Mapping 49 quantitative trait loci at high resolution through sequencing-based genotyping of rice recombinant inbred lines

Theoretical and Applied Genetics

Volumn 122, Issue 2, 2011, Pages 327-340

  Wang, Lu ^a   Wang, Ahong ^a   Huang, Xuehui ^a   Zhao, Qiang ^a   Dong, Guojun ^b   Qian, Qian ^b   Sang, Tao ^a,c   Han, Bin ^a,d  

^a INSTITUTE OF PLANT PHYSIOLOGY AND ECOLOGY   (China)

^b INSTITUTE OF PLANT PROTECTION   (China)

^c MICHIGAN STATE UNIVERSITY   (United States)

^d Chinese Academy of Sciences and China National Center for Bioinformation   (China)

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL TRAITS; BREAK-POINTS; CANDIDATE GENES; COMPLEX TRAITS; GENETIC BASIS; GENETIC MARKERS; GENOMIC REGIONS; GENOTYPING; HIGH RESOLUTION; ORYZA SATIVA; PHENOTYPIC VARIATIONS; QTL ANALYSIS; QUANTITATIVE TRAIT LOCUS; RECOMBINANT INBRED LINES;

GENES; MAPPING;

PLANTS (BOTANY);

JAPONICA; ORYZA SATIVA;

ARTICLE; CHINA; CHROMOSOME MAP; CROP; CROSS BREEDING; GENETIC MARKER; GENETIC RECOMBINATION; GENETICS; INFLORESCENCE; METHODOLOGY; PHENOTYPE; PLANT; PLANT GENE; PLANT SEED; QUANTITATIVE TRAIT LOCUS; RICE;

CHINA; CHROMOSOME MAPPING; CROPS, AGRICULTURAL; CROSSES, GENETIC; GENES, PLANT; GENETIC MARKERS; INFLORESCENCE; ORYZA SATIVA; PHENOTYPE; PLANT SHOOTS; QUANTITATIVE TRAIT LOCI; RECOMBINATION, GENETIC; SEEDS;

EID: 79952254766     PISSN: 00405752     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00122-010-1449-8     Document Type: Article

References (53)

1. Ashikari M, Sakakibara H, Lin S, Yamamoto T, Takashi T, Nishimura A, Angeles ER, Qian Q, Kitano H, Matsuoka M (2005) Cytokinin oxidase regulates rice grain production. Science 309:741-745
2. Bennewitz J, Reinsch N, Kalm E (2002) Improved confidence intervals in quantitative trait loci mapping by permutation bootstrapping. Genetics 160:1673-1686
3. Broman KW, Wu H, Sen S, Churchill GA (2003) R/qtl: QTL mapping in experimental crosses. Bioinformatics 19:889-890
4. Da Y, Vanraden PM, Schook LB (2000) Detection and parameter estimation for quantitative trait loci using regression models and multiple markers. Genet Sel Evol 32:357-381
5. Doebley J, Stec A, Hubbard L (1997) The evolution of apical dominance in maize. Nature 386:485-488
6. Fan C, Xing Y, Mao H, Lu T, Han B, Xu C, Li X, Zhang Q (2006) GS3, a major QTL for grain length and weight and minor QTL for grain width and thickness in rice, encodes a putative transmembrane protein. Theor Appl Genet 112:1164-1171
7. Frary A, Nesbitt TC, Grandillo S, Knaap E, Cong B, Liu J, Meller J, Elber R, Alpert KB, Tanksley SD (2000) fw2.2: a quantitative trait locus key to the evolution of tomato fruit size. Science 289:85-88
8. Gautier M, Barcelona RR, Fritz S, Grohs C, Druet T, Boichard D, Eggen A, Meuwissen THE (2006) Fine mapping and physical characterization of two linked quantitative trait loci affecting milk fat yield in dairy cattle on BTA26. Genetics 172:425-436
9. Goff SA, Ricke D, Lan TH, Presting G, Wang R, Dunn M, Glazebrook J, Sessions A, Oeller P, Varma H, Hadley D, Hutchison D, Martin C, Katagiri F, Lange BM, Moughamer T, Xia Y, Budworth P, Zhong J, Miguel T, Paszkowski U, Zhang S, Colbert M, Sun WL, Chen L, Cooper B, Park S, Wood TC, Mao L, Quail P, Wing R, Dean R, Yu Y, Zharkikh A, Shen R, Sahasrabudhe S, Thomas A, Cannings R, Gutin A, Pruss D, Reid J, Tavtigian S, Mitchell J, Eldredge G, Scholl T, Miller RM, Bhatnagar S, Adey N, Rubano T, Tusneem N, Robinson R, Feldhaus J, Macalma T, Oliphant A, Briggs S (2002) A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). Science 296:92-100
10. Grisart B, Coppieters W, Farnir F, Karim L, Ford C, Berzi P, Cambisano N, Mni M, Reid S, Simon P, Spelman R, Georges M, Snell R (2002) Positional candidate cloning of a QTL in dairy cattle: identification of a missense mutation in the bovine DGAT1 gene with major effect on milk yield and composition. Genome Res 12:222-231
11. Harjes C, Rocheford TR, Bai L, Brutnell TP, Kandianis CB, Sowinski SG, Stapleton AE, Vallabhaneni R, Williams M, Wurtzel ET, Yan J, Buckler ES (2008) Natural genetic variation in Lycopene Epsilon Cyclase tapped for maize biofortification. Science 319:330-333
12. Harushima Y, Yano M, Shomura A, Sato M, Shimano T, Kuboki Y, Yamamoto T, Lin SY, Antonio BA, Parco A, Kajiya H, Huang N, Yamamoto K, Nagamura Y, Kurata N, Khush GS, Sasaki T (1998) A high-density rice genetic linkage map with 2275 markers using a single F2 population. Genetics 148:479-494
13. Hittalmani S, Huang N, Courtois B, Venuprasad R, Shashidhar HE, Zhuang JY, Zheng KL, Liu GF, Wang GC, Sidhu JS, Srivantaneeyakul S, Singh VP, Bagali PG, Prasanna HC, McLaren G, Khush GS (2003) Identification of QTL for growthand grain yield-related traits in rice across nine locations of Asia. Theor Appl Genet 107:679-690
14. Huang X, Feng Q, Qian Q, Zhao Q, Wang L, Wang A, Guan J, Fan D, Weng Q, Huang T, Dong G, Sang T, Han B (2009) Highthroughput genotyping by whole-genome resequencing. Genome Res 19:1068-1076
15. International Rice Genome Sequencing Project (2005) The map-based sequence of the rice genome. Nature 436:793-800
16. Ishimaru K (2003) Identification of a locus increasing rice yield and physiological analysis of its function. Plant Physiol 133:1083-1090
17. Ishimaru K, Ono K, Kashiwagi T (2004) Identification of a new gene controlling plant height in rice using the candidate-gene strategy. Planta 218:388-395
18. Ishimaru K, Yano M, Aoki N, Ono K, Hirose Y, Lin SY, Monna L, Sasaki T, Ohsugi R (2001) Toward the mapping of physiological and agronomic characters on a rice function map: QTL analysis and comparison between QTLs and expressed sequence tags. Theor Appl Genet 102:793-800
19. Jiang GH, Xu CG, Li XH, He YQ (2004) Characterization of the genetic basis for yield and its component traits of rice revealed by doubled haploid population. Acta Genetica Sinica 31:63-72
20. Jin J, Huang W, Gao JP, Yang J, Shi M, Zhu MZ, Luo D, Lin HX (2008) Genetic control of rice plant architecture under domestication. Nat Genet 40:1365-1369
21. Kao CH, Zeng ZB, Teasdale RD (1999) Multiple interval mapping for quantitative trait loci. Genetics 152:1203-1216
22. Kashiwagi T, Ishimaru K (2004) Identification and functional analysis of a locus for improvement of lodging resistance in rice. Plant Physiol 134:676-683
23. Konishi S, Izawa T, Lin SY, Ebana K, Fukuta Y, Sasaki T, Yano M (2006) An SNP caused loss of seed shattering during rice domestication. Science 312:1392-1396
24. Lander ES, Schork NJ (1994) Genetic dissection of complex traits. Science 265:2037-2048
25. Lander ES, Green P, Abrahamson J, Barlow A, Daly MJ, Lincoln SE, Newberg LA (1987) MAPMAKER: an interactive computer package for constructing primary genetic linkage maps of experimental and natural populations. Genomics 1:174-181
26. Li C, Zhou A, Sang T (2006) Rice domestication by reducing shattering. Science 311:1936-1939
27. Li ZF, Wan JM, Xia JF, Zhai HQ (2003) Mapping quantitative trait loci underlying appearance quality of rice grains (Oryza sativa L.). Acta Genetica Sinica 30:251-259
28. Lin HX, Ashikari M, Yamanouchi U, Sasaki T, Yano M (2002) Identification and characterization of a quantitative trait locus, Hd9, controlling heading date in rice. Breed Sci 52:35-41
29. Liu X, Zhang H, Li H, Li N, Zhang Y, Zhang Q, Wang S, Wang Q, Wang H (2008) Fine-mapping quantitative trait loci for body weight and abdominal fat traits: effects of marker density and sample size. Poult Sci 87:1314-1319
30. Mackay TFC (2001) The genetic architecture of quantitative traits. Annu Rev Genet 35:303-339
31. Mauricio R (2001) Mapping quantitative trait loci in plants: uses and caveats for evolutionary biology. Nat Rev Genet 2:370-381
32. Mei HW, Li ZK, Shu QY, Guo LB, Wang YP, Yu XQ, Ying CS, Luo LJ (2005) Gene actions of QTLs affecting several agronomic traits resolved in a recombinant inbred rice population and two backcross populations. Theor Appl Genet 110(4):649-659
33. Mei HW, Xu JL, Li ZK, Yu XQ, Guo LB, Wang YP, Ying CS, Luo LJ (2006) QTLs influencing panicle size detected in two reciprocal introgressive line (IL) populations in rice (Oryza sativa L.). Theor Appl Genet 112:648-656
34. Qi J, Qian Q, Bu Q, Li S, Chen Q, Sun J, Liang W, Zhou Y, Chu C, Li X, Ren F, Palme K, Zhao B, Chen J, Chen M, Li C (2008) Mutation of the rice Narrow leaf1 gene, which encodes a novel protein, affects vein patterning and polar auxin transport. Plant Physiol 147:1947-1959
35. Sasaki A, Ashikari M, Ueguchi-Tanaka M, Itoh H, Nishimura A, Swapan D, Ishiyama K, Saito T, Kobayashi M, Khush GS, Kitano H, Matsuoka M (2002) Green revolution: a mutant gibberellin-synthesis gene in rice. Nature 416:701-702
36. Shomura A, Izawa T, Ebana K, Ebitani T, Kanegae H, Konishi S, Yano M (2008) Deletion in a gene associated with grain size increased yields during rice domestication. Nat Genet 40:1023-1028
37. Song XJ, Huang W, Shi M, Zhu MZ, Lin HX (2007) A QTL for rice grain width and weight encodes a previously unknown RING-type E3 ubiquitin ligase. Nat Genet 39:623-630
38. Sutter N, Bustamante CD, Chase K, Gray MM, Zhao K, Zhu L, Padhukasahasram B, Karlins E, Davis S, Jones PG, Quignon P, Johnson GS, Parker HG, Fretwell N, Mosher DS, Lawler DF, Satyaraj E, Nordborg M, Lark KG, Wayne RK, Ostrander EA (2007) A single IGF1 allele is a major determinant of small size in dogs. Science 316:112-115
39. Tadege M, Sheldon CC, Helliwell CA, Upadhyaya NM, Dennis ES, Peacock WJ (2003) Reciprocal control of flowering time by OsSOC1 in transgenic Arabidopsis and by FLC in transgenic rice. Plant Biotechnol J 1(5):361-369
40. Tanksley SD (1993) Mapping polygenes. Annu Rev Genet 27:205-233
41. Van Laere AS, Nguyen M, Braunschweig M, Nezer C, Collette C, Moreau L, Archibald AL, Haley CS, Buys N, Tally M, Andersson G, Georges M, Andersson L (2003) A regulatory mutation in IGF2 causes a major QTL effect on muscle growth in the pig. Nature 425:832-836
42. Visscher PM, Thompson R, Haley CS (1996) Confidence intervals in QTL mapping by bootstrapping. Genetics 143:1013-1020
43. Wan XY, Wan JM, Jiang L, Wang JK, Zhai HQ (2006) QTL analysis for rice grain length and fine mapping of an identified QTL with stable and major effects. Theor Appl Genet 112:1258-1270
44. Wang S, Basten CJ, Zeng ZB (2007) Windows QTL Cartographer 2.5. Department of Statistics, North Carolina State University, Raleigh
45. Xue W, Xing Y, Weng X, Zhao Y, Tang W, Wang L, Zhou H, Yu S, Xu C, Li X, Zhang Q (2008) Natural variation in Ghd7 is an important regulator of heading date and yield potential in rice. Nat Genet 40:761-767
46. Yamamoto T, Sasaki T, Yano M (1997) Genetic analysis of spreading stub using indica/japonica backcrossed progenies in rice. Breed Sci 47:141-144
47. Yan CJ, Liang GH, Chen F, Li X, Tang SZ, Yi CD, Tian S, Lu JF, Gu MH (2003) Mapping quantitative trait loci associated with rice grain shape based on an indica/japonica backcross population. Acta Genetica Sinica 30:711-716
48. Yano M, Katayose Y, Ashikari M, Yamanouchi U, Monna L, Fuse T, Baba T, Yamamoto K, Umehara Y, Nagamura Y, Sasaki T (2000) Hd1, a major photoperiod sensitivity quantitative trait locus in rice, is closely related to the Arabidopsis flowering time gene CONSTANS. Plant Cell 12:2473-2484
49. Yu J, Hu S, Wang J, Wong GK, Li S, Liu B, Deng Y, Dai L, Zhou Y, Zhang X, Cao M, Liu J, Sun J, Tang J, Chen Y, Huang X, Lin W, Ye C, Tong W, Cong L, Geng J, Han Y, Li L, Li W, Hu G, Huang X, Li W, Li J, Liu Z, Li L, Liu J, Qi Q, Liu J, Li L, Li T, Wang X, Lu H, Wu T, Zhu M, Ni P, Han H, Dong W, Ren X, Feng X, Cui P, Li X, Wang H, Xu X, Zhai W, Xu Z, Zhang J, He S, Zhang J, Xu J, Zhang K, Zheng X, Dong J, Zeng W, Tao L, Ye J, Tan J, Ren X, Chen X, He J, Liu D, Tian W, Tian C, Xia H, Bao Q, Li G, Gao H, Cao T, Wang J, Zhao W, Li P, Chen W, Wang X, Zhang Y, Hu J, Wang J, Liu S, Yang J, Zhang G, Xiong Y, Li Z, Mao L, Zhou C, Zhu Z, Chen R, Hao B, Zheng W, Chen S, Guo W, Li G, Liu S, Tao M, Wang J, Zhu L, Yuan L, Yang H (2002) A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science 296:79-92
50. Yu CY, Liu YQ, Jiang L, Wang CM, Zhai HQ, Wan JM (2005) QTLs mapping and genetic analysis of tiller angle in rice (Oryza sativa L.). Acta Genetica Sinica 32:948-954
51. Yu B, Lin Z, Li H, Li X, Li J, Wang Y, Zhang X, Zhu Z, Zhai W, Wang X, Xie D, Sun C (2007) TAC1, a major quantitative trait locus controlling tiller angle in rice. Plant J 52:891-898
52. Yue B, Xue WY, Luo LJ, Xing YZ (2006) QTL analysis for flag leaf characteristics and their relationships with yield and yield traits in rice. Acta Genetica Sinica 33:824-832
53. Zhang Q (2007) Strategies for developing Green Super Rice. Proc Natl Acad Sci USA 104:16402-16409