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

Theoretical and Applied Genetics

Volumn 120, Issue 7, 2010, Pages 1415-1441

  Nayak, Spurthi N ^a,b   Zhu, Hongyan ^c,d   Varghese, Nicy ^a   Datta, Subhojit ^c,e   Choi, Hong Kyu ^c,f   Horres, Ralf ^g   Jüngling, Ruth ^g   Singh, Jagbir ^a,h   Kishor, P B Kavi ^b   Sivaramakrishnan, S ^h   Hoisington, Dave A ^a   Kahl, Günter ^g,i   Winter, Peter ⁱ   Cook, Douglas R ^c   Varshney, Rajeev K ^a,j  

^a INTERNATIONAL CROPS RESEARCH INSTITUTE FOR THE SEMI ARID TROPICS ICRISAT   (India)

^b OSMANIA UNIVERSITY   (India)

^c UNIVERSITY OF CALIFORNIA   (United States)

^d UNIVERSITY OF KENTUCKY   (United States)

^e INDIAN INSTITUTE OF PULSES RESEARCH   (India)

^f Dong A University   (South Korea)

^g GOETHE UNIVERSITY   (Germany)

^h ACHARYA N G RANGA AGRICULTURAL UNIVERSITY   (India)

ⁱ GENXPRO GMBH   (Germany)

^j INTERNATIONAL MAIZE AND WHEAT IMPROVEMENT CENTER CIMMYT   (Mexico)

more..

Author keywords

[No Author keywords available]

Indexed keywords

ANCHOR POINT; CHICKPEA ACCESSION; CICER ARIETINUM; GENE-BASED MARKERS; GENETIC MAP; GENETIC MARKERS; GENOMIC LIBRARIES; INFORMATION CONTENTS; LINKAGE GROUPS; MAPPING POPULATIONS; MEDICAGO; MEDICAGO TRUNCATULA; MICRO SATELLITE; POLYMORPHIC MARKERS; SIMPLE SEQUENCE REPEATS; SINGLE-NUCLEOTIDE POLYMORPHISM MARKERS; SSR MARKERS; SYNTENY;

GENES;

MICROSATELLITE DNA;

ARTICLE; BARREL MEDIC; CHICKPEA; CHROMOSOME MAP; EXPRESSED SEQUENCE TAG; GENE LIBRARY; GENE LOCUS; GENETIC LINKAGE; GENETIC MARKER; GENETICS; GENOTYPE; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PHYLOGENY; PLANT GENE; SEQUENCE HOMOLOGY; SINGLE NUCLEOTIDE POLYMORPHISM; VARIABLE NUMBER OF TANDEM REPEAT;

BASE SEQUENCE; CHROMOSOME MAPPING; CICER; EXPRESSED SEQUENCE TAGS; GENE LIBRARY; GENES, PLANT; GENETIC LOCI; GENETIC MARKERS; GENOTYPE; LINKAGE (GENETICS); MEDICAGO TRUNCATULA; MICROSATELLITE REPEATS; MINISATELLITE REPEATS; MOLECULAR SEQUENCE DATA; PHYLOGENY; POLYMORPHISM, SINGLE NUCLEOTIDE; SEQUENCE HOMOLOGY, NUCLEIC ACID;

CICER ARIETINUM; MEDICAGO; MEDICAGO TRUNCATULA;

EID: 77953129466     PISSN: 00405752     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00122-010-1265-1     Document Type: Article

References (45)

1. Akkaya MS, Bhagwat AA, Cregan PB (1992) Length polymorphism of simple sequence repeat DNA in soybean. Genetics 132: 1131-1139.
2. Ameline-Torregrosa C, Wang BB, O'Bleness MS, Deshpande S, Zhu H, Roe B, Young ND, Cannon SB (2008) Identification and characterization of nucleotide-binding site-leucine-rich repeat genes in the model plant Medicago truncatula. Plant Physiol 146: 5-21.
3. Arumuganathan K, Earle ED (1991) Nuclear DNA content of some important plant species. Plant Mol Biol Rep 9: 208-219.
4. 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.
5. Cannon SB, Sterck L, Rombauts S, Sato S, Wang X, Mudge J, Vasdewani J, Cheung F, Gouzy JP, Schiex T, Spanngl M, Schoof H, Nicholson C, Humphays S, Mayer K, Rogers J, Quetier F, Oldroyd GED, Debelle F, Cook DR, Town CD, Roe BA, Tabata S, van de Peer Y, Young ND (2006) Legume genome evolution viewed through the Medicago truncatula and Lotus japonicus genomes. Proc Natl Acad Sci USA 103: 14959-14964.
6. Choi HK, Kim D, Uhm T, Limpens E, Lim H, Mun JH, Kalo P, Penmetsa RV, Seres A, Kulikova O, Roe BA, Bisseling T, Kiss GB, Cook DR (2004a) A sequence-based genetic map of Medicago truncatula and comparison of marker colinearity with M. sativa. Genetics 166: 1463-1502.
7. Choi HK, Mun JH, Kim DJ, Zhu H, Baek JM, Mudge J, Roe B, Ellis N, Doyle J, Kiss GB, Young ND, Cook DR (2004b) Estimating genome conservation between crop and model legume species. Proc Natl Acad Sci USA 101: 15289-15294.
8. Choi HK, Luckow MA, Doyle J, Cook DR (2006) Development of nuclear gene-derived molecular markers linked to legume genetic maps. Mol Genet Genomics 276: 56-70.
9. Choudhary S, Sethy NK, Shokeen B, Bhatia S (2006) Development of sequence-tagged microsatellite site markers for chickpea (Cicer arietinum L.). Mol Ecol Notes 6: 3-95.
10. Cregan PB, Bhagwat AA, Akkaya MS, Rongwen J (1994) Microsatellite fingerprinting and mapping of soybean. Meth Mol Cell Biol 5: 49-61.
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.
12. Douglas SE (2008) DNA strider: an inexpensive sequence analysis package for the Macintosh. Mol Biotechnol 3: 37-45.
13. Grube RC, Radwanski ER, Jahn M (2000) Comparative genetics of disease resistance within the Solanaceae. Genetics 155: 873-887.
14. 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: 163-185.
15. Huettel B, Santra D, Muehlbauer J, Kahl G (2002) Resistance gene analogues of chickpea (Cicer arietinum L.): isolation, genetic mapping and association with a Fusarium resistance gene cluster. Theor Appl Genet 105: 479-490.
16. Hulbert SH, Webb CA, Smith SM, Sun Q (2001) Resistance gene complexes: evolution and utilization. Annu Rev Phytopathol 39: 285-312.
17. Hüttel B, Winter P, Weising K, Choumane W, Weigand F (1999) Seguence-tagged microsatellite site markers for chickpea (Cicer arietinum L.). Genome 42: 210-217.
18. Jayashree B, Punna R, Prasad P, Bantte K, Hash CT, Chandra S, Hoisington DA, Varshney RK (2006) A database of simple sequence repeats from cereal and legume expressed sequence tags mined in silico: survey and evaluation. In Silico Biol 6: 0054.
19. Kosambi DD (1944) The estimation of map distance from recombination values. Ann Eugen 12: 172-175.
20. Kulikova O, Gualtieri G, Geurts R, Kim DJ, Cook D, Huguet T, de Jong JH, Fransz PF, Bisseling T (2001) Integration of the FISH pachytene and genetic maps of Medicago truncatula. Plant J 27: 49-58.
21. Ladizinsky G, Adler A (1976) The origin of chickpea (Cicer arietinum L.). Euphytica 25: 211-217.
22. Lander ES, Green P, Abrahamson J, Barlow A, Daly MJ, Lincoln SE, Newburg L (1987) MAPMAKER: an interactive computer package for constructing primary genetic linkage maps of experimental and natural populations. Genomics 1: 174-181.
23. 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: 492-510.
24. Meyers BC, Dickerman AW, Michelmore RW, Sivaramakrishnan S, Sobral BW, Young ND (1999) Plant disease resistance genes encode members of an ancient and diverse protein family within the nucleotide-binding superfamily. Plant J 20: 317-332.
25. Mun JH, Kim DJ, Choi HK, Gish J, Debellé F, Mudge J, Denny R, Endré G, Dénarié J, Kiss GB, Roe B, Young ND, Cook DR (2006) Distribution of microsatellites in the genome of Medicago truncatula: a resource of genetic markers that integrate genetic and physical maps. Genetics 172: 2541-2555.
26. Pfaff T, Kahl G (2003) Mapping of gene-specific markers on the genetic map of chickpea (Cicer arietinum L.). Mol Genet Genomics 269: 243-251.
27. Rakshit S, Winter P, Tekeoglu M, Juarez Muñoz J, Pfaff T, Benko-Iseppon AM, Muehlbauer FJ, Kahl G (2003) DAF marker tightly linked to a major locus for Ascochyta blight resistance in chickpea (Cicer arietinum L.). Euphytica 132: 23-30.
28. Sambrook J, Russell DR (2001) Molecular cloning: a laboratory manual, 3rd edn. Cold Spring Harbor Laboratory Press, Cold Spring Harbor.
29. Sethy NK, Shokeen B, Bhatia S (2003) Isolation and characterization of sequence-tagged microsatellite sites markers in chickpea (Cicer arietinum L.). Mol Ecol Notes 3: 428-430.
30. Sethy NK, Choudhary S, Shokeen B, Bhatia S (2006a) Identification of microsatellite markers from Cicer reticulatum: molecular variation and phylogenetic analysis. Theor Appl Genet 112: 347-357.
31. Sethy NK, Shokeen B, Edwards KJ, Bhatia S (2006b) Development of microsatellite markers and analysis of intraspecific genetic variability in chickpea (Cicer arietinum L.). Theor Appl Genet 112: 1416-1428.
32. Sharma KD, Winter P, Kahl G, Muehlbauer FJ (2004) Molecular mapping of Fusarium oxysporum f. sp. ciceris race 3 resistance gene in chickpea. Theor Appl Genet 108: 1243-1248.
33. Singh R, Sharma P, Varshney RK, Sharma SK, Singh NK (2008) Chickpea improvement: role of wild species and genetic markers. Biotechnol Genet Eng Rev 25: 267-314.
34. Tekeoglu M, Tullu A, Kaiser WJ, Muehlbauer FJ (2000) Inheritance and linkage of two genes that confer resistance to fusarium wilt in chickpea. Crop Sci 40: 1247-1251.
35. Temnykh S, Declerck G, Lukashova A, Lipovich L, Cartinhour S, McCouch S (2001) Computational and experimental analysis of microsatellites in rice (Oryza sativa L.): frequency, length variation, transposon associations, and genetic marker potential. Genome Res 11: 1441-1452.
36. Varshney RK, Thiel T, Stein N, Langridge P, Graner A (2002) In silico analysis on frequency and distribution of microsatellites in ESTs of some cereal species. Cell Mol Biol Lett 7: 537-546.
37. Varshney RK, Graner A, Sorrells ME (2005) Genic microsatellite markers in plants: features and applications. Trends Biotechnol 23: 48-55.
38. Varshney RK, Hoisington DA, Tyagi AK (2006) Advances in cereal genomics and applications in crop breeding. Trends Biotechnol 24: 490-499.
39. Varshney RK, Mahender T, Aggrawal RK, Börner A (2007) Genic molecular markers in plants: development and applications. In: Varshney RK, Tuberosa R (eds) Genomic assisted crop improvement: genomics approaches and platforms. Springer, The Netherlands, pp 13-30.
40. Varshney RK, Close TJ, Singh NK, Hoisington DA, Cook DR (2009a) Orphan legume crops enter the genomics era!. Curr Opin Plant Biol 12: 202-210.
41. 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 283-304.
42. 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: 90-101.
43. 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: 1155-1163.
44. Zhu H, Cannon SB, Young ND, Cook DR (2002) Phylogeny and genomic organization of the TIR and non-TIR NBS-LRR resistance gene family in Medicago truncatula. Mol Plant Microbe Interact 15: 529-539.
45. Zhu H, Choi HK, Cook DR, Shoemaker RC (2005) Bridging model and crop legumes through comparative genomics. Plant Physiol 137: 1189-1196.