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.

Yi Bi,Xinyu Wang,Lei Qu,Kangshu Lan,Jie Li,Xiaoyue Song,Chuanying Pan,Libang He,Xianyong Lan

doi:10.3389/fvets.2020.00406

Yi Bi, Xinyu Wang + Show 7 more

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https://doi.org/10.3389/fvets.2020.00406

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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, r2 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.

Highlights

The growth differentiation factor 9 (GDF9) gene is a unique member of the transforming growth factor β (TGFβ) superfamily [1], as its protein has six Cys, being different from others in this superfamily that have seven or nine Cys [2, 3]
Its greatest expression is in the ovary while it is widely expressed in 20 different tissues such as the hypothalamus, pituitary, and uterus [4, 5]; GDF9 Variants and Goat Fecundity this indicates that it affects different physiological pathways and metabolism, as well as phenotypic expression to some degree [6]
In Shaanbei white cashmere (SBWC), Lubei White, Jining Gray, Inner Mongolia cashmere, and Laiwu black goat breeds, the G allele is the major allele in V397I [22, 23, 26], but among the Xinong Saanen dairy goat, Big foot black goat, Guanzhong dairy goat, Jintang black goat, and Yimeng black goat, the A allele is associated with larger litter sizes [27, 28]

Summary

Introduction

The growth differentiation factor 9 (GDF9) gene is a unique member of the transforming growth factor β (TGFβ) superfamily [1], as its protein has six Cys, being different from others in this superfamily that have seven or nine Cys [2, 3]. Based on relevant study and data from the National Center for Biotechnology Information Search database (NCBI), 45 SNP loci have been identified in the goat GDF9 gene [9]. 15 SNPs were identified to have significant associations with litter size in more than 30 goat breeds [10,11,12]. Three missense mutations, A240V [17], Q320P [18,19,20], and V397I [21, 22], and three synonymous mutations, L61L [23], N121N [24], and L141L [25, 26], were found to have high mutant frequencies and be significantly associated with litter size in different breeds. The gap in research regarding the combined effects of multiple loci needed to be addressed

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