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Detection of genome-wide genetic variation is one of the primary goals in bovine genomics. Genomes of several cattle breeds have been sequenced so far to understand the genetic variation associated with important phenotypes. Red Chittagong Cattle (RCC) is a locally adopted and disease-resistant indicine cattle breed in Bangladesh. In this study, we describe the first genome sequence of the RCC breed and in silico analyses of identified functional variants. Deep sequencing of a RCC bull genome on the NanoBall sequencing platform generated approximately 110 Gb paired-end data, resulting in 31X of genome coverage. Quality filtering retained 360,711,803 paired-end reads. Of the filtered reads, 99.8% were mapped to the bovine reference genome (ARSUCD1.2). A total of 17. 8 million Single nucleotide variants (SNVs) and 2.1 insertions and deletions (INDELs) were identified in the RCC genome. Ts/Tv ratio was computed and found to be 2.21. In total, 332 4621 variants were novel compared with dbSNP data (NCBI dbSNP bovine build 150). Functional annotation identified 54961 SNVs exonic regions, 63.75% of which were synonymous, whereas 30.42% were non-synonymous changes. The percentage of coding INDELs was 0.25% (Frameshift deletion 0.19% and Frameshift insertion 0.06%). We identified 120 variants in 26 candidates for five diseases-foot and mouth disease (FMD), Mastitis, Parasite, para-tuberculosis, and tick. Of the 120 variants, 50 were non-synonymous / frameshift (NS/FS), while 70 were synonymous/non-frameshift (SS/NFS). The identified catalog of genomic variants in RCC may establish a paradigm for cattle research in Bangladesh by filling the void and providing a database for genome-wide variation for future functional studies in RCC.

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.

A rare case of windpuff was diagnosed in 7 months old two domestic pigeons due to itching and scratching with inanimate objects caused by lice infestation reported in Begumganj upazila hospital, Noakhali district, Bangladesh. This is the first case of domestic pigeon recorded in Bangladesh and the aim of this case study is to determine the causal agent, treatment and management procedure of windpuff. Parasitological examination of feathers revealed the presence ofColumbicola columbae,a dorso-ventrally flattened biting type louse. Using needle puncture was able to release the ballooning condition and the pigeons were treated with antimicrobial drug (Enrofloxacin @10mg/kg body weight) through drinking water along with multivitamin and ectoparasiticidal drug (Ivermectin @0.4mg/kg body weight). Both the pigeon was successfully recovered without any further complications within four days.

Growth differentiation factor 9 (GDF9) and bone morphogenetic protein 15 (BMP15) are two crucial fecundity genes 15 associated with litter size traits in the goat. Our previous study on GDF9 and BMP15 genes detected single nucleotide polymorphisms (SNPs) associated with litter size in Bangladeshi Black Bengal goats. In this study, Jamunapari and crossbred goats of Bangladesh were screened 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 goats (50 Jamunapari and 50 crossbred) was used in Polymerase Chain Reaction (PCR) to amplify the exon 2 of the GDF9 and exon 2 of the BMP15 gene. PCR products were sequenced employing the BigDye Terminator cycle sequencing protocol, to identify SNPs. A generalized linear model was utilized 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, 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 (PICBMP15 were moderately polymorphic (PIC≥0.25). The genotypes at the G1330T locus had a significant (p

Inappropriate antimicrobial treatment can pose a risk for developing resistance against antimi-crobial drugs in bacteria. Close human contact might have a higher chance of being transmitted to humans from sheep if the sheep population is a potential reservoir of zoonotic pathogens such as shiga toxin-producing Escherichia coli (E. coli) (STEC). Therefore, this study aimed to exam-ine the sheep population in rural Bangladesh for antimicrobial resistant STEC. We screened 200 faecal samples collected from sheep in three Upazila from the Chattogram district. Phenotypical-ly 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 genes- blaTEM, sul1 and sul2. In total, 123 of the 200 tested samples were confirmed positive E. coli by cul-tured based methods. PCR results show 17(13.8%) E. coli isolates harboured ≥ one virulent gene (stx1 or/and stx2) of STEC. Six of the tested STEC isolates exhibited blaTEM gene; eight STEC isolates had sul1 gene, and sul2 gene was detected in ten STEC isolates. To our knowledge, this study is the first to reveal a significant proportion of STEC isolated from sheep in rural Bangla-desh harbouring antimicrobial resistance genes.

Identification of prolificacy associated genetic markers remains vital in goat breeding industry since an increase in litter size can generate significant profit. Black Bengal is a prolific goat breed in Bangladesh. There are no inland reports on polymorphisms associated with fertility of Black Bengal goats in Bangladesh. In this study, we investigated two major fecundity genes-bone morphogenetic protein 15 (BMP15) and growth differentiation factor 9 (GDF9) in order to detect any possible mutations in these two genes in Bangladeshi Black Bengal goats. We identified six single nucleotide polymorphisms (SNP), of which five (C735A, C743A, G754T, C781A, and C808G) in BMP15 exon 2 and one (T1173A) in GDF9 exon 2. We also studied their association with litter size. Association analysis results show that polymorphism at the 735, 754 and 781 nucleotide positions of BMP15 exon 2 had significant association with litter size in Black Bengal goat. The effect of parity was also highly significant (p