Home > 2019, 38(8) > Identification of SNP markers correlated with the tolerance of low-salinity challenge in swimming crab (Portunus trituberculatus)

Citation: Yanyan Feng, Dening Zhang, Jianjian Lv, Baoquan Gao, Jian Li, Ping Liu. Identification of SNP markers correlated with the tolerance of low-salinity challenge in swimming crab (Portunus trituberculatus). ACTA OCEANOLOGICA SINICA, 2019, 38(8): 41-47. doi: 10.1007/s13131-019-1428-0

2019, 38(8): 41-47. doi: 10.1007/s13131-019-1428-0

Identification of SNP markers correlated with the tolerance of low-salinity challenge in swimming crab (Portunus trituberculatus)

1.  Key Laboratory of Sustainable Development of Marine Fisheries of Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China

Corresponding author: Jian Li, lijian@ysfri.ac.cn

Received Date: 2018-07-19
Web Publishing Date: 2019-08-01

Fund Project: The Modern Agro-industry Technology Research System under contract No. CARS-48; the program of Shandong Leading Talent under contract No. LJNY2015002; the National Natural Science Foundation of China under contract No. 31472275; the Qingdao Industrial Development Program (Science and Technology Benefit Special Project) under contract No. 17-3−3−62−nsh.

Water salinity condition is an important factor for artificial propagation of the swimming crab (Portunus trituberculatus). Low salinity (LS)-resistant strains are preferred by crab industries. Single nucleotide polymorphism (SNP), the third generation of molecular markers, can be utilized in the breeding of LS-resistant species of P. trituberculatus. Our earlier study identified 615 genes differentially expressed in low-salinity stress compared to the controls. Although thousands of SNP loci have been found, it is hard to identify a SNP marker in correlation with a desired trait. In this study, time-of-flight mass spectrometry (TOF-MS), as an efficient method to select SNPs for the tolerance of LS challenge, was utilized for SNP typing. Fifty gene segments were amplified based on comparative transcriptomics in our earlier study, a total of 18 511 bp DNA fragments were amplified, and eighty-five SNP markers were found. The frequency of the SNPs was estimated to be 0.46 per 100 base pairs of DNA sequences. The rate of the conversion mutation was 81%, while the transversion mutation was 19%. The mutation rate of the G/T (C/A), A/T and G/C was 26%, 12% and 7%, respectively. Eight SNP markers were found to significantly correlate with the adaption of low salinity. Of the eight SNP markers, three linked-SNPs were found in the cuticle proportion gene, and another three SNPs were found in three new genes, and the rest two were found in aquaporin gene and chloride channel gene. The development of these SNP markers found in our study could be primarily used for breeding LS-resistant strains of P. trituberculatus.

Key words: Portunus trituberculatus , low salinity , time-of-flight mass spectrometry , single nucleotide polymorphism , SNP

[1]

Aitken N, Smith S, Schwarz C, et al. 2004. Single nucleotide polymorphism (SNP) discovery in mammals: a targeted-gene approach. Molecular Ecology, 13(6): 1423–1431.

[2]

Arias A, Freire R, Boudry P, et al. 2009. Single nucleotide polymorphism for population studies in the scallops Aequipecten opercularis and Mimachlamys varia. Conservation Genetics, 10(5): 1491–1495.

[3]

Black IV W C, Baer C F, Antolin M F, et al. 2001. Population genomics: genome-wide sampling of insect populations. Annual Review of Entomology, 46: 441–469.

[4]

Bray W, Lawrence A L, Leung-Trujillo J. 1994. The effect of salinity on growth and survival of Penaeus vannamei, with observations on the interaction of IHHN virus and salinity. Aquaculture, 122(2–3): 133–146.

[5]

Chen R, Davydov E V, Sirota M, et al. 2010. Non-synonymous and synonymous coding SNPs show similar likelihood and effect size of human disease association. PLoS One, 5(10): e13574.

[6]

Cui Zhaoxia, Liu Yuan, Wang Hongxia, et al. 2012. Isolation and characterization of microsatellites in Portunus trituberculatus. Conservation Genetics Resources, 4(2): 251–255.

[7]

Dai Aiyun, Feng Zhongqi, Song Yuzhi, et al. 1977. Primary investigation on the fishery biology of the Portunus trituberculatus. Chinese Journal of Zoology (in Chinese), (2): 30–33.

[8]

Dai Aiyun, Yang Siqiong, Song Yuzhi, et al. 1986. Marine Crabs in China Sea (in Chinese). Beijing: China Ocean Press, 194–195

[9]

Germer S, Higuchi R. 1999. Single-tube genotyping without oligonucleotide probes. Genome Research, 9(1): 72–78

[10]

Harding R M, Fullerton S M, Griffiths R C, et al. 1997. Archaic African and Asian lineages in the genetic ancestry of modern humans. American Journal of Human Genetics, 60(4): 772–789

[11]

Hirschhorn J N, Sklar P, Lindblad-Toh K, et al. 2000. SBE-TAGS: an array-based method for efficient single-nucleotide polymorphism genotyping. Proceedings of the National Academy of Sciences of the United States of America, 97(22): 12164–12169.

[12]

Holliday R, Grigg G W. 1993. DNA methylation and mutation. Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis, 285(1): 61–67.

[13]

Ji Dongsheng. 2005. Techniques of pond-farming of swimming crab, Portunus trituberculatus. Special Economic Animal and Plant (in Chinese), 8(3): 12–13.

[14]

Jin Yulin, Kong Lingfeng, Yu Hong, et al. 2014. Development, inheritance and evaluation of 55 novel single nucleotide polymorphism markers for parentage assignment in the Pacific oyster (Crassostrea gigas). Genes & Genomics, 36(2): 129–141.

[15]

Komar A A. 2007. SNPs, silent but not invisible. Science, 315(5811): 466–467.

[16]

Kumlu M, Eroldogan O T, Saglamtimur B. 2001. The effects of salinity and added substrates on growth and survival of Metapenaeus monoceros (Decapoda: Penaeidae) post-larvae. Aquaculture, 196(1–2): 177–188.

[17]

Kumlu M, Jones D A. 1995. Salinity tolerance of hatchery-reared postlarvae of Penaeus indicus H. Milne Edwards originating from India. Aquaculture, 130(2–3): 287–296.

[18]

Kwok P Y. 2001. Methods for genotyping single nucleotide polymorphisms. Annual Review of Genomics and Human Genetics, 2(2): 235–258.

[19]

Lai E, Riley J, Purvis I, et al. 1998. A 4-Mb high-density single nucleotide polymorphism-based map around human APOE. Genomics, 54(1): 31–38.

[20]

Li Xihong, Cui Zhaoxia, Liu Yuan, et al. 2013. Polymorphisms of anti-lipopolysaccharide factors in the swimming crab Portunus trituberculatus and their association with resistance/susceptibility to Vibrio alginolyticus. Fish & Shellfish Immunology, 34(6): 1560–1568.

[21]

Li Shuzhen, Wan Huirong, Ji Heyi, et al. 2009. SNP discovery based on CATS and genotyping in the finless porpoise (Neophocaena phocaenoides). Conservation Genetics, 10(6): 2013–2019.

[22]

Li W H, Sadler L A. 1991. Low nucleotide diversity in man. Genetics, 129(2): 513–523

[23]

Livak K J, Marmaro J, Todd J A. 1995. Towards fully automated genome-wide polymorphism screening. Nature Genetics, 9(4): 341–342.

[24]

Lv Jianjian, Liu Ping, Wang Yu, et al. 2013. Transcriptome analysis of Portunus trituberculatus in response to salinity stress provides insights into the molecular basis of osmoregulation. PLoS One, 8(12): e82155.

[25]

Ma Hongyu, Ma Qunqun, Ma Chunyan, et al. 2011. Isolation and characterization of gene-derived single nucleotide polymorphism (SNP) markers in Scylla paramamosain. Biochemical Systematics and Ecology, 39(4-6): 419–424.

[26]

Morin P A, Aitken N C, Rubio-Cisneros N, et al. 2007. Characterization of 18 SNP markers for sperm whale (Physeter macrocephalus). Molecular Ecology Notes, 7(4): 626–630.

[27]

Nickerson D A, Taylor S L, Weiss K M, et al. 1998. DNA sequence diversity in a 9. 7-kb region of the human lipoprotein lipase gene. Nature Genetics, 19(3): 233–240.

[28]

Péqueux A. 1995. Osmotic regulation in crustaceans. Journal of Crustacean Biology, 15(1): 1–60.

[29]

Petrov D A, Hartl D L. 1999. Patterns of nucleotide substitution in Drosophila and mammalian genomes. Proceedings of the National Academy of Sciences of the United States of America, 96(4): 1475–1479.

[30]

Piatek A S, Tyagi S, Pol A C, et al. 1998. Molecular beacon sequence analysis for detecting drug resistance in Mycobacterium tuberculosis. Nature Biotechnology, 16(4): 359–363.

[31]

Rafalski A. 2002. Applications of single nucleotide polymorphisms in crop genetics. Current Opinion in Plant Biology, 5(2): 94–100.

[32]

Rouse D B, Kartamulia I. 1992. Influence of salinity and temperature on molting and survival of the Australian freshwater crayfish (Cherax tenuimanus). Aquaculture, 105(1): 47–52.

[33]

Ruscoe I M, Shelley C C, Williams G R. 2004. The combined effects of temperature and salinity on growth and survival of juvenile mud crabs (Scylla serrata Forskål). Aquaculture, 238(1–4): 239–247.

[34]

Sauvage C, Bierne N, Lapègue S, et al. 2007. Single Nucleotide polymorphisms and their relationship to codon usage bias in the Pacific oyster Crassostrea gigas. Gene, 406(1–2): 13–22.

[35]

Schütz E, Von Ahsen N, Oellerich M. 2000. Genotyping of eight thiopurine methyltransferase mutations: three-color multiplexing, " two-color/shared” anchor, and fluorescence-quenching hybridization probe assays based on thermodynamic nearest-neighbor probe design. Clinical Chemistry, 46(11): 1728–1737

[36]

Shen L X, Basilion J P, Stanton V P Jr. 1999. Single-nucleotide polymorphisms can cause different structural folds of mRNA. Proceedings of the National Academy of Sciences of the United States of America, 96(14): 7871–7876.

[37]

Smith C T, Elfstrom C M, Seeb L W, et al. 2005. Use of sequence data from rainbow trout and Atlantic salmon for SNP detection in Pacific salmon. Molecular Ecology, 14(13): 4193–4203.

[38]

Sommer S S, Groszbach A, Bottema C. 1992. PCR amplification of specific alleles (PASA) is a general method for rapidly detecting known single-base changes. Biotechniques, 12(1): 82–87

[39]

Soyel H I, Kumlu M. 2003. The effects of salinity on postlarval growth and survival of Penaeus semisulcatus (Decapoda: Penaeidae). Turkish Journal of Zoology, 27(3): 221–225

[40]

Stickney H L, Schmutz J, Woods I G, et al. 2002. Rapid mapping of zebrafish mutations with SNPs and oligonucleotide microarrays. Genome Research, 12(12): 1929–1934.

[41]

Storey J D, Tibshirani R. 2003. Statistical significance for genomewide studies. Proceedings of the National Academy of Sciences of the United States of America, 100(16): 9440–9445.

[42]

Syvänen A C. 1999. From gels to chips: " minisequencing” primer extension for analysis of point mutations and single nucleotide polymorphisms. Human Mutation, 13(1): 1–10.

[43]

Taillon-Miller P, Gu Zhijie, Li Qun, et al. 1998. Overlapping genomic sequences: a treasure trove of single-nucleotide polymorphisms. Genome Research, 8(7): 748–754.

[44]

Tran H T T, Takeshima Y, Surono A, et al. 2005. A G-to-A transition at the fifth position of intron-32 of the dystrophin gene inactivates a splice-donor site both in vivo and in vitro. Molecular Genetics and Metabolism, 85(3): 213–219.

[45]

Wang Jun, Chuang Karen, Ahluwalia M, et al. 2005. High-throughput SNP genotyping by single-tube PCR with Tm-shift primers. Biotechniques, 39(6): 885–893.

[46]

Wang D G, Fan Jianbing, Siao C J, et al. 1998. Large-scale identification, mapping, and genotyping of single-nucleotide polymorphisms in the human genome. Science, 280(5366): 1077–1082.

[47]

Xue Junzeng, Du Nanshan, Lai Wei, et al. 1997. A review of studies on Portunus trituberculatus in China. Donghai Marine Science (in Chinese), 15(4): 60–65

[48]

Yu Yang, Wei Jiankai, Zhang Xiaojun, et al. 2014. SNP discovery in the transcriptome of White Pacific Shrimp Litopenaeus vannamei by next generation sequencing. PLoS One, 9(1): e87218.

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Identification of SNP markers correlated with the tolerance of low-salinity challenge in swimming crab (Portunus trituberculatus)

Yanyan Feng, Dening Zhang, Jianjian Lv, Baoquan Gao, Jian Li, Ping Liu