Genome sequencing of captive white tigers from Bangladesh.

OBJECTIVES: The Bengal tiger Panthera tigris tigris, is an emblematic animal for Bangladesh. Despite being the apex predator in the wild, their number is decreasing due to anthropogenic activities such as hunting, urbanization, expansion of agriculture and deforestation. By contrast, captive tigers are flourishing due to practical conservation efforts. Breeding within the small captive population can produce inbreeding depression and genetic bottlenecks, which may limit the success of conservation efforts. Despite past decades of research, a comprehensive database on genetic variation in the captive and wild Bengal tigers in Bangladesh still needs to be included. Therefore, this research aimed to investigate the White Bengal tiger genome to create a resource for future studies to understand variation underlying important functional traits. DATA DESCRIPTION: Blood samples from Chattogram Zoo were collected for three white Bengal tigers. Genomic DNA for all collected samples were extracted using a commercial DNA extraction kit. Whole genome sequencing was performed using a DNBseq platform. We generated 77 Gb of whole-genome sequencing (WGS) data for three white Bengal tigers (Average 11X coverage/sample). The data we generated will establish a paradigm for tiger research in Bangladesh by providing a genomic resource for future functional studies on the Bengal white tiger.

Identification of polymorphisms in GDF9 and BMP15 genes in Jamunapari and crossbred goats in Bangladesh.

Polymorphisms in growth differentiation factor 9 (GDF9) and bone morphogenetic protein 15 (BMP15) genes have been found to be associated with litter size in goats across the globe. Our previous study detected single-nucleotide polymorphisms (SNPs) in GDF9 and BMP15 genes associated with litter size in Black Bengal, Bangladesh's primary native goat breed. However, Jamunapari and crossbred goats in Bangladesh are yet to be investigated for litter size-associated polymorphisms. In this study, we screened Jamunapari and crossbred (50% Black Bengal × 50% Jamunapari) goats to identify polymorphisms in the GDF9 and BMP15 genes and to assess the association between identified SNPs and litter size. The genomic DNA from 100 female goats (50 Jamunapari and 50 crossbred) was used in polymerase chain reactions (PCRs) to amplify exon 2 of the GDF9 and exon 2 of the BMP15 genes. PCR products were sequenced employing the BigDye Terminator cycle sequencing protocol to identify SNPs. We used a generalized linear model to perform the association analysis for identified SNPs and litter size. Seven SNPs were identified, of which four, C818CT, G1073A, G1189A, and G1330T, were in the GDF9 gene and three, G616T, G735A, and G811A, were in the BMP15 gene. G735A was a synonymous SNP, whereas the remaining were non-synonymous SNPs. Identified SNP loci in GDF9 were low polymorphic (PIC < 0.25), while loci in BMP15 were moderately polymorphic (PIC ≥ 0.25). The genotypes at the G1330T locus had a significant (p < 0.05) difference in litter size in Jamunapari goats, but no significant difference was observed for all genotypes at other loci. Therefore, the G1330T loci could be useful as a marker in marker-assisted selection for litter size traits in goats of Bangladesh.

Occurrence of Shiga toxin-producing Escherichia coli carrying antimicrobial resistance genes in sheep on smallholdings in Bangladesh.

BACKGROUND: Shiga toxin-producing Escherichia coli (STEC) are zoonotic foodborne pathogens and a significant concern with the emergence of antibiotic resistance. Close human contact might have a higher chance of being transmitted to humans from sheep if the sheep population is a potential reservoir of antimicrobial-resistant STEC. Therefore, this study aimed to examine the sheep population in rural Bangladesh for antimicrobial-resistant STEC. METHODS: We screened 200 faecal samples collected from sheep in three Upazilas from the Chattogram district. Randomisation of sampling was not performed due to the smaller flock size (two to six animals per smallholding). Phenotypically positive E. coli isolates were examined for two Shiga toxin-producing genes - stx1 and stx2. PCR-positive STEC isolates were investigated for the presence of antimicrobial resistance (AMR) genes - blaTEM , sul1 and sul2. RESULTS: In total, 123 of the 200 tested samples were confirmed positive E. coli using culture-based methods. PCR results show 17 (13.8%) E. coli isolates harboured ≥ one virulent gene (stx1 or/and stx2) of STEC. The AMR profile of STEC isolates was determined utilising the disc diffusion method. Of the STEC isolates, 82, 76, 71 and 71% were susceptible to chloramphenicol, gentamicin, ciprofloxacin and ampicillin. In contrast, 47% of isolates were resistant to trimethoprim-sulfamethoxazole, and 41% were resistant to amoxicillin. In addition, six of the tested STEC isolates exhibited the blaTEM  gene; eight STEC isolates had the sul1 gene, and the sul2 gene was detected in ten STEC isolates. CONCLUSION: To our knowledge, this study is the first to reveal a substantial percentage of STEC isolated from sheep in rural Bangladesh harbouring AMR genes.

Polymorphism of fecundity genes (BMP15 and GDF9) and their association with litter size in Bangladeshi prolific Black Bengal goat.

Goat farming in Bangladesh is primarily centred on indigenous Black Bengal goat, a highly prolific breed. Searching for genetic markers associated with prolificacy in this breed is vital for the country's goat breeding industry. However, there are no reports on polymorphisms associated with the fertility of Bangladeshi Black Bengal goats. This study investigated two major fecundity genes-bone morphogenetic protein 15 (BMP15) and growth differentiation factor 9 (GDF9) to detect any possible mutations in these two genes associated with litter size in Black Bengal goats. Blood samples were collected from 40 raised goats in Hathazari Government Goat Farm, Bangladesh. Genomic DNA was extracted; PCR amplification was performed; and sequencing of PCR products was performed to detect polymorphism loci in the target genes. Five SNPs viz. C735A, C743A, G754T, C781A and C808G were detected in exon 2 of BMP15 gene. A SNP (T1173A) was detected in GDF9 exon 2. Association results show that SNPs at the 735, 754 and 781 nucleotide positions of BMP15 exon 2 had a significant association with litter size in Black Bengal goat. The effect of parity was also highly significant (P < 0.001) on litter size. For the first time, this study explored SNP loci in fecundity genes in Bangladeshi prolific Black Bengal goats. Further studies with many genetically unrelated animals for assessing the association of these loci and others in the fecundity genes with litter size may be useful.