A new ALF from Litopenaeus vannamei and its SNPs related to WSSV resistance

Li, Jingwen; Yu, Yang; Li, Fuhua; Zhang, Xiaojun; Xiang, Jianhai

doi:10.1007/s00343-015-4010-4

Cited by 11 publications

(5 citation statements)

References 45 publications

(42 reference statements)

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“…The present study applied the GMDR method in shrimp WSSV resistance association analysis for the first time. The loci in LvALFs related to WSSV resistance of shrimp found in our previous studies were also involved2425. In the present study, a three-factor model consisted of loci from unigene34569, unigene16729 and nLvALF2 showed significant association with viral resistance.…”

Section: Discussionsupporting

confidence: 71%

“…All loci showing associations with WSSV resistance identified in this study and those in our previous study2425 were used for GMDR analyses to detect the combined effects. The best interaction models from two-loci to four-loci were shown in Table 2.…”

Section: Resultsmentioning

confidence: 99%

“…Meanwhile, SNPs located in nLvALF1 and nLvALF2 (loci nLvALF1 g.1370, g.1419 and nLvALF2 g.2422, g.2466, g.2529) which was proved to be potentially associated with WSSV resistance in previous reports2425 were also chosen for the interaction analysis. Through the cross-validation strategy, GMDR divided various combinations of genotypes into ‘high’ or ‘low’ risk genotypes19.…”

Section: Methodsmentioning

confidence: 99%

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Gene set based association analyses for the WSSV resistance of Pacific white shrimp Litopenaeus vannamei

et al. 2017

Sci Rep

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White Spot Syndrome Virus (WSSV) is regarded as a virus with the strongest pathogenicity to shrimp. For the threshold trait such as disease resistance, marker assisted selection (MAS) was considered to be a more effective approach. In the present study, association analyses of single nucleotide polymorphisms (SNPs) located in a set of immune related genes were conducted to identify markers associated with WSSV resistance. SNPs were detected by bioinformatics analysis on RNA sequencing data generated by Illimina sequencing platform and Roche 454 sequencing technology. A total of 681 SNPs located in the exons of immune related genes were selected as candidate SNPs. Among these SNPs, 77 loci were genotyped in WSSV susceptible group and resistant group. Association analysis was performed based on logistic regression method under an additive and dominance model in GenABEL package. As a result, five SNPs showed associations with WSSV resistance at a significant level of 0.05. Besides, SNP-SNP interaction analysis was conducted. The combination of SNP loci in TRAF6, Cu/Zn SOD and nLvALF2 exhibited a significant effect on the WSSV resistance of shrimp. Gene expression analysis revealed that these SNPs might influence the expression of these immune-related genes. This study provides a useful method for performing MAS in shrimp.

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Section: Discussionsupporting

confidence: 71%

Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

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Gene set based association analyses for the WSSV resistance of Pacific white shrimp Litopenaeus vannamei

et al. 2017

Sci Rep

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“…So far, several genes associated with disease resistance have been reported in aquatic animals. Polymorphism of LvALF and TRAF6 was reported to be associated with the resistance to WSSV in shrimp (Wang et al, 2011;Liu et al, 2014b;Liu et al, 2014a;Yu et al, 2017;Zhang Q. et al, 2019). A major quantitative trait locus (QTL) for the resistance of Atlantic salmon (Salmo salar) against infectious pancreatic necrosis (IPN) was discovered, which has been already applied in marker-assisted breeding of IPN-resistant fish (Houston et al, 2008;Moen et al, 2009;Woldemariam et al, 2020).…”

Section: Introductionmentioning

confidence: 99%

Comparison of Gene Expression Between Resistant and Susceptible Families Against VPAHPND and Identification of Biomarkers Used for Resistance Evaluation in Litopenaeus vannamei

Zhang

Luo

et al. 2021

Front. Genet.

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Acute hepatopancreatic necrosis disease (AHPND) has caused a heavy loss to shrimp aquaculture since its outbreak. Vibrio parahaemolyticus (VPAHPND) is regarded as one of the main pathogens that caused AHPND in the Pacific white shrimp Litopenaeus vannamei. In order to learn more about the mechanism of resistance to AHPND, the resistant and susceptible shrimp families were obtained through genetic breeding, and comparative transcriptome approach was used to analyze the gene expression patterns between resistant and susceptible families. A total of 95 families were subjected to VPAHPND challenge test, and significant variations in the resistance of these families were observed. Three pairs of resistant and susceptible families were selected for transcriptome sequencing. A total of 489 differentially expressed genes (DEGs) that presented in at least two pairwise comparisons were screened, including 196 DEGs highly expressed in the susceptible families and 293 DEGs in the resistant families. Among these DEGs, 16 genes demonstrated significant difference in all three pairwise comparisons. Gene set enrichment analysis (GSEA) of all 27,331 expressed genes indicated that some energy metabolism processes were enriched in the resistant families, while signal transduction and immune system were enriched in the susceptible families. A total of 32 DEGs were further confirmed in the offspring of the detected families, among which 19 genes were successfully verified. The identified genes in this study will be useful for clarifying the genetic mechanism of shrimp resistance against Vibrio and will further provide molecular markers for evaluating the disease resistance of shrimp in the breeding program.

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“…Different ALFs exhibited diverse antibacterial and antiviral activities in E. carinicauda (Lv et al, 2018) and F. chinensis (Yang et al, 2015). In our previous studies, mutations in LvALF gene have been regarded as the important immune factor in L. vannamei with WSSV resistance (Liu et al, 2014a; Liu et al, 2014b). Several polymorphisms of PtALF in the swimming crab ( Portunus trituberculatus ) were reported to be associated with resistance and susceptibility to Vibrio alginolyticus (Li et al, 2013).…”

Section: Discussionmentioning

confidence: 99%

Identification of Single Nucleotide Polymorphisms Related to the Resistance Against Acute Hepatopancreatic Necrosis Disease in the Pacific White Shrimp Litopenaeus vannamei by Target Sequencing Approach

Zhang

Wang

et al. 2019

Front. Genet.

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Acute hepatopancreatic necrosis disease (AHPND) is a major bacterial disease in Pacific white shrimp Litopenaeus vannamei farming, which is caused by Vibrio parahaemolyticus . AHPND has led to a significant reduction of shrimp output since its outbreak. Selective breeding of disease-resistant broodstock is regarded as a key strategy in solving the disease problem. Understanding the relationship between genetic variance and AHPND resistance is the basis for marker-assisted selection in shrimp. The purpose of this study was to identify single nucleotide polymorphisms (SNPs) associated with the resistance against AHPND in L. vannamei . In this work, two independent populations were used for V. parahaemolyticus challenge and the resistant or susceptible shrimp were evaluated according to the survival time after Vibrio infection. The above two populations were genotyped separately by a SNP panel designed based on the target sequencing platform using a pooling strategy. The SNP panel contained 508 amplicons from DNA fragments distributed evenly along the genome and some immune-related genes of L. vannamei . By analyzing the allele frequency in the resistant and susceptible groups, 30 SNPs were found to be significantly associated with the resistance of the shrimp against V. parahaemolyticus infection (false discovery rate corrected at P < 0.05). Three SNPs were further validated by individual genotyping in all samples of population 1. Our study illustrated that target sequencing and pooling sequencing were effective in identifying the markers associated with economic traits, and the SNPs identified in this study could be used as molecular markers for breeding disease-resistant shrimp.

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A new ALF from Litopenaeus vannamei and its SNPs related to WSSV resistance

Cited by 11 publications

References 45 publications

Gene set based association analyses for the WSSV resistance of Pacific white shrimp Litopenaeus vannamei

Gene set based association analyses for the WSSV resistance of Pacific white shrimp Litopenaeus vannamei

Comparison of Gene Expression Between Resistant and Susceptible Families Against VPAHPND and Identification of Biomarkers Used for Resistance Evaluation in Litopenaeus vannamei

Identification of Single Nucleotide Polymorphisms Related to the Resistance Against Acute Hepatopancreatic Necrosis Disease in the Pacific White Shrimp Litopenaeus vannamei by Target Sequencing Approach

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