Identification, evaluation, and application of the genomic-SSR loci in ramie

• Autorzy: Luan M.-B. , Yang Z.-M. , Zhu J.-J. , Deng X. , Liu C.-C. , Wang X.-F. , Xu Y. , Sun Z.-M. , Chen J.-H.
• Języki publikacji: EN

Abstrakty

EN

To provide a theoretical and practical foundation for ramie genetic analysis, simple sequence repeats (SSRs) were identified in the ramie genome and employed in this study. From the 115 369 sequences of a specific-locus amplified fragment library, a type of reduced representation library obtained by high-throughput sequencing, we identified 4774 sequences containing 5064 SSR motifs. SSRs of ramie included repeat motifs with lengths of 1 to 6 nucleotides, and the abundance of each motif type varied greatly. We found that mononucleotide, dinucleotide, and trinucleotide repeat motifs were the most prevalent (95.91%). A total of 98 distinct motif types were detected in the genomic-SSRs of ramie. Of them, The A/T mononucleotide motif was the most abundant, accounting for 41.45% of motifs, followed by AT/TA, accounting for 20.30%. The number of alleles per locus in 31 polymorphic microsatellite loci ranged from 2 to 7, and observed and expected heterozygosities ranged from 0.04 to 1.00 and 0.04 to 0.83, respectively. Furthermore, molecular identity cards (IDs) of the germplasms were constructed employing the ID Analysis 3.0 software. In the current study, the 26 germplasms of ramie can be distinguished by a combination of five SSR primers including Ibg5-5, Ibg3-210, Ibg1-11, Ibg6-468, and Ibg6-481. The allele polymorphisms produced by all SSR primers were used to analyze genetic relationships among the germplasms. The similarity coefficients ranged from 0.41 to 0.88. We found that these 26 germplasms were clustered into five categories using UPGMA, with poor correlation between germplasm and geographical distribution. Our study is the first large-scale SSR identification from ramie genomic sequences. We have further studied the SSR distribution pattern in the ramie genome, and proposed that it is possible to develop SSR loci from genomic data for population genetics studies, linkage mapping, quantitative trait locus mapping, cultivar fingerprinting, and as genetic diversity studies.

• Wydawca: -
• Czasopismo: Acta Societatis Botanicorum Poloniae
• Rocznik: 2016
• Tom: 85
• Numer: 3
• Opis fizyczny: Article 3510 [12p.], fig.,ref.

Twórcy

autor

Luan M.-B.

• Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences/Key laboratory of Stemfiber Biomass and Engineering Microbiology, Ministry of Agriculture, 348 West Xianjiahu Road, Changsha, Hunan, China

autor

Yang Z.-M.

• Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences/Key laboratory of Stemfiber Biomass and Engineering Microbiology, Ministry of Agriculture, 348 West Xianjiahu Road, Changsha, Hunan, China

autor

Zhu J.-J.

• Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences/Key laboratory of Stemfiber Biomass and Engineering Microbiology, Ministry of Agriculture, 348 West Xianjiahu Road, Changsha, Hunan, China

autor

Deng X.

• Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences/Key laboratory of Stemfiber Biomass and Engineering Microbiology, Ministry of Agriculture, 348 West Xianjiahu Road, Changsha, Hunan, China

autor

Liu C.-C.

• Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences/Key laboratory of Stemfiber Biomass and Engineering Microbiology, Ministry of Agriculture, 348 West Xianjiahu Road, Changsha, Hunan, China

autor

Wang X.-F.

• Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences/Key laboratory of Stemfiber Biomass and Engineering Microbiology, Ministry of Agriculture, 348 West Xianjiahu Road, Changsha, Hunan, China

autor

Xu Y.

• Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences/Key laboratory of Stemfiber Biomass and Engineering Microbiology, Ministry of Agriculture, 348 West Xianjiahu Road, Changsha, Hunan, China

autor

Sun Z.-M.

• Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences/Key laboratory of Stemfiber Biomass and Engineering Microbiology, Ministry of Agriculture, 348 West Xianjiahu Road, Changsha, Hunan, China

autor

Chen J.-H.

• Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences/Key laboratory of Stemfiber Biomass and Engineering Microbiology, Ministry of Agriculture, 348 West Xianjiahu Road, Changsha, Hunan, China

Bibliografia

• 1. Xiong HP. Ma lei zuo wu yu zhong xue [Bast-fiber crops breeding]. Beijing: China Agricultural Science and Technology Press; 2008.
• 2. Luan MB, Zou ZZ, Zhu JJ. Development of a core collection for ramie by heuristic search based on SSR markers. Biotechnol Biotechnol Equip. 2014;28:798–804. http://dx.doi.org/10.1080/13102818.2014.953768
• 3. Zhu TT, Yu CM, Wang YZ. Preliminary evaluation on nutritional value for ramie [Boehmeria nivea (L.) Gaud.] Zhongzhu No. 1 and Zhongzhu No. 2. Plant Fiber Scinence in China. 2014;36(3):113–121.
• 4. Kaur S, Panesar PS, Bera MB, Kaur V. Simple sequence repeat markers in genetic divergence and marker-assisted selection of rice cultivars: a review. Crit Rev Food Sci Nutr. 2015;55:41–49. http://dx.doi.org/10.1080/10408398.2011.646363
• 5. Zhang DD, Hua YP, Wang XH, Zhao H, Shi L. A high-density genetic map identifies a novel major QTL for boron efficiency in oilseed rape (Brassica napus L.). PLoS One. 2014;9:e112089. http://dx.doi.org/10.1371/journal.pone.0112089
• 6. Kalia RK, Rai MK, Kalia S, Singh R, Dhawan AK. Microsatellite markers: an overview of the recent progress in plants. Euphytica. 2011;177:309–334. http://dx.doi.org/10.1007/s10681-010-0286-9
• 7. Powell W, Machray GC, Provan J. Polymorphism revealed by simple sequence repeats. Trends Plant Sci. 1996;1:215–222. http://dx.doi.org/10.1016/S1360-1385(96)86898-0
• 8. Zhang XW, Ye ZW, Wang TK, Xiong HR, Yuan XL. Characterization of the global transcriptome for cotton (Gossypium hirsutum L.) anther and development of SSR marker. Gene. 2014;551:206–213. http://dx.doi.org/10.1016/j.gene.2014.08.058
• 9. Singh R, Kumar S, Kashyap PL, Srivastava AK, Mishra S. Identification and characterization of microsatellite from Alternaria brassicicola to assess cross-species transferability and utility as a diagnostic marker. Mol Biotechnol. 2014;56:1049–1059. http://dx.doi.org/10.1007/s12033-014-9784-7
• 10. Wang XL, Xu F, Li L, Zhang YP, Ding YD. Development of 39 novel polymorphic microsatellite markers for the giant mottled eel Anguilla marmorata and cross-amplification in other eel species. Conserv Genet Resour. 2014;6:865–871. http://dx.doi.org/10.1007/s12686-014-0227-3
• 11. Noakes AG, Best T, Staton ME, Koch J, Romero-Severson J. Cross amplification of 15 EST-SSR markers in the genus Fraxinus. Conserv Genet Resour. 2014;6:969–970. http://dx.doi.org/10.1007/s12686-014-0260-2
• 12. Zhang Y, Dai SL, Hong Y, Song XB. Application of genomic SSR locus polymorphisms on the identification and classification of chrysanthemum cultivars in China. PLoS One. 2014;9:e104856. http://dx.doi.org/10.1371/journal.pone.0104856
• 13. Lei YT, Zhao YY, Yu F, Li Y, Dou QW. Development and characterization of 53 polymorphic genomic-SSR markers in Siberian wildrye (Elymus sibiricus L.). Conserv Genet Resour. 2014;6:861–864. http://dx.doi.org/10.1007/s12686-014-0225-5
• 14. Luo R, Wu WL, Zhang Y, Li YH. SSR marker and its application to crop genetics and breeding. Genomics Appl Biol. 2010;29:137–143.
• 15. Liu G, Zhang DQ, Xie YJ, Gu ZJ, Zhang HY. Rapid screening and transferability analysis of genomic-SSR and EST-SSR primers in eucalypt. Scientia Silvae Sinicae. 2013;49:127–133.
• 16. Chen JH, Luan MB, Song SF. Isolation and characterization of EST-SSRs in the ramie. Afr J Microbiol Res. 2011;5:3504–3508.
• 17. Liu TM, Zhu SY, Fu LL. Development and characterization of 1827 expressed sequence tag-derived simple sequence repeat markers in ramie (Boehmeria nivea L. Gaud). PLoS One. 2013;8:e60346. http://dx.doi.org/10.1371/journal.pone.0060346
• 18. Jiang YB, J YC, Zhou JL. Isolation and characterization of microsatellites from ramie [Boehmeria nivea (L.) Gaud.]. Acta Agronomica Sinica. 2007;33:158–162.
• 19. Guan L, Zhang Z, Wang XW, Xue HB. Evaluation and application of the SSR loci in apple genome. Scientia Agricultura Sinica. 2011;44:4415–4428.
• 20. Ibrahim C, Visam G, Jens A, Sami D, Anne F. Development of genomic simple sequence repeat markers in opium poppy by next-generation sequencing. Mol Breed. 2014;34:323–334. http://dx.doi.org/10.1007/s11032-014-0036-0
• 21. Sun XW, Liu DY, Zhang XF, Li WB, Liu H. SLAF-seq: an efficient method of large-scale de novo SNP discovery and genotyping using high-throughput sequencing. PLoS One. 2013;8:e58700. http://dx.doi.org/10.1371/journal.pone.0058700
• 22. van Bakel H, Stout JM, Cote AG, Tallon CM, Sharpe AG .The draft genome and transcriptome of Cannabis sativa. Genome Biol. 2011;12:R102. http://dx.doi.org/10.1186/gb-2011-12-10-r102
• 23. Zhang J, Wu YT, Guo WZ. Fast screening of microsatellite markers in cotton with page/silver staining. Acta Gossypii Sinica. 2000;12:267–269.
• 24. Yeh FC, Yang RC, Boyle T. POPGENE version 1.31. Quick user guide. Edmonton, AB: University of Alberta and Center for International Forestry Research; 1999.
• 25. Rohlf FJ. NTSYSpc. Numerical Taxonomy and Multivariate Analysis System. Version 2.1. New York, NY: Applied Biostatistics Inc., Exeter Software; 2000.
• 26. Cai B, Li CH, Yao QH, Zhou J, Tao JM, Zhang Z. Analysis of SSRs in grape genome and development of SSR database. Journal of Nanjing Agricultural University. 2009;32:28–32.
• 27. Tóth G, Gáspári Z, Jurka J. Microsatellites in different eukaryotic genomes: survey and analysis. Genome Res. 2000;10:967–981. http://dx.doi.org/10.1101/gr.10.7.967
• 28. Li CY, Li JB, Zhou XG, Dong AR, Xu MH. Frequency and distribution of microsatellites in the whole genome of rice blast fungus, Magnaporthe grisea. Chinese Journal of Rice Science. 2004;18:269–273.
• 29. Haraoglu H, Lee CM, Meyer W. Survey of simple sequence repeats in complete fungal genomes. Mol Biol Evol. 2005;22:639–649. http://dx.doi.org/10.1093/molbev/msi057
• 30. Lu JB, Li JQ, Lu J, Zhan QW. Design of SSR primers and verification of e-PCR in non-coding regions of sorghum genome. Seed. 2010;29:1–6.
• 31. Gao YM, Han YQ, Tang H, Sun DM, Wang YJ, Wang WD. Analysis of simple sequence repeats in rhizobium genome. Scientia Agricultura Sinica. 2008;41:2992–2998.
• 32. Sia EA, Kokoska RJ, Dominska M, Greenwell P, Petes TD. Microsatellite instability in yeast: dependence on repeat unit size and DNA mismatch repair genes. Mol Cell Biol. 1997;17:2851–2858. http://dx.doi.org/10.1128/MCB.17.5.2851
• 33. Harry B, Schlötterer C. Long microsatellite alleles in Drosophila melanogaster have a downward mutation bias and short persistence times, which cause their genome-wide under representation. Genetics. 2000;155:1213–1220.
• 34. Xu Y, Chen JH, Li Y. Development of EST-SSR and genomic-SSR in Chinese fir. Journal of Nanjing Forestry University. 2014;38:9–14.
• 35. Zhang H, Wang XM, Wang DJ. Survey of SSRs in foxtail millet genome and development of SSR markers. Mol Plant Breed. 2013;11:30–36.
• 36. Braulio J, Rodrigo AC, Gabriela AA. Identifying novel polymorphic microsatellites from cultivated flax (Linum usitatissimum L.) following data mining. Plant Mol Biol Report. 2011;29:753–759. http://dx.doi.org/10.1007/s11105-010-0270-5
• 37. Schorderet DF, Gartler SM. Analysis of CpG suppression inmethylated and nonmethylated species. Proc Natl Acad Sci USA. 1992;89:957–961. http://dx.doi.org/10.1073/pnas.89.3.957
• 38. Morgante M, Hanafey M, Powell W. Microsatellites are preferentially associated with nonrepetitive DNA in plant genome. Nat Genet. 2002;30:194–200. http://dx.doi.org/10.1038/ng822
• 39. Lee SB, Kaittanis C, Jansen RK, Hosterler JB, Tallon LJ, Town CD, et al. The complete chloroplast genome sequence of Gossypium hisutum: organization and phylogenetic relationships to other angiosperms. BMC Genomics. 2006;7:61–72. http://dx.doi.org/10.1186/1471-2164-7-61
• 40. Shang MZ, Liu F, Hua JP, Wang KB. Analysis on codon usage of chloroplast genome of Gossypium hirsutum. Scientia Agricultura Sinica. 2011;44:245–253.
• 41. Yin TM, Zhang XY, Gunter LE. Microsatellite primer resource for Populus developed from the mapped sequence scaffolds of the nisqually-1 genome. New Phytol. 2009;181:498–503. http://dx.doi.org/10.1111/j.1469-8137.2008.02663.x
• 42. Cavagnaro PF, Senalik DA, Yang LM. Genome-wide characterization of simple sequence repeats in cucumber (Cucumis sativus L.). BMC Genomics. 2010;11:569. http://dx.doi.org/10.1186/1471-2164-11-569
• 43. Qi Z, Huang L, Zhu R, Xin D, Liu C. A high-density genetic map for soybean based on specific length amplified fragment sequencing. PLoS One. 2014;9:e104871. http://dx.doi.org/10.1371/journal.pone.0104871
• 44. Li B, Tian L, Zhang JY. Construction of a high-density genetic map based on large-scale markers developed by specific length amplified fragment sequencing (SLAF-seq) and its application to QTL analysis for isoflavone content in glycine max. BMC Genomics. 2014;15:1086. http://dx.doi.org/10.1186/1471-2164-15-1086
• 45. Sangwan I, Obrian MR. Identification of a soybean protein that interacts with GAGA element dinucleotide repeat DNA. Plant Physiol. 2002;129:1788–1794. http://dx.doi.org/10.1104/pp.002618

Identyfikatory

DOI

10.5586/asbp.3510