Whole-genome sequencing to identify candidate genes for litter size and to uncover the variant function in goats (Capra hircus).

To select candidate genes for goat prolificacy, we managed six multi- and six single-kid female goats at the same feeding level and in the same management mode over a 4-year period. These goats showed stable differences in litter size over five continuous parturition records. Whole-genome re-sequencing was used in all 12 to select candidate genes, namely, AURKA , ENDOG , SOX2 , RORA , GJA10 , RXFP2 , CDC25C , and NANOS3 , by the strength of their differentiation signals. Most of the selected genes were enriched in the coiled coil process and ovarian development, which suggests that the coiled coil process has a potential regulatory effect on fecundity. Detection of the distribution of variants and association analyses with litter size in 400 goats showed that NANOS3 exon mutations may lead to a transformation of the protein structure. The variation in CDC25C , ENDOG , and NANOS3 showed a significant association with litter size. These results can contribute to the improvement of reproduction traits in the artificial breeding of goats. • Some candidate genes, such as ENDOG, RORA, SMAD5, RXFP2, CDC25C and NANOS3 , was selected out by the strongest differentiation signals. • The coiled coil process and ovarian development enriched most genes at selective regions. • NANOS3 mutations may lead to the protein structure transformation, and variations in CDC25C, ENDOG and NANOS3 showed association with litter size [ABSTRACT FROM AUTHOR]