Genetic Diversity and Genetic Differentiation of Populations of Golden-Backed Carp (Cyprinus carpio var. Jinbei) in Traditional Rice Fields in Guizhou, China

Abstract

The aim of this study was to assess the current status of the germplasm resources of golden-backed carp (Cyprinus carpio var. Jinbei) cultured in paddy fields in Guizhou Province, China. Five populations of golden-backed carp in Liping County, Jinping County, Huangping County, Congjiang County and Duyun City in Guizhou Province were subjected to high-throughput sequencing by 2b-RAD technology, and their genetic diversity and genetic differentiation were analysed. Based on sequencing, 44,896 SNP loci were obtained, and all five population genetic diversity indicators showed low diversity. In the NJ tree, the Congjiang and Liping populations were mixed together, and the other three groups formed a cluster. A cross-validation error box plot and pong cluster plot were constructed to show the K value results. When K = 1, the cross-validation error rate was the lowest. Principal component analysis showed that the Duyun population formed a group separate from the group comprising the other four populations. The genetic differentiation index and genetic distances between the Duyun population and the remaining four populations were greater than 0.05, indicating population differentiation. The genetic diversity of the five populations of golden-backed carp in Guizhou Province was low, the genetic differentiation of the Duyun population was the most significant, and the Duyun population was separate from the other four groups.

Genetic Diversity of Fish in Aquaculture and of Common Carp (Cyprinus carpio) in Traditional Rice–Fish Coculture

“…This suggests that traditional agricultural systems play a role in in situ conservation of the genetic diversity of carp cocultured in paddies in southern Zhejiang Province. The C. carpio preserved in the traditional rice-fish coculture system is a landrace that has well adapted to the paddy environment, with strong resistance to pests and diseases and adaptation to the fierce habitat changes during rice cultivation [58,59]. In the traditional agricultural system, the conservation of carp depends on the recognition, collection, and introduction of new strains by local smallholders, resulting in the diversity accumulation of genotypes and alleles in landraces [60,61].…”

Genetic Diversity and Population Structure of Coilia nasus Revealed by 2b-RAD Sequencing

“…The Hardy–Weinberg equilibrium p -value (HW-P) and the nucleotide diversity (Pi) were calculated using VCF tools software (Version 0.1.14) [ 31 ]. The expected heterozygosity (He), observed heterozygosity (Ho), and effective number of alleles (Ne) were calculated with reference to Ji et al [ 22 ].…”

“…For instance, based on 2b-RAD sequencing, the low genetic diversity of five golden-backed carp ( Cyprinus carpio var. Jinbei ) populations in Guizhou, China, was revealed [ 22 ]. Based on RAD sequencing, significant genetic differentiation of Monopterus albus in different regions of China was identified [ 23 ].…”