SCRAPIE is a prion disease of sheep and goats, and is characterised by the accumulation of pathologically folded prion protein (PrP) derived from host-encoded PrP. For sheep, over 40 polymorphisms of PrP have been described

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 (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 goat, but no significant difference was observed for all genotypes at other loci. This study provides additional molecular markers that would be useful for future research on the litter size trait in goats of Bangladesh.

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.

Growth differentiation factor 9 (GDF9) and bone morphogenetic protein 15 (BMP15) are two crucial fecundity genes 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 (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 goat, but no significant difference was observed for all genotypes at other loci. This study provides additional molecular markers that would be useful for future research on the litter size trait in goats of Bangladesh.

No abstract