Origin of domesticated Qingtian paddy-field carp and its genetic differentiation from wild common carp populations

Common carp is the first domesticated fish species in the world, which is the main fish candidate for being cocultured with rice in paddy fields. There are several strains of rice field-domesticated common carp in China, such as Qingtian (paddy-field) carp, Congjiang Carp, Wuyi Carp etc. Unfortunately, their geographical origins were unclear and the adaptability to rice field of these common carp varieties have not yet been well studied. Here we used 2b-RAD simplified genome sequencing to obtain 108,813 SNP markers from two paddy-field carp populations (Qingtian and Wuyi Mountain) and eight wild carp populations to explore the phylogenetic relationship and differences between the Qingtian paddy field carp and the other neighboring wild and domesticated carp populations. Compared with the wild carp populations, the levels of nucleotide diversity of the two paddy-field carp populations were lower. The neighbor-joining (NJ) tree, principal component analysis (PCA), and population structure analysis all showed three clusters of the carp populations: Qingtian paddy-field carps as one of the clusters, paddy-field carps from Wuyi Mountain areas the second and all the wild common carp populations the third. Qingtian paddy-field carps were clearly separated from other populations, which was consistent with the population differentiation index (Fst) analysis. All these analyses indicated that Qingtian paddy-field carps showed the closest relationship with the Oujiang wild carp population (OJ), and less close to all other populations, providing clear evidence of the geographical origin of Qingtian paddy-field carp from Oujiang River. With wild carps as the control group and paddy-field carps as the selection group, 180 genes with a selection signature were obtained. The gene ontology (GO) classification and enrichment analysis showed that the genes with a selection signature were enriched in the pathway related to signal transduction function. We can thus conclude that Qingtian paddy field carp of the Asia first GIAHS rice-fish coculture system were originated from the domestication from the local Oujiang wild common carp population, which showed a clear genetic adaptive evolution in genes with function in signal transduction. These findings will help us to further disclose the domestication effects on fish that leading us better understanding the adaptive mechanism of fish to the rice field environment.