Molecular markers for identifying a new selected variety of Pacific white shrimp Litopenaeus vannamei

Yang Yu; Xiaojun Zhang; Jingwen Liu; Fuhua Li; Hao Huang; Yijun Li; Xiaolin Liu; Jianhai Xiang

doi:10.1007/s00343-014-3232-1

Your Location：

Home >

Browse articles >

Molecular markers for identifying a new selected variety of Pacific white shrimp Litopenaeus vannamei

OriginalPaper | Updated：2023-05-16

- Molecular markers for identifying a new selected variety of Pacific white shrimp Litopenaeus vannamei
- Molecular markers for identifying a new selected variety of Pacific white shrimp Litopenaeus vannamei
- 海洋湖沼学报（英文） 2015年33卷第1期页码：1-10
- Affiliations：
  
  1. Key Laboratory of Experimental Marine Biology Institute of Oceanology Chinese Academy of Sciences
  2. University of Chinese Academy of Sciences
  3. Hainan Nanjiang Marine Biotechnique Company Limited
  4. Northwest Agriculture and Forestry University
- Author bio：
- Funds：
  
  Supported by the National High Technology Research and Development Program of China (863 Program) (Nos. 2012AA10A404, 2012AA092205)
- DOI：10.1007/s00343-014-3232-1
  中图分类号：
- 网络首发：2014-10-27，
  
  纸质出版：2015
- Accepted：
Scan QR Code
Molecular markers for identifying a new selected variety of Pacific white shrimp Litopenaeus vannamei[J]. 海洋湖沼学报（英文）, 2015,33(1):1-10.

Yu, Y., Zhang, X., Liu, J. et al. Molecular markers for identifying a new selected variety of Pacific white shrimp Litopenaeus vannamei, ., Chin. J. Ocean. Limnol. 33, 1–10 (2015). https://doi.org/10.1007/s00343-014-3232-1
Molecular markers for identifying a new selected variety of Pacific white shrimp Litopenaeus vannamei[J]. 海洋湖沼学报（英文）, 2015,33(1):1-10. DOI： 10.1007/s00343-014-3232-1.

Yu, Y., Zhang, X., Liu, J. et al. Molecular markers for identifying a new selected variety of Pacific white shrimp Litopenaeus vannamei, ., Chin. J. Ocean. Limnol. 33, 1–10 (2015). https://doi.org/10.1007/s00343-014-3232-1 DOI：

摘要

Abstract

Selective breeding of the Pacific white shrimp Litopenaeus vannamei during the last decade has produced new varieties exhibiting high growth rates and disease resistance. However

the identification of new varieties of shrimps from their phenotypic characters is difficult. This study introduces a new approach for identifying varieties of shrimps using molecular markers of microsatellites and mitochondrial control region sequences. The method was employed to identify a new selected variety

Kehai No. 1 (KH-1)

from three representative stocks (control group): Zhengda; Tongwei; and a stock collected from Fujian Province

which is now cultured in mainland China. By pooled genotyping of KH-1 and the control group

five microsatellites showing differences between KH-1 and the control group were screened out. Individual genotyping data confirmed the results from pooled genotyping. The genotyping data for the five microsatellites were applied to the assignment analysis of the KH-1 group and the control group using the partial Bayesian assignment method in GENECLASS2. By sequencing the mitochondrial control regions of individuals from the KH-1 and control group

four haplotypes were observed in the KH-1 group

whereas 14 haplotypes were obtained in the control group. By combining the microsatellite assignment analysis with mitochondrial control region analysis

the average accuracy of identification of individuals in the KH-1 group and control group reached 89%. The five selected microsatellite loci and mitochondrial control region sequences were highly polymorphic and could be used to distinguish new selected varieties of L. vannamei from other populations cultured in China.

关键词

Keywords

references

Alcivar-Warren A, Meehan-Meola D, Park S W, Xu Z, Delaney M, Zuniga G. 2007. ShrimpMap: a low-density, microsatellite-based linkage map of the pacific whiteleg shrimp, Litopenaeus vannamei: identification of sexlinked markers in linkage group 4. J. Shellfish. Res., 26(4): 1 259–1 277.

Argue B J, Arce S M, Lotz J M, Moss S M. 2002. Selective breeding of Pacific white shrimp (Litopenaeus vannamei) for growth and resistance to Taura Syndrome Virus. Aquaculture, 204(3–4): 447–460.

Baudouin L. 2004. Analytical bayesian approach for assigning individuals to populations. Journal of Heredity, 95(3): 217–224.

Bredemeijer G M M, Cooke R J, Ganal M W, Peeters R, Isaac P, Noordijk Y, Rendell S, Jackson J, Roder M S, Wendehake K, Dijcks M, Amelaine M, Wickaert V, Bertrand L, Vosman B. 2002. Construction and testing of a microsatellite database containing more than 500 tomato varieties. Theor. Appl. Genet., 105(6–7): 1 019–1 026.

Carlsson J, McDowell J R, Diaz-Jaimes P, Carlsson J E L, Boles S B, Gold J R, Graves J E. 2004. Microsatellite and mitochondrial DNA analyses of Atlantic bluefin tuna (Thunnus thynnus thynnus) population structure in the Mediterranean Sea. Molecular Ecology, 13(11): 3 345–3 356.

Chu K H, Li C P, Tam Y K, Lavery S. 2003. Application of mitochondrial control region in population genetic studies of the shrimp Penaeus. Mol. Ecol. Notes, 3(1): 120–122.

Collins H E, Li H Z, Inda S E, Anderson J, Laiho K, Tuomilehto J, Seldin M F. 2000. A simple and accurate method for determination of microsatellite total allele content differences between DNA pools. Hum. Genet., 106(2): 218–226.

Cryer N C, Butler D R, Wilkinson M J. 2005. High throughput, high resolution selection of polymorphic microsatellite loci for multiplex analysis. Plant Methods, 1.

Esselink G D, Smulders M J M, Vosman B. 2003. Identification of cut rose (Rosa hybrida) and rootstock varieties using robust sequence tagged microsatellite site markers. Theor. Appl. Genet., 106(2): 277–286.

Gitterle T, Rye M, Salte D, Cock J, Johansen H, Lozano C, Suarez J A, Qjerde B. 2005. Genetic (co)variation in harvest body weight and survival in Penaeus (Litopenaeus) vannamei under standard commercial conditions. Aquaculture, 243(1–4): 83–92.

Gjedrem T, Fimland E. 1995. Potential benefits from high health and genetically improved shrimp stocks. Swimming Through Troubled Water. p.60–65.

Huang Y C, Yin Z X, Weng S P, He J G, Li S D. 2012. Selective breeding and preliminary commercial performance of Penaeus vannamei for resistance to white spot syndrome virus (WSSV). Aquaculture, 364:111–117.

Huelsenbeck J P, Ronquist F. 2001. MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics, 17: 754–755.

Kause A, Ritola O, Paananen T, Wahlroos H, Mantysaari E A. 2005. Genetic trends in growth, sexual maturity and skeletal deformations, and rate of inbreeding in a breeding programme for rainbow trout (Oncorhynchus mykiss). Aquaculture, 247(1–4): 177–187.

Kimura T, Shi Y Z, Shoda M, Kotobuki K, Matsuta N, Hayashi T, Ban Y, Yamamoto T. 2002. Identification of Asian pear varieties by SSR analysis. Breeding Science, 52(2): 115–121.

Kirov G, Williams N, Sham P, Craddock N, Owen M J. 2000. Pooled genotyping of microsatellite markers in parentoffspring trios. Genome Res., 10(1): 105–115.

Liu Z J, Cordes J F. 2004. DNA marker technologies and their applications in aquaculture genetics. Aquaculture, 238(1–4): 1–37.

Lu X, Wang H X, Liu B Z, Xiang J H. 2011. An effective method for parentage determination of the clam (Meretrix meretrix) based on SSR and COI markers. Aquaculture, 318(1–2): 223–228.

Mccusker M R, Paterson I G, Bentzen P. 2008. Microsatellite markers discriminate three species of North Atlantic wolffishes (Anarhichas spp.). J. Fish. Biol., 72(2): 375–385.

Meehan D, Xu Z, Zuniga G, Alcivar-Warren A. 2003. High frequency and large number of polymorphic microsatellites in cultured shrimp, Penaeus (Litopenaeus) vannamei [Crustacea: Decapoda]. Mar. Biotechnol., 5(4): 311–330.

Oetting W S, Lee H K, Flanders D J, Wiesner G L, Sellers T A, King R A. 1995. Linkage analysis with multiplexed short tandem repeat polymorphisms using infrared fluorescence and M13 tailed primers. Genomics, 30(3): 450–458.

O’Reilly P, Wright J M. 1995. The evolving technology of DNA fingerprinting and its application to fisheries and aquaculture. J. Fish. Biol., 47: 29–55.

Paetkau D, Slade R, Burden M, Estoup A. 2004. Genetic assignment methods for the direct, real-time estimation of migration rate: a simulation-based exploration of accuracy and power. Molecular Ecology, 13(1): 55–65.

Pearse D, Wooninck L, Dean C, Garza J C. 2007. Identification of northeastern Pacific rockfish using multilocus nuclear DNA genotypes. Transactions of the American Fisheries Society, 136(1): 272–280.

Piry S, Alapetite A, Cornuet J M, Paetkau D, Baudouin L, Estoup A. 2004. GENECLASS2: a software for genetic assignment and first-generation migrant detection. Journal of Heredity, 95(6): 536–539.

Rannala B, Mountain J L. 1997. Detecting immigration by using multilocus genotypes. P. Natl. Acad. Sci. USA, 94(17): 9 197–9 201.

Rasmussen R S, Morrissey M T. 2009. Application of DNA-based methods to identify fish and seafood substitution on the commercial market. Compr. Rev. Food. Sci. F., 8(2): 118–154.

Renshaw M A, Saillant E, Broughton R E, Gold J R. 2006. Application of hypervariable genetic markers to forensic identification of ‘wild’ from hatchery-raised red drum, Sciaenops ocellatus. Forensic Science International, 156(1): 9–15.

Rozas J, Sanchez-DelBarrio J C, Messeguer X, Rozas R. 2003. DnaSP, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics, 19(18): 2 496–2 497.

Santos C A, Rossini B C, Marques C G, Galetti P M, Freitas P D. 2012. Characterization and genomic annotation of polymorphic EST-SSR loci in Litopenaeus vannamei shrimp. Aquaculture Research, 43(10): 1 567–1 570.

Sellars M J, Arce S M, Hertzler P L. 2012. Triploidy induction in the Pacific white shrimp Litopenaeus vannamei: an assessment of induction agents and parameters, embryo viability, and early larval survival. Mar. Biotechnol., 14(6): 740–751.

Shaw S H, Carrasquillo M M, Kashuk C, Puffenberger E G, Chakravarti A. 1998. Allele frequency distributions in pooled DNA samples: applications to mapping complex disease genes. Genome. Res., 8(2): 111–123.

Simmons M, Mickett K, Kucuktas H, Li P, Dunham R, Liu Z J. 2006. Comparison of domestic and wild channel catfish (Ictalurus punctatus) populations provides no evidence for genetic impact. Aquaculture, 252(2–4): 133–146.

Smith C T, Grant W S, Seeb L W. 2005. A rapid, highthroughput technique for detecting Tanner crabs Chionoecetes bairdi illegally taken in Alaska’s snow crab fishery. Transactions of the American Fisheries Society, 134(3): 620–623.

Sorenson L, McDowell J R, Knott T, Graves J E. 2013. Assignment test method using hypervariable markers for blue marlin (Makaira nigricans) stock identification. Conservation Genetics Resources, 5(1): 293–297.

Storset A, Strand C, Wetten M, Sissel K, Rarnstad A. 2007. Response to selection for resistance against infectious pancreatic necrosis in Atlantic salmon (Salmo salar L.). Aquaculture, 272: S62–S68.

Swofford D L. 2002. PAUP*: Phylogenetic Analysis Using Parsimony and Other Methods, Version 4.0b10. Sinauer Associates, MA (2002).

Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S. 2011. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol. Biol. Evol., 28(10): 2 731–2 739.

Valles-Jimenez R, Gaffney P M, Perez-Enriquez R. 2006. RFLP analysis of the mtDNA control region in white shrimp (Litopenaeus vannamei) populations from the eastern Pacific. Marine Biology, 148(4): 867–873.

Vaseeharan B, Rajakamaran P, Jayaseelan D, Anita Yeshvadha V. 2013. Molecular markers and their application in genetic diversity of Penaeid shrimps. Aquacult. Int., 21(2): 219–241.

Wright J M, Bentzen P. 1994. Microsatellites—genetic-markers for the future. Rev. Fish. Biol. Fisher., 4(3): 384–388.

You E M, Chiu T S, Liu K F, Tassanakajon A, Klinbunga S, Triwitayakorn K, de la Pena L D, Li Y, Yu H T. 2008. Microsatellite and mitochondrial haplotype diversity reveals population differentiation in the tiger shrimp (Penaeus monodon) in the Indo-Pacific region. Anim. Genet., 39(3): 267–277.

Zhang L S, Yang C J, Zhang Y, Li L, Zhang X M, Zhang Q L, Xiang J H. 2007. A genetic linkage map of Pacific white shrimp (Litopenaeus vannamei): sex-linked microsatellite markers and high recombination rates. Genetica, 131(1): 37–49.

浏览量

Downloads

CSCD

文章被引用时，请邮件提醒。

Submit

工具集

关联资源

Profile and development of microsatellite primers for Acanthogobius ommaturus based on high-throughput sequencing technology

Analysis of novel immune-related genes and microsatellite markers in the transcriptome of Paphia undulata

Isolation and characterization of genic microsatellites from de novo assembly transcriptome in the bivalve Ruditapes philippinarum

A novel male-associated marker for sex identification in Ussuri catfish Pseudobagrus ussuriensis

Peritrophin-like protein from Litopenaeus vannamei (LvPT) involved in white spot syndrome virus (WSSV) infection in digestive tract challenged with reverse gavage