Isolation and characterization of microsatellite markers and analysis of genetic diversity in Chinese jujube (Ziziphus jujuba Mill.)

PLoS ONE

Volumn 9, Issue 6, 2014, Pages

  Wang, Siqi ^a   Liu, Ying ^a   Liying, Ma ^a   Liu, Huabo ^a   Tang, Yan ^a   Wu, Liping ^a   Wang, Zhe ^a   Li, Yingyue ^a   Wu, Rongling ^a   Pang, Xiaoming ^a  

^a BEIJING FORESTRY UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CONTROLLED STUDY; CULTIVAR; GENE CLUSTER; GENETIC POLYMORPHISM; GENETIC SCREENING; GENETIC VARIABILITY; GENOME ANALYSIS; GENOTYPE; GEOGRAPHIC ORIGIN; JUJUBE; MICROSATELLITE MARKER; MOLECULAR CLONING; NONHUMAN; PLANT GENOME; POLYMERASE CHAIN REACTION; SIMPLE SEQUENCE REPEAT; CHINA; GENE LIBRARY; GENE LOCUS; GENETICS; ISOLATION AND PURIFICATION; METABOLISM; NUCLEOTIDE MOTIF; NUCLEOTIDE REPEAT; PHYLOGENY; ZIZIPHUS;

MICROSATELLITE DNA; PLANT DNA; PRIMER DNA;

CHINA; DNA PRIMERS; DNA, PLANT; GENE LIBRARY; GENETIC LOCI; GENETIC VARIATION; MICROSATELLITE REPEATS; NUCLEOTIDE MOTIFS; PHYLOGENY; POLYMORPHISM, GENETIC; REPETITIVE SEQUENCES, NUCLEIC ACID; ZIZIPHUS;

EID: 84903123826     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0099842     Document Type: Article

References (62)

1. Liu M, Zhao Z (2009) Germplasm resources and production of jujube in China. ISHS Acta Horticulturae 840: 25-32.
2. Cyong J-C, Hanabusa K (1980) Cyclic adenosine monophosphate in fruits of Zizyphus jujuba. Phytochemistry 19: 2747-2748.
3. Li JW, Fan LP, Ding SD, Ding XL (2007) Nutritional composition of five cultivars of Chinese jujube. Food chemistry 103: 454-460.
4. Zhang YL, Guo H, Chen JP, Li JK (2005) Effects of juice of fructus Zipiphi jujubae on blood lipid level and body function in mice. Chinese Journal of Clinical Rehabilitation 9: 247-249 (in Chinese with English abstract). (Pubitemid 40824174)
5. Mahajan R, Chopda M (2009) Phyto-Pharmacology of Ziziphus jujuba Mill.-A plant review. Pharmacognosy Reviews 3: 320.
6. State Forestry Administration (2011) China Forestry Statistical Yearbook. Beijing: China Forestry Publishing House (in Chinese).
7. Liu MJ, Wang M (2009) Germplasm resources of Chinese jujube. Beijing: China Forestry Publishing House (in Chinese).
8. Wang YL (2001) Prospects of extension for propagation techniques for green cuttages in Jujube. Economic Forest Researches 9: 59-60 (in Chinese).
9. Smith J, Smith O (1992) Fingerprinting crop varieties. Advances in agronomy 47: 85-140.
10. Peng JY, Shu HR, Sun ZX, Peng SQ (2000) RAPD analysis of germplasm resources on Chinese date. Acta Horticulturae Sinica 27: 171-176 (in Chinese with English abstract).
11. Bai RX (2008) Studies on genetic diversity and core collection construction of Ziziphus jujube germplasm resources using AFLP and SRAP markers [PhD thesis]: Hebei Agricultural University (in Chinese with English abstract).
12. Vosman B (1998) The use of molecular markers for the identification of tomato cultivars. Molecular tools for screening biodiversity. Berlin: Springer. pp. 382-387.
13. Wu YQ, Huang Y (2007) An SSR genetic map of Sorghum bicolor (L.) Moench and its comparison to a published genetic map. Genome 50: 84-89. (Pubitemid 46882799)
14. Yuan SX, Ge L, Liu C, Ming J (2013) The development of EST-SSR markers in Lilium regale and their cross-amplification in related species. Euphytica 189: 393-419.
15. Lu JY, Mao YM, Shen LY, Peng SQ, Liu M (2005) Application of AFLP markers for identification of hybrids from open pollinated Dongzao (Ziziphus jujuba Mill.) progenies. Acta Horticulturae Sinica 32: 680-683 (in Chinese with English abstract).
16. Shen LY (2005) Construction of genetic linkage map and mapping QTL for some traits in Chinese jujube (Ziziphus jujuba Mill.) [PhD thesis]: Hebei Agricultural University (in Chinese with English abstract).
17. El-Kassaby YA, Lstibůrek M, Liewlaksaneeyanawin C, Slavov GT, Howe GT (2007) Breeding without breeding: approach, example, and proof of concept. Citeseer pp. 43-54.
18. Zane L, Bargelloni L, Patarnello T (2002) Strategies for microsatellite isolation: a review. Molecular Ecology 11: 1-16. (Pubitemid 34108467)
19. Ma QH, Wang GX, Liang LS (2011) Development and characterization of SSR markers in Chinese jujube (Ziziphus jujuba Mill.) and its related species. Scientia Horticulturae 129: 597-602.
20. Varshney RK, Graner A, Sorrells ME (2005) Genic microsatellite markers in plants: features and applications. Trends in Biotechnology 23: 48-55. (Pubitemid 40075526)
21. Liu J, Liu HB, Ma LY, Wang SQ, Gao J, et al. (2014) A Chinese jujube (Ziziphus jujuba Mill.) fruit-expressed sequence tag (EST) library: Annotation and ESTSSR characterization. Scientia Horticulturae 165: 99-105.
22. Nunome T, Negoro S, Kono I, Kanamori H, Miyatake K, et al. (2009) Development of SSR markers derived from SSR-enriched genomic library of eggplant (Solanum melongena L.). Theoretical and Applied Genetics 119: 1143-1153.
23. Wang X, Trigiano R, Windham M, DeVries R, Scheffler B, et al. (2007) A simple PCR procedure for discovering microsatellites from small insert libraries. Molecular Ecology Notes 7: 558-561. (Pubitemid 47035487)
24. Appleby N, Edwards D, Batley J (2009) New technologies for ultra-high throughput genotyping in plants. Methods in Molecular Biology 513: 19-39.
25. Mammadov JA, Chen W, Ren R, Pai R, Marchione W, et al. (2010) Development of highly polymorphic SNP markers from the complexity reduced portion of maize [Zea mays L.] genome for use in marker-assisted breeding. Theoretical and Applied Genetics 121: 577-588.
26. Hendre PS, Phanindranath R, Annapurna V, Lalremruata A, Aggarwal RK (2008) Development of new genomic microsatellite markers from robusta coffee (Coffea canephora Pierre ex A. Froehner) showing broad cross-species transferability and utility in genetic studies. BMC Plant Biology 8: 51.
27. Jena SN, Srivastava A, Rai KM, Ranjan A, Singh SK, et al. (2012) Development and characterization of genomic and expressed SSRs for levant cotton (Gossypium herbaceum L.). Theoretical and Applied Genetics 124: 565-576.
28. Dirlewanger E, Cosson P, Tavaud M, Aranzana J, Poizat C, et al. (2002) Development of microsatellite markers in peach [Prunus persica (L.) Batsch] and their use in genetic diversity analysis in peach and sweet cherry (Prunus avium L.). Theoretical and Applied Genetics 105: 127-138. (Pubitemid 36059368)
29. Tang S, Yu JK, Slabaugh B, Shintani K, Knapp J (2002) Simple sequence repeat map of the sunflower genome. Theoretical and Applied Genetics 105: 1124-1136. (Pubitemid 36053137)
30. Wang YW, Samuels TD, Wu YQ (2011) Development of 1,030 genomic SSR markers in switchgrass. Theoretical and Applied Genetics 122: 677-686.
31. Tsukazaki H, Nunome T, Fukuoka H, Kanamori H, Kono I, et al. (2007) Isolation of 1,796 SSR clones from SSR-enriched DNA libraries of bunching onion (Allium fistulosum). Euphytica 157: 83-94. (Pubitemid 47338849)
32. Mir RR, Banerjee S, Das M, Gupta V, Tyagi AK, et al. (2009) Development and characterization of large-scale simple sequence repeats in jute. Crop science 49: 1687-1694.
33. Hirata M, Cai H, Inoue M, Yuyama N, Miura Y, et al. (2006) Development of simple sequence repeat (SSR) markers and construction of an SSR-based linkage map in Italian ryegrass (Lolium multiflorum Lam.). Theoretical and Applied Genetics 113: 270-279. (Pubitemid 43961558)
34. Perumal R, Nimmakayala P, Erattaimuthu SR, No EG, Reddy UK, et al. (2008) Simple sequence repeat markers useful for sorghum downy mildew (Peronosclerospora sorghi) and related species. BMC Genetics 9: 77.
35. Sethy NK, Shokeen B, Edwards KJ, Bhatia S (2006) Development of microsatellite markers and analysis of intraspecific genetic variability in chickpea (Cicer arietinum L.). Theoretical and Applied Genetics 112: 1416-1428.
36. Cai HW, Inoue M, Yuyama N, Takahashi W, Hirata M, et al. (2005) Isolation, characterization and mapping of simple sequence repeat markers in zoysiagrass (Zoysia spp.). Theoretical and Applied Genetics 112: 158-166. (Pubitemid 41738323)
37. Cai HW, Yuyama N, Tamaki H, Yoshizawa A (2003) Isolation and characterization of simple sequence repeat markers in the hexaploid forage grass timothy (Phleum pratense L.). Theor Appl Genet 107: 1337-1349. (Pubitemid 37496538)
38. Danin-Poleg Y, Reis N, Tzuri G, Katzir N (2001) Development and characterization of microsatellite markers in Cucumis. Theoretical and Applied Genetics 102: 61-72. (Pubitemid 32143376)
39. Li M, Yuyama N, Luo L, Hirata M, Cai H (2009) In silico mapping of 1758 new SSR markers developed from public genomic sequences for sorghum. Molecular Breeding 24: 41-47.
40. Rahimmalek M, Tabatabaei BES, Arzani A, Khorrami M (2011) Development and characterization of microsatellite markers for genomic analysis of yarrow (Achillea millefolium L.). Genes & Genomics 33: 475-482.
41. Botstein D, White RL, Skolnick M, Davis RW (1980) Construction of a genetic linkage map in man using restriction fragment length polymorphisms. American journal of human genetics 32: 314.
42. Cipriani G, Marrazzo MT, Di Gaspero G, Pfeiffer A, Morgante M, et al. (2008) A set of microsatellite markers with long core repeat optimized for grape (Vitis spp.) genotyping. BMC Plant Biol 8: 127.
43. Butler JM (2006) Genetics and genomics of core short tandem repeat loci used in human identity testing. Journal of forensic sciences 51: 253-265.
44. Fisher P, Richardson T, Gardner R (1998) Characteristics of single-and multicopy microsatellites from Pinus radiata. Theoretical and Applied Genetics 96: 969-979. (Pubitemid 28290189)
45. Stagel A, Portis E, Toppino L, Rotino GL, Lanteri S (2008) Gene-based microsatellite development for mapping and phylogeny studies in eggplant. BMC Genomics 9: 357.
46. Rallo P, Dorado G, Martin A (2000) Development of simple sequence repeats (SSRs) in olive tree (Olea europaea L.). Theoretical and Applied Genetics 101: 984-989.
47. Yu KF, Park SJ, Poysa V (1999) Abundance and variation of microsatellite DNA sequences in beans (Phaseolus and Vigna). Genome 42: 27-34. (Pubitemid 29174492)
48. Barthe S, Gugerli F, Barkley NA, Maggia L, Cardi C, et al. (2012) Always look on both sides: phylogenetic information conveyed by simple sequence repeat allele sequences. PLOS One 7: e40699.
49. Richards CM, Volk GM, Reilley AA, Henk AD, Lockwood DR, et al. (2009) Genetic diversity and population structure in Malus sieversii, a wild progenitor species of domesticated apple. Tree Genetics & Genomes 5: 339-347.
50. Ashworth VE, Clegg MT (2003) Microsatellite markers in avocado (Persea americana Mill.): genealogical relationships among cultivated avocado genotypes. Journal of Heredity 94: 407-415. (Pubitemid 37296661)
51. Zhang JJ, Shu QY, Liu ZA, Ren HX, Wang LS, et al. (2012) Two EST-derived marker systems for cultivar identification in tree peony. Plant Cell Reports 31: 299-310.
52. Zhang ZS, Liu GP, He RP, Liu F (2010) Breeding of a new crack-resistant jujube cultivar ' Muzao kanglie 1 '. China Fruits: 5-7.
53. Murray M, Thompson WF (1980) Rapid isolation of high molecular weight plant DNA. Nucleic acids research 8: 4321-4326.
54. Nunome T, Negoro S, Miyatake K, Yamaguchi H, Fukuoka H (2006) A protocol for the construction of microsatellite enriched genomic library. Plant Molecular Biology Reporter 24: 305-312. (Pubitemid 351344715)
55. Schuelke M (2000) An economic method for the fluorescent labeling of PCR fragments. Nature biotechnology 18: 233-234.
56. Amos W, Hoffman J, Frodsham A, Zhang L, Best S, et al. (2007) Automated binning of microsatellite alleles: problems and solutions. Molecular Ecology Notes 7: 10-14. (Pubitemid 46046571)
57. Park SDE (2001) Trypanotolerance in west african cattle and the population genetic effects of selection [PhD thesis]. Ireland: University of Dublin.
58. Excoffier L, Lischer HE (2010) Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows. Molecular Ecology Resources 10: 564-567.
59. Federici CT, Fang DQ, Scora RW, Roose ML (1998) Phylogenetic relationships within the genus Citrus (Rutaceae) and related genera as revealed by RFLP and RAPD analysis. Theoretical and Applied Genetics 96: 812-822. (Pubitemid 28295150)
60. Pang XM, Hu CG, Deng XX (2003) Phylogenetic relationships among Citrus and its relatives as revealed by SSR markers. Acta Genetica Sinica 30: 81-87.
61. Ge HM, Ren M (2011) DataTrans1.0: A Software for Microsatellite Data Processing Based on Excel Macro. Molecular Plant Breeding 9: 1359-1365.
62. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S (2013) MEGA6: Molecular Evolutionary Genetics Analysis version 6.0. Molecular Biology and Evolution 30: 2725-2729.