Molecular characterization of the recombinant inbred line population derived from a japonica-indica rice cross

Euphytica

Volumn 159, Issue 1-2, 2008, Pages 73-82

  Liu, Guangjie ^a,b,c   Bernhardt, John L ^a   Jia, Melissa H ^b   Wamishe, Yeshi A ^a,b   Jia, Yulin ^b,c  

^a UNIVERSITY OF ARKANSAS   (United States)

^b USDA ARS Dale Bumpers National Rice Research Center   (United States)

^c CHINA NATIONAL RICE RESEARCH INSTITUTE   (China)

Author keywords

Cluster analysis; Linkage map; Recombinant inbred line; Rice; SSR marker

Indexed keywords

JAPONICA; LISSORHOPTRUS ORYZOPHILUS;

EID: 36749030694     PISSN: 00142336     EISSN: 15735060     Source Type: Journal    
DOI: 10.1007/s10681-007-9459-6     Document Type: Article

References (56)

1. Andaya CB, Tai TH (2005) Fine mapping of the rice low phytic (lpa1) locus. Theor Appl Genet 111:489-495
2. Andaya VC, Mackill DJ (2003) QTLs conferring cold tolerance at the booting stage of rice using recombinant inbred lines from a japonica × indica cross. Theor Appl Genet 106:1084-1090
3. Antonio BA, Inoue T, Kajiya H, Nagamura Y, Kurata N, Minobe Y, Yano M, Nakagahra M, Sasaki T (1996) Comparison of genetic distance and order of DNA markers in five populations of rice. Genome 39:946-956
4. Boerma HR, Narvel JM, Jakkula LR, Alvernaz J, Lee GJ, Carter TE Jr, Bailey MA, Mian MAR, Lee SH (2004) Registration of NC113 soybean mapping population. Crop Sci 44:704-706
5. Cheng S, Min S (2000) Rice cultivars in China: current status and prospects. China Rice (1):13-16
6. Cho YG, McCouch SR, Kuiper M, Kang MR, Pot J, Groenen JTM, Eun MY (1998) Integrated map of AFLP, SSLP and RFLP markers using a recombinant inbred population of rice (Oryza sativa L.). Theor Appl Genet 97:370-380
7. Conaway-Bormans CA, Marchetti MA, Johnson CW, McClung AM, Park WD (2003) Molecular markers linked to the blast resistance gene Pi-z in rice for use in marker-assisted selection. Theor Appl Genet 107:1014-1020
8. Cryder CM, Corgan JN, Urquhart NS, Clason D (1991) Isozyme analysis of progeny derived from Allium fistulosum × Allium cepa × Allium cepa. Theor Appl Genet 82:337-345
9. Dreisigacker S, Zhang P, Warburton ML, VanGinkle M, Hoisington D, Bohn M, Melchinger AE (2004) SSR and pedigree analyses of genetic diversity among CIMMYT wheat lines targeted to different megaenvironments. Crop Sci 44:381-388
10. Gadish I, Zamir D (1986) Differential zygotic abortion in an interspecific Lycopersicon cross. Genome 29:156-159
11. Gardiner JM, Coe EH, Melia-Hancock S, Hoisington DA, Chao S (1993) Development of a core RFLP map in maize using an immortalized F2 population. Genetics 134:917-930
12. Gebhardt C, Ritter E, Debener T, Schachtschabel U, Walkemeir B, Uhrig H, Salamini F (1989) RFLP analysis and linkage mapping in Solanum tuberosum. Theor Appl Genet 78:65-75
13. Gethi JG, Labate JA, Lamkey KR, Smith ME, Kresovich S (2002) SSR variation in imported US. maize inbred lines. Crop Sci 42:951-957
14. He P, Li JZ, Zheng XW, Shen LS, Lu CF, Chen Y, Zhu LH (2001) Comparison of molecular linkage maps and agronomic trait loci between DH and RIL populations derived from the same rice cross. Crop Sci 41:1240-1246
15. Heckenberger M, Bohn M, Ziegle JS, Joe LK, Hauser JD, Hutton M, Melchinger AE (2002) Variation of DNA fingerprints among accessions within maize inbred lines and implications for identification of essentially derived varieties I. Genetic and technical sources of variation in SSR data. Mol Breed 10:181-191
16. Heun M, Kennedy AE, Anderson JA, Lapitan NLV, Sorrells ME, Tanksley SD (1991) Construction of a restriction fragment length polymorphism map for barley (Hordeum vulgare). Genome 34:437-447
17. Jia Y, Wang Z, Fjellstrom RG, Moldenhauer KAK, Azam MA, Correll J, Lee FN, Xia Y, Rutger JN (2004) Rice Pi-ta gene confers resistance to the major pathotypes of the rice blast fungus in the United States. Phytopathology 94:296-301
18. Jia Y, Wamishe Y, Jia MH, Lin J, Eizenga GC, Gibbons JW, Moldenhauer KAK, Correll JC (2005) Two major resistance genes confer resistance to race shift isolates overcoming blast resistance gene Pi-ta. http://www.uark.edu/depts/ agripub/Publications/researchseries/529.3.pdf. Cited 8 Mar 2007
19. Jiang W, Zhou M, Li T (2002) Anatomical study on the chalkiness formation of early indica rice. J Zhejiang Univ (Sci ed) 29:459-463
20. Kosambi DD (1944) The estimation of map distances from recombination values. Ann Eugen 12:172-175
21. International Rice Genome Sequencing Project (2005) The map-based sequence of the rice genome. Nature 436:793-800
22. Larson SR, Rutger JN, Young KA, Raboy V (2000) Isolation and genetic mapping of a non-lethal rice (Oryza sativa L.) low phytic acid 1 mutation. Crop Sci 40:1397-1405
23. Lee FN, Cartwright RD, Jia Y, Correll JC, Moldenhauer KAK, Gibbons JW, Boyett V, Zhou E, Boza E, Seyran E (2005) A preliminary characterization of the rice blast fungus on 'Bank' rice. http://www.uark.edu/depts/agripub/ Publications/researchseries/529.3.pdf. Cited 23 Feb 2007
24. Liedl B, Anderson NO (1993) Reproductive barriers: identification, uses and circumvention. Plant Breed Rev 11:11-154
25. Lu H, Romero-Severson J, Bernardo R (2002) Chromosomal regions associated with segregation distortion in maize. Theor Appl Genet 105:622-628
26. Mangelsdorf PC, Jones DF (1926) The expression of mendelian factors in the gametophyte of maize. Genetics 11:423-455
27. McCouch SR, Teytelman L, Xu Y, Lobos KB, Clare K, Walton M, Fu B, Magirang R, Li Z, Xing Y, Zhang Q, Kono I, Fjellstrom R, DeClerck G, Schneider D, Cartinhour S, Ware D, Stein L (2002) Development and mapping of 2240 new SSR markers for rice (Oryza sativa L.). DNA Res 9:199-207
28. Nakagahra M (1986) Geographic distribution of gametophyte genes in wide crosses of rice cultivars. In: Khush GS (ed) Rice genetics. Proceedings of the international rice genetics symposium, IRRI, Manila, pp 73-82
29. Nandi S, Subudhi PK, Senadhira D, Manigbas NL, Sen-Mandi S, Huang N (1997) Mapping QTLs for submergence tolerance in rice by AFLP analysis and selective genotyping. Mol Gen Genet 255:1-8
30. Nei M (1972) Genetic distance between populations. Am Nat 106:283-292
31. Ni J, Colowit PM, Mackill DJ (2002) Evaluation of genetic diversity in rice subspecies using microsatellite markers. Crop Sci 42:601-607
32. Peng JH, Korol AB, Fahima T, Roder MS, Ronin YI, Li YC, Nevo E (2000) Molecular genetic maps in wild emmer wheat, Triticum dicoccoides: genome-wide coverage, massive negative interference, and putative Quasi-linkage. Genome Res 10:1509-1531
33. Pinson SRM, Capdevielle FM, Oard JH (2005) Confirming QTLs and finding additional loci conditioning sheath blight resistance in rice using recombinant inbred lines. Crop Sci 45:503-510
34. Rutger JN, Tai TH (2005) Registration of K/Z mapping population of rice. Crop Sci 45:2671-2672
35. Rutger JN, Raboy V, Moldenhauer KAK, Bryant RJ, Lee FN, Gibbons JW (2004) Registration of KBNT lpa1-1 low phytic acid germplasm of rice. Crop Sci 44:363
36. Saito T, Hirai K, Way MO (2005) The rice water weevil, Lissorhoptrus oryzophilus Kuschel (Coleoptera:Curculionidae). Appl Entomol Zool 40:31-39
37. Schwemmle J (1968) Selective fertilization in Oenothera. Adv Genet 14:225-324
38. Shen B, Cheng N (1999) Character of physiological and biochemical changes during chalkiness formation in early indica rice varieties. Acta Bot Boreali-Occidentalia Sin 19:290-295
39. Stout MJ, Riggio MR (2002) Variation in susceptibility of rice lines to infestation by the rice water weevil (Coleoptera: Curculionidae). J Agric Urban Entomol 19:205-216
40. Tabien RE, Li Z, Paterson AH, Marchetti MA, Stansel JW, Pinson SRM (2000) Mapping of four major rice blast resistance genes from 'Lemont' and 'Teqing' and evaluation of their combinatorial effect for field resistance. Theor Appl Genet 101:1215-1225
41. Tai T, Tanksley SD (1990) A rapid and inexpensive method for isolation of total DNA from dehydrated plant tissue. Plant Mol Biol Rep 8:297-303
42. Tan GX, Weng QM, Ren X, Huang Z, Zhu LL, He GC (2004) Two whitebacked planthopper resistance genes in rice share the same loci with those for brown planthopper resistance. Heredity 92:212-217
43. Tanksley SD (1984) Linkage relationships and chromosomal locations of enzyme-coding genes in pepper, Capsicum annum. Chromosoma 89:352-360
44. Temnykh S, Park WD, Ayres N, Cartinhour S, Hauck N, Lipovich L, Cho YG, Ishii T, McCouch SR (2000) Mapping and genome organization of microsatellite sequences in rice (Oryza sativa L.). Theor Appl Genet 100:697-712
45. Uga Y, Fukuta Y, Cai HW, Iwata H, Ohsawa R, Morishima H, Fujimura T (2003) Mapping QTLs influencing rice floral morphology using recombinant inbred lines derived from a cross between Oryza sativa L. and Oryza rufipogon Griff. Theor Appl Genet 107:218-226
46. Wang GL, Mackill DJ, Bonman JM, McCouch SR, Champoux MC, Nelson RJ (1994) RFLP mapping of genes conferring complete and partial resistance to blast in a durably resistant rice cultivar. Genetics 136:1421-1434
47. Wang Z, Jia Y, Rutger JN, Xia Y (2007) Rapid survey for presence of a blast resistance gene Pi-ta in rice cultivars using the dominant DNA markers derived from portions of the Pi-ta gene. Plant Breed 126:36-42
48. Way MO (2003) Rice arthropod pests and their management in the United States. In: Smith CW, Dilday RH (eds) Rice: origin, history, technology, and production. Wiley, Hoboken, NJ
49. Xiao J, Li J, Yuan L, Tanksley SD (1996) Identification of QTLs affecting traits of agronomic importance in recombinant inbred population derived from a subspecific rice cross. Theor Appl Genet 92:230-244
50. 2, backcross, doubled haploid, and recombinant inbred populations in rice (Oryza sativa L.). Mol Gen Genet 253:535-545
51. Yan W, Dilday RH, Tai TH, Gibbons JW, McNew RW, Rutger JN (2005) Differential response of rice germplasm to straighthead induced by arsenic. Crop Sci 45:1223-1228
52. Zhang Z, Stout MJ, Shang H, Pousson RC (2004) A method for rearing the rice water weevil, Lissorhoptrus oryzophilus (Coleoptera: Curculionidae), in the laboratory. Coleopt Bull 58:644-651
53. Zhang ZH, Su L, Li W, Chen W, Zhu YG (2005a) A major QTL conferring cold tolerance at the early seedling stage using recombinant inbred lines of rice (Oryza sativa L.). Plant Sci 168:527-534
54. Zhang ZH, Yu SB, Yu T, Huang Z, Zhu YG (2005b) Mapping quantitative trait loci (QTLs) for seedling-vigor using recombinant inbred lines of rice (Oryza sativa L.). Field Crops Res 91:161-170
55. Zhao B, Deng Q, Zhang Q, Li J, Ye S, Liang Y, Peng Y, Li P (2006) Analysis of segregation distortion of molecular markers in F2 population of rice. Acta Genet Sin 33:449-457
56. Zhuang JY, Ma WM, Wu JL, Chai RY, Lu J, Fan YY, Jin MZ, Leung H, Zheng KL (2002) Mapping of leaf and neck blast resistance genes with resistance gene analog, RAPD and RFLP in rice. Euphytica 128:363-370