Variants of pri-miR-26a-5p polymorphisms are associated with values for chicken egg production variables and affects abundance of mature miRNA.

MicroRNAs (miRNAs) are a class of endogenous non-coding RNAs that have an important role in post-transcriptional regulation. Previous analysis of the chicken ovary transcriptome indicated there was a differential abundance of miR-26a-5p in sexually mature and immature hens. In this study, ten single nucleotide polymorphism (SNP) sites in miR-26a-5p primary transcripts (pri-miR-26a-5p) were identified using Sanger sequencing on PCR products in three chicken breeds, among which, the rs316365438(C > T)SNP was associated with age at first egg (AFE) and total number of eggs at 32 weeks (E32). The hens with the TT genotype of the rs316365438(C > T)SNP had an earlier AFE and greater E32 than those with CC and CT genotypes. Due to the presence of linkage disequilibrium (LD) in SNPs, there were only two dominant haplotypes. The two dominant haplotypes with different free-energy and secondary structure were identified and the overexpression vectors were constructed. Overexpression of mature miR-26a-5p from TCTACGCACG haplotype was greater than that from the TTTATATACA haplotype. In summary, the polymorphisms of pri-miR-26a-5p are associated with chicken egg production traits and affect the transcript abundance of the mature miR-26a-5p.