Abstract
Gerbera (Gerbera hybrida) is one of the most important cut and pot flowers marketed worldwide. Few molecular markers and no SSR (simple sequence repeat) markers were available for gerbera breeding and genetic studies. Through in silico analysis of 8,670 unigene sequences assembled from 16,998 gerbera expressed sequence tags (ESTs) in the GenBank, we identified 893 SSR loci, corresponding to 10.3% of the gerbera unigene sequences or one SSR in every 5.16 kb of the ESTs in the gerbera transcriptome. The majority of SSR loci contain dinucleotide (42.8%) or trinucleotide (25.6%) repeats, while fewer contain tetranucleotide (6.4%), pentanucleotide (9.1%) and hexanucleotide (16.1%) repeats. AG (37%) and AAT (7.3%) were the most abundant motifs identified. Out of 115 primer pairs designed, 99 (86.1%) amplified discrete PCR products of the expected sizes, while 67 (67.7%) detected polymorphism among seven gerbera cultivars representing three plant types (cut flower, pot, and garden) propagated by two methods (seed or tissue culture). The number of alleles at these SSR loci ranged from 2 to 6, with an average of 2.7 alleles per locus. The PIC value of 67 polymorphic SSR markers was 0.13–0.80, with an average of 0.51. Sixty-eight ESTs targeted by the 115 SSR markers have putative gene functions, and two marker loci may have potential to be associated with disease resistance or flowering time. The availability of these gerbera EST-SSR markers should facilitate the use of molecular markers in gerbera breeding and genetic studies.
References
Anonymous (2001) Classic gerbera with a new look. http://www.flowercouncil.org/uk/news/fpnews/Productnieuws_2001/mrt2001_Gerbera.asp?Source. Accessed 4 Feb 2004
Bhatiaa R, Singha KP, Jhangb T, Sharmab TR (2009) Assessment of clonal fidelity of micropropagated gerbera plants by ISSR markers. Sci Hortic 119:208–211
Deng Z, Harbaugh BK (2008) Progress in breeding for disease resistance and stress tolerance in caladium, gerbera, and lisianthus. Acta Hortic 766:399–403
Fraser LG, Harvey CF, Crowhurst RN, De Silva HN (2004) EST–derived microsatellites from Actinidia species and their potential for mapping. Theor Appl Genet 108:1010–1016
Kloos WE, George CG, Sorge LK (2005) Inheritance of powdery mildew resistance and leaf macrohair density in Gerbera hybrida. HortScience 40:1246–1251
Kofler R, Schlötterer C, Lelley T (2007) SciRoKo: a new tool for whole genome microsatellite search and investigation. Bioinformatics 23:1683–1685
Kumpatla SP, Mukhopadhyay S (2005) Mining and survey of simple sequence repeats in expressed sequence tags of dicotyledonous species. Genome 48:985–998
Laitinen RAE, Immanen J, Auvinen P, Rudd S, Alatalo E, Paulin L, Ainasoja M, Kotilainen M, Koskela S, Teeri TH, Elomaa P (2005) Analysis of the floral transcriptome uncovers new regulators of organ determination and gene families related to flower organ differentiation in Gerbera hybrida (Asteraceae). Genome Res 15:475–486
Li YC, Korol AB, Fahima T, Nevo E (2004) Microsatellites within genes: structure, function, and evolution. Mol Biol Evol 21:991–1007
Mata TLD, Segeren MI, Fonseca AS, Colombo CA (2009) Genetic divergence among gerbera accessions evaluated by RAPD. Sci Hortic 121:92–96
Rogers MN, Tjia BO (1990) Gerbera production. Timber Press, Portland
Rungis D, Bérubé Y, Zhang J, Ralph S, Ritland CE, Ellis BE, Douglas C, Bohlmann J, Ritland K (2004) Robust simple sequence repeat markers for spruce Picea spp. from expressed sequence tags. Theor Appl Genet 109:1283–1294
Saha MC, Mian RA, Eujayl I, Zwonitzer JC, Wang L, May GD (2004) Tall fescue EST–SSR markers with transferability across several grass species. Theor Appl Genet 109:783–791
Scott KD, Eggler P, Seaton G, Rosetto M, Ablett EM, Lee LS, Henry RJ (2000) Analysis of SSRs derived from grape ESTs. Theor Appl Genet 100:723–726
Teeri TH, Elomaa P, Kotilainen M, Albert VA (2006) Mining plant diversity: Gerbera as a model system for plant developmental and biosynthetic research. BioEssays 28:756–767
Varshney RK, Thiel T, Stein N, Langride P, Graner A (2002) In silico analysis on frequency and distribution of microsatellites in ESTs of some cereal species. Cell Mol Biol Letter 7:537–546
Varshney RK, Graner A, Sorrells ME (2005) Genic microsatellite markers in plants: features and applications. Trends Biotechnol 23:48–55
Acknowledgments
The authors thank Drs. Jeremy Edwards and John Scott for giving us access to use their NanoDrop 1000 spectrophotometer and Mastercycler Gradient thermocycler and Joyce Jones and Gail Bowman for technical assistance.
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Gong, L., Deng, Z. EST-SSR markers for gerbera (Gerbera hybrida). Mol Breeding 26, 125–132 (2010). https://doi.org/10.1007/s11032-009-9380-x
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DOI: https://doi.org/10.1007/s11032-009-9380-x