Advertisement

Tree Genetics & Genomes

, Volume 10, Issue 5, pp 1271–1279 | Cite as

Genome-wide characterization and selection of expressed sequence tag simple sequence repeat primers for optimized marker distribution and reliability in peach

  • Chunxian ChenEmail author
  • Clive H. Bock
  • William R. Okie
  • Fred G. GmitterJr.
  • Sook Jung
  • Dorrie Main
  • Tom G. Beckman
  • Bruce W. Wood
Original Paper

Abstract

Simple sequence repeats (SSR) in Prunus expressed sequence tags (EST) were mined, and flanking primers designed and used for genome-wide characterization and selection of primers to optimize marker distribution and reliability in peach. A total of 4,770 and 9,029 SSRs were identified from 12,618 contigs and 34,238 singlets, from which 3,695 and 6,849 primers were designed, respectively. Alignment of the 10,544 forward and reverse primer sequences (21,088 queries) against the peach reference genome at 9e-03 resulted in 23,553 hits (96,621 alignments) with 16,885 queries, and “no hits found” (NHF) for the remaining 4,203 queries. A majority of aligned primers had only one hit/alignment on the peach scaffolds, and the distribution of the 5,500 singly aligned primers (pairs) on each 500-kb genome interval was determined. The average number of ESR-SSR primers per 500-kb interval was 10.8. The primers were categorized into eight subgroups based on the difference between the genome amplicon size and expressed amplicon size of each primer, with 288 primers of optimized distribution and reliability selected for genotype evaluation. Only 2 of the 288 primers failed in all 4 peach cultivars screened, with an overall successful primer/sample rate of 97.2 %. The average number of alleles detected in the four cultivars was 3.84. The polymorphism information content (PIC) values suggested that a majority of the 288 primers had a high rate of allele polymorphism among the four peach cultivars. The advantages of genome-wide analysis of EST-SSR primers and options to improve the polymorphism rate are discussed.

Keywords

Microsatellite Short tandem repeat (STR) Marker-assisted selection (MAS) Variety authentication Reference genome 

Notes

Acknowledgments

The authors thank Bryan Blackburn, Luke Quick, and Minling Zhang for their technical assistance. The research is partially supported by the USDA National Program of Plant Genetic Resources, Genomics and Genetic Improvement (Project number 6606-21000-004-006) and an USDA National Institute of Food and Agriculture Specialty Crop Research Initiative project (2009-51181- 06036).

Data archiving statement

All Prunus EST sequences and accession numbers are available at the National Center for Biotechnology Information EST database (http://www.ncbi.nlm.nih.gov/nucest/?term=Prunus). The peach (Prunus persica) reference genome assembly (version 1.0) is available at the Genome Database for Rosaceae (http://www.rosaceae.org/species/Prunus_persica/genome_v1.0), so is the mined Prunus EST-SSR primer information (http://www.rosaceae.org/node/336118). The 10545 EST-SSR forward and reverse primers and the selected 288 primers are attached as ESM Tables 2 and 3, respectively.

Supplementary material

11295_2014_759_MOESM1_ESM.docx (14 kb)
ESM 1 (DOCX 14 kb)
11295_2014_759_MOESM2_ESM.xlsx (1.3 mb)
ESM 2 (XLSX 1316 kb)
11295_2014_759_MOESM3_ESM.docx (33 kb)
ESM 3 (DOCX 33 kb)

References

  1. Agarwal M, Shrivastava N, Padh H (2008) Advances in molecular marker techniques and their applications in plant sciences. Plant Cell Rep 27:617–631PubMedCrossRefGoogle Scholar
  2. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25:3389–3402PubMedCrossRefPubMedCentralGoogle Scholar
  3. Blenda AV, Wechter WP, Reighard GL, Baird WV, Abbott AG (2006) Development and characterisation of diagnostic AFLP markers in Prunus persica for its response to peach tree short life syndrome. J Hortic Sci Biotechnol 81:281–288Google Scholar
  4. Blenda AV, Verde I, Georgi LL, Reighard GL, Forrest SD, Munoz-Torres M, Baird WV, Abbott AG (2007) Construction of a genetic linkage map and identification of molecular markers in peach rootstocks for response to peach tree short life syndrome. Tree Genet Genomes 3:341–350CrossRefGoogle Scholar
  5. Bliss FA, Arulsekar S, Foolad MR, Becerra V, Gillen AM, Warburton ML, Dandekar AM, Kocsisne GM, Mydin KK (2002) An expanded genetic linkage map of Prunus based on an interspecific cross between almond and peach. Genome 45:520–529PubMedCrossRefGoogle Scholar
  6. Chen X, Sullivan PF (2003) Single nucleotide polymorphism genotyping: biochemistry, protocol, cost and throughput. Pharmacogenomics J 3:77–96Google Scholar
  7. Chen C, Gmitter FG Jr (2013) Mining of haplotype-based expressed sequence tag single nucleotide polymorphisms in citrus. BMC Genomics 14:746Google Scholar
  8. Chen C, Zhou P, Choi YA, Huang S, Gmitter FG (2006) Mining and characterizing microsatellites from citrus ESTs. Theor Appl Genet 112:1248–1257PubMedCrossRefGoogle Scholar
  9. Chen C, Bowman KD, Choi YA, Dang PM, Rao MN, Huang S, Soneji JR, McCollum TG, Gmitter FG (2008) EST-SSR genetic maps for Citrus sinensis and Poncirus trifoliata. Tree Genet Genome 4:1–10CrossRefGoogle Scholar
  10. Chen C, Bock CH, Beckman TG (2014) Sequence analysis reveals genomic factors affecting EST-SSR primer performance and polymorphism. Mol Genet Genomics. doi: 10.1007/s00438-014-0875-8
  11. Cipriani G, Lot G, Huang WG, Marrazzo MT, Peterlunger E, Testolin R (1999) AC/GT and AG/CT microsatellite repeats in peach [Prunus persica (L) Batsch]: isolation, characterisation and cross-species amplification in Prunus. Theor Appl Genet 99:65–72CrossRefGoogle Scholar
  12. Doyle JJ, Doyle JL (1987) A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem Bul 19:11–15Google Scholar
  13. Horner DS, Pavesi G, Castrignano T, De Meo PD, Liuni S, Sammeth M, Picardi E, Pesole G (2010) Bioinformatics approaches for genomics and post genomics applications of next-generation sequencing. Brief Bioinform 11:181–197PubMedCrossRefGoogle Scholar
  14. Howad W, Yamamoto T, Dirlewanger E, Testolin R, Cosson P, Cipriani G, Monforte AJ, Georgi L, Abbott AG, Arus P (2005) Mapping with a few plants: using selective mapping for microsatellite saturation of the Prunus reference map. Genetics 171:1305–1309PubMedCrossRefPubMedCentralGoogle Scholar
  15. Huang X, Madan A (1999) CAP3: A DNA sequence assembly program. Genome Res 9:868–877PubMedCrossRefPubMedCentralGoogle Scholar
  16. International Peach Genome I, Verde I, Abbott AG, Scalabrin S, Jung S, Shu S, Marroni F, Zhebentyayeva T, Dettori MT, Grimwood J, Cattonaro F, Zuccolo A, Rossini L, Jenkins J, Vendramin E, Meisel LA, Decroocq V, Sosinski B, Prochnik S, Mitros T, Policriti A, Cipriani G, Dondini L, Ficklin S, Goodstein DM, Xuan P, Del Fabbro C, Aramini V, Copetti D, Gonzalez S, Horner DS, Falchi R, Lucas S, Mica E, Maldonado J, Lazzari B, Bielenberg D, Pirona R, Miculan M, Barakat A, Testolin R, Stella A, Tartarini S, Tonutti P, Arus P, Orellana A, Wells C, Main D, Vizzotto G, Silva H, Salamini F, Schmutz J, Morgante M, Rokhsar DS (2013) The high-quality draft genome of peach (Prunus persica) identifies unique patterns of genetic diversity, domestication and genome evolution. Nat Genet 45:487–494PubMedCrossRefGoogle Scholar
  17. Jung S, Jesudurai C, Staton M, Du Z, Ficklin S, Cho I, Abbott A, Tomkins J, Main D (2004) GDR (Genome Database for Rosaceae): integrated web resources for Rosaceae genomics and genetics research. BMC Bioinformatics 5:130PubMedCrossRefPubMedCentralGoogle Scholar
  18. Jung S, Staton M, Lee T, Blenda A, Svancara R, Abbott A, Main D (2008) GDR (Genome Database for Rosaceae): integrated web-database for Rosaceae genomics and genetics data. Nucleic Acids Res 36:D1034–D1040.Google Scholar
  19. Jung S, Ficklin SP, Lee T, Cheng CH, Blenda A, Zheng P, Yu J, Bombarely A, Cho I, Ru S, Evans K, Peace C, Abbott AG, Mueller LA, Olmstead MA, Main D (2014) The Genome Database for Rosaceae (GDR): year 10 update. Nucleic Acids Res 42:D1237–1244PubMedCrossRefPubMedCentralGoogle Scholar
  20. Kayesh E, Zhang YY, Liu GS, Bilkish N, Sun X, Leng XP, Fang JG (2013) Development of highly polymorphic EST-SSR markers and segregation in F(1) hybrid population of Vitis vinifera L. Genet Mol Res 12:3871–3878PubMedCrossRefGoogle Scholar
  21. Kong Q, Zhang G, Chen W, Zhang Z, Zou X (2012) Identification and development of polymorphic EST-SSR markers by sequence alignment in pepper, Capsicum annuum (Solanaceae). Am J Bot 99:e59–61PubMedCrossRefGoogle Scholar
  22. Lambert P, Hagen LS, Arus P, Audergon JM (2004) Genetic linkage maps of two apricot cultivars ( Prunus armeniaca L.) compared with the almond Texas x peach Earlygold reference map for Prunus. Theor Appl Genet 108:1120–1130PubMedCrossRefGoogle Scholar
  23. Lambert P, Pascal T (2011) Mapping Rm2 gene conferring resistance to the green peach aphid (Myzus persicae Sulzer) in the peach cultivar "Rubira (R)". Tree Genet Genome 7:1057–1068CrossRefGoogle Scholar
  24. Liu K, Muse SV (2005) PowerMarker: an integrated analysis environment for genetic marker analysis. Bioinformatics 21:2128–2129PubMedCrossRefGoogle Scholar
  25. McCarthy S (1993) USDA's Plant Genome Research Program. Bull Med Libr Assoc 81:278–281PubMedPubMedCentralGoogle Scholar
  26. Miah G, Rafii MY, Ismail MR, Puteh AB, Rahim HA, Islam Kh N, Latif MA (2013) A review of microsatellite markers and their applications in rice breeding programs to improve blast disease resistance. Int J Mol Sci 14:22499–22528PubMedCrossRefPubMedCentralGoogle Scholar
  27. Mohanty P, Sahoo L, Parida K, Das P (2013) Development of polymorphic EST-SSR markers in Macrobrachium rosenbergii by data mining. Conserv Genet Resour 5:133–136CrossRefGoogle Scholar
  28. Morgante M, Hanafey M, Powell W (2002) Microsatellites are preferentially associated with nonrepetitive DNA in plant genomes. Nat Genet 30:194–200PubMedCrossRefGoogle Scholar
  29. Muthamilarasan M, Venkata Suresh B, Pandey G, Kumari K, Parida SK, Prasad M (2013) Development of 5123 Intron-length polymorphic markers for large-scale genotyping applications in foxtail millet. DNA Res 21:41–52Google Scholar
  30. Oetting WS, Lee HK, Flanders DJ, Wiesner GL, Sellers TA, King RA (1995) Linkage analysis with multiplexed short tandem repeat polymorphisms using infrared fluorescence and M13 tailed primers. Genomics 30:450–458PubMedCrossRefGoogle Scholar
  31. Ogundiwin EA, Peace CP, Gradziel TM, Parfitt DE, Bliss FA, Crisosto CH (2009) A fruit quality gene map of Prunus. BMC Genomics 10:587PubMedCrossRefPubMedCentralGoogle Scholar
  32. Okie WR (1998) Handbook of peach and nectarine varieties: performance in the Southeastern United States and Index of Names. The National Technical Information Service, Springfield, VAGoogle Scholar
  33. Ott J, Rabinowitz D (1997) The effect of marker heterozygosity on the power to detect linkage disequilibrium. Genetics 147:927–930PubMedPubMedCentralGoogle Scholar
  34. Pettersson A, Winer ES, Wekslerzangen S, Lernmark A, Jacob HJ (1995) Predictability of heterozygosity scores and polymorphism information-content values for rat genetic-markers. Mamm Genome 6:512–520PubMedCrossRefGoogle Scholar
  35. Rozen S, Skaletsky H (2000) Primer3 on the WWW for general users and for biologist programmers. Methods Mol Biol (Clifton, NJ) 132:365–386Google Scholar
  36. Tang J, Vosman B, Voorrips RE, van der Linden CG, Leunissen JA (2006) QualitySNP: a pipeline for detecting single nucleotide polymorphisms and insertions/deletions in EST data from diploid and polyploid species. BMC Bioinformatics 7:438PubMedCrossRefPubMedCentralGoogle Scholar
  37. Terwilliger JD, Ding YL, Ott J (1992) On the relative importance of marker heterozygosity and intermarker distance in gene-mapping. Genomics 13:951–956PubMedCrossRefGoogle Scholar
  38. Thiel T, Michalek W, Varshney RK, Graner A (2003) Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley (Hordeum vulgare L.). Theor Appl Genet 106:411–422PubMedGoogle Scholar
  39. Verde I, Bassil N, Scalabrin S, Gilmore B, Lawley CT, Gasic K, Micheletti D, Rosyara UR, Cattonaro F, Vendramin E, Main D, Aramini V, Blas AL, Mockler TC, Bryant DW, Wilhelm L, Troggio M, Sosinski B, Aranzana MJ, Arus P, Iezzoni A, Morgante M, Peace C (2012) Development and evaluation of a 9K SNP array for peach by internationally coordinated SNP detection and validation in breeding germplasm. PLoS One 7:e35668PubMedCrossRefPubMedCentralGoogle Scholar
  40. Warburton ML, Becerra-Velasquez VL, Goffreda JC, Bliss FA (1996) Utility of RAPD markers in identifying genetic linkages to genes of economic interest in peach. Theor Appl Genet 93:920–925PubMedCrossRefGoogle Scholar
  41. Wendel JF, Cronn RC, Alvarez I, Liu B, Small RL, Senchina DS (2002) Intron size and genome size in plants. Mol Biol Evol 19:2346–2352PubMedCrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2014

Authors and Affiliations

  • Chunxian Chen
    • 1
    Email author
  • Clive H. Bock
    • 1
  • William R. Okie
    • 1
  • Fred G. GmitterJr.
    • 2
  • Sook Jung
    • 3
  • Dorrie Main
    • 3
  • Tom G. Beckman
    • 1
  • Bruce W. Wood
    • 1
  1. 1.USDA, ARS, SEFTNRLByronUSA
  2. 2.Citrus Research and Education CenterUniversity of FloridaLake AlfredUSA
  3. 3.Department of HorticultureWashington State UniversityPullmanUSA

Personalised recommendations