Genome wide characterization of short tandem repeat markers in sweet orange (Citrus sinensis)

PLoS ONE

Volumn 9, Issue 8, 2014, Pages

  Biswas, Manosh Kumar ^a   Xu, Qiang ^a   Mayer, Christoph ^b   Deng, Xiuxin ^a  

^a HUAZHONG AGRICULTURAL UNIVERSITY   (China)

^b ZOOLOGISCHES FORSCHUNGSMUSEUM ALEXANDER KOENIG   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

PRIMER RNA; MICROSATELLITE DNA;

ALLELE; ARTICLE; AT RICH SEQUENCE; CHROMOSOME 4; COMPARATIVE GENOMIC HYBRIDIZATION; COMPUTER MODEL; CONTROLLED STUDY; DINUCLEOTIDE REPEAT; GC RICH SEQUENCE; GENE AMPLIFICATION; GENE FREQUENCY; GENE FUNCTION; GENETIC ANALYSIS; GENETIC ASSOCIATION; GENETIC LINKAGE; GENETIC POLYMORPHISM; LABORATORY TEST; MICROSATELLITE MARKER; NONHUMAN; PLANT GENETICS; PLANT GENOME; POPULATION STRUCTURE; PROTEIN ASSEMBLY; SHORT TANDEM REPEAT; SIMPLE SEQUENCE REPEAT; SWEET ORANGE; BIOLOGY; CHROMOSOME MAP; GENETICS; GENOTYPE; HIGH THROUGHPUT SEQUENCING; MOLECULAR GENETICS; NUCLEIC ACID DATABASE; PLANT CHROMOSOME; REPRODUCIBILITY;

CHROMOSOME MAPPING; CHROMOSOMES, PLANT; CITRUS SINENSIS; COMPUTATIONAL BIOLOGY; DATABASES, NUCLEIC ACID; GENE FREQUENCY; GENOME, PLANT; GENOME-WIDE ASSOCIATION STUDY; GENOTYPE; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; MICROSATELLITE REPEATS; MOLECULAR SEQUENCE ANNOTATION; POLYMORPHISM, GENETIC; REPRODUCIBILITY OF RESULTS;

EID: 84923349693     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0104182     Document Type: Article

References (41)

1. Weber JL, Wong C (1993) Mutation of human short tandem repeats. Hum Mol Genet 2: 1123-1128. (Pubitemid 23244988)
2. Kruglyak S, Durrett RT, Schug MD, Aquadro CF (1998) Equilibrium distributions of microsatellite repeat length resulting from a balance between slippage events and point mutations. Proc Natl Acad Sci U S A 95: 10774-10778. (Pubitemid 28413144)
3. Richard GF, Kerrest A, Dujon B (2008) Comparative genomics and molecular dynamics of DNA repeats in eukaryotes. Microbiol Mol Biol Rev 72: 686-727.
4. Sonah H, Deshmukh RK, Sharma A, Singh VP, Gupta DK, et al. (2011) Genome-wide distribution and organization of microsatellites in plants: an insight into marker development in Brachypodium. PLoS One 6: e21298.
5. Mayer C, Leese F, Tollrian R (2010) Genome-wide analysis of tandem repeats in Daphnia pulex - a comparative approach. BMC Genomics 11:277.
6. FAOSTAT (2012) Food and Agriculture Organization of the United Nations, Rome: FAO.
7. Arumuganathan K, Earle E (1991) Nuclear DNA content of some important plant species. Plant Molecular Biology Reporter 9: 208-218.
8. Biswas MK, Chai L, Amar MH, Zhang X, Deng XX (2011) Comparative analysis of genetic diversity in Citrus germplasm collection using AFLP, SSAP, SAMPL and SSR markers. Scientia Horticulturae 129: 798-803.
9. Biswas MK, Chai L, Mayer C, Xu Q, Guo W, et al. (2012) Exploiting BAC-end sequences for the mining, characterization and utility of new short sequences repeat (SSR) markers in Citrus. Molecular Biology Reports: 1-14.
10. Biswas MK, Xu Q, Deng XX (2010) Utility of RAPD, ISSR, IRAP and REMAP markers for the genetic analysis of Citrus spp. Scientia Horticulturae 124: 254-261.
11. Ollitrault F, Terol J, Pina JA, Navarro L, Talon M, et al. (2010) Development of SSR markers from Citrus clementina (Rutaceae) BAC end sequences and interspecific transferability in Citrus. Am J Bot 97: e124-129.
12. Chen C, Zhou P, Choi YA, Huang S, Gmitter FG Jr (2006) Mining and characterizing microsatellites from citrus ESTs. Theor Appl Genet 112: 1248-1257.
13. Cheng YJ, Guo WW, Yi HL, Pang XM, Deng X (2003) An efficient protocol for genomic DNA extraction fromCitrus species. Plant Molecular Biology Reporter 21: 177-178.
14. Bohra A, Dubey A, Saxena RK, Penmetsa RV, Poornima KN, et al. (2011) Analysis of BAC-end sequences (BESs) and development of BES-SSR markers for genetic mapping and hybrid purity assessment in pigeonpea (Cajanus spp.). BMC Plant Biol 11: 56.
15. Ruiz C, Paz Breto M, Asíns MJ (2000) A quick methodology to identify sexual seedlings in citrus breeding programs using SSR markers. Euphytica 112: 89-94. (Pubitemid 30203187)
16. Cardle L, Ramsay L, Milbourne D, Macaulay M, Marshall D, et al. (2000) Computational and experimental characterization of physically clustered simple sequence repeats in plants. Genetics 156: 847-854.
17. Temnykh S, DeClerck G, Lukashova A, Lipovich L, Cartinhour S, et al. (2001) Computational and experimental analysis of microsatellites in rice (Oryza sativa L.): frequency, length variation, transposon associations, and genetic marker potential. Genome Res 11: 1441-1452. (Pubitemid 32771552)
18. Mun JH, Kim DJ, Choi HK, Gish J, Debelle F, et al. (2006) Distribution of microsatellites in the genome of Medicago truncatula: a resource of genetic markers that integrate genetic and physical maps. Genetics 172: 2541-2555.
19. Kuntal H, Sharma V, Daniell H (2012) Microsatellite analysis in organelle genomes of Chlorophyta. Bioinformation 8: 255-259.
20. Cavagnaro PF, Senalik DA, Yang L, Simon PW, Harkins TT, et al. (2010) Genome-wide characterization of simple sequence repeats in cucumber (Cucumis sativus L.). BMC Genomics 11: 569.
21. Labbé J, Murat C, Morin E, Tacon F, Martin F (2011) Survey and analysis of simple sequence repeats in the Laccaria bicolor genome, with development of microsatellite markers. Current Genetics 57: 75-88.
22. Murat C, Riccioni C, Belfiori B, Cichocki N, Labbe J, et al. (2011) Distribution and localization of microsatellites in the Perigord black truffle genome and identification of new molecular markers. Fungal Genet Biol 48: 592-601.
23. Li B, Xia Q, Lu C, Zhou Z, Xiang Z (2004) Analysis on frequency and density of microsatellites in coding sequences of several eukaryotic genomes. Genomics Proteomics Bioinformatics 2: 24-31.
24. Zhang L, Zuo K, Zhang F, Cao Y, Wang J, et al. (2006) Conservation of noncoding microsatellites in plants: implication for gene regulation. BMC Genomics 7: 323.
25. Duval A, Hamelin R (2002) Genetic instability in human mismatch repair deficient cancers. Ann Genet 45: 71-75. (Pubitemid 34823865)
26. Vassileva V, Millar A, Briollais L, Chapman W, Bapat B (2002) Genes involved in DNA repair are mutational targets in endometrial cancers with microsatellite instability. Cancer Res 62: 4095-4099. (Pubitemid 34791080)
27. Morgante M, Hanafey M, Powell W (2002) Microsatellites are preferentially associated with nonrepetitive DNA in plant genomes. Nat Genet 30: 194-200.
28. Peng JH, Lapitan NL (2005) Characterization of EST-derived microsatellites in the wheat genome and development of eSSR markers. Funct Integr Genomics 5: 80-96. (Pubitemid 40425089)
29. Toth G, Gaspari Z, Jurka J (2000) Microsatellites in different eukaryotic genomes: survey and analysis. Genome Research 10: 967-981. (Pubitemid 30608632)
30. Subramanian S, Mishra RK, Singh L (2003) Genome-wide analysis of microsatellite repeats in humans: their abundance and density in specific genomic regions. Genome Biol 4: R13.
31. Weng Y, Azhaguvel P, Michels GJ Jr, Rudd JC (2007) Cross-species transferability of microsatellite markers from six aphid (Hemiptera: Aphididae) species and their use for evaluating biotypic diversity in two cereal aphids. Insect Mol Biol 16: 613-622. (Pubitemid 47481036)
32. Shama S, Meyuhas O (1996) The translational cis-regulatory element of mammalian ribosomal protein mRNAs is recognized by the plant translational apparatus. Eur J Biochem 236: 383-388. (Pubitemid 26098819)
33. Martienssen RA, Colot V (2001) DNA methylation and epigenetic inheritance in plants and filamentous fungi. Science 293: 1070-1074. (Pubitemid 32758076)
34. da Maia LC, de Souza VQ, Kopp MM, de Carvalho FI, de Oliveira AC (2009) Tandem repeat distribution of gene transcripts in three plant families. Genet Mol Biol 32: 822-833.
35. Hong CP, Piao ZY, Kang TW, Batley J, Yang TJ, et al. (2007) Genomic distribution of simple sequence repeats in Brassica rapa. Mol Cells 23: 349-356. (Pubitemid 47181050)
36. Read BA, Kegel J, Klute MJ, Kuo A, Lefebvre SC, et al. (2013) Pan genome of the phytoplankton Emiliania underpins its global distribution. Nature 499: 209-213.
37. Ellegren H (2000) Heterogeneous mutation processes in human microsatellite DNA sequences. Nat Genet 24: 400-402.
38. Wierdl M, Dominska M, Petes TD (1997) Microsatellite instability in yeast: dependence on the length of the microsatellite. Genetics 146: 769-779. (Pubitemid 27290966)
39. Cavagnaro PF, Chung SM, Manin S, Yildiz M, Ali A, et al. (2011) Microsatellite isolation and marker development in carrot - genomic distribution, linkage mapping, genetic diversity analysis and marker transferability across Apiaceae. BMC Genomics 12: 386.
40. Zhang LY, Bernard M, Leroy P, Feuillet C, Sourdille P (2005) High transferability of bread wheat EST-derived SSRs to other cereals. Theor Appl Genet 111: 677-687. (Pubitemid 41204209)
41. Zhao H, Yu J, You FM, Luo M, Peng J (2011) Transferability of microsatellite markers from Brachypodium distachyon to Miscanthus sinensis, a potential biomass crop. J Integr Plant Biol 53: 232-245.