Development of universal genetic markers based on single-copy orthologous (COSII) genes in Poaceae

Plant Cell Reports

Volumn 32, Issue 3, 2013, Pages 379-388

  Liu, Hailan ^a   Guo, Xiaoqin ^b   Wu, Jiasheng ^b   Chen, Guo Bo ^c   Ying, Yeqing ^b  

^a SICHUAN AGRICULTURAL UNIVERSITY   (China)

^b ZHEJIANG A F UNIVERSITY   (China)

^c UNIVERSITY OF QUEENSLAND   (Australia)

Author keywords

COSII genes; Poaceae; Polymorphism; Transferability

Indexed keywords

BRACHYPODIUM; POACEAE; SETARIA ITALICA; SORGHUM (GENUS); ZEA MAYS;

EID: 84873991861     PISSN: 07217714     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00299-012-1371-4     Document Type: Article

References (47)

1. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSIBLAST: a new generation of protein database search programs. Nucleic Acids Res 25: 3389-3402.
2. Anderson JA, Churchill GA, Autrique JE, Tanksley SD, Sorrells ME (1993) Optimizing parental selection for genetic linkage maps. Genome 36: 181-186.
3. Bagge M, Xia XC, Lubbersted T (2007) Functional markers in wheat. Curr Opin Plant Biol 10: 211-216.
4. Barkley NA, Newman ML, Wang ML, Hotchkiss MW, Pederson GA (2005) Assessment of the genetic diversity and phylogenetic relationships of a temperate bamboo collection by using transferred EST-SSR markers. Genome 48: 731-737.
5. Becker J, Heum M (1995) Barley microsatellites: allele variation and mapping. Plant Mol Biol 27: 835-845.
6. Botstein D, White RL, Skolnick M, Davis RW (1980) Construction of a genetic linkage map in man using restriction fragment length polymorphisms. Am J Hum Genet 32: 314-331.
7. Chapman MA, Chang JC, Weisman D, Kesseli RV, Burke JM (2007) Universal markers for comparative mapping and phylogenetic analysis in the Asteraceae (Compositae). Theor Appl Genet 115: 747-755.
8. Chen SL, Li DZ, Zhu GH (2006) Flora of China (Poaceae vol. 22). Science Press, Beijing.
9. Chen SY, Lin YT, Lin CW, Chen WY, Yang CH, Ku HM (2010) Transferability of rice SSR markers to bamboo. Euphytica 175: 23-33.
10. Chenna R, Sugawara H, Koike T, Lopez R, Gibson TJ, Higgins DG, Thompson JD (2003) Multiple sequence alignment with the Clustal series of program. Nucleic Acids Res 31: 3497-3500.
11. Das M, Bhattacharya S, Pal A (2005) Generation and characterization of SCARs by cloning and sequencing of RAPD products: a strategy for species-specific marker development in bamboo. Ann Bot 95: 835-841.
12. Das M, Bhattacharya S, Basak J, Pal A (2007) Phylogenetic relationships among the bamboo species as revealed by morphological characters and polymorphism analyses. Biol Plantarum 51: 667-672.
13. Doyle JJ, Doyle JL (1987) A rapid isolation procedure for small quantities of fresh leaf materials. Phytochem Bull 19: 11-15.
14. Friar E, Kochert G (1994) A study of genetic variation and evolution of Phyllostachys (Bambusoideae: Poaceae) using nuclear restriction fragment length polymorphisms. Theor Appl Genet 89: 265-270.
15. Ganal MW, Altmann T, Roder MS (2009) SNP identification in crop plants. Curr Opin Plant Biol 12: 211-217.
16. Gui YJ, Wang S, Quan LY, Zhou CP, Long SB, Zheng HJ, Jin L, Zhang XY, Ma NX, Fan LJ (2007) Genome size and sequence composition of moso bamboo: a comparative study. Sci China C Life Sci 50: 1-6.
17. Kowalski SP, Lan TH, Feldmann KA, Paterson AH (1994) Comparative mapping of Arabidopsis thaliana and Brassica oleracea chromosomes reveals islands of conserved organization. Genetics 138: 499-510.
18. Lin XC, Ruan XS, Lou YF, Guo XQ, Fang W (2009) Genetic similarity among cultivars of Phyllostachys pubescens. Plant Syst Evol 277: 67-73.
19. Lin LF, Tang HB, Compton RO, Lemke C, Rainville LK, Wang X, Rong J, Rana MK, Paterson AH (2011) Comparative analysis of Gossypium and Vitis genomes indicates genome duplication specific to the Gossypium lineage. Genomics 97: 313-320.
20. Liu HL, Lin YA, Chen GB, Shen YO, Liu J, Zhang SZ (2012) Genome-scale identification of resistance gene analogs and the development of their intron length polymorphism markers in maize. Mol Breed 29: 437-447.
21. Mohan M, Nair S, Bhagwat A, Krishna TG, Yano M, Bhatia CR, Sasaki T (1997) Genome mapping, molecular markers and marker-assisted selection in crop plants. Mol Breed 3: 87-103.
22. Mukherjee AK, Ratha S, Dhar S, Debata AK, Acharya PK, Mandal S, Panda PC, Mahapatra AK (2010) Genetic relationships among 22 taxa of bamboo revealed by ISSR and EST-based random primers. Biochem Genet 48: 1015-1025.
23. Nayak A, Rout GR, Das P (2003) Evaluation of the genetic variability in bamboo using RAPD markers. Plant Soil Environ 49: 24-28.
24. Nicholas KB, Nicholas HB (1997) GeneDoc: a tool for editing and annotating multiple sequence alignments. http://www. nrbsc. org/gfx/genedoc/index. html.
25. Peleman JD, van der Voort JR (2003) Breeding by design. Trends Plant Sci 8: 330-334.
26. Qiu LJ, Guo Y, Li Y, Wang XB, Zhou GA, Liu ZX, Zhou SR, Li XH, Ma YZ, Wang JK, Wan JM (2011) Novel gene discovery of crops in China: status, challenging, and perspective. Acta Agronomica Sinica 37: 1-17.
27. Quraishi UM, Abrouk M, Bolot S, Pont C, Throude M, Guilhot N, Confolent C, Bortolini F, Praud S, Murigneux A, Charmet G, Salse J (2009) Genomics in cereals: from genome-wide conserved orthologous set (COS) sequences to candidate genes for trait dissection. Funct Integr Genomics 9: 473-484.
28. Rohlf FJ (2000) NTSYS-pc: Numerical taxonomy and multivariate analysis system, version 2. 10e. Exeter Software, Setauket, New York.
29. Sharma RK, Gupta P, Sharma V, Sood A, Mohapatra T, Ahuja PS (2008) Evaluation of rice and sugarcane SSR markers for phylogenetic and genetic diversity analyses in bamboo. Genome 51: 91-103.
30. Sharma V, Bhardwaj P, Kumar R, Sharma RK, Sood A, Ahuja PS (2009) Identification and cross-species amplification of EST derived SSR markers in different bamboo species. Conserv Genet 10: 721-724.
31. Sun X, Cao Y, Yang Z, Xu C, Li X, Wang S, Zhang Q (2004) Xa26, a gene conferring resistance to Xanthomonas oryzae pv. oryzae in rice, encodes an LRR receptor kinase-like protein. Plant J 37: 517-527.
32. Sungkaew S, Stapleton CMA, Salamin N, Hodkinson TR (2009) Non-monophyly of the woody bamboos (Bambuseae; Poaceae): a multi-gene region phylogenetic analysis of Bambusoideae s. s. J Plant Res 122: 95-108.
33. Svenning S, Lamark T, Krause K, Johansen T (2011) Plant NBR1 is a selective autophagy substrate and a functional hybrid of the mammalian autophagic adapters NBR1 and p62/SQSTM1. Autophagy 7: 993-1010.
34. Tang HB, Bowers JE, Wang XY, Ming R, Alam M, Paterson AH (2008) Synteny and collinearity in plant genomes. Science 320: 486-488.
35. Tang DQ, Lu JJ, Fang W, Zhang S, Zhou MB (2010) Development, characterization and utilization of GenBank microsatellite markers in Phyllostachys pubescens and related species. Mol Breed 25: 299-311.
36. Vos P, Hogers R, Bleeker M, Reijans M, van de Lee T, Hornes M, Frijters A, Pot J, Peleman J, Kuiper M, Zabeau Marc (1995) AFLP: a new technique for DNA fingerprinting. Nucleic Acids Res 23: 4407-4414.
37. Wang XS, Zhao XQ, Zhu J, Wu WR (2005) Genome-wide investigation of intron length polymorphisms and their potential as molecular markers in rice (Oryza sativa L.). DNA Res 12: 417-427.
38. Williams JGK, Kubelik AR, Livak KJ, Rafalski JA, Tingey SV (1990) DNA polymorphism amplified by arbitrary primers are useful as genetic markers. Nucleic Acids Res 18: 6531-6535.
39. Wu FN, Muller LA, Crouzillat D, Petiard V, Tanksley SD (2006) Combining bioinformatics and phylogenetics to identify large sets of single-copy orthologous genes (COSII) for comparative, evolutionary and systematic studies: a test case in the euasterid plant clade. Genetics 174: 1407-1420.
40. Wu FN, Eannetta NT, Xu YM, Durrett R, Mazourek M, Jahn MM, Tanksley SD (2009a) A COSII genetic map of the pepper genome provides a detailed picture of synteny with tomato and new insights into recent chromosome evolution in the genus Capsicum. Theor Appl Genet 118: 1279-1293.
41. Wu FN, Eannetta NT, Xu YM, Tanksley SD (2009b) A detailed synteny map of the eggplant genome based on conserved ortholog set II (COSII) markers. Theor Appl Genet 118: 927-935.
42. Wu FN, Eannetta NT, Xu YM, Plieske J, Ganal M, Pozzi C, Bakaher N, Tanksley SD (2010) COSII genetic maps of two diploid Nicotiana species provide a detailed picture of synteny with tomato and insights into chromosome evolution in tetraploid N. tabacum. Theor Appl Genet 120: 809-827.
43. Xu SB, Tao YF, Yang ZQ, Chu JY (2002) A simple and rapid methods used for silver staining and gel preservation. Hereditas (Beijing) 24: 335-336.
44. Yan WH, Wang P, Chen HX, Zhou HJ, Li QP, Wang CR, Ding ZH, Zhang YS, Yu SB, Xing YZ, Zhang QF (2011) A major QTL, Ghd8, plays pleiotropic roles in regulating grain productivity, plant height, and heading date in rice. Mol Plant 4: 319-330.
45. Yang Z, Sun X, Wang S, Zhang Q (2003) Genetic and physical mapping of a new gene for bacterial blight resistance in rice. Theor Appl Genet 106: 1467-1472.
46. Yang L, Jin GL, Zhao XQ, Zheng Y, Xu ZH, Wu WR (2007) PIP: a database of potential intron polymorphism markers. Bioinformatics 23: 2174-2177.
47. Zhang S, Tang DQ (2007) A review on application of DNA marker in bamboos and its limits. J Bamboo Res 26: 10-14.