revealed by mtDNA sequence variation

Locus minimization in breed prediction using artificial neural network approach

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