Two Novel Rare Strongly Linked Missense SNPs (P27R and A85G) Within the GDF9 Gene Were Significantly Associated With Litter Size in Shaanbei White Cashmere (SBWC) Goats

Abstract

Growth differentiation factor 9 (GDF9) is a high-fertility candidate gene that plays a crucial role in early folliculogenesis in female mammals. In this study, direct sequencing was used to screen possible SNP loci in the goat GDF9 gene. Three SNP loci, p.proline27alanine (P27R), p.leucine61leucine (L61L), and p.alanine85glycine (A85G), were identified in Shaanbei white cashmere (SBWC) goats. Among the three SNPs, two rare missense SNP loci (P27R and A85G) were discovered to be strongly linked with each other ( D ′ value = 0.926, r 2 value = 0.703). Both P27R and A85G loci had two genotypes: wild type and heterozygous type. A85G exerted a significant effect on litter size ( P = 0.029) in SBWC goats, and the heterozygous genotype was superior in comparison with the wild type. The heterozygous genotype was also superior in P27R but no significant association was found. However, the combination genotypes of P27R and A85G were identified to have superior effects on litter size ( P = 3.8E−15). This information suggested that these two SNPs influenced litter size in goats synergistically. Combining this information with our previous studies, we propose that the GDF9 gene is the principal high-fertility candidate gene and that the A85G locus is a promising SNP that affects litter size in goats. These results may fill a research gap regarding rare mutations as well as provide crucial molecular markers that could be useful in marker-assisted selection (MAS) goat rearing when selecting superior individuals.

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

“…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).…”

“…Marker-assisted selection (MAS), combined with conventional selective breeding programs, is the most effective approach for improving reproductive traits (Ahlawat et al, 2015). Genetic evidence showed the significant influence of Bone Morphogenetic Protein 15 (BMP15) and Growth Differentiation Factor 9 (GDF9) on the fecundity of goats (Zhao et al, 2016;Arefnejad et al, 2018;Bi et al, 2020). Meanwhile, several polymorphisms in the candidate genes like BMP15 and GDF9 have been reported for their associations with prolificacy traits in different goat populations (Wang et al, 2011;Jalbani et al, 2017;Ghoreishi et al, 2019).…”

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

“…Jamunapari goats with heterozygous GT genotype had a significantly smaller litter size than the GG genotype at the G1330T locus. Novel and rare missense SNP in the GDF9 gene have been reported considerably associated with litter size in the Shaanbei White Cashmere goat (Bi et al 2020). Previous studies recorded both positive (Feng et al 2011;Wang et al 2013) and negative (Wang et al 2019a) effects of the mutant allele of the G1089A(V397I) locus on the litter size trait in goats.…”

Mutation Analysis and Restriction Site Mapping of GDF9 in Indonesian Bligon Goat

“…An evolutionary mechanism that produces random (rather than selection-driven) changes in allele frequencies in a population over time was called genetic drift. Bi et al (2020) reported that three SNPs of the GDF9 (p.proline27alanine (P27R), p.leucine61leucine (L61L), and p.alanine85glycine (A85G)) were identified in Shaanbei white cashmere (SBWC) goats. Two SNPs are missense mutations (P27R and A85G) among the three SNPs.…”