Genetic diversity and relationship of Indian cattle inferred from microsatellite and mitochondrial DNA markers

Sharma, Rekha; Kishore, Amit; Mukesh, Manishi; Ahlawat, Sonika; Maitra, A.; Pandey, Anjula; Tantia, M. S.

doi:10.1186/s12863-015-0221-0

Cited by 98 publications

(95 citation statements)

References 39 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…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%

“…Microsatellite markers have been widely used to evaluate the genetic diversity of indigenous cattle breeds (FAO, 2011). Genetic diversity has been investigated in a number of developing countries on breeds such as the Ankole longhorn (Ndumu et al 2008;Kugonza et al 2011) and Afrikaner cattle breeds (Pienaar et al 2014) as well as a number of indigenous cattle breeds in Mozambique (Bessa et al 2009), Cuba (Acosta et al 2013), Cameroon (Ngono-Ema et al 2014 and India (Sharma et al 2015).…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

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

Sanarana

Visser

Bosman

et al. 2015

Trop Anim Health Prod

View full text Add to dashboard Cite

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.

show abstract

Section: Discussionsupporting

confidence: 85%

Section: Introductionmentioning

confidence: 99%

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

Sanarana

Visser

Bosman

et al. 2015

Trop Anim Health Prod

View full text Add to dashboard Cite

show abstract

“…The study showed lower F st values using 760,139 SNPs from 777k chip among B. indicus breeds (0.066–0.093) compared to F st among B. taurus breeds (0.159) indicating comparatively less divergence among B. indicus breeds. A higher F st value (13.3%) considering a larger diverse panel of B. indicus breeds genotyped with microsatellite markers has previously been reported (Sharma et al., ). Results of PCA analysis for genotype data of 120 purebred animals using pruned 777k data having 138,451 SNPs showed that the first and second PC clearly separated the B. taurus from the B. indicus breeds (Figure a), while all four B. indicus breeds clustered together expect a few Red Sindhi animals (Figure b).…”

Section: Discussionmentioning

confidence: 65%

Suitability of existing commercial single nucleotide polymorphism chips for genomic studies in Bos indicus cattle breeds and their Bos taurus crosses

Nayee

Sahana

Gajjar

et al. 2018

J Animal Breeding Genetics

View full text Add to dashboard Cite

Bos indicus cattle breeds are genetically distinct from Bos taurus breeds. We examined the performance of three SNP arrays, the Illumina BovineHD BeadChip (777k; Illumina Inc.), the Illumina BovineSNP50 BeadChip (50k) and the GeneSeek 70k Indicus chip (75Ki; GeneSeek) in four B. indicus breeds (Gir, Kankrej, Sahiwal and Red Sindhi) and their B. taurus crosses, along with two B. taurus breeds, Holstein and Jersey. More SNPs on both Illumina SNP chips were monomorphic in B. indicus breeds (average 20.3%-29.3% on the 777k chip, 35.5%-45.5% on the 50k chip) than in Holstein (19.7% on the 777k chip, 17.1% on the 50k chip). The proportion of monomorphic SNPs on the 75Ki chip was much lower, 4% (2.8%-7%) in B. indicus breeds, while it was 33.5% in Holstein. With on average 164,357 heterozygous loci in B. indicus breeds, the 777k SNP chip has sufficient heterozygous loci to design a chip customized for B. indicus breeds. Principal component analysis clearly differentiated B. indicus from B. taurus breeds. Differentiation among B. indicus breeds was only achieved by plotting the third and fifth principal components using 777k genotype data. Admixture analysis showed that many B. indicus animals, previously believed to be of pure origin, are in fact had mixed ancestry. The extent of linkage disequilibrium showed comparatively higher effective population sizes in four B. indicus breeds compared to two B. taurus breeds. The results of admixture analyses show that it is important to assess the genomic composition of a bull before using it in a breeding programme.

show abstract

“…Population subdivision could be one of the possible causes for the observed heterozygosity deficit considering the fact that samples were collected from different geographical locations of the native breed tract. However, it also needs to be mentioned that much higher deviations from HWE have been reported in Brazilian (19.5 % breed × locus combina- Sharma et al, 2015).…”

Section: Test For Hardy-weinberg Equilibriummentioning

confidence: 93%

Short tandem repeat (STR) based genetic diversity and relationship of indigenous Niger cattle

et al. 2017

View full text Add to dashboard Cite

Abstract. The diversity of cattle in Niger is predominantly represented by three indigenous breeds: Zebu Arabe, Zebu Bororo and Kuri. This study aimed at characterizing the genetic diversity and relationship of Niger cattle breeds using short tandem repeat (STR) marker variations. A total of 105 cattle from all three breeds were genotyped at 27 STR loci. High levels of allelic and gene diversity were observed with an overall mean of 8.7 and 0.724 respectively. The mean inbreeding estimate within breeds was found to be moderate with 0.024, 0.043 and 0.044 in Zebu Arabe, Zebu Bororo and Kuri cattle respectively. The global F statistics showed low genetic differentiation among Niger cattle with about 2.6 % of total variation being attributed to between-breed differences. Neighbor-joining tree derived from pairwise allele sharing distance revealed Zebu Arabe and Kuri clustering together while Zebu Bororo appeared to be relatively distinct from the other two breeds. High levels of admixture were evident from the distribution of pairwise inter-individual allele sharing distances that showed individuals across populations being more related than individuals within populations. Individuals were assigned to their respective source populations based on STR genotypes, and the percent correct assignment of Zebu Bororo (87.5 to 93.8 %) was consistently higher than Zebu Arabe (59.3 to 70.4 %) and Kuri (80.0 to 83.3 %) cattle. The qualitative and quantitative tests for mutation drift equilibrium revealed absence of genetic bottleneck events in Niger cattle in the recent past. High genetic diversity and poor genetic structure among indigenous cattle breeds of Niger might be due to historic zebu-taurine admixture and ongoing breeding practices in the region. The results of the present study are expected to help in formulating effective strategies for conservation and genetic improvement of indigenous Niger cattle breeds.

show abstract

Genetic diversity and relationship of Indian cattle inferred from microsatellite and mitochondrial DNA markers

Cited by 98 publications

References 39 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

Suitability of existing commercial single nucleotide polymorphism chips for genomic studies in Bos indicus cattle breeds and their Bos taurus crosses

Short tandem repeat (STR) based genetic diversity and relationship of indigenous Niger cattle

Contact Info

Product

Resources

About