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. 2019 Aug 2:10:700.
doi: 10.3389/fgene.2019.00700. eCollection 2019.

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

Qian Zhang  1   2   3 , Yang Yu  1   2 , Quanchao Wang  1 , Fei Liu  1 , Zheng Luo  1   3 , Chengsong Zhang  1   2 , Xiaojun Zhang  1   2 , Hao Huang  4 , Jianhai Xiang  1   2 , Fuhua Li  1   2   5
Affiliations

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

Qian Zhang et al. Front Genet. .

Abstract

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.

Keywords: association analysis; disease resistance; penaeid shrimp; single nucleotide polymorphism; target sequencing.

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Figures

Figure 1
Figure 1
Accumulated mortality rates of populations 1 and 2 infected with V. parahaemolyticus and PBS. PL1, population 1; PL2, population 2.
Figure 2
Figure 2
-log10(adjusted P) of 1556 SNPs (filtering out 10 false-positive sites) in a combined population and the threshold for significance is FDR-corrected P < 0.05.
Figure 3
Figure 3
-log10(adjusted P) of three SNPs, including loci Marker15416_294, Marker8720_486, and Marker1077_61 located in the fragment of Marker15416, (A) Marker8720 (B), and Marker1077 (C), respectively.
Figure 4
Figure 4
Expression profile of LvALF6 and LvPI3K regulatory subunit in hepatopancreas, gill, and hemocytes at different times after V. parahaemolyticus infection (P < 0.01). Relative transcription level of LvALF in hepatopancreas (A), gill (B) and hemocytes (C); Relative transcription level of LvPI3K in hepatopancreas (D), gill (E) and hemocytes (F).
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