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

Abstract

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.

Detection of Polymorphisms in BMP15 and GDF9 Genes and Their Associations with Reproductive Traits in Black Bengal Goat of Bangladesh

“…Maitra et al (2016) reported G as the major allele for G735A and C for C808G polymorphisms in the BMP15 gene of Indian BBG with allelic frequencies of 0.635 and 0.741, respectively and are close to the current estimation. However, the estimated genotypic and allelic frequencies of the BMP15 (K245K and E270Q) gene in BBG (Das et al, 2021), in Jamunapari, and Crossbred (for K245K) (Shaha et al, 2022) differed slightly from the present estimation. The genotypic and allelic frequencies of the GDF9 gene (A273V) estimated in this study differed slightly from those observed in Indian goat breeds (Ahlawat et al, 2012) and Beetal goats (Hadizadeh et al, 2014) respectively.…”

“…In the follow-up research, Ahlawat et al (2015) genotyped these three non-synonymous polymorphisms in Indian BBG and confirmed the C818T (A273V) polymorphism, consistent with this study. However, the identified g.3764C>T SNP of GDF9 in the studied BBG population has also been reported in prolific Beetal goats (Hadizadeh et al, 2014), Cameroon native goats (Wouobeng et al, 2020), and Jamunapari and crossbred goats (Shaha et al, 2022) that supports the present finding. In the history of recorded polymorphisms, the identified SNP loci in the exon region of the GDF9 gene of different goat breeds were similar different from our identified SNP (Feng et al, 2011;An et al, 2012;Arefnejad et al, 2018;Ghoreishi et al, 2019;Bi et al, 2020;Das et al, 2021).…”

“…For G735A (K245K) polymorphism, Das et al (2021) reported parity-wise mean litter size as 1.92, 2.64, and 2.88, respectively in BBG. Likewise, Shaha et al (2022) also found the mean litter size in Jamunapari and Crossbred goats as 2.00 and 1.50, respectively, for the same SNP (G735A) of BMP15 gene and is homogenous to the present findings. In contrast, Wang et al (2011) observed AA, AB, and BB genotypes (for 456T→G, 466C→G, 510C→T, and 511T→C SNPs) in the exon 2 of BMP15, where the BB genotype always appeared to have the maximum litter size at the three consecutive parities and the average litter size was found as 1.62±0.32, 1.60±0.42, and 2.28±0.93, respectively (p<0.05).…”

“…Conversely, Polley et al (2009) found GDF9 as monomorphic in Indian BBG, while Das et al (2021) found GDF9 as polymorphic with dissociation of genotypes on litter size in Bangladeshi BBG. Moreover, Shaha et al (2022) reported C818T with amino acid replacement A273V in the exon 2 of the GDF9 gene in Jamunapari and Crossbred goats in Bangladesh, where CC and CT genotypes had mean litter sizes of 1.50 and 1.83 in both of the breeds, which is close to this findings.…”

“…Ahlawat et al (2016) found a significant association between single nucleotide polymorphisms (SNPs) in the BMPR1B, BMP15, and GDF9 genes and litter size in Indian Black Bengal goats. Shaha et al (2022) reported that a non-synonymous mutation at the G1330T locus of the GDF9 gene had significantly affected litter size in the Jamunapari goat of Bangladesh. Three SNPs (C735A, G754T, and C781A based on NCBI GenBank reference sequence: NM_001285588.1) of the BMP15 gene had a significant association with litter size in Bangladeshi BBG (Das et al, 2021).…”