Genetic diversity and population structure of indigenous chicken of Bangladesh using microsatellite markers.

OBJECTIVE: The objectives of this study were to investigate the genetic diversity, population structure and relatedness among the five chicken populations of Bangladesh using microsatellite markers. METHODS: A total of 161 individuals representing 5 chicken populations (non-descript Deshi [ND], naked neck [NN], hilly [HI], Aseel [AS], and red jungle fowl [JF]) were included in this study to investigate genetic diversity measures, population structure, genetic distance and phylogenetic relationships. Genotyping was performed using 16 selected polymorphic microsatellite markers distributed across 10 chromosomes. RESULTS: The average observed and expected heterozygosity, mean number of alleles and polymorphic information content were found to be 0.67±0.01, 0.70±0.01, 10.7 and 0.748, respectively in the studied populations. The estimated overall fixation index across the loci (F), heterozygote deficiency within (FIS) and among (FIT) chicken populations were 0.04±0.02, 0.05 and 0.16, respectively. Analysis of molecular variance analysis revealed 88.07% of the total genetic diversity was accounted for within population variation and the rest 11.93% was incurred with population differentiation (FST). The highest pairwise genetic distance (0.154) was found between ND and AS while the lowest distance was between JF and AS (0.084). Structure analysis depicted that the studied samples can be categorized into four distinct types or varieties (ΔK = 3.74) such as ND, NN, and HI where AS and JF clustered together as an admixed population. The Neighbor-Joining phylogenetic tree and discriminant analysis of principal component also showed close relatedness among three chicken varieties namely AS, HI, and JF. CONCLUSION: The results reflected that indigenous chicken of Bangladesh still possess rich genetic diversity but weak differentiation among the studied populations. This finding provides some important insight on genetic diversity measures that could support the designing and implementing of future breeding plans for indigenous chickens of Bangladesh.

Serological and Molecular Evidence of Q Fever in Domestic Ruminants in Bangladesh.

The objective of this study was to know the herd and animal level prevalence of Q fever in domestic ruminants in some selected districts in Bangladesh. Randomly collected 111 bulk milk and 94 sera samples of cattle, sheep, and goats were tested by indirect ELISA (iELISA). DNA extracted from 23 aborted fetal membranes was analyzed by real time (rt) PCR. The positive cut-off value of iELISA in bulk milk and individual animal sera was ≥30% and ≥40%, respectively. The overall herd level prevalence of Q fever in dairy cattle was 15.6%. The prevalence of Q fever in dairy cattle was significantly higher in Sirajganj in comparison to Satkhira District (P < 0.01). The overall seroprevalence of Q fever in domestic ruminants was 5.06%. Although statistically insignificant, the seroprevalence of Q fever was relatively higher in sheep (9.52%) in comparison to goats (3.33%) and cattle (3.57%). Out of 23 aborted fetal membranes, only one sheep placenta was positive in rt PCR. Q fever is present in all of the three important species of domestic ruminants in Bangladesh. It may have some role in sheep abortion as the seroprevalence is relatively higher and also one sheep placenta is rt PCR positive.

Contrasting evolution of diversity at two disease-associated chicken genes.

There have been significant evolutionary pressures on the chicken during both its speciation and its subsequent domestication by man. Infectious diseases are expected to have exerted strong selective pressures during these processes. Consequently, it is likely that genes associated with disease susceptibility or resistance have been subject to some form of selection. Two genes involved in the immune response (interferon-gamma and interleukin 1-beta) were selected for sequencing in diverse chicken populations from Pakistan, Sri Lanka, Bangladesh, Kenya, Senegal, Burkina Faso and Botswana, as well as six outgroup samples (grey, green, red and Ceylon jungle fowl and grey francolin and bamboo partridge). Haplotype frequencies, tests of neutrality, summary statistics, coalescent simulations and phylogenetic analysis by maximum likelihood were used to determine the population genetic characteristics of the genes. Networks indicate that these chicken genes are most closely related to the red jungle fowl. Interferon-gamma had lower diversity and considerable coding sequence conservation, which is consistent with its function as a key inflammatory cytokine of the immune response. In contrast, the pleiotropic cytokine interleukin 1-beta had higher diversity and showed signals of balancing selection moderated by recombination, yielding high numbers of diverse alleles, possibly reflecting broader functionality and potential roles in more diseases in different environments.