Development of simple sequence repeat (SSR) markers from a genome survey of Chinese bayberry (Myrica rubra)

BMC Genomics

Volumn 13, Issue 1, 2012, Pages

  Jiao, Yun ^a   Jia, Hui min ^a   Li, Xiong wei ^a   Chai, Ming liang ^a   Jia, Hui juan ^a   Chen, Zhe ^b   Wang, Guo yun ^c   Chai, Chun yan ^d   van de Weg, Eric ^e   Gao, Zhong shan ^a  

^a ZHEJIANG UNIVERSITY   (China)

^b BGI SHENZHEN   (China)

^c Fruit Research Institute   (China)

^d Forestry Technology Extension Center   (China)

^e WAGENINGEN UNIVERSITY   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

DINUCLEOTIDE; HEXANUCLEOTIDE; NUCLEOTIDE; PENTANUCLEOTIDE; TETRANUCLEOTIDE; TRINUCLEOTIDE; UNCLASSIFIED DRUG;

ARTICLE; CHINA; CHINESE BAYBERRY; GENE LOCUS; GENE MAPPING; GENETIC LINKAGE; GENETIC VARIABILITY; GENOME SIZE; GENOTYPE; HETEROZYGOSITY; MOLECULAR PHYLOGENY; MYRICA ADENOPHORA; MYRICA CERIFERA; MYRICA NANA; MYRICACEAE; NONHUMAN; NUCLEOTIDE SEQUENCE; PLANT GENOME; POPULATION DISTRIBUTION; SIMPLE SEQUENCE REPEAT; UNITED STATES;

BASE SEQUENCE; CHINA; CLUSTER ANALYSIS; EVOLUTION, MOLECULAR; EXPRESSED SEQUENCE TAGS; GENOME, PLANT; MICROSATELLITE REPEATS; MYRICA; POLYMORPHISM, GENETIC;

MORELLA; MORELLA CERIFERA; MORELLA RUBRA; MYRICA; MYRICA ADENOPHORA;

EID: 84861337742     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-13-201     Document Type: Article

References (35)

1. Chen K, Xu C, Zhang B, Ferguson IB. Red bayberry: botany and horticulture, in Horticultural Reviews 2004, 83-114. John Wiley & Sons, Inc, Oxford, Jules Janick, 30.
2. Zhang B, Kang MX, Xie QP, Xu B, Sun CD, Chen KS, Wu YL. Anthocyanins from Chinese bayberry extract protect beta cells from oxidative stress-mediated injury via HO-1 upregulation. J Agr Food Chem 2011, 59(2):537-545.
3. Terakawa M, Kikuchi S, Kanetani S, Matsui K, Yumoto T, Yoshimaru H. Characterization of 13 polymorphic microsatellite loci for an evergreen tree, Myrica rubra. Mol Ecol Notes 2006, 6(3):709-711.
4. Zhang SM, Xu CJ, Gao ZS, Chen KS, Wang GY. Development and characterization of microsatellite markers for Chinese bayberry (Myrica rubra Sieb. & Zucc.). Conserv Genet 2009, 10(5):1605-1607.
5. Xie XB, Qiu YY, Ke LP, Zheng XL, Wu GT, Chen JQ, Qi XJ, Ahn S. Microsatellite primers in red bayberry, myrica rubra (Myricaceae). Am J Bot 2011, 98(4):E93-E95. 10.3732/ajb.1000271, 21613157.
6. Xie R-J, Zhou J, Wang G-Y, Zhang S-M, Chen L, Gao Z-S. Cultivar identification and genetic diversity of chinese bayberry (Myrica rubra) accessions based on fluorescent SSR markers. Plant Mol Biol Rep 2011, 29(3):554-562.
7. Zhang SM, Gao ZS, Xu CJ, Chen KS. Genetic diversity of Chinese bayberry (Myrica rubra Sieb. et Zucc.) accessions revealed by Amplified Fragment Length Polymorphism. HortSci 2009, 44(2):487-491.
8. Cheng YJ, Zhang R, Zhu AD, Wang XJ, Yu J, Zhang HR, Gao JS, Deng XX. Development of Juglans regia SSR Markers by data mining of the EST database. Plant Mol Biol Rep 2010, 28(4):646-653.
9. Aravanopoulos FA, Ganopoulos IV, Avramidou E, Fasoula DA, Diamantidis G. Assessing inter- and intra-cultivar variation in Greek Prunus avium by SSR markers. Plant Genet Resour-C 2010, 8(3):242-248.
10. Audergon JM, Bourguiba H, Khadari B, Krichen L, Trifi-Farah N, Santoni S. Grafting versus seed propagated apricot populations: two main gene pools in Tunisia evidenced by SSR markers and model-based Bayesian clustering. Genetica 2010, 138(9-10):1023-1032. 2948653, 20838857.
11. Baudouin L, Martinez RT, Berger A, Dollet M. Characterization of the genetic diversity of the Tall coconut (Cocos nucifera L.) in the Dominican Republic using microsatellite (SSR) markers. Tree Genet Genomes 2010, 6(1):73-81.
12. Wu YQ, Wang YW, Samuels TD. Development of 1,030 genomic SSR markers in switchgrass. Theor Appl Genet 2011, 122(4):677-686. 10.1007/s00122-010-1477-4, 20978736.
13. Goff SA. A draft sequence of the rice genome (Oryza sativa L. ssp. japonica) (April, pg 92, 2002). Science 2005, 309(5736):879-879.
14. Wang J, Chen C, Na J-K, Yu Q, Hou S, Paull R, Moore P, Alam M, Ming R. Genome-wide comparative analyses of microsatellites in papaya. Tropical Plant Biology 2008, 1(3):278-292.
15. Schuelke M. An economic method for the fluorescent labeling of PCR fragments. Nat Biotechnol 2000, 18(2):233-234. 10.1038/72708, 10657137.
16. Nei M. Genetic Distance between Populations. Am Nat 1972, 106(949):283-292.
17. Batzoglou S, Jaffe DB, Stanley K, Butler J, Gnerre S, Mauceli E, Berger B, Mesirov JP, Lander ES. ARACHNE: A whole-genome shotgun assembler. Genome Res 2002, 12(1):177-189. 10.1101/gr.208902, 155255, 11779843.
18. Watanabe KN, Hirano R, Ishii H, Oo TH, Gilani SA, Kikuchi A. Propagation management methods have altered the genetic variability of two traditional mango varieties in Myanmar, as revealed by SSR. Plant Genet Resour-C 2011, 9(3):404-410.
19. Chen C, Zhou P, Choi Y, Huang S, Gmitter F. Mining and characterizing microsatellites from citrus ESTs. Theor Appl Genet 2006, 112(7):1248-1257. 10.1007/s00122-006-0226-1, 16474971.
20. Fraser LG, Harvey CF, Crowhurst RN, De Silva HN. EST-derived microsatellites from Actinidia species and their potential for mapping. Theor Appl Genet 2004, 108(6):1010-1016. 10.1007/s00122-003-1517-4, 15067386.
21. McCouch SR, Cho YG, Ishii T, Temnykh S, Chen X, Lipovich L, Park WD, Ayres N, Cartinhour S. Diversity of microsatellites derived from genomic libraries and GenBank sequences in rice (Oryza sativa L.). Theor Appl Genet 2000, 100(5):713-722.
22. Sosinski B, Gannavarapu M, Hager LD, Beck LE, King GJ, Ryder CD, Rajapakse S, Baird WV, Ballard RE, Abbott AG. Characterization of microsatellite markers in peach [Prunus persica (L.) Batsch]. Theor Appl Genet 2000, 101(3):421-428.
23. Cuc LM, Mace ES, Crouch JH, Quang VD, Long TD, Varshney RK. Isolation and characterization of novel microsatellite markers and their application for diversity assessment in cultivated groundnut (Arachis hypogaea). BMC Plant Biol 2008, 8.
24. Kapila RK, Yadav RS, Plaha P, Rai KN, Yadav OP, Hash CT, Howarth CJ. Genetic diversity among pearl millet maintainers using microsatellite markers. Plant Breeding 2008, 127(1):33-37.
25. Lu J, Huang H, Ren ZB, Hunter W, Dowd SE, Dang P. Mining and validating grape (Vitis L.) ESTs to develop EST-SSR markers for genotyping and mapping. Mol Breeding 2011, 28(2):241-254.
26. Feng C, Chen M, Xu CJ, Bai L, Yin XR, Li X, Allan AC, Ferguson IB, Chen KS. Transcriptomic analysis of Chinese bayberry (Myrica rubra) fruit development and ripening using RNA-Seq. BMC Genomics 2012, 13(1):19. 10.1186/1471-2164-13-19, 3398333, 22244270.
27. Han Y, Zheng D, Vimolmangkang S, Khan MA, Beever JE, Korban SS. Integration of physical and genetic maps in apple confirms whole-genome and segmental duplications in the apple genome. J Exp Bot 2011, 62(14):5117-5130. 10.1093/jxb/err215, 3193016, 21743103.
28. Xie XB, Qiu YY, Zheng XL, Qi XJ, Qiu LJ, Huang ZP, Wang T, Liang SM. Studies on the crossing between Myrica rubra and M. nana and embryo culture in vitro of hybrid F1. Journal of Fruit Science 2009, 26(4):507-510.
29. Cheng YP, Chien CT, Lin TP. Population genetics of geographically restricted and widespread species of Myrica (Myricaceae). J Hered 2000, 91(1):61-66. 10.1093/jhered/91.1.61, 10739129.
30. Erickson DL, Hamrick JL. Genetic and clonal diversity for Myrica cerifera along a spatiotemporal island chronosequence. Heredity 2003, 90(1):25-32. 10.1038/sj.hdy.6800172, 12522422.
31. Myers RM, Maniatis T, Lerman LS. Detection and localization of single base changes by denaturing gradient gel-electrophoresis. Method Enzymol 1987, 155:501-527.
32. Bassam BJ, Caetanoanolles G. Silver staining of DNA in polyacrylamide gels. Appl Biochem Biotech 1993, 42(2-3):181-188.
33. Liu KJ, Muse SV. PowerMarker: an integrated analysis environment for genetic marker analysis. Bioinformatics 2005, 21(9):2128-2129. 10.1093/bioinformatics/bti282, 15705655.
34. Hampl V, Pavlicek A, Flegr J. Construction and bootstrap analysis of DNA fingerprinting-based phylogenetic trees with the freeware program FreeTree: application to trichomonad parasites. Int J Syst Evol Micr 2001, 51:731-735.
35. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S. MEGA5: Molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 2011, 28(10):2731-2739. 10.1093/molbev/msr121, 3203626, 21546353.