Limits...
Genome-wide Single Nucleotide Polymorphism Analyses Reveal Genetic Diversity and Structure of Wild and Domestic Cattle in Bangladesh.

Uzzaman MR, Edea Z, Bhuiyan MS, Walker J, Bhuiyan AK, Kim KS - Asian-australas. J. Anim. Sci. (2014)

Bottom Line: The mean expected heterozygosity varied from 0.42±0.14 in zebu to 0.148±0.14 in gayal with significant heterozygosity deficiency of 0.06 (F IS) in the latter.Results of population structure and principal component analyses suggest that gayal is distinct from Bos indicus and that the two zebu populations were weakly structured.This study provides basic information about the genetic diversity and structure of Bangladeshi cattle and the semi-domesticated gayal population that can be used for future appraisal of breed utilization and management strategies.

View Article: PubMed Central - PubMed

Affiliation: Department of Animal Breeding and Genetics, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh .

ABSTRACT
In spite of variation in coat color, size, and production traits among indigenous Bangladeshi cattle populations, genetic differences among most of the populations have not been investigated or exploited. In this study, we used a high-density bovine single nucleotide polymorphism (SNP) 80K Bead Chip derived from Bos indicus breeds to assess genetic diversity and population structure of 2 Bangladeshi zebu cattle populations (red Chittagong, n = 28 and non-descript deshi, n = 28) and a semi-domesticated population (gayal, n = 17). Overall, 95% and 58% of the total SNPs (69,804) showed polymorphisms in the zebu and gayal populations, respectively. Similarly, the average minor allele frequency value was as high 0.29 in zebu and as low as 0.09 in gayal. The mean expected heterozygosity varied from 0.42±0.14 in zebu to 0.148±0.14 in gayal with significant heterozygosity deficiency of 0.06 (F IS) in the latter. Coancestry estimations revealed that the two zebu populations are weakly differentiated, with over 99% of the total genetic variation retained within populations and less than 1% accounted for between populations. Conversely, strong genetic differentiation (FST = 0.33) was observed between zebu and gayal populations. Results of population structure and principal component analyses suggest that gayal is distinct from Bos indicus and that the two zebu populations were weakly structured. This study provides basic information about the genetic diversity and structure of Bangladeshi cattle and the semi-domesticated gayal population that can be used for future appraisal of breed utilization and management strategies.

No MeSH data available.


Related in: MedlinePlus

Genetic structure of three cattle populations inferred using structure 2.3.4 (Pritchard et al., 2000). Each individual animal is represented using a single vertical line divided by k colors, where k is the number of clusters assumed and the length of the colored segment represents the individual’s estimated proportion of membership to a particular cluster.
© Copyright Policy
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4150168&req=5

f2-ajas-27-10-1381: Genetic structure of three cattle populations inferred using structure 2.3.4 (Pritchard et al., 2000). Each individual animal is represented using a single vertical line divided by k colors, where k is the number of clusters assumed and the length of the colored segment represents the individual’s estimated proportion of membership to a particular cluster.

Mentions: The first and the second principal components (PC1 and PC2) explained 90.24% of the total variation and evidently distinguish the two zebu populations from gayal. The results coincided well with the STRUCTURE output at K = 2 and K = 3 (Figure 2). The output at K = 2 seems plausible; it clearly distinguished the gayal from B. indicus populations (RC and ND) with some level of gene flow between the breeds. The output at K = 3 suggests higher admixture than expected in ND and RC, which does not agree with the PCA result in this study. This might be because of the influence of exotic blood due to indiscriminate crossbreeding. Approximately 11% of the gayal population is considered to share common ancestry with the ND and RC populations.


Genome-wide Single Nucleotide Polymorphism Analyses Reveal Genetic Diversity and Structure of Wild and Domestic Cattle in Bangladesh.

Uzzaman MR, Edea Z, Bhuiyan MS, Walker J, Bhuiyan AK, Kim KS - Asian-australas. J. Anim. Sci. (2014)

Genetic structure of three cattle populations inferred using structure 2.3.4 (Pritchard et al., 2000). Each individual animal is represented using a single vertical line divided by k colors, where k is the number of clusters assumed and the length of the colored segment represents the individual’s estimated proportion of membership to a particular cluster.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4150168&req=5

f2-ajas-27-10-1381: Genetic structure of three cattle populations inferred using structure 2.3.4 (Pritchard et al., 2000). Each individual animal is represented using a single vertical line divided by k colors, where k is the number of clusters assumed and the length of the colored segment represents the individual’s estimated proportion of membership to a particular cluster.
Mentions: The first and the second principal components (PC1 and PC2) explained 90.24% of the total variation and evidently distinguish the two zebu populations from gayal. The results coincided well with the STRUCTURE output at K = 2 and K = 3 (Figure 2). The output at K = 2 seems plausible; it clearly distinguished the gayal from B. indicus populations (RC and ND) with some level of gene flow between the breeds. The output at K = 3 suggests higher admixture than expected in ND and RC, which does not agree with the PCA result in this study. This might be because of the influence of exotic blood due to indiscriminate crossbreeding. Approximately 11% of the gayal population is considered to share common ancestry with the ND and RC populations.

Bottom Line: The mean expected heterozygosity varied from 0.42±0.14 in zebu to 0.148±0.14 in gayal with significant heterozygosity deficiency of 0.06 (F IS) in the latter.Results of population structure and principal component analyses suggest that gayal is distinct from Bos indicus and that the two zebu populations were weakly structured.This study provides basic information about the genetic diversity and structure of Bangladeshi cattle and the semi-domesticated gayal population that can be used for future appraisal of breed utilization and management strategies.

View Article: PubMed Central - PubMed

Affiliation: Department of Animal Breeding and Genetics, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh .

ABSTRACT
In spite of variation in coat color, size, and production traits among indigenous Bangladeshi cattle populations, genetic differences among most of the populations have not been investigated or exploited. In this study, we used a high-density bovine single nucleotide polymorphism (SNP) 80K Bead Chip derived from Bos indicus breeds to assess genetic diversity and population structure of 2 Bangladeshi zebu cattle populations (red Chittagong, n = 28 and non-descript deshi, n = 28) and a semi-domesticated population (gayal, n = 17). Overall, 95% and 58% of the total SNPs (69,804) showed polymorphisms in the zebu and gayal populations, respectively. Similarly, the average minor allele frequency value was as high 0.29 in zebu and as low as 0.09 in gayal. The mean expected heterozygosity varied from 0.42±0.14 in zebu to 0.148±0.14 in gayal with significant heterozygosity deficiency of 0.06 (F IS) in the latter. Coancestry estimations revealed that the two zebu populations are weakly differentiated, with over 99% of the total genetic variation retained within populations and less than 1% accounted for between populations. Conversely, strong genetic differentiation (FST = 0.33) was observed between zebu and gayal populations. Results of population structure and principal component analyses suggest that gayal is distinct from Bos indicus and that the two zebu populations were weakly structured. This study provides basic information about the genetic diversity and structure of Bangladeshi cattle and the semi-domesticated gayal population that can be used for future appraisal of breed utilization and management strategies.

No MeSH data available.


Related in: MedlinePlus