Whole-genome resequencing reveals genetic diversity and signatures of selection in mono-female grass carp (Ctenopharyngodon idella)

Grass carp (Ctenopharyngodon idella) is an important aquaculture species in China even in the world, and the production of mono-female population can effectively increase its yield as its females grow faster than males. Assessing the genetic basis of mono-female population is of great importance for breeding and culture, and the detection of signature of selection may shed light on genes and mutations associated with important phenotypic traits. In this study, whole-genome resequencing technology was employed to detect the genetic variation in wild populations of grass carp from the Yangtze River and the Pearl River, as well as in a mono-female population based on combining gynogenesis with sex-reversal breeding method. A total of 9,510,648 informative single nucleotide polymorphisms (SNPs) were identified across the three populations. The mean observed heterozygosity (Ho) and mean expected heterozygosity (He) of SNPs were calculated to be 0.2139 and 0.2894, 0.2313 and 0.2888, and 0.2523 and 0.2418 in the Yangtze River, Pearl River and mono-female population, respectively. The genetic distance between the mono-female population and the wild populations indicated that there was a moderate genetic differentiation between the three populations. Furthermore, analysis of run of homozygosity (ROH) revealed that the mono-female population exhibited a lower level of genomic inbreeding (inbreed coefficient = 0.075) compared to higher levels in the Yangtze River (inbreeding coefficient = 0.2410) and Pearl River populations (inbreed coefficient = 0.1894). Short ROHs were more frequently observed in the mono-female population, while long ROHs were more common in the Yangtze River and the Pearl River populations, providing insight into the population history of grass carp. Using the Yangtze River and Pearl River populations as references, 646 and 594 genes with hypothesized selection signature were identified by selective sweeps in the mono-female population, respectively. These genes were involved in 25 KEGG pathways associated with some important traits, such as growth (esm1 and zbed1), reproduction (ccnb1 and ptpn13), development (grin1a, mcc and brd2) and immune response (npr2, psmb9a, psmb8, tap2 and h2a). These results will be helpful for the molecular marker-assisted breeding and development conservation strategies of grass carp germplasm resources.