Transcriptome and MassARRAY analysis for identification of transcripts and SNPs for growth traits of the swimming crab Portunus trituberculatus

Lv, Jianjian; Zhang, Dening; Gao, Bingbo; Liu, Ping; Li, Jian

doi:10.1016/j.gene.2015.04.050

Cited by 25 publications

(16 citation statements)

References 45 publications

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“…The expression of X-box binding protein 1 (PmXbp1) during ovarian development in wild P. monodon broodstock and association between its SNP and growthrelated parameters were observed: expression of genotype A (corresponding to a T/T349 SNP) was significantly greater than that of juveniles carrying pattern B (corresponding to a T/ C349 SNP) (Prasertlux et al, 2015). The growth-related genes were screened using paired-end sequencing technology in the swimming crab Portunus trituberculatus in China (Lv et al, 2015b). One growth-associated SNP was identified, which was located in hemocyanin as a result of association analysis.…”

Section: Growth Traitsmentioning

confidence: 99%

Single nucleotide polymorphism markers with applications in aquaculture and assessment of its impact on natural populations

Wenne

2017

Aquat. Living Resour.

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-An increase in aquatic animal production can be achieved by extending aquaculture areas geographically, utilizing new species for culture, and using new technologies. Among new technologies useful for the increase of aquaculture production is the application of genetics and genomics. New molecular tools that benefit aquaculture have been developed. There has been a large number of experimental and review papers published concerning molecular markers and the range of their applications, including aquaculture and food product analyses. Analysis of single nucleotide polymorphisms (SNPs) has emerged as genotyping technology with wide and significant applications in aquaculture. SNPs can be used for construction of genetic linkage maps, finding quantitative trait loci (QTL) for useful traits like growth, body weight, grilsing, thermal and low oxygen tolerance, resistance to stress and diseases, mapping sex determination loci and identification of progeny in selection and chromosome manipulation experiments, assessment of genomic selectionand marker assisted selection in aquaculture. Genome-wide association studies (GWAS) facilitate the finding associations between SNPs and a trait in related or unrelated specimens. However, many traits are complex and can be controlled by number of QTL. Genotyping by genome reduction complexity sequencing emerged as an efficient and applicable technology in genomic selection. Identification of genes, sequences and nucleotides (substitutions) directly influencing phenotypic variations opens the possibility of marker-assisted selection for desirable characters in culture. SNP and QTL associations can be enhanced using genome editing technology. Examples of successful applications of SNPs in aquaculture of fish, crustacean and mollusk species, representing most geographic areas, and ecological risks assessment are reviewed.

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Section: Growth Traitsmentioning

confidence: 99%

Single nucleotide polymorphism markers with applications in aquaculture and assessment of its impact on natural populations

Wenne

2017

Aquat. Living Resour.

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“…Measurement of miRNA expression levels and elucidation of the regulatory relationship between miRNA and its corresponding mRNA target are important to clarify pathways and biological processes including biotic and abiotic stress responses (Rao et al 2014). Transcriptome analyses of P. trituberculatus growth (Lv et al 2015) and responses to salinity challenged (Lv et al 2013) by high-throughput nextgeneration sequencing technology have been reported; however, the study or experimental identification of miRNAs has been no performed.…”

Section: Electronic Supplementary Materialsmentioning

confidence: 99%

The identification and characteristics of salinity-related microRNAs in gills of Portunus trituberculatus

Liu

Gao

et al. 2016

Cell Stress and Chaperones

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MicroRNAs (miRNAs) are small noncoding RNAs that post-transcriptionally regulate gene expression in organisms. To understand the underlying mechanisms behind the molecular response of the crab to low salt-stress, highthroughput Illumina/Solexa deep sequencing technology was used to investigate the expression profiles of miRNAs under low salinity challenged. Two mixed RNA pool libraries of gill tissues from low salinity challenged (LC) and the control groups (NC) were sequenced on the Illumina platform. A total of 6,166,057 and 7,032,973 high-quality reads were obtained from the NC and LC libraries, respectively. Sixty-seven miRNAs consisting of 16 known and 51 novel ones were identified, among which, 12 miRNAs were differentially expressed in LC compared to NC. Thirty-four of the target genes predicted were differentially expressed in the opposite direction to the miRNAs, which were involved in crucial processes related to osmoregulation by gene ontology (GO) functional enrichment analysis, such as anion transport processes (GO:0006820) and chitin metabolic process (GO:0006030). These results provide a basis for further investigation of the miRNA-modulating networks in osmoregulation of Portunus trituberculatus.

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“…Sequencing chromatograms were visually analyzed using the Vector NTI Suite 11.0 (Invitrogen), and SNPs were detected as overlapping nucleotide peaks. SNPs were genotyped in the 90 crabs from SG and RG with the MassARRAY platform (Sequenom, San Diego, CA, USA) by the way of Lv (Lv et al 2015). Each SNP site allele frequencies were calculated by SPSS 17.0 and processed the Pearson's chi-square test to confirm their association with salt-tolerant trait.…”

Section: Single Nucleotide Polymorphism Loci Detection and Genotypingmentioning

confidence: 99%

Effects of salinity acclimation and eyestalk ablation on Na+, K+, 2Cl− cotransporter gene expression in the gill of Portunus trituberculatus:a molecular correlate for salt-tolerant trait

Zhang

Ping

et al. 2016

Cell Stress and Chaperones

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The Na− cotransporter (NKCC) is an important gene in ion transport. In order to elucidate its function, and regulatory mechanisms, in salinity acclimation, the complete cDNA sequence of NKCC (4218 bp) from Portunus trituberculatus (PtNKCC) was first cloned and characterized. It was found to encode 1055 amino acids containing conserved AA-permease and SLC12 motifs. Results show that PtNKCC is expressed to the greatest extent in gills. High salinity stress exposure led to significant increases (9.6-fold) of PtNKCC mRNA expression in the gills 12 h after treatment, declining to less than the levels seen in the control group between 48 and 72 h. During low salinity stress, expression levels of PtNKCC in gills were found to be upregulated at each sampling time, reaching their peak after 6 h (a 12.4-fold increase). Eyestalk ablation also triggered an 11.3-fold increase in PtNKCC mRNA, while re-injection with eyestalk homogenates significantly reduced the expression of PtNKCC mRNA. Four single nucleotide polymorphisms (SNPs) were detected in the PtNKCC open reading frame, and one SNP was associated with salt tolerance. Our results indicate that PtNKCC plays an important role in the salinity acclimation of P. trituberculatus, while there may be a compound present in the XOSG that inhibits the expression of PtNKCC.

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Transcriptome and MassARRAY analysis for identification of transcripts and SNPs for growth traits of the swimming crab Portunus trituberculatus

Cited by 25 publications

References 45 publications

Single nucleotide polymorphism markers with applications in aquaculture and assessment of its impact on natural populations

Single nucleotide polymorphism markers with applications in aquaculture and assessment of its impact on natural populations

The identification and characteristics of salinity-related microRNAs in gills of Portunus trituberculatus

Effects of salinity acclimation and eyestalk ablation on Na+, K+, 2Cl− cotransporter gene expression in the gill of Portunus trituberculatus:a molecular correlate for salt-tolerant trait

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