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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

Individual animal clustering-based principal component analysis.
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f1-ajas-27-10-1381: Individual animal clustering-based principal component analysis.

Mentions: The PCA results clustered the RC and ND as one population, whereas the gayal population was observed as a separate cluster (Figure 1). Within the gayal cluster, a few were outgroups. This is likely because a few hybrid individuals were noted within the studied gayal population. The structure output also revealed the same genetic architecture in the two zebu populations, with some introgressions of genes from domestic cattle (i.e., zebu) to the gayal population and vice versa. This might be due to inter-specific hybridization among the Bos species (zebu, taurine, gayal, and yak) which has been documented in South and Southeast Asian cultures (Tanaka et al., 2011). The admixed zebu and gayal individuals in the studied population might be due to sampling errors despite they have the phenotypic resemblance and every precautions were taken during sampling. It is notable that the remnant of inheritance in admixed individuals is very difficult to trace phenotypically in some cases. In addition, the pedigree information is almost unknown to farmers in Bangladesh perspective. The bottleneck of genetic features in the gayal population might be because of inbreeding within a small population. In fact the geographic distribution of gayal habitats is very specific where people of several tribal families used to keep their animals together in a form of small group in the particular territory. Random mating occurs in that small sub-population over the years despite hierarchy of breeding bulls is a question. Moreover, the chance of interbreeding among the sub-population is negligible. This faulty breeding practices and lack of scientific management leads to increase homogeneity within the small group. However, our attempts unveiled the genetic architecture of gayal for the first time and above all, gave us hints to take immediate attention from different scientific institutes of Bangladesh to overcome the bottlenecks.


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)

Individual animal clustering-based principal component analysis.
© Copyright Policy
Related In: Results  -  Collection

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

f1-ajas-27-10-1381: Individual animal clustering-based principal component analysis.
Mentions: The PCA results clustered the RC and ND as one population, whereas the gayal population was observed as a separate cluster (Figure 1). Within the gayal cluster, a few were outgroups. This is likely because a few hybrid individuals were noted within the studied gayal population. The structure output also revealed the same genetic architecture in the two zebu populations, with some introgressions of genes from domestic cattle (i.e., zebu) to the gayal population and vice versa. This might be due to inter-specific hybridization among the Bos species (zebu, taurine, gayal, and yak) which has been documented in South and Southeast Asian cultures (Tanaka et al., 2011). The admixed zebu and gayal individuals in the studied population might be due to sampling errors despite they have the phenotypic resemblance and every precautions were taken during sampling. It is notable that the remnant of inheritance in admixed individuals is very difficult to trace phenotypically in some cases. In addition, the pedigree information is almost unknown to farmers in Bangladesh perspective. The bottleneck of genetic features in the gayal population might be because of inbreeding within a small population. In fact the geographic distribution of gayal habitats is very specific where people of several tribal families used to keep their animals together in a form of small group in the particular territory. Random mating occurs in that small sub-population over the years despite hierarchy of breeding bulls is a question. Moreover, the chance of interbreeding among the sub-population is negligible. This faulty breeding practices and lack of scientific management leads to increase homogeneity within the small group. However, our attempts unveiled the genetic architecture of gayal for the first time and above all, gave us hints to take immediate attention from different scientific institutes of Bangladesh to overcome the bottlenecks.

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