Association mapping for yield and grain quality traits in rice (Oryza sativa L.)

Genetics and Molecular Biology

Volumn 33, Issue 3, 2010, Pages 515-524

  Borba, Tereza Cristina de Oliveira ^a   Brondani, Rosana Pereira Vianello ^a   Breseghello, Flávio ^a   Coelho, Alexandre Siqueira Guedes ^b   Mendonça, João Antônio ^a   Rangel, Paulo Hideo Nakano ^a   Brondani, Claudio ^a  

^a EMBRAPA ARROZ E FEIJÃO   (Brazil)

^b FEDERAL UNIVERSITY OF GOIÁS   (Brazil)

Author keywords

Association analysis; Core collection; Genetic structure

Indexed keywords

AMYLOSE;

ARTICLE; CONTROLLED STUDY; GENE FREQUENCY; GENE LINKAGE DISEQUILIBRIUM; GENETIC VARIABILITY; GERMPLASM; GRAIN; NONHUMAN; PHENOTYPE; POPULATION STRUCTURE; QUANTITATIVE TRAIT LOCUS MAPPING; RICE; STRUCTURE ANALYSIS;

ORYZA SATIVA;

EID: 77957292157     PISSN: 14154757     EISSN: 16784685     Source Type: Journal    
DOI: 10.1590/S1415-47572010005000065     Document Type: Article

References (43)

1. Abadie T, Cordeiro CMT, Fonseca JR, Alves RBN, Burle ML, Brondani C, Rangel PHN, Castro EM, Silva HT, Freire MS, et al. (2005) Constructing a rice core collection for Brazil. Pesq Agropec Bras 40:129-136.
2. Agrama HA, Eizenga GC and Yan W (2007) Association mapping of yield and its components in rice cultivars. Mol Breed 19:341-356.
3. Aluko G, Martinez C, Tohme J, Castano C, Bergman C and Oard JH (2004) QTL mapping of grain quality traits from the interspecific cross Oryza sativa x O. glaberrima. Theor Appl Genet 109:630-639.
4. Ayres NM, McClung A, Larkin PD, Bligh HFJ, Jones CA and Park WD (1997) Microsatellites and a single nucleotide polymorphism differentiate apparent amylose classes in an extended pedigree of US rice germplasm. Theor Appl Genet 94:773-781.
5. Bao JS, Corke H and Sun M (2006) Microsatellites, single nucleotide polymorphisms and a sequence tagged site in starch-synthesizing genes in relation to starch physicochemical properties in nonwaxy rice (Oryza sativa L.). Theor Appl Genet 113:1185-1196.
6. Breseghello F and Sorrels ME (2006a) Association mapping of kernel size and milling quality in wheat (Triticum aestivum L.) cultivars. Genetics 172:1165-1177.
7. Breseghello F and Sorrels ME (2006b) Association analysis as a strategy for improvement of qualitative traits in plants. Crop Sci 46:1323-1330.
8. Brondani C, Rangel PHN, Brondani RPV and Ferreira ME (2002) QTL mapping and introgression of yield related traits from Oryza glumaepatula to cultivated rice (Oryza sativa) using microsatellite markers. Theor Appl Genet 104:1192-1203.
9. Brondani RPV and Grattapaglia D (2001) Cost-effective method to synthesize a fluorescent internal DNA standard for automated fragment sizing. Biotechniques 31:793-800.
10. Buntjer JB, Sorensen AP and Peleman JD (2005) Haplotype diversity: The link between statistical and biological association. Trends Plant Sci 10:466-471.
11. Campos H (1983) Estatística Experimental Não-Paramétrica. 4a edição. ESALQ, Piracicaba, 349 pp.
12. Cho YC, Suh JP, Choi IS, Hong HC, Baek MK, Kang KH, Kim YG, Ahn SN, Choi HC, Hwang HG, et al. (2003) QTLs analysis of yield and its related traits in wild rice relative Oryza rufipogon. Treat Crop Res 4:19-29.
13. Cruz CD (1997) Programa Genes: Aplicativo Computacional em Genética e Estatística. 1a edição. Editora UFV, Viçosa, 442 pp.
14. Fan CC, Yu XQ, Xing YZ, Xu CG, Luo LJ and Zhang Q (2005) The main effects, epistatic effects and environmental interactions of QTLs on the cooking and eating quality of rice in a doubled-haploid line population. Theor Appl Genet 110:1445-1452.
15. Ferreira ME and Grattaplaglia D (2006) Genética de associação em plantas. In: Borém A and Caixeta, ET (eds) Marcadores Moleculares. Editora UFV, Viçosa, pp 273-306.
16. Flint-Garcia AS, Thornsberry JM and Buckler ES (2003) Structure of linkage disequilibrium in plants. Annu Rev Plant Biol 54:357-374.
17. Garris AJ, McCouch SR and Kresovich S (2003) Population structure and its effect on haplotype diversity and linkage disequilibrium surrounding the xa5 locus of rice (Oryza sativa L.). Genetics 165:759-769.
18. Garris AJ, Tai TH, Coburn J, Kresovich S and McCouch S (2005) Genetic structure and diversity in Oryza sativa L. Genetics 169:1631-1638.
19. Hardy OJ and Vekemans X (2002) SPAGeDi: A versatile computer program to analyse spatial genetic structure at the individual or population levels. Mol Ecol Notes 2:618-620.
20. He P, Li SG, Qian Q, Ma YQ, Li JZ, Wang WM, Chen Y and Zhu LH (1999) Genetic analysis of rice grain quality. Theor Appl Genet 98:502-508.
21. Jannink JL, Bink CAMM and Jansen RC (2001) Using complex plant pedigrees to map valuable genes. Trends Plant Sci 6:337-342.
22. Jiang GH, Xu CG, Li XH and He YQ (2004) Characterization of the genetic basis for yield and its component traits of rice revealed by doubled haploid population. Yi Chuan Xue Bao 31:63-72.
23. Juliano B (1979) Amylose analysis - A review. In: Chemical Aspects of Rice Grain Quality. IRRI, Los Banõs, pp 251-260.
24. Khush GS (1997) Origin, dispersal, cultivation and variation of rice. Plant Mol Biol 35:25-34.
25. Kraakman ATW, Niks RF, van den Berg PMMM, Stam P and van Eeuwijk FA (2004) Linkage disequilibrium of yield and yield stability in modern spring barley cultivars. Genetics 168:435-446.
26. Lanceras JC, Huang ZL, Naivikul O, Vanavichit A, Ruanjaichon V and Tragoonrung S (2000) Mapping of genes for cooking and eating qualities in Thai jasmine rice (KDML105). DNA Res 7:93-101.
27. Lu H, Redus MA, Coburn JR, Rutger JN, McCouch SR and Tai TH (2005) Population structure and breeding patterns of 145 U.S. rice cultivars based on SSR marker analysis. Crop Sci 45:66-76.
28. Marri PR, Sarla N, Reddy LV and Siddiq EA (2005) Identification and mapping of yield and yield related QTLs from an Indian accession of Oryza rufipogon. BMC Genet 6:1-14.
29. Patron NJ, Smith AM, Fahy BF, Hylton CM, Naldrett MJ, Rossnagel BG and Denyer K (2002) The altered pattern of amylose accumulation in the endosperm of low-amylose barley cultivars is attributable to a single mutant allele of granule-bound starch synthase I with a deletion in the 5'-non-coding region. Plant Physiol 130:190-198.
30. Peleman JD and van der Voort JR (2003) Breeding by design. Trends Plant Sci 8:330-334.
31. Pritchard JK, Stephens M and Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155:945-959.
32. Remington DL, Thornsberry JM, Matsuoka Y, Wilson LM, Whitt SR, Doebley J, Kresovich S, Goodman MM and Buckler ES (2001) Structure of linkage disequilibrium and phenotypic associations in the maize genome. Proc Natl Acad Sci USA 98:11479-11484.
33. Risch N and Zhang H (1996) Mapping quantitative trait loci with extreme discordant pairs, sampling considerations. Am J Hum Genet 58:836-843.
34. Rostoks NT, Ramsay L, Mackenzie K, Cardle L, Bhat PR, Roose ML, Svensson JT, Stein N, Varshney RK, Marshall DF, et al. (2006). Recent history of artificial outcrossing facilitates whole-genome association mapping in elite inbred crop varieties. Proc Natl Acad Sci USA 103:18656-18661.
35. Septiningsih EM, Prasetiyono J, Lubis E, Tai TH, Tjubaryat T, Moeljopawiro S and McCouch S (2003) Identification of quantitative trait loci for yield and yield components in an advanced backcross population derived from the Oryza sativa variety IR64 and the wild relative O. rufipogon. Theor Appl Genet 107:1419-1432.
36. Skot L, Humphreys MO and Armstead I (2005) An association mapping approach to identify flowering time genes in natural populations of Lolium perenne (L.). Mol Breed 15:233-245.
37. Storey JD (2002) A direct approach to false discovery rates. J R Stat Soc Ser B 64:479-498.
38. Tan YF, Li JX, Yu SB, Xing YZ, Xu CG and Zhang Q (1999) The three important traits for cooking and eating quality of rice grains are controlled by a single locus in na elite rice hybrid, Shanyou 63. Theor Appl Genet 99:642-648.
39. Yu JG, Pressoir WH, Briggs I, Bi IV, Yamasaki M, Doebley JF, McMullen MD, Gaut BS, Nielsen DM, Holland JB, et al. (2006) A unified mixed-model method for association mapping that accounts for multiple levels of relatedness. Nat Genet 38:203-208.
40. Yu SB, Li JX, Xu CG, Tan YF, Gao YJ, Li XH, Zhang Q and Maroof MAS (1997) Importance of epistasis as the genetic basis of heterosis in an elite rice hybrid. Proc Natl Acad Sci USA 94:9226-9231.
41. Zhou PH, Tan YF, He YQ, Xu C and Zhang Q (2003) Simultaneous improvement for four quality traits of Zhenshan 97, an elite parent of hybrid rice, by molecular marker-assisted selection. Theor Appl Genet 106:326-331.
42. Zhu C, Gore M, Buckler ES and Yu J (2008) Status and prospects of association mapping in plants. Plant Genome 1:5-20.
43. Zondervan KT and Cardon LR (2004) The complex interplay among factors that influence allelic association. Nat Rev Genet 5:89-100.