Population structure and diversity of Duyun "Red Carp"

The "Red Carp" from Duyun, Guizhou Province is a product of the traditional rice farming model, with relatively rich genetic diversity, making it an ideal material for breed selection. To enrich the genetic background data of rice field carps in Guizhou Province and provide a theoretical basis for the rational development, utilization, and protection of rice field carp germplasm resources, we used mitochondrial DNA Cyt b gene sequencing technology to explore the population structure and diversity of the "Red Carp" from Duyun and adjacent areas. The results show that a total of 45 variable sites were detected in 253 Cyt b genes, defining 23 haplotypes. The 'Red Carp' from Duyun exhibited 9 haplotypes, 5 of which shared with the control rice field carp, accounting for 76.19% of the total sample size. Phylogenetic and neural network results indicate that the Duyun "Red Carp" is a hybrid population composed of two highly differentiated sub-species groups with minor genetic differences, namely Cyprinus carpio haematopterus Temminck and C. carpio rubrofuscus Lacépède. These sub-species shared the same maternal origin with domestic carp varieties and the control paddy field carp. For the Duyun "Red Carp", Hap22 was shared among individuals belonging to C. carpio haematopterus sub-species, while four unique haplotypes were exclusive to this sub-species, Additionally, four shared haplotypes were present in C. carpio rubrofuscus sub-species. Genetic diversity and differentiation analysis reveal that the two subspecies populations of Duyun "Red Carp" had a low level of genetic variation, both exhibiting characteristics such as high H_d and low π. The C. c. haematopterus subspecies was moderately differentiated from the control paddy field carp; while the sub-species of C. carpio rubrofuscus showed a high degree of differentiation from the Jinping Carp, but a relatively low level of differentiation from the other three control paddy field carp populations. However, due to geographical isolation and selective pressure during domestication, founder effects and genetic drift, their genetic diversity had decreased, resulting in genetic differentiation from the control populations. The study indicates that there is limited genetic exchange among the rice field carp populations in Duyun and its adjacent areas, with different genetic structures within and between populations.