Assessment of genetic diversity and population structure of Vietnamese indigenous cattle populations by microsatellites

Pham, Lan Doan; Ngoc, Duy; Bình, Nguyễn Trọng; Nam, Le Quang; Ba, Nguyen Van; Thủy, Trần Thị Thu; Hoan, Tran Xuan; Cuong, Vu Chi; Kadarmideen, Haja N.

doi:10.1016/j.livsci.2013.04.006

Cited by 23 publications

(17 citation statements)

References 24 publications

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“…The heterozygosity values observed in the current study were comparable to the values reported in indigenous cattle from Vietnam (Pham et al 2013), Cameroon (Ngono Ema et al 2014) and in India (Sharma et al 2015). High gene diversity levels are normally associated with long-term natural selection for adaptation and the historic admixture of different populations (Ojango et al 2011).…”

Section: Discussionsupporting

confidence: 85%

Genetic diversity in South African Nguni cattle ecotypes based on microsatellite markers

Sanarana

Visser

Bosman

et al. 2015

Trop Anim Health Prod

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The Nguni cattle breed is a landrace breed adapted to different ecological regions of South Africa. A number of ecotypes are recognised based on phenotype within the breed, but it is not known if they are genetically distinct. In this study molecular characterization was performed on Makhathini (MAK), Pedi (PED), Shangaan (SHA) and Venda (VEN) Nguni cattle ecotypes. Two Nguni cattle populations, not kept as separate ecotypes, from University of Fort Hare (UFH) and Agricultural Research Council Loskop South farm (LOS) were also included. Genotypic data was generated for 189 unrelated Nguni cattle selected based on pedigree records using 22 microsatellite markers. The expected heterozygosity values varied from 69% (UFH) to 72% PED with a mean number of alleles ranging from 6.0 to 6.9. The F ST estimate demonstrated that 4.8% of the total genetic variation was due to the genetic differentiation between the populations and 92.2% accounted for differences within the populations. The genetic distances and structure analysis revealed the closest relationship between MAK, PEDI and SHA ecotypes, followed by SHA and VEN. The UFH population clustered with the MAK ecotype, indicating that they are more genetically similar, while the LOS cattle grouped as a distinct cluster. Results suggest that the genetic differentiation between the PED and SHA ecotypes is low and can be regarded as one ecotype based on 2 limited genetic differences. The results of this study can be applied as a point of reference for further genetic studies towards conservation of Nguni cattle ecotypes.

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Section: Discussionsupporting

confidence: 85%

Genetic diversity in South African Nguni cattle ecotypes based on microsatellite markers

Sanarana

Visser

Bosman

et al. 2015

Trop Anim Health Prod

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“…The statistical analysis methods used here were similar to our previous study for diversity of Vietnamese cattle populations (Pham et al 2013). In brief, we used an Excel add-in MS_tools.xla (Park 2001) to check for data errors and removal of duplicated samples or genetically identical individuals.…”

Section: Discussionmentioning

confidence: 99%

“…The methods to extract DNA extraction, amplify PCR and genotype microsatellites have been described before in (Pham et al 2013). In summary, we used AccuPREP Genomic DNA extraction kit (Cat.No.…”

Section: Dna Extraction Pcr Amplification and Microsatellite Genotypingmentioning

confidence: 99%

Molecular genetic diversity and genetic structure of Vietnamese indigenous pig populations

Pham

Ngoc

Nam

et al. 2013

J Animal Breeding Genetics

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The study characterized genetic diversity and genetic structure of five indigenous pig populations (Ha Lang, Muong Te, Mong Cai, Lung and Lung Pu), two wild pig populations (Vietnamese and Thai wild pigs) and an exotic pig breed (Yorkshire) using FAO/ISAG recommended 16 microsatellite markers in 236 samples. All estimated loci were very polymorphic indicated by high values of polymorphism information content (from 0.76 in S0225 to 0.92 in Sw2410). Indigenous populations had very high level of genetic diversity (mean He = 0.75); of all indigenous breeds, Lung Pu showed highest mean number of alleles (MNA = 10.1), gene diversity (He = 0.82), allele richness (5.33) and number of private alleles (10). Thirteen percentage of the total genetic variation observed was due to differences among populations. The neighbour-joining dendrogram obtained from Nei's standard genetic distance differentiated eight populations into four groups including Yorkshire, two wild populations, Mong Cai population and a group of four other indigenous populations. The Bayesian clustering with the admixture model implemented in Structure 2.1 indicated seven possible homogenous clusters among eight populations. From 79% (Ha Lang) to 98% (Mong Cai). individuals in indigenous pigs were assigned to their own populations. The results confirmed high level of genetic diversity and shed a new light on genetic structure of Vietnam indigenous pig populations.

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“…Microsatellite analyses have provided useful genetic information for African, European, mid-South American and Asian cattle breeds as reported by Dadi et al (2008), Padilla et al (2009), Acosta et al (2013) and Pham et al (2013), respectively. Microsatellites have been effectively exploited to evaluate genetic diversity among cattle populations (Sun et al 2007).…”

Section: Introductionmentioning

confidence: 99%

Genetic diversity and structure of native Egyptian cattle populations and French-Egyptian Cross via DNA-microsatellite

Faid-Allah¹,

Ghoneim²,

Elbetagy³

et al. 2018

JITV

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This study investigates genetic diversity and structure of native Egyptian cattle populations, called Baladi, as Saidi from Southern Egypt, Menufi from Mid-Delta and their F1 crosses with the French Tarentaise breed using DNA Microsatellite markers. A total of unrelated 97 individuals were genotyped utilizing eight SSR primers (ETH10, ETH225, BM1818, BM1824, BM2113, SPS115, TGLA53 and TGLA126). All utilized SSR were found to be polymorphic. The highest and lowest numbers of alleles detected were 16 and 6 at TGLA53 and SPS115 loci, respectively. Baladi-Tarentaise crosses (Bal-Tar) had the highest number of alleles over all. The PIC values of 7 loci were higher than 0.5, indicating high allelic variation of utilized markers. Estimated PIC values were up to 0.898, 0.866 and 0.873 for TGLA53 genotyped in Saidi, Menufi and Bal-Tar, respectively. Hobs values were lower than the expected ones in the native populations accompanied with positive values for Fis and significant deviation from HWE indicating inbreeding trend in native populations. Structure analysis indicated three ancestral genetic backgrounds. The native populations share two main backgrounds in almost equal percentages, while the Bal-Tar had the third one. The three populations showed low percentage of admixture. The studied Mediterranean cattle populations that belong to Egypt and France seem to have differentiated from each other with only little genetic exchange between the geographically isolated populations so local cattle is very similar.

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Assessment of genetic diversity and population structure of Vietnamese indigenous cattle populations by microsatellites

Cited by 23 publications

References 24 publications

Genetic diversity in South African Nguni cattle ecotypes based on microsatellite markers

Genetic diversity in South African Nguni cattle ecotypes based on microsatellite markers

Molecular genetic diversity and genetic structure of Vietnamese indigenous pig populations

Genetic diversity and structure of native Egyptian cattle populations and French-Egyptian Cross via DNA-microsatellite

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