Assessment of Microsatellite Genetic Diversity of Cultured Eriocheir sinensis Populations from Jiangsu and Anhui

Abstract

Eriocheir sinensis, commonly known as the Chinese mitten crab, is widely distributed in China from the Liaohe River in the north to the Pearl River in the south and in the shallow waters of the estuary into the sea, among which the population in the Yangtze River system has the largest yield and the most delicious taste, and is favored by domestic consumers. It is an important breeding species in the Chinese fishing industry. Since artificial breeding began in the 1980s, the production of Chinese mitten crabs has increased, and this species has become one of the most economically important crabs in the world and the most economically important freshwater crab in China. From the perspective of aquaculture areas, the Yangtze River Basin region accounts for over 80% of the total output in China, with Jiangsu and Anhui provinces ranking first and third, respectively. Therefore, the culture of Chinese mitten crabs in Jiangsu and Anhui plays a pivotal role in the country. After more than 30 years of development, China has established ecological and large-scale breeding systems for juvenile crabs. Therefore, artificial seedlings dominate the market but are mainly distributed in coastal areas such as Jiangsu. However, to reduce production costs, some breeding farms blindly introduce Chinese mitten crabs to one another, and do not perform germplasm detection during breeding, causing germplasm resources to be random and mixed, which directly affects the quality of juvenile crabs and results in the risk of germplasm decline. To evaluate the genetic background of cultured Chinese mitten crab populations in Jiangsu and Anhui in odd-number years, and to provide a scientific basis for subsequent genetic improvement and breeding of new varieties, 10 pairs of highly polymorphic microsatellite markers (simple sequence repeats) were used to analyze the genetic diversity and genetic structure of six cultured populations with 177 individuals in total. Each population contained 28–30 adult individuals with an approximate sex ratio. The leg muscle of the sampled crabs was extracted, and genomic DNA was extracted according to the instructions of the genome extraction kit (TianGen DP304). The microsatellite primers were modified using fluorescent labels (FAM and HEX) prior to PCR, and the PCR products were subjected to capillary electrophoresis. Genemarker 2.2 software was used to interpret typing results. The number of alleles (Na), effective number of alleles (Ne), expected heterozygosity (He), observed heterozygosity (Ho), inbreeding coefficient (Fis), and genetic distance (Dn) were calculated using Popgene 1.32 software, and Hardy-Weinberg equilibrium analysis was performed using the Markov chain method. PIC_CALC 0.6 software calculates polymorphism information content (PIC). Analysis of molecular variance (AMOVA) and the coefficient of genetic differentiation (Fst) were performed using Arlequin 3.5 software. A UPGMA tree was constructed based on inter-population genetic distance using MEGA 4.0 software. According to the frequency of alleles, mutation-drift equilibrium was detected using Bottleneck software. Genetic structure analysis was performed using the Structure 2.3.4 software. The results showed that the genetic diversity levels of the six cultured populations of E. sinensis were high and similar (Na=16.0–18.4, Ne=10.1–12.4, Ho=0.759–0.836, He=0.897–0.916, PIC=0.870–0.892). Genetic distance among populations (0.015–0.277) and the coefficient of genetic differentiation (Fst: 0.001–0.011) were low, and genetic variation among populations accounted for only 0.47% of the total variation in AMOVA. These analyses consistently indicated no significant genetic differentiation among the populations. The phylogenetic tree showed that the six cultured populations had a common ancestor and that the Gaochun population had further relationships with the other populations. Owing to its high genetic diversity, the Gaochun population can be used as a base population for mass selection. Genetic structure analysis showed that the genetic composition of each cultured population was diverse, and the proportions were similar. In this study, the inbreeding coefficient (Fis) of 10 loci in six populations had 43 positive values and 17 negative values, and there were both positive and negative values in each population, indicating that there was not only inbreeding to a certain extent but also a small amount of distant breeding in the six cultured populations of Chinese mitten crabs.The results of genetic structure analysis showed that the number of optimal genetic cluster groups was K=3. However, the chaotic genetic structures among the three groups failed to gather into a relatively independent group. Furthermore, each population had a genetic composition similar to those of the three genetic lineage sources. Considering the high level of genetic diversity in these populations, it is possible that the parental population sources are more complex. This indicated that the cultured population of Chinese mitten crabs had a large number of exogenous genetic hybrids.In conclusion, the genetic diversity of cultured Chinese mitten crab populations in the Jiangsu and Anhui areas is still high, which has potential development and utilization value, but there may be germplasm confounding. Therefore, it is necessary to conduct further studies on the breeding population during the subsequent breeding of improved varieties, such as using molecular markers with high sensitivity that can be used to identify different water systems to analyze the sources of mixed germplasm, and conducting germplasm detection before breeding to purify the germplasm and make reasonable and sustainable use of its germplasm resources.

Keywords

• eriocheir sinensis
• genetic diversity
• microsatellite
• cultured population