Development and use of genic molecular markers (GMMs) for construction of a transcript map of chickpea (Cicer arietinum L.)
详细信息 查看全文
- 作者：Neha Gujaria (1) (2)
Ashish Kumar (1)
Preeti Dauthal (1)
Anuja Dubey (1)
Pavana Hiremath (1)
A. Bhanu Prakash (1)
Andrew Farmer (3)
Mangla Bhide (2)
Trushar Shah (1)
Pooran M. Gaur (1)
Hari D. Upadhyaya (1)
Sabhyata Bhatia (4)
Douglas R. Cook (5)
Greg D. May (3)
Rajeev K. Varshney (1) (6) - 刊名：Theoretical and Applied Genetics
- 出版年：2011
- 出版时间：May 2011
- 年：2011
- 卷：122
- 期：8
- 页码：1577-1589
- 全文大小：502KB
- 参考文献：1. Alderborn A, Kristofferson A, Hammerling U (2000) Determination of single-nucleotide polymorphisms by real-time pyrophosphate DNA sequencing. Genome Res 10:1249-258 CrossRef
2. Andersen JR, Lübberstedt T (2003) Functional markers in plants. Trends Plant Sci 8:554-60 CrossRef
3. Arumuganathan K, Earle ED (1991) Estimation of nuclear DNA content of plants by some important plant species. Plant Mol Biol Rep 9:208-18 CrossRef
4. Borevitz JO, Liang D, Plouffe D, Chang HS, Zhu T, Weigel D, Berry CC, Winzeler E, Chory J (2003) Large-scale identification of single-feature polymorphisms in complex genomes. Genome Res 13:513-23 CrossRef
5. Bryan GJ, Stephenson P, Collins A, Kirby J, Smith JB, Gale MD (1999) Low levels of DNA sequence variation among adapted genotypes of hexaploid wheat. Theor Appl Genet 99:192-98 CrossRef
6. Buhariwalla HK, Jayashree B, Eshwar K, Crouch JH (2005) Development of ESTs from chickpea roots and their use in diversity analysis of the / Cicer genus. BMC Plant Biol 5:16 CrossRef
7. Ching A, Rafalski A (2002) Rapid genetic mapping of ESTs using SNP pyrosequencing and indel analysis. Cell Mol Biol Lett 7:803-10
8. Choi IY, Hyten DL, Matukumalli LK, Song Q, Chaky JM, Quigley CV, Chase K, Lark KG, Reiter RS, Yoon MS, Hwang EY, Yi SI, Young ND, Shoemaker RC, van Tassel CP, Specht JE, Cregan PB (2007) A soybean transcript map: gene distribution, haplotype and single-nucleotide polymorphism analysis. Genetics 176:685-96 CrossRef
9. Choudhary S, Sethy NK, Shokeen BA, Bhatia S (2006) Development of sequence-tagged microsatellite site markers for chickpea ( / Cicer arietinum L.). Mol Ecol Notes 6:3-5 CrossRef
10. Choudhary S, Sethy NK, Shokeen BA, Bhatia S (2009) Development of chickpea EST-SSR markers and analysis of allelic variation across related species. Theor Appl Genet 118:591-08 CrossRef
11. Cuc LM, Mace E, Crouch J, Quang VD, Long TD, Varshney RK (2008) Isolation and characterization of novel microsatellite markers and their application for diversity assessment in cultivated groundnut ( / Arachis hypogaea). BMC Plant Biol 8:55 CrossRef
12. Fan JB, Oliphant A, Shen R, Kermani BG, Garcia F, Gunderson KL, Hansen M, Steemers F, Butler SL, Deloukas P, Galver L, Hunt S, Mcbride C, Bibikova M, Rubano T, Chen J, Wickham E, Doucet D, Chang W, Campbell D, Zhang B, Kruglyak S, Bentley D, Haas J, Rigault P, Zhou L, Stuelpnagel J, Chee MS (2003) Highly parallel SNP genotyping. Cold Spring Harb Symp Quant Biol 68:69-8 CrossRef
13. Feltus FA, Singh HP, Lohithaswa HC, Schulze SR, Silva TD, Paterson AH (2006) A comparative genomics strategy for targeted discovery of single-nucleotide polymorphisms and conserved-noncoding sequences in orphan crops. Plant Physiol 140:1183-191 CrossRef
14. Gaitán-Solís E, Choi IY, Quigley C, Cregan P, Tohme J (2008) Single nucleotide polymorphisms in common bean: their discovery and genotyping using a multiplex detection system. Plant Genome 1:125-34 CrossRef
15. Gil J, Nadal S, Luna D, Moreno MT, De Haro A (1996) Variability of some physico-chemical characters in Desi and Kabuli chickpea types. J Sci Food Agric 71:179-84 CrossRef
16. Gupta PK, Rustgi S (2004) Molecular markers from the transcribed/expressed region of the genome in higher plants. Funct Integr Genomics 4:139-62 CrossRef
17. Gupta PK, Varshney RK (2000) The development and use of microsatellite markers for genetic analysis and plant breeding with emphasis on bread wheat. Euphytica 113:163-85 CrossRef
18. Hüttel B, Winter P, Weising K, Choumane W, Weigand F (1999) Sequence-tagged microsatellite site markers for chickpea ( / Cicer arietinum L.). Genome 42:210-17
19. Hyten DL, Song O, Fickus EW, Quigley CV, Lim JS, Choi IY, Hwang EY, Pastor Corrales M, Cregan PB (2010) High-throughput SNP discovery and assay development in common bean. BMC Genomics 11:475 CrossRef
20. Ibrikci H, Knewtson SJB, Grusak MA (2003) Chickpea leaves as a vegetable green for humans: evaluation of mineral composition. J Sci Food Agric 83:945-50 CrossRef
21. Jayashree B, Bhanuprakash A, Jami A, Reddy SP, Nayak S, Varshney RK (2009) Perl module and PISE wrappers for the integrated analysis of sequence data and SNP features. BMC Res Notes 2:92 CrossRef
22. Kosambi DD (1944) The estimation of map distance from recombination values. Ann Eugen 12:172-75 CrossRef
23. Kota R, Varshney RK, Prasad M, Zhang H, Stein N, Graner A (2008) EST-derived single nucleotide polymorphism markers for assembling genetic and physical maps of the barley genome. Funct Integr Genomics 8:223-33 CrossRef
24. Lander ES, Green P, Abrahamson J, Barlow A, Daley M, Lincoln S, Newburg L (1987) MAPMAKER: an interactive computer package for constructing primary genetic linkage maps of experimental and natural populations. Genomics 1:174-81 CrossRef
25. Lichtenzveig J, Scheuring C, Dodge J, Abbo S, Zhang HB (2005) Construction of BAC and BIBAC libraries and their applications for generation of SSR markers for genome analysis of chickpea, / Cicer arietinum L. Theor Appl Genet 110:492-10 CrossRef
26. Millan T, Winter P, Jungling R, Gil J, Rubio J, Cho S, Cobos MJ, Iruela M, Rajesh PN, Tekeoglu M, Kahl G, Muehlbauer FJ (2010) A consensus genetic map of chickpea ( / Cicer arietinum L.) based on 10 mapping populations. Euphytica 175:175-89 CrossRef
27. Muchero W, Diop NN, Bhat PR, Fenton RD, Wanamaker S, Pottorff M, Hearne S, Cisse N, Fatokun C, Ehlers JD, Roberts PA, Close TJ (2009) A consensus genetic map of cowpea [ / Vigna unguiculata (L) Walp.] and synteny based on EST-derived SNPs. Proc Natl Acad Sci USA 106:18159-8164 CrossRef
28. Nasu S, Suzuki J, Ohta R, Hasegawa K, Yui R, Kitazawa N, Monna L, Minobe Y (2002) Search for and analysis of single nucleotide polymorphisms (SNPs) in rice ( / Oryza sativa, / Oryza rufipogon) and establishment of SNP markers. DNA Res 9:163-71 CrossRef
29. Nayak SN, Zhu H, Varghese N, Datta S, Choi H-K, Horres R, Jüngling R, Singh J, Kavi Kishor PB, Sivaramakrihnan S, Hoisington DA, Kahl G, Winter P, Cook DR, Varshney RK (2010) Integration of novel SSR and gene-based SNP marker loci in the chickpea genetic map and establishment of new anchor points with / Medicago truncatula genome. Theor Appl Genet 120:1415-441 CrossRef
30. Nelson M, Phan H, Ellwood S, Moolhuijzen P, Hane J, Williams A, O’Lone C, Fosu-Nyarko J, Scobie M, Cakir M, Jones M, Bellgard M, Ksiazkiewicz M, Wolko B, Barker S, Oliver R, Cowling W (2006) The first gene-based map of / Lupinus angustifolius L.—location of domestication genes and conserved synteny with / Medicago truncatula. Theor Appl Genet 113:225-38 CrossRef
31. Ooijen Van (2006) JoinMap? 4: software for the calculation of genetic linkage maps in experimental populations. Kyazma B.V., Wageningen, The Netherlands
32. Pfaff T, Kahl G (2003) Mapping of gene-specific markers on the genetic map of chickpea ( / Cicer arietinum L.). Mol Genet Genomics 269:243-51
33. Qi LL, Echalier B, Chao S, Lazo GR, Butler GE, Anderson OD, Akhunov ED, Dvorak J, Linkiewicz AM, Ratnasiri A, Bermudez-Kandianis J, Dubcovsky CE, Greene RA, Kantety R, La Rota CM, Munkvold JD, Sorrells SF, Sorrells ME, Dilbirligi M, Sidhu D, Erayman M, Randhawa HS, Sandhu D, Bondareva SN, Gill KS, Mahmoud AA, Ma, Miftahudin XF, Gustafson JP, Conley EJ, Nduati V, Gonzalez Hernandez JL, Anderson JA, Peng JH, Lapitan NLV, Hossain KG, Kalavacharla V, Kianian SF, Pathan MS, Zhang DS, Nguyen HT, Choi DW, Fenton RD, Close TJ, McGuire PE, Qualset CO, Gill BS (2004) A chromosome bin map of 16,000 expressed sequence tag loci and distribution of genes among the three genomes of polyploid wheat. Genetics 168:701-12 CrossRef
34. Radhika P, Gowda SJM, Kadoo NY, Mhase LB, Jamadagni BM, Sainani MN, Chandra S, Gupta VS (2007) Development of an integrated intraspecific map of chickpea ( / Cicer arietinum L.) using two recombinant inbred line populations. Theor Appl Genet 115:209-16 CrossRef
35. Rafalski JA (2002) Novel genetic mapping tools in plants SNPs and LD-based approaches. Plant Sci 162:329-33 CrossRef
36. Rajesh PN, Muehlbauer FJ (2008) Discovery and detection of single nucleotide polymorphism (SNP) in coding and genomic sequences in chickpea ( / Cicer arietinum L.). Euphytica 162:291-00 CrossRef
37. Raju NL, Gnanesh BN, Lekha P, Jayashree B, Pande S, Hiremath PJ, Byregowda M, Singh NK, Varshney RK (2010) The first set of EST resource for gene discovery and marker development in pigeonpea ( / Cajanus cajan L.). BMC Plant Biol 10:45 CrossRef
38. Rodi CP, Darnhofer PB, Stanssens P, Zabeau M, van den Boom D (2002) A strategy for the rapid discovery of disease markers using the MassARRAY system. BioTechniques 32:62-9
39. Rostoks N, Ramsay L, Mackenzie K, Cardle L, Bhat PR, Roose ML, Svensson JT, Stein N, Varshney RK, Marshall DF, Graner A, Close TJ, Waugh R (2006) Recent history of artificial outcrossing facilitates whole-genome association mapping in elite inbred crop varieties. Proc Natl Acad Sci USA 103:18656-8661 CrossRef
40. Sato K, Nankaku N, Takeda K (2009) A high-density transcript linkage map of barley derived from a single population. Heredity 103:110-17 CrossRef
41. Sethy N, Shokeen B, Edwards K, Bhatia S (2006) Development of microsatellite markers and analysis of intraspecific genetic variability in chickpea ( / Cicer arietinum L.). Theor Appl Genet 112:1416-428 CrossRef
42. Singh A, Singh IK, Verma PK (2008) Differential transcript accumulation in / Cicer arietinum L. in response to a chewing insect / Helicoverpa armigera and defence regulators correlate with reduced insect performance. J Exp Bot 59:2379-392 CrossRef
43. Stein N, Prasad M, Scholz U, Thiel T, Zhang H, Wolf M, Kota R, Varshney RK, Perovic D, Grosse I, Graner A (2007) A 1,000-loci transcript map of the barley genome: new anchoring points for integrative grass genomics. Theor Appl Genet 114:823-39 CrossRef
44. Thiel T, Kota R, Grosse I, Stein N, Graner A (2004) SNP2CAPS: a SNP and INDEL analysis tool for CAPS marker development. Nucleic Acids Res 32:e5 CrossRef
45. Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22:4673-680 CrossRef
46. Thudi M, Senthilvel S, Bottley A, Hash CT, Reddy AR, Feltus AF, Paterson AH, Hoisington DA, Varshney RK (2010) A comparative assessment of the utility of PCR-based marker systems in pearl millet. Euphytica 174:253-60 CrossRef
47. Varshney RK (2010) Gene-based marker systems in plants: high throughput approaches for discovery and genotyping. In: Jain SM, Brar DS (eds) Molecular techniques in crop improvement. Springer, The Netherlands, pp 119-42 CrossRef
48. Varshney RK, Graner A, Sorrells ME (2005a) Genomics-assisted breeding for crop improvement. Trends Plant Sci 10:621-30 CrossRef
49. Varshney RK, Graner A, Sorrells ME (2005b) Genic microsatellite markers in plants: features and applications. Trends Biotechnol 23:48-5 CrossRef
50. Varshney RK, Nayak S, Jayashree B, Eshwar K, Upadhyaya HD, Hoisington DA (2007) Development of cost-effective SNP assays for chickpea genome analysis and breeding. SAT eJournal 3:1-
51. Varshney RK, Thiel T, Sretenovic-Rajicic T, Baum M, Valkoun J, Guo P, Grando S, Ceccarelli S, Graner A (2008) Identification and validation of a core set of informative genic SSR and SNP markers for assaying functional diversity in barley. Mol Breed 22:1-3 CrossRef
52. Varshney RK, Hiremath P, Lekha P, Kashiwagi J, Balaji J, Deokar AA, Vadez V, Srinivasan R, Xiao Y, Gaur PM, Siddique KHM, Town CD, Hoisington DA (2009a) A comprehensive resource of drought- and salinity-responsive ESTs for gene discovery and marker development in chickpea ( / Cicer arietinum L.). BMC Genomics 10:523 CrossRef
53. Varshney RK, Hoisington DA, Nayak SN, Graner A (2009b) Molecular plant breeding: methodology and achievements. In: Somers D, Langridge P, Gustafson PJ (eds) Plant genomics: methods and protocols. The Humana Press, Totowa, pp 283-04
54. Voorips RE (2002) Mapchart: software for the graphical presentation of linkage maps and QTLs. J Hered 93:77-8 CrossRef
55. Winter P, Pfaff T, Udupa SM, Hüttel B, Sharma PC, Sahi S, Arrequin-Espinoza R, Weigand F, Muehlbauer FJ, Kahl G (1999) Characterization and mapping of sequence-tagged microsatellite sites in the chickpea ( / C. arietinum L.). Mol Gen Genet 262:90-01 CrossRef
56. Winter P, Benko-Iseppon AM, Hüttel B, Ratnaparkhe M, Tullu A, Sonnante G, Pfaff T, Tekeoglu M, Santra D, Sant VJ, Rajesh PN, Kahl G, Muehlbauer FJ (2000) A linkage map of the chickpea ( / Cicer arietinum L.) genome based on the recombinant inbred lines from a / C. arietinum?×? / C. reticulatum cross: localization of resistance genes for / Fusarium races 4 and 5. Theor Appl Genet 101:1155-163 CrossRef
57. Wu J, Maehara T, Shimokawa T, Yamamoto S, Harada C, Takazaki Y, Ono N, Mukai Y, Koike K, Yazaki J, Fujii F, Shomura A, Ando T, Kono I, Waki K, Yamamoto K, Yano M, Matsumoto T, Sasaki T (2002) A comprehensive rice transcript map containing 6591 expressed sequence tag sites. Plant Cell 14:525-35 CrossRef
58. Zhu YL, Song QJ, Hyten DL, Tassell CPV, Matukumalli LK, Grimm DR, Hyatt SM, Fickus EW, Young ND, Cregan PB (2003) Single-nucleotide polymorphisms in soybean. Genetics 163:1123-134 - 作者单位：Neha Gujaria (1) (2)
Ashish Kumar (1)
Preeti Dauthal (1)
Anuja Dubey (1)
Pavana Hiremath (1)
A. Bhanu Prakash (1)
Andrew Farmer (3)
Mangla Bhide (2)
Trushar Shah (1)
Pooran M. Gaur (1)
Hari D. Upadhyaya (1)
Sabhyata Bhatia (4)
Douglas R. Cook (5)
Greg D. May (3)
Rajeev K. Varshney (1) (6)
1. International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, 502324, Andhra Pradesh, India
2. Dr. Hari Singh Gaur University, Sagar, 470003, Madhya Pradesh, India
3. National Centre for Genome Resources (NCGR), Santa Fe, NM, 87505, USA
4. National Institute for Plant Genome Research (NIPGR), New Delhi, 110067, India
5. University of California, Davis (UC-Davis), Davis, CA, 95616, USA
6. CGIAR Generation Challenge Programme (GCP), c/o CIMMYT, 06600, Mexico, DF, Mexico - ISSN：1432-2242
文摘
A transcript map has been constructed by the development and integration of genic molecular markers (GMMs) including single nucleotide polymorphism (SNP), genic microsatellite or simple sequence repeat (SSR) and intron spanning region (ISR)-based markers, on an inter-specific mapping population of chickpea, the third food legume crop of the world and the first food legume crop of India. For SNP discovery through allele re-sequencing, primer pairs were designed for 688 genes/expressed sequence tags (ESTs) of chickpea and 657 genes/ESTs of closely related species of chickpea. High-quality sequence data obtained for 220 candidate genic regions on 2-0 genotypes representing 9 Cicer species provided 1,893 SNPs with an average frequency of 1/35.83?bp and 0.34 PIC (polymorphism information content) value. On an average 2.9 haplotypes were present in 220 candidate genic regions with an average haplotype diversity of 0.6326. SNP2CAPS analysis of 220 sequence alignments, as mentioned above, provided a total of 192 CAPS candidates. Experimental analysis of these 192 CAPS candidates together with 87 CAPS candidates identified earlier through in silico mining of ESTs provided scorable amplification in 173 (62.01%) cases of which predicted assays were validated in 143 (82.66%) cases (CGMM). Alignments of chickpea unigenes with Medicago truncatula genome were used to develop 121 intron spanning region (CISR) markers of which 87 yielded scorable products. In addition, optimization of 77 EST-derived SSR (ICCeM) markers provided 51 scorable markers. Screening of easily assayable 281 markers including 143 CGMMs, 87 CISRs and 51 ICCeMs on 5 parental genotypes of three mapping populations identified 104 polymorphic markers including 90 markers on the inter-specific mapping population. Sixty-two of these GMMs together with 218 earlier published markers (including 64 GMM loci) and 20 other unpublished markers could be integrated into this genetic map. A genetic map developed here, therefore, has a total of 300 loci including 126 GMM loci and spans 766.56?cM, with an average inter-marker distance of 2.55?cM. In summary, this is the first report on the development of large-scale genic markers including development of easily assayable markers and a transcript map of chickpea. These resources should be useful not only for genome analysis and genetics and breeding applications of chickpea, but also for comparative legume genomics.