Detection of genetic variations of five MMAF-related genes and their associations with litter size in goat

Abstract

Background: Multiple morphological abnormalities of the sperm flagella (MMAF) makes an assignable contribution to male infertility, including QRICH2 , CFAP43 , CFAP44 , CFAP69 , CCDC39 , AKAP4 and DNAH1 gene. This work studied 28 putative indel mutations of MMAF related genes including QRICH2 , CFAP69 , CFAP43 , CCDC39 and DNAH1 gene and their correlation with the first-born litter sizes of 769 Shaanbei white cashmere (SBWC) goats. Results: Electrophoresis and DNA sequencing analysis showed the 11-bp indel within QRICH2 ( QRICH2 -P4), the three indel variations in CFAP69 ( CFAP69 -P4, CFAP69 -P6 and CFAP69 -P7) and the 27-bp indel of DNAH1 ( DNAH1 -P1) were found to be polymorphic. The 27-bp indel variation within DNAH1 was not in consistent with HWE and the other four indel of QRICH2 and CFAP69 were in consistent with HWE. The linkage disequilibrium (LD) analysis showed the 8-bp indel ( CFAP69 -P4) and the 6-bp indel ( CFAP69- P6) within CFAP69 were in complete LD with each other (D'=0.99, r 2 =1.00). The 27-bp indel mutation within DNAH1 was strongly significantly associated with first-born litter sizes of SBWC goats ( P ＜0.01) and the average litter size of II genotype was significantly greater than ID and DD genotypes ( P = 0.003). In single-lamb and multi-lamb of goat groups, the genotype distributions of the 27-bp indel was significantly different ( P = 0.002). While the 11-bp indel variation of QRICH2 and three indel mutations (P4, P6 and P7) of CFAP69 identified were not ( P ＞0.05). Conclusions: These findings suggest the 27-bp indels in the goat DNAH1 can be used as an effective molecular marker for marker-assisted selection of goats reproduction breeding in the future.