Molecular characterizations of a novel putative DNA-binding protein LvDBP23 in marine shrimp L. vannamei tissues and molting stages

Genome survey and high-resolution backcross genetic linkage map construction of the ridgetail white prawn Exopalaemon carinicauda applications to QTL mapping of growth traits

BACKGROUND

High-resolution genetic linkage map is critical for QTL mapping, genome sequence assembly and marker-assisted selection in aquaculture species. The ridgetail white prawn Exopalaemon carinicauda is one of the most economic shrimp species naturally distributed in the coasts of eastern China and western Korea. However, quite limited genomics and genetics information have been exploited for genetic improvement of economic traits in this species.

RESULTS

In the present study, we conducted genome survey and constructed high-resolution genetic linkage maps of the ridgetail white prawn with reciprocal-cross mapping family genotyped using next-generation sequencing approaches. The estimated genome size was 9.33 Gb with a heterozygosity of 0.26% and a repeat sequence ratio of 76.62%. 65,772 protein-coding genes were identified by genome annotation. A total of 10,384 SNPs were used to high-throughput genotyping and assigned to 45 linkage groups (LGs) from reciprocal backcross families of E. carinicauda, and the average marker distances were 0.73 cM and 0.55 cM, respectively. Based on the high-resolution linkage map, twenty-three QTLs related to five growth traits were detected. All QTLs could explain 8.8-15.7% of the total growth-traits variation.

CONCLUSIONS

The genome size of E. carinicauda was estimated more accurately by genome survey analysis, which revealed basic genomic architecture. The first high-resolution backcross genetic linkage map and QTLs related to growth traits will provide important information for QTL fine mapping, genome assembly and genetic improvement of E. carinicauda and other palaemon shrimps.

Molecular characterization of a p38 MAPK from Litopenaeus vannamei and its expression during the molt cycle and following pathogen infection

The p38 mitogen-activated protein kinase (MAPK), a serine/threonine-specific protein kinase, has been reported to be involved in innate immunity, development and muscle differentiation. To explore the function of p38 in shrimp, partial cDNA sequence of p38 in Litopenaeus vannamei (designated as Lv-p38) was characterized and the expression of Lv-p38 in hepatopancreas of the shrimp after being infected with Vibrio parahaemolyticus and in muscle of the shrimp at different molt stages was detected by quantitative RT-PCR in this study. The results showed that the open reading frame of Lv-p38 was 1098 bp and encoded a protein of 365 amino acids. The protein of Lv-p38 which showed close phylogenetic relationship to Marsupenaeus japonicus p38 had a conserved TGY motif and serine/threonine protein kinase (S_TKc) domain. The expression of Lv-p38 was detected in all tested tissues, especially in the hepatopancreas and muscle. The expression of Lv-p38 in the hepatopancreas was different from that of the control at the 24th hour after the injection of V. parahaemolyticus and in the muscle significantly increased at stage C but decreased at other stages during molt, illustrating that Lv-p38 could be involved in pathogen infection and the molt cycle of shrimp. In conclusion, we identified Lv-p38 and studied its role in pathogen infection and molting, which might facilitate our understanding of the function of p38 in innate immunity and growth during molt of shrimp.

Identifications of captive and wild tilapia species existing in Hawaii by mitochondrial DNA control region sequence

Background

The tilapia family of the Cichlidae includes many fish species, which live in freshwater and saltwater environments. Several species, such as O. niloticus, O. aureus, and O. mossambicus, are excellent for aquaculture because these fish are easily reproduced and readily adapt to diverse environments. Historically, tilapia species, including O. mossambicus, S. melanotheron, and O. aureus, were introduced to Hawaii many decades ago, and the state of Hawaii uses the import permit policy to prevent O. niloticus from coming into the islands. However, hybrids produced from O. niloticus may already be present in the freshwater and marine environments of the islands. The purpose of this study was to identify tilapia species that exist in Hawaii using mitochondrial DNA analysis.

Methodology/Principal Findings

In this study, we analyzed 382 samples collected from 13 farm (captive) and wild tilapia populations in Oahu and the Hawaii Islands. Comparison of intraspecies variation between the mitochondrial DNA control region (mtDNA CR) and cytochrome c oxidase I (COI) gene from five populations indicated that mtDNA CR had higher nucleotide diversity than COI. A phylogenetic tree of all sampled tilapia was generated using mtDNA CR sequences. The neighbor-joining tree analysis identified seven distinctive tilapia species: O. aureus, O. mossambicus, O. niloticus, S. melanotheron, O. urolepies, T. redalli, and a hybrid of O. massambicus and O. niloticus. Of all the populations examined, 10 populations consisting of O. aureus, O. mossambicus, O. urolepis, and O. niloticus from the farmed sites were relatively pure, whereas three wild populations showed some degree of introgression and hybridization.

Conclusions/Significance

This DNA-based tilapia species identification is the first report that confirmed tilapia species identities in the wild and captive populations in Hawaii. The DNA sequence comparisons of mtDNA CR appear to be a valid method for tilapia species identification. The suspected tilapia hybrids that consist of O. niloticus are present in captive and wild populations in Hawaii.

Molecular characterization of differentially expressed TXNIP gene and its association with porcine carcass traits

Thioredoxin interacting protein (TXNIP), which plays a regulatory role in lipid metabolism and immune regulation, is down-regulated expressed in F(1) hybrids Landrace × Yorkshire skeletal muscle. Here we described the molecular characterization of porcine TXNIP gene. The full-length cDNA contains a coding sequence of 1,176 bp nucleotides with untranslated regions of 263 bp at 5'-end and 441 bp at 3'-end, respectively. The predicted molecular mass and isoelectric point of porcine TXNIP is 43.81 kDa and 7.385, respectively. The deduced 391 amino acids exhibit high identity with other mammalian TXNIP. The TXNIP gene contains eight coding exons and seven non coding introns, spans approximately 3,348 bp. The expression of porcine TXNIP mRNA is almost absent in Landrace × Yorkshire and lower level in 6-month-old pigs during skeletal muscle development. Other stages and breeds were high level expressed. Statistical analysis showed the TXNIP gene polymorphism (c.575-4T>C) was different between F(1) hybrids and their parents, was highly associated with dressing percentage (DP) and thorax-waist fat thickness (TFT) in the Yorkshire × Meishan F(2) population. The possible role of TXNIP was discussed.