Genetic diversity of the cultured giant freshwater prawn (Macrobrachium rosenbergii) in China based on microsatellite markers

Skim-Sequencing Based Genotyping Reveals Genetic Divergence of the Wild and Domesticated Population of Black Tiger Shrimp (Penaeus monodon) in the Indo-Pacific Region

The domestication of a wild-caught aquatic animal is an evolutionary process, which results in genetic discrimination at the genomic level in response to strong artificial selection. Although black tiger shrimp (Penaeus monodon) is one of the most commercially important aquaculture species, a systematic assessment of genetic divergence and structure of wild-caught and domesticated broodstock populations of the species is yet to be documented. Therefore, we used skim sequencing (SkimSeq) based genotyping approach to investigate the genetic structure of 50 broodstock individuals of P. monodon species, collected from five sampling sites (n = 10 in each site) across their distribution in Indo-Pacific regions. The wild-caught P. monodon broodstock population were collected from Malaysia (MS) and Japan (MJ), while domesticated broodstock populations were collected from Madagascar (MMD), Hawaii, HI, USA (MMO), and Thailand (MT). After various filtering process, a total of 194,259 single nucleotide polymorphism (SNP) loci were identified, in which 4983 SNP loci were identified as putatively adaptive by the pcadapt approach. In both datasets, pairwise F_ST estimates high genetic divergence between wild and domesticated broodstock populations. Consistently, different spatial clustering analyses in both datasets categorized divergent genetic structure into two clusters: (1) wild-caught populations (MS and MJ), and (2) domesticated populations (MMD, MMO and MT). Among 4983 putatively adaptive SNP loci, only 50 loci were observed to be in the coding region. The gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses suggested that non-synonymous mutated genes might be associated with the energy production, metabolic functions, respiration regulation and developmental rates, which likely act to promote adaptation to the strong artificial selection during the domestication process. This study has demonstrated the applicability of SkimSeq in a highly duplicated genome of P. monodon specifically, across a range of genetic backgrounds and geographical distributions, and would be useful for future genetic improvement program of this species in aquaculture.

Investigation of growth retardation in Macrobrachium rosenbergii based on genetic/epigenetic variation and molt performance

Giant freshwater prawn, Macrobrachium rosenbergii is an important freshwater aquaculture species worldwide, and China contributes the most to its global production. However, in recent years in China, many prawns have shown serious growth retardation, which is referred to as "iron prawn." To explore the mechanism behind this phenomenon, we compared the difference between these "iron prawns" and normal prawns in three aspects-changes in genetic diversity, DNA methylation, and transcriptomes-as well as comparing differences in their molt performance. The results are as follows: first, compared with normal prawns, "iron prawns" showed no significant decrease in genetic diversity, but they did show obvious genetic differentiation, and different DNA methylation levels were observed. The genetic and epigenetic variations that existed between "iron prawn" and normal prawn indicated the influence of germplasm on growth performance. Second, transcriptome analysis revealed 1813 differentially expressed genes (DEGs) between the "iron prawn" and normal prawn, and the DEGs mainly enriched the glucose metabolism- and immune-related pathways, such as in glycolysis/gluconeogenesis metabolism, insulin secretion, glucagon signaling pathway, antigen processing and presentation, as well as in complement and coagulation cascades. Enrichment analysis indicated the importance of the glucose level and pathogen attacks to growth performance in the "iron prawn." Finally, a comparison of the molt performance showed that the length of the molt cycle in the "iron prawn" was comparable to normal prawns with the same size, but the specific growth was much lower in the "iron prawn." This result suggested that lower body weight gain per molt cycle should be responsible for growth retardation in the "iron prawn," but not in the longer molt cycle. The results in this study provided fundamental information about the mechanism behind growth retardation in M. rosenbergii.

Effects of microcystin-LR on the immune dysfunction and ultrastructure of hepatopancreas in giant freshwater prawn Macrobrachium rosenbergii

Microcystins (MCs), produced by cyanobacteria, can strongly inhibit the activity of protein phosphatase, and exhibit strong hepatotoxicity. Macrobrachium rosenbergii is an important aquaculture economic species. Cyanobacterial blooms occur frequently during the culture of M. rosenbergii. However, the effects of MCs on the M. rosenbergii immune function have not been studied. In the present study, M. rosenbergii were exposed to environment-related concentrations of MC-LR type (0.5 and 5 μg/L) for 3 weeks. Hepatopancreatic histology was investigated, and antioxidant enzymes activity, acid phosphatase, alkaline phosphatase and lysozyme activity in hepatopancreas were also analyzed. Results showed that MC-LR could damage M. rosenbergii hepatopancreas, induce hepatopancreatic apoptosis and antioxidant dysfunctions. The expression profiles of major immune-related genes after MC-LR exposure were also detected. Some genes with antibacterial functions were suppressed, and the expression of apoptosis-related genes were up-regulated. After MC-LR exposure, the cumulative mortality of M. rosenbergii infected with Vibrio vulnificus and Aeromonas hydrophila were much higher than the control in a time-dose dependent manner. These results indicated the potential negative influence of MC-LR on the immune function of M. rosenbergii.

Genetic Diversity and Structure Analysis of Percocypris pingi (Cypriniformes: Cyprinidae): Implications for Conservation and Hatchery Release in the Yalong River

Percocypris pingi is a near threatened cyprinid species, which has suffered a dramatic decline due to anthropogenic factors. As one response to this decline, hatchery release for P. pingi has been conducted in the lower reaches of the Yalong River since 2012. To understand the conservation status of this species and the potential impact of the release of hatchery-reared fish, we studied the genetic diversity and population structure of wild and hatchery populations of P. pingi. Two hatchery populations (Jinping [JPH] and Ya’an [YAH]) and two wild populations (Muli [MLW] and Woluo [WLW]) of P. pingi were analyzed based on microsatellite markers and the mitochondrial DNA control region. The results showed that P. pingi possesses moderate levels of genetic diversity, with observed heterozygosities ranging from 0.657 to 0.770 and nucleotide diversities ranging from 0.00212 to 0.00491. Our results also suggested WLW harbors considerable proportions of genetic diversity in this species and serves as a refuge for P. pingi during anthropogenic disturbance, thus playing an important role for the conservation of P. pingi populations. Microsatellite and mitochondrial markers both indicated close genetic relationships between YAH and MLW, JPH and WLW, respectively. The results to some extent reflected the geographical provenances for original broodstocks of the two hatchery populations, which provide some practical guidance for hatchery release of P. pingi. The existence of remarkable genetic divergence distributed along limited geographical range (approximately 10 kilometers) suggests the two wild populations should be regarded at least as two distinct evolutionary significant units (ESUs) and management units (MUs). Considering reduced intra-population genetic variation in hatchery population for release and significant genetic compositions of the two hatchery populations, some appropriate breeding strategies were proposed to benefit conservation of P. pingi.