Identification of Candidate Genes for Twinning Births in Dezhou Donkeys by Detecting Signatures of Selection in Genomic Data

Twinning trait in donkeys is an important manifestation of high fecundity, but few reports are available elucidating its genetic mechanism. To explore the genetic mechanism underlying the twin colt trait in Dezhou donkeys, DNA from 21 female Dezhou donkeys that had birthed single or twin colts were collected for whole-genome resequencing. F(ST), θπ and Tajima’s D were used to detect the selective sweeps between single and twin colt fecundity in the Dezhou donkey groups. Another set of 20 female Dezhou donkeys with single or multiple follicles during estrus were selected to compare concentrations of reproductive hormone including follicle-stimulating hormone (FSH), luteinizing hormone (LH), estradiol (E(2)) and progesterone (P(4)). Four candidate genes including ENO2, PTPN11, SOD2 and CD44 were identified in the present study. The CD44 gene had the highest F(ST) value, and ENO2, PTPN11 and SOD2 were screened by two joint analyses (F(ST) and θπ, θπ and Tajima’s D). There was no significant difference in the LH, FSH and P(4) levels between the two groups (p > 0.05); however, the serum E(2) content in the multi-follicle group was significantly higher than that in the single-follicle group (p < 0.05). The identified candidate genes may provide new insights into the genetic mechanism of donkey prolificacy and may be useful targets for further research on high reproductive efficiency.