Genetic variability and relationships among six grass carp Ctenopharyngodon idella populations in China estimated using EST-SNP Markers

Abstract

The grass carp, which is one of the most important farmed fish species in China, is widely distributed in different river basins. In this study, 21 single nucleotide polymorphism markers, developed in the grass carp expressed sequence tag database, were used with the snapshot genotyping method to analyze the genetic structure of six grass carp populations (SS, JL, HH, YJ, NX, and FS) from the Yangtze River and the Pearl River. The effective numbers of alleles (Ne) of the six grass carp populations was 1.7680–1.8038, the observed heterozygosity (Ho) was 0.5938–0.6305, the expected heterozygosity (He) was 0.4420–0.4443, and the polymorphic information content (PIC) was 0.3241–0.3403. The PIC, Ne, and He of the JL population were the highest among all populations, whereas those of the YJ population were the lowest. The NJ tree analysis based on genetic distance of the grass carp populations revealed that the six populations clustered into two branches: the SS, JL, and HH populations clustered first into one branch, which then clustered with YJ population; the FS and NX populations constituted a separate branch. The established genetic structures and phylogenetic relationships of some of the grass carp populations of the Yangtze River and Pearl River may lay the foundation for selecting core breeding populations.