Bioinformatics analysis and the association of polymorphisms within the caprine GDF9 gene promoter with economically useful traits in Damani goats

Abstract

The blood sample from 60 Damani does were collected and genomic DNA was extracted, and DNA integrity were investigated. A 447 bp promoter fragment of the GDF9 gene was amplified and Sanger sequenced for the identification of GDF9 gene polymorphism. Three novel SNPs were identified at positions g. 97(T > A), g. 142 (G > G) and g. 313(C > T) in the promoter region of the caprine GDF9 gene which significantly (P < 0.05) influenced litter size, body measurement, and milk production traits in Damani goats. The genotype CT of SNP1 significantly (P < 0.05) improved litter size, genotype GG of SNP2 significantly (P < 0.05) enhanced milk production, while the genotypes CC of SNP3 significant (P < 0.05) increased body measurement traits in Damani goats. Moreover, in SNP1 loss of 3 transcription factors (TF) binding sites occurred, SNP2 caused loss of two TFs binding sites, and SNP3 caused loss of a single TF binding site. Similarly, SNP1 and SNP2 caused the gain of three new potential TF binding sites, and SNP3 caused gain of two new TF binding sites. It is concluded that caprine GDF9 gene could be used as a candidate gene for litter size, milk production and body measurement traits in Damani goats through marker-assisted selection for future breeding program.

Keywords:

• Damani goat
• caprine GDF9
• SNPs
• litter size
• body measurement traits

Authors contribution

R.K and A.K conceived the idea, performed experiment, and wrote the manuscript. S.M.S, I.A MSQ, F.A.K, NAK, AAA, and DMA assisted in analysis, editing and revision the draft manuscript. R.K supervised overall research and analyzed the data.

Disclosure statement

No potential conflict of interest was reported by the author(s).

Additional information

Funding

The authors extend their appreciation to the Deanship of Scientific Research at King Khaled University for supporting this work through small Groups Project under grant number [RGP.1/381/1443].