Identification of a Quantitative Trait Loci (QTL) Associated with Ammonia Tolerance in the Pacific White Shrimp (Litopenaeus Vannamei)

Overview

Journal BMC Genomics

Publisher Biomed Central

Specialty Genetics

Date 2020 Dec 3

PMID 33267780

Citations 5

Authors

Digang Zeng

Chunling Yang

Qiangyong Li

Weilin Zhu

Xiuli Chen

Min Peng

Xiaohan Chen

Yong Lin

Huanling Wang

Hong Liu

Jingzhen Liang

Qingyun Liu

Yongzhen Zhao

Affiliations

Soon will be listed here.

Abstract

Background: Ammonia is one of the most common toxicological environment factors affecting shrimp health. Although ammonia tolerance in shrimp is closely related to successful industrial production, few genetic studies of this trait are available.

Results: In this study, we constructed a high-density genetic map of the Pacific white shrimp (Litopenaeus vannamei) using specific length amplified fragment sequencing (SLAF-seq). The constructed genetic map contained 17,338 polymorphic markers spanning 44 linkage groups, with a total distance of 6360.12 centimorgans (cM) and an average distance of 0.37 cM. Using this genetic map, we identified a quantitative trait locus (QTL) that explained 7.41-8.46% of the phenotypic variance in L. vannamei survival time under acute ammonia stress. We then sequenced the transcriptomes of the most ammonia-tolerant and the most ammonia-sensitive individuals from each of four genetically distinct L. vannamei families. We found that 7546 genes were differentially expressed between the ammonia-tolerant and ammonia-sensitive individuals. Using QTL analysis and the transcriptomes, we identified one candidate gene (annotated as an ATP synthase g subunit) associated with ammonia tolerance.

Conclusions: In this study, we constructed a high-density genetic map of L. vannamei and identified a QTL for ammonia tolerance. By combining QTL and transcriptome analyses, we identified a candidate gene associated with ammonia tolerance. Our work provides the basis for future genetic studies focused on molecular marker-assisted selective breeding.

Citing Articles

Genome-wide QTL and eQTL mapping reveal genes associated with growth rate trait of the Pacific white shrimp (Litopenaeus vannamei).

Chen X, Peng M, Yang C, Li Q, Feng P, Zhu W BMC Genomics. 2024; 25(1):414.

PMID: 38671371 PMC: 11046935. DOI: 10.1186/s12864-024-10328-9.

The sORF-Encoded Peptides, ATP Synthase Subunits, Facilitate WSSV Duplication in Shrimp.

Huo L, Lu P, Li D, Shi X Viruses. 2022; 14(11).

PMID: 36366547 PMC: 9692589. DOI: 10.3390/v14112449.

Animal board invited review: Widespread adoption of genetic technologies is key to sustainable expansion of global aquaculture.

Houston R, Kriaridou C, Robledo D Animal. 2022; 16(10):100642.

PMID: 36183431 PMC: 9553672. DOI: 10.1016/j.animal.2022.100642.

Genome-wide association study identified genes associated with ammonia nitrogen tolerance in .

Fu S, Liu J Front Genet. 2022; 13:961009.

PMID: 36072655 PMC: 9441690. DOI: 10.3389/fgene.2022.961009.

Genome-Wide Analyses of Heat Shock Protein Superfamily Provide New Insights on Adaptation to Sulfide-Rich Environments in (Annelida, Echiura).

Liu D, Qin Z, Wei M, Kong D, Zheng Q, Bai S Int J Mol Sci. 2022; 23(5).

PMID: 35269857 PMC: 8910992. DOI: 10.3390/ijms23052715.

References

Liu D, Ma C, Hong W, Huang L, Liu M, Liu H . Construction and analysis of high-density linkage map using high-throughput sequencing data. PLoS One. 2014; 9(6):e98855. PMC: 4048240. DOI: 10.1371/journal.pone.0098855. View

Zhang L, Yang C, Zhang Y, Li L, Zhang X, Zhang Q . A genetic linkage map of Pacific white shrimp (Litopenaeus vannamei): sex-linked microsatellite markers and high recombination rates. Genetica. 2006; 131(1):37-49. DOI: 10.1007/s10709-006-9111-8. View

Zhang Y, Wang L, Xin H, Li D, Ma C, Ding X . Construction of a high-density genetic map for sesame based on large scale marker development by specific length amplified fragment (SLAF) sequencing. BMC Plant Biol. 2013; 13:141. PMC: 3852768. DOI: 10.1186/1471-2229-13-141. View

Liang Z, Liu R, Zhao D, Wang L, Sun M, Wang M . Ammonia exposure induces oxidative stress, endoplasmic reticulum stress and apoptosis in hepatopancreas of pacific white shrimp (Litopenaeus vannamei). Fish Shellfish Immunol. 2016; 54:523-8. DOI: 10.1016/j.fsi.2016.05.009. View

Singh V, Mangalam A, Dwivedi S, Naik S . Primer premier: program for design of degenerate primers from a protein sequence. Biotechniques. 1998; 24(2):318-9. DOI: 10.2144/98242pf02. View

Yu Y, Zhang X, Yuan J, Li F, Chen X, Zhao Y . Genome survey and high-density genetic map construction provide genomic and genetic resources for the Pacific White Shrimp Litopenaeus vannamei. Sci Rep. 2015; 5:15612. PMC: 4621519. DOI: 10.1038/srep15612. View

Zhu M, Zhao S . Candidate gene identification approach: progress and challenges. Int J Biol Sci. 2007; 3(7):420-7. PMC: 2043166. DOI: 10.7150/ijbs.3.420. View

Li B, Tian L, Zhang J, Huang L, Han F, Yan S . Construction of a high-density genetic map based on large-scale markers developed by specific length amplified fragment sequencing (SLAF-seq) and its application to QTL analysis for isoflavone content in Glycine max. BMC Genomics. 2014; 15:1086. PMC: 4320444. DOI: 10.1186/1471-2164-15-1086. View

Mortazavi A, Williams B, McCue K, Schaeffer L, Wold B . Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods. 2008; 5(7):621-8. DOI: 10.1038/nmeth.1226. View

10.

Cruz P, Ibarra A, Mejia-Ruiz H, Gaffney P, Perez-Enriquez R . Genetic variability assessed by microsatellites in a breeding program of Pacific white shrimp (Litopenaeus vannamei). Mar Biotechnol (NY). 2003; 6(2):157-64. DOI: 10.1007/s10126-003-0017-5. View

11.

Marazza D, Bornens P, Le Gal Y . Effect of ammonia on survival and adenylate energy charge in the shrimp Palaemonetes varians. Ecotoxicol Environ Saf. 1996; 34(2):103-8. DOI: 10.1006/eesa.1996.0050. View

12.

Li H, Durbin R . Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009; 25(14):1754-60. PMC: 2705234. DOI: 10.1093/bioinformatics/btp324. View

13.

Qiu L, Shi X, Yu S, Han Q, Diao X, Zhou H . Changes of Ammonia-Metabolizing Enzyme Activity and Gene Expression of Two Strains in Shrimp Under Ammonia Stress. Front Physiol. 2018; 9:211. PMC: 5876294. DOI: 10.3389/fphys.2018.00211. View

14.

Wei Q, Wang Y, Qin X, Zhang Y, Zhang Z, Wang J . An SNP-based saturated genetic map and QTL analysis of fruit-related traits in cucumber using specific-length amplified fragment (SLAF) sequencing. BMC Genomics. 2014; 15:1158. PMC: 4367881. DOI: 10.1186/1471-2164-15-1158. View

15.

Grattapaglia D, Bertolucci F, Sederoff R . Genetic mapping of QTLs controlling vegetative propagation in Eucalyptus grandis and E. urophylla using a pseudo-testcross strategy and RAPD markers. Theor Appl Genet. 2013; 90(7-8):933-47. DOI: 10.1007/BF00222906. View

16.

Xu X, Chao J, Cheng X, Wang R, Sun B, Wang H . Mapping of a Novel Race Specific Resistance Gene to Phytophthora Root Rot of Pepper (Capsicum annuum) Using Bulked Segregant Analysis Combined with Specific Length Amplified Fragment Sequencing Strategy. PLoS One. 2016; 11(3):e0151401. PMC: 4798474. DOI: 10.1371/journal.pone.0151401. View

17.

Zhu Y, Yin Y, Yang K, Li J, Sang Y, Huang L . Construction of a high-density genetic map using specific length amplified fragment markers and identification of a quantitative trait locus for anthracnose resistance in walnut (Juglans regia L.). BMC Genomics. 2015; 16:614. PMC: 4539690. DOI: 10.1186/s12864-015-1822-8. View

18.

Lu X, Kong J, Meng X, Cao B, Luo K, Dai P . Identification of SNP markers associated with tolerance to ammonia toxicity by selective genotyping from de novo assembled transcriptome in Litopenaeus vannamei. Fish Shellfish Immunol. 2017; 73:158-166. DOI: 10.1016/j.fsi.2017.12.005. View

19.

Andriantahina F, Liu X, Huang H . Genetic map construction and quantitative trait locus (QTL) detection of growth-related traits in Litopenaeus vannamei for selective breeding applications. PLoS One. 2013; 8(9):e75206. PMC: 3783498. DOI: 10.1371/journal.pone.0075206. View

20.

Zhao Z, Gu H, Sheng X, Yu H, Wang J, Huang L . Genome-Wide Single-Nucleotide Polymorphisms Discovery and High-Density Genetic Map Construction in Cauliflower Using Specific-Locus Amplified Fragment Sequencing. Front Plant Sci. 2016; 7:334. PMC: 4800193. DOI: 10.3389/fpls.2016.00334. View