Skip to main content
SpringerLink
Log in
Book cover

Diagnostics in Plant Breeding pp 443–465Cite as

Molecular Diagnostics in Rice (Oryza sativa)

  • Chapter
  • First Online:

  • 2834 Accesses

Abstract

Rice grain yield and its quality are quantitatively inherited. These traits are controlled by their genetic constitution, and environmental factors including light, temperature, fertilizers, and biotic stress. With completion of the rice genome sequence, dissection of the genetic basis of yield traits as well as rice quality advanced substantially. Hundreds of quantitative trait loci (QTL) for these traits were identified on the basis of molecular linkage maps. Dozens of disease and insect resistant QTL/genes were identified as well. Numerous markers linked to major QTL were anchored in the process of fine mapping. Map-based cloning of QTL isolated dozens of genes controlling yield components, rice quality, and biotic stress tolerance. Functional markers were developed based on these functional genes. These linked markers and functional markers started to play important roles in developing rice varieties with higher quality, higher yield potential, and greater yield stability.

This is a preview of subscription content, log in via an institution.

Chapter
USD   29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD   169.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD   219.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD   219.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Learn about institutional subscriptions

References

  • Ashikari M (2005) Cytokinin oxidase regulates rice grain production. Science 309(5735):741–745

    PubMed  CAS  Google Scholar 

  • Ashikari M, Sakakibara H, Lin SY, Yamamoto T, Takashi H, Nishimura A, Angeles EA, Qian Q, Kitana H, Matsuoka M (2005) Cytokinin oxidase regulates rice grain production. Science 309:741–745

    PubMed  CAS  Google Scholar 

  • Ashikawa I, Hayashi N, Yamane H, Kanamori H, Wu J, Matsumoto T, Ono K, Yano M (2008) Two adjacent nucleotide-binding site-leucine-rich repeat class genes are required to confer Pikm-specific rice blast resistance. Genetics 180(4):2267–2276

    PubMed  CAS  Google Scholar 

  • Ballini E, Morel JB, Droc G, Price A, Courtois B, Notteghem JL, Tharreau D (2008) A genome-wide meta-analysis of rice blast resistance genes and quantitative trait loci provides new insights into partial and complete resistance. Mol Plant Microbe Interact 21(7):859–868

    PubMed  CAS  Google Scholar 

  • Bryan GT, Wu KS, Farrall L, Jia Y, Hershey HP, McAdams SA, Faulk KN, Donaldson GK, Tarchini R, Valent B (2000) A single amino acid difference distinguishes resistant and susceptible alleles of the rice blast resistance gene Pi-ta. Plant Cell 12(11):2033–2046

    PubMed  CAS  Google Scholar 

  • Buttery RG, Ling LC, Juliano BO (1982) 2-Acety-1-pyrroline: an important aroma component of cooked rice. Chem Ind 12:958–959

    Google Scholar 

  • Cagampang GB, Perez CM, Juliano BO (1973) A gel consistency test for eating quality of rice. J Sci Food Agric 24(12):1589–1594

    PubMed  CAS  Google Scholar 

  • Chen H, Xu C, Li X, Lin Y, Zhang Q (2005) Transgenic indica rice plants harboring a synthetic cry2A* gene of Bacillus thuringiensis exhibit enhanced resistance against lepidopteran rice pests. Theor Appl Genet 111(7):1330–1337

    PubMed  CAS  Google Scholar 

  • Chen X, Shang J, Chen D, Lei C, Zou Y, Zhai W, Liu G, Xu J, Ling Z, Cao G, Ma B, Wang Y, Zhao X, Li S, Zhu L (2006) A B-lectin receptor kinase gene conferring rice blast resistance. Plant J 46(5):794–804

    PubMed  CAS  Google Scholar 

  • Chen H, Zhang G, Zhang Q, Lin Y (2008a) Effect of transgenic Bacillus thuringiensis rice lines on mortality and feeding behavior of rice stem borers (Lepidoptera: Crambidae). J Econ Entomol 101(1):182–189

    PubMed  CAS  Google Scholar 

  • Chen S, Yang Y, Shi W, Ji Q, He F, Zhang Z, Cheng Z, Liu X, Xu M (2008b) Badh2, encoding betaine aldehyde dehydrogenase, inhibits the biosynthesis of 2-acetyl-1-pyrroline, a major component in rice fragrance. Plant Cell 20(7):1850–1861

    PubMed  CAS  Google Scholar 

  • Chen M, Shelton A, Ye GY (2011) Insect-resistant genetically modified rice in China: from research to commercialization. Annu Rev Entomol 56:81–101

    PubMed  CAS  Google Scholar 

  • Chu Z (2006) Promoter mutations of an essential gene for pollen development result in disease resistance in rice. Genes Dev 20(10):1250–1255

    PubMed  CAS  Google Scholar 

  • Clair St DA (2010) Quantitative disease resistance and quantitative resistance loci in breeding. Annu Rev Phytopathol 48(1):247–268

    Google Scholar 

  • Deka S, Barthakur S (2010) Overview on current status of biotechnological interventions on yellow stem borer Scirpophaga incertulas (Lepidoptera: Crambidae) resistance in rice. Biotechnol Adv 28(1):70–81

    PubMed  CAS  Google Scholar 

  • Doi K, Izawa T, Fuse T, Yamanouchi U, Kubo T, Shimatani Z, Yano M, Yoshimura A (2004) Ehd1, a B-type response regulator in rice, confers short-day promotion of flowering and controls FT-like gene expression independently of Hd1. Genes Dev 18(8):926–936

    PubMed  CAS  Google Scholar 

  • Du B, Zhang W, Liu B, Hu J, Wei Z, Shi Z, He R, Zhu L, Chen R, Han B, He G (2009) Identification and characterization of Bph14, a gene conferring resistance to brown planthopper in rice. Proc Natl Acad Sci U S A 106(52):22163–22168

    PubMed  CAS  Google Scholar 

  • Fan CC, Yu XQ, Xing YZ, Xu CG, Luo LJ, Zhang QF (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

    PubMed  CAS  Google Scholar 

  • 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(6):1164–1171

    PubMed  CAS  Google Scholar 

  • Fan C, Yu S, Wang C, Xing Y (2009) A causal C-A mutation in the second exon of GS3 highly associated with rice grain length and validated as a functional marker. Theor Appl Genet 118(3):465–472

    PubMed  CAS  Google Scholar 

  • Fujita N, Kubo A, Suh DS, Wong KS, Jane JL, Ozawa K, Takaiwa F, Inaba Y, Nakamura Y (2003) Antisense inhibition of isoamylase alters the structure of amylopectin and the physicochemical properties of starch in rice endosperm. Plant Cell Physiol 44:607–618

    PubMed  CAS  Google Scholar 

  • Fukuoka S, Saka N, Koga H, Ono K, Shimizu T, Ebana K, Hayashi N, Takahashi A, Hirochika H, Okuno K, Yano M (2009) Loss of function of a proline-containing protein confers durable disease resistance in rice. Science 325(5943):998–1001

    PubMed  CAS  Google Scholar 

  • Gale MD, Devos KM (1998) Comparative genetics in the grasses. Proc Natl Acad Sci U S A 95(5):1971–1974

    PubMed  CAS  Google Scholar 

  • Gao Z (2003) Map-based cloning of the ALK gene, which controls the gelatinization temperature of rice. Sci China C Life Sci 46(6):661. doi:10.1360/03yc0099

    PubMed  CAS  Google Scholar 

  • 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(5565):92–100

    PubMed  CAS  Google Scholar 

  • Gregory P, Newton AC, Ingram JSI (2009) Integrating pests and pathogens into the climate change/food security debate. J Exp Bot 60(10):2827–2838

    PubMed  CAS  Google Scholar 

  • Gu K, Yang B, Tian D, Wu L, Wang D, Sreekala C, Yang F, Chu Z, Wang GL, White FF, Yin Z (2005) R gene expression induced by a type-III effector triggers disease resistance in rice. Nature 435(7045):1122–1125

    PubMed  CAS  Google Scholar 

  • Han B, Xue Y, Li J, Deng XW, Zhang Q (2007) Rice functional genomics research in China. Philos Trans R Soc Lond B Biol Sci 362(1482):1009–1021

    PubMed  CAS  Google Scholar 

  • Hayama R, Yokoi S, Tamaki S, Yano M, Shimamoto K (2003) Adaptation of photoperiodic control pathways produces short-day flowering in rice. Nature 422(6933):719–722

    PubMed  CAS  Google Scholar 

  • Hayashi N, Inoue H, Kato T, Funao T, Shirota M, Shimizu T, Kanamori H, Yamane H, Hayano-Saito Y, Matsumoto T, Yano M, Takatsuji H (2010) Durable panicle blast-resistance gene Pb1 encodes an atypical CC-NBS-LRR protein and was generated by acquiring a promoter through local genome duplication. Plant J 64(3):498–510

    PubMed  CAS  Google Scholar 

  • Hirano H-Y, Sano Y (1991) Molecular characterization of the waxy locus of rice (Oryza sativa). Plant Cell Physiol 32(7):989–997

    CAS  Google Scholar 

  • Hong X, Sasaki T, Yano M (2003) Fine mapping and characterization of quantitative trait loci Hd4 and Hd5 controlling heading date in rice. Breed Sci 53:51–59

    Google Scholar 

  • Hu KM, Qiu DY, Shen XL, Li XH, Wang SP (2008) Isolation and manipulation of quantitative trait loci for disease resistance in rice using a candidate gene approach. Mol Plant 1(5):786–793

    PubMed  CAS  Google Scholar 

  • Huang Z, He G, Shu L, Li X, Zhang Q (2001) Identification and mapping of two brown planthopper resistance genes in rice. Theor Appl Genet 102:929–934

    CAS  Google Scholar 

  • Huang X, Qian Q, Liu Z, Sun H, He S, Luo D, Xia G, Chu C, Li J, Fu X (2009) Natural variation at the DEP1 locus enhances grain yield in rice. Nat Genet 41(4):494–497

    PubMed  CAS  Google Scholar 

  • Ikeda K, Nagasawa N, Nagato Y (2005) ABERRANT PANICLE ORGANIZATION1 temporally regulates meristem identity in rice. Dev Biol 282(2):349–360

    PubMed  CAS  Google Scholar 

  • Ikeda K, Yasuno N, Oikawa T, Iida S, Nagato Y, Maekawa M, Kyozuka J (2009) Expression level of ABERRANT PANICLE ORGANIZATION1 determines rice inflorescence form through control of cell proliferation in the meristem. Plant Physiol 150(2):736–747

    Google Scholar 

  • Isshiki M, Morino K, Nakajima M, Okagaki RJ, Wessler SR, Izawa T, Shimamoto K (1998) A naturally occurring functional allele of the rice waxy locus has a GT to TT mutation at the 5′ splice site of the first intron. Plant J 15(1):133–138

    PubMed  CAS  Google Scholar 

  • Ito T, Motohashi R, Kuromori T, Mizukado S, Sakurai T, Kanahara H, Seki M, Shinozaki K (2002) A new resource of locally transposed Dissociation elements for screening gene-knockout lines in silico on the Arabidopsis genome. Plant Physiol 129(4):1695–1699

    PubMed  CAS  Google Scholar 

  • Iyer AS, McCouch SR (2004) The rice bacterial blight resistance gene xa5 encodes a novel form of disease resistance. Mol Plant Microbe Interact 17(12):1348–1354

    PubMed  CAS  Google Scholar 

  • Jiao Y, Wang Y, Xue D, Wang J, Yan M, Liu G, Dong G, Zeng D, Lu Z, Zhu X, Qian Q, Li J (2010) Regulation of OsSPL14 by OsmiR156 defines ideal plant architecture in rice. Nat Genet 42(6):541–544

    PubMed  CAS  Google Scholar 

  • Jin J, Huang W, Gao J-P, Yang J, Shi M, Zhu M-Z, Luo D, Lin H-X (2008) Genetic control of rice plant architecture under domestication. Nat Genet 40(11):1365–1369

    PubMed  CAS  Google Scholar 

  • Khush GS (2005) What it will take to Feed 5.0 Billion Rice consumers in 2030. Plant Mol Biol 59(1):1–6

    PubMed  CAS  Google Scholar 

  • Kojima S, Takahashi Y, Kobayashi Y, Monna L, Sasaki T, Araki T, Yano M (2002) Hd3a, a rice ortholog of the Arabidopsis FT gene, promotes transition to flowering downstream of Hd1 under short-day conditions. Plant Cell Physiol 43(10):1096–1105

    PubMed  CAS  Google Scholar 

  • Kou Y, Wang S (2010) Broad-spectrum and durability: understanding of quantitative disease resistance. Curr Opin Plant Biol 13(2):181–185

    PubMed  CAS  Google Scholar 

  • Kovach MJ, Calingacion MN, Fitzgerald MA, McCouch SR (2009) The origin and evolution of fragrance in rice (Oryza sativa L.). Proc Natl Acad Sci U S A 106(34):14444–14449

    PubMed  CAS  Google Scholar 

  • Lee SK, Song MY, Seo YS, Kim HK, Ko S, Cao PJ, Suh JP, Yi G, Roh JH, Lee S, An G, Hahn TR, Wang GL, Ronald P, Jeon JS (2009) Rice Pi5-mediated resistance to magnaporthe oryzae requires the presence of two coiled-coil-nucleotide-binding-leucine-rich repeat genes. Genetics 181(4):1627–1638

    PubMed  CAS  Google Scholar 

  • Li ZK, Pinson SRM, Marchetti MA, Stansel JW, Park WD (1995) Characterization of quantitative trait loci (QTLs) in cultivated rice contributing to field resistance to sheath blight (Rhizoctonia solani). Theor Appl Genet 91:382–388

    CAS  Google Scholar 

  • Li ZK, Pinson SRM, Park WD, Paterson AH, Stansel JW (1997) Epistasis for three grain yield components in rice (Oryza sativa L.). Genetics 145:453–465

    PubMed  CAS  Google Scholar 

  • Li X, Qian Q, Fu Z, Wang Y, Xiong G, Zeng D, Wang X, Liu X, Teng S, Hiroshi F, Yuan M, Luo D, Han B, Li J (2003) Control of tillering in rice. Nature 422(6932):618–621

    PubMed  CAS  Google Scholar 

  • Li P, Wang Y, Qian Q, Fu Z, Wang M, Zeng D, Li B, Wang X, Li J (2007) LAZY1 controls rice shoot gravitropism through regulating polar auxin transport. Cell Res 17(5):402–410

    PubMed  CAS  Google Scholar 

  • Lin F, Chen S, Que Z, Wang L, Liu X, Pan Q (2007) The blast resistance gene Pi37 encodes a nucleotide binding site leucine-rich repeat protein and is a member of a resistance gene cluster on rice chromosome 1. Genetics 177(3):1871–1880

    PubMed  CAS  Google Scholar 

  • Lin H, Liang ZW, Sasaki T, Yano M (2003) Fine mapping and characterization of quantitative trait loci Hd4 and Hd5 controlling heading date in rice. Breeding science 53:51–59

    PubMed  CAS  Google Scholar 

  • Liu X, Lin F, Wang L, Pan Q (2007) The in silico map-based cloning of Pi36, a rice coiled-coil nucleotide-binding site leucine-rich repeat gene that confers race-specific resistance to the blast fungus. Genetics 176(4):2541–2549

    PubMed  CAS  Google Scholar 

  • Liu T, Zhang H, Xing Y (2011) Quantitative trait loci for the number of grains per panicle dependent on or independent of heading date in rice (Oryza sativa L.). Breed Sci 61(2):142–150

    Google Scholar 

  • Mao H, Sun S, Yao J, Wang C, Yu S, Xu C, Li X, Zhang Q (2010) Linking differential domain functions of the GS3 protein to natural variation of grain size in rice. Proc Natl Acad Sci U S A A107(45):19579–19584

    Google Scholar 

  • Matsubara K, Yamanouchi U, Wang ZX, Minobe Y, Izawa T, Yano M (2008) Ehd2, a rice ortholog of the maize INDETERMINATE1 gene, promotes flowering by up-regulating Ehd1. Plant Physiol 148(3):1425–1435

    PubMed  CAS  Google Scholar 

  • McDonald BA, Linde C (2002) Pathogen population genetics, evolutionary potential, and durable resistance. Annu Rev Phytopathol 40:349–379

    PubMed  CAS  Google Scholar 

  • McNally KL, Childs KL, Bohnert R, Davidson RM, Zhao K, Ulat VJ, Zeller G, Clark RM, Hoen DR, Bureau TE, Stokowski R, Ballinger DG, Frazer KA, Cox DR, Padhukasahasram B, Bustamante CD, Weigel D, Mackill DJ, Bruskiewich RM, Ratsch G, Buell CR, Leung H, Leach JE (2009) Genomewide SNP variation reveals relationships among landraces and modern varieties of rice. Proc Natl Acad Sci U S A 106(30):12273–12278

    PubMed  CAS  Google Scholar 

  • 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 110:649–659

    PubMed  CAS  Google Scholar 

  • Mew TW (1987) Current status and further prospects of research on bacterial blight of rice. Annu Rev Phytopathol 25:359–382

    Google Scholar 

  • Miura K, Ikeda M, Matsubara A, Song XJ, Ito M, Asano K, Matsuoka M, Kitano H, Ashikari M (2010) OsSPL14 promotes panicle branching and higher grain productivity in rice. Nat Genet 42(6):545–549

    PubMed  CAS  Google Scholar 

  • Oerke E (2004) Safeguarding production—losses in major crops and the role of crop protection. Crop Prot 23(4):275–285

    Google Scholar 

  • Oerke E-C (2006) Crop losses to animal pests, plant pathogens, and weeds. Encycl Pest Manage. doi:10.1081/E-EPM-120009897

  • Ookawa T, Hobo T, Yano M, Murata K, Ando T, Miura H, Asano K, Ochiai Y, Ikeda M, Nishitani R, Ebitani T, Ozaki H, Angeles ER, Hirasawa T, Matsuoka M (2010) New approach for rice improvement using a pleiotropic QTL gene for lodging resistance and yield. Nat Commun 1(8):132

    PubMed  Google Scholar 

  • Parniske M, Hammond-Kosack KE, Golstein C, Thomas CM, Jones DA, Harrison K, Wulff BB, Jones JD (1997) Novel disease resistance specificities result from sequence exchange between tandemly repeated genes at the Cf-4/9 locus of tomato. Cell 91(6):821–832

    PubMed  CAS  Google Scholar 

  • Poland JA, Balint-Kurti PJ, Wisser RJ, Pratt RC, Nelson RJ (2009) Shades of gray: the world of quantitative disease resistance. Trends Plant Sci 14(1):21–29

    PubMed  CAS  Google Scholar 

  • Qu S, Liu G, Zhou B, Bellizzi M, Zeng L, Dai L, Han B, Wang GL (2006) The broad-spectrum blast resistance gene Pi9 encodes a nucleotide-binding site-leucine-rich repeat protein and is a member of a multigene family in rice. Genetics 172(3):1901–1914

    PubMed  CAS  Google Scholar 

  • Römer P, Recht S, Strauß T, Elsaesser J, Schornack S, Boch J, Wang S, Lahaye T (2010) Promoter elements of rice susceptibility genes are bound and activated by specific TAL effectors from the bacterial blight pathogen, Xanthomonas oryzae pv. oryzae. New Phytol 187(4):1048–1057

    PubMed  Google Scholar 

  • Ronald P, Dardick C (2006) Plant and animal pathogen recognition receptors signal through non-RD kinases. PLoS Pathog 2(1):e2

    PubMed  Google Scholar 

  • Shang J, Tao Y, Chen X, Zou Y, Lei C, Wang J, Li X, Zhao X, Zhang M, Lu Z, Xu J, Cheng Z, Wan J, Zhu L (2009) Identification of a new rice blast resistance gene, Pid3, by genomewide comparison of paired nucleotide-binding site-leucine-rich repeat genes and their pseudogene alleles between the two sequenced rice genomes. Genetics 182(4):1303–1311

    PubMed  CAS  Google Scholar 

  • Sheng CF, Sheng SY, Gao LD, Xuan JW (2003) Pest status and loss assessment of crop damage caused by the rice borers, Chilo suppressalis and Tryporyza incertulas in China. Entomol Knowl 40:289–294

    Google Scholar 

  • Shi W, Chen S, Xu M (2008) Discovery of a new fragrance allele and the development of functional markers for the breeding of fragrant rice varieties. Mol Breed 22:185–192

    CAS  Google Scholar 

  • 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(8):1023–1028

    PubMed  CAS  Google Scholar 

  • Song WY, Wang GL, Chen LL, Kim HS, Pi LY, Holsten T, Gardner J, Wang B, Zhai WX, Zhu LH, Fauquet C, Ronald P (1995) A receptor kinase-like protein encoded by the rice disease resistance gene, Xa21. Science 270(5243):1804–1806

    PubMed  CAS  Google Scholar 

  • 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(5):623–630

    PubMed  CAS  Google Scholar 

  • Spielmeyer W (2002) Semidwarf (sd-1), “green revolution” rice, contains a defective gibberellin 20-oxidase gene. Proc Natl Acad Sci U S A 99(13):9043–9048

    PubMed  CAS  Google Scholar 

  • Sun X, Cao Y, Yang Z, Xu C, Li X, Wang S, Zhang Q (2004) Xa26, a gene conferring resistance to Xanthomonas oryzae pv. oryzae in rice, encodes an LRR receptor kinase-like protein. Plant J 37(4):517–527

    PubMed  CAS  Google Scholar 

  • Takahashi Y (2001) Hd6, a rice quantitative trait locus involved in photoperiod sensitivity, encodes the alpha subunit of protein kinase CK2. Proc Natl Acad Sci U S A 98(14):7922–7927

    PubMed  CAS  Google Scholar 

  • Takahashi Y, Teshima KM, Yokoi S, Innan H, Shimamoto K (2009) Variations in Hd1 proteins, Hd3a promoters, and Ehd1 expression levels contribute to diversity of flowering time in cultivated rice. Proc Natl Acad Sci U S A 106(11):4555–4560

    PubMed  CAS  Google Scholar 

  • Tamura M, Tachida H (2011) Evolution of the number of LRRs in plant disease resistance genes. Mol Genet Genomics 285(5):393–402

    PubMed  CAS  Google Scholar 

  • Tan L, Li X, Liu F, Sun X, Li C, Zhu Z, Fu Y, Cai H, Wang X, Xie D, Sun C (2008) Control of a key transition from prostrate to erect growth in rice domestication. Nat Genet 40(11):1360–1364

    PubMed  CAS  Google Scholar 

  • Tanaka K (2000) Toxicity of insecticides to predators of rice planthoppers: Spiders, the mirid bug and the dryinid wasp. Appl Entomol Zool 35(1):177–187

    CAS  Google Scholar 

  • Tang W, Xu C, Li X, Lin Y, Zhang Q (2006) Development of insect-resistant transgenic indica rice with a synthetic cry1C * gene. Chin Sci Bull 18(1):1–10

    CAS  Google Scholar 

  • Terao T, Nagata K, Morino K, Hirose T (2010) A gene controlling the number of primary rachis branches also controls the vascular bundle formation and hence is responsible to increase the harvest index and grain yield in rice. Theor Appl Genet 120(5):875–893

    PubMed  CAS  Google Scholar 

  • Tian Z, Qian Q, Liu Q, Yan M, Liu X, Yan C, Liu G, Gao Z, Tang S, Zeng D, Wang Y, Yu J, Gu M, Li J (2009) Allelic diversities in rice starch biosynthesis lead to a diverse array of rice eating and cooking qualities. Proc Natl Acad Sci U S A 106(51):21760–21765

    PubMed  CAS  Google Scholar 

  • Tu J, Zhang G, Datta K, Xu C, He Y, Zhang Q, Khush GS, Datta SK (2000) Field performance of transgenic elite commercial hybrid rice expressing bacillus thuringiensis delta-endotoxin. Nat Biotechnol 18(10):1101–1104

    PubMed  CAS  Google Scholar 

  • Unnevehr LJ, Duff B, Juliano BO (1992) Consumer demand for rice grain quality. International Rice Research Institute/International Development Research Center, Manila/Ottawa

    Google Scholar 

  • Virk PS, Khush GS, Peng S (2004) Breeding to enhance yield potential of rice at IRRI: the ideotype approach. Int Rice Res Notes 29(1):5–9

    Google Scholar 

  • Wang ZX, Yano M, Yamanouchi U, Iwamoto M, Monna L, Hayasaka H, Katayose Y, Sasaki T (1999) The Pib gene for rice blast resistance belongs to the nucleotide binding and leucine-rich repeat class of plant disease resistance genes. Plant J 19(1):55–64

    PubMed  Google Scholar 

  • Wang L, Wang A, Huang XH, Zhao Q, Dong GJ, Qian Q, Sang T, Han B (2011a) Mapping 49 quantitative trait loci at high resolution through sequencing-based genotyping of rice recombinant inbred lines. Theor Appl Genet 122:327–340

    PubMed  Google Scholar 

  • Wang C, Chen S, Yu S (2011b) Functional markers developed from multiple loci in GS3 for fine marker-assisted selection of grain length in rice. Theor Appl Genet 122:905–913

    PubMed  Google Scholar 

  • Wei X, Xu J, Guo H, Jiang L, Chen S, Yu C, Zhou Z, Hu P, Zhai H, Wan J (2010) DTH8 suppresses flowering in rice, influencing plant height and yield potential simultaneously. Plant Physiol 153(4):1747–1758

    PubMed  CAS  Google Scholar 

  • Weng J, Gu S, Wan X, Gao H, Guo T, Su N, Lei C, Zhang X, Cheng Z, Guo X, Wang J, Jiang L, Zhai H, Wan J (2008) Isolation and initial characterization of GW5, a major QTL associated with rice grain width and weight. Cell Res 18(12):1199–1209

    PubMed  CAS  Google Scholar 

  • White FF, Yang B (2009) Host and pathogen factors controlling the rice-Xanthomonas oryzae interaction. Plant Physiol 150(4):1677–1686

    PubMed  CAS  Google Scholar 

  • Wu C, Li X, Yuan W, Chen G, Kilian A, Li J, Xu C, Zhou DX, Wang S, Zhang Q (2003) Development of enhancer trap lines for functional analysis of the rice genome. Plant J 35(3):418–427

    PubMed  CAS  Google Scholar 

  • Wu C, You C, Li C, Long T, Chen G, Byrne ME, Zhang Q (2008) RID1, encoding a Cys2/His2-type zinc finger transcription factor, acts as a master switch from vegetative to floral development in rice. Proc Natl Acad Sci U S A 105(35):12915–12920

    PubMed  CAS  Google Scholar 

  • Xiang Y, Cao Y, Xu C, Li X, Wang S (2006) Xa3, conferring resistance for rice bacterial blight and encoding a receptor kinase-like protein, is the same as Xa26. Theor Appl Genet 113(7):1347–1355

    PubMed  CAS  Google Scholar 

  • Xing Y, Zhang Q (2010) Genetic and molecular bases of rice yield. Annu Rev Plant Biol 61:421–442

    PubMed  CAS  Google Scholar 

  • Xing YZ, Tan YF, Hua JP, Sun XL, Xu CG, Zhang Q (2002) Characterization of the main effects, epistatic effects and their environmental interactions of QTLs in the genetic basis of yield traits in rice. Theor Appl Genet 105:248–257

    PubMed  CAS  Google Scholar 

  • Xu XF, Mei HW, Luo LJ, Cheng XN, Li ZK (2002) RFLP-facilitated investigation of the quantitative resistance of rice to brown planthopper (Nilaparvata lugens). Theor Appl Genet 104:248–253

    PubMed  CAS  Google Scholar 

  • Xu WH, Wang YS, Liu GZ, Chen X, Tinjuangjun P, Pi LY, Song WY (2006) The autophosphorylated Ser686, Thr688, and Ser689 residues in the intracellular juxtamembrane domain of XA21 are implicated in stability control of rice receptor-like kinase. Plant J 45(5):740–751

    PubMed  CAS  Google Scholar 

  • 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(6):761–767

    PubMed  CAS  Google Scholar 

  • Yamamoto T, Lin H, Sasaki T, Yano M (2000) Identification of heading date quantitative trait locus Hd6 and characterization of its epistatic interactions with Hd2 in rice using advanced backcross progeny. Genetics 154(2):885–891

    PubMed  CAS  Google Scholar 

  • Yamamura K, Nishimori M, Ueda Y, Yokosuka T (2006) How to analyze long-term insect population dynamics under climate change: 50-year data of three insect pests in paddy fields. Popul Ecol 48:31–48

    Google Scholar 

  • Yan WH, Wang P, Chen HX, Zhou HJ, Li QP, Wang CR, Ding ZH, Zhang YS, Yu SB, Xing YZ, Zhang QF (2011) A major QTL, Ghd8, plays pleiotropic roles in regulating grain productivity, plant height, and heading date in rice. Mol Plant 4(2):319–330

    PubMed  CAS  Google Scholar 

  • Yano M, Nagamura Y, Kurata N, Minobe Y, Sasaki T (1997) Identification of quantitative trait loci controlling heading date in rice using a high-density linkage map. Theor Appl Genet 95:1025–1032

    CAS  Google Scholar 

  • 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(12):2473–2484

    PubMed  CAS  Google Scholar 

  • Yano M, Kojima S, Takahashi Y, Lin H, Sasaki T (2001) Genetic control of flowering time in rice, a short-day plant. Plant Physiol 127(4):1425–1429

    PubMed  CAS  Google Scholar 

  • Yoshimura S, Katayose Y, Toki S, Wang ZX, Kono I, Yano M, Iwata N, Sasaki T (1998) Expression of Xa1, a bacterial blight resistance gene in rice, is induced by bacterial inoculation. Proc Natl Acad Sci U S A 95:1663–1668

    PubMed  CAS  Google Scholar 

  • 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, Li J, Liu Z, Qi Q, 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, Xu J, Zhang K, Zheng X, Dong J, Zeng W, Tao L, Ye J, Tan J, Chen X, He J, Liu D, Tian W, Tian C, Xia H, Bao Q, Li G, Gao H, Cao T, Zhao W, Li P, Chen W, Zhang Y, Hu 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, Tao M, Zhu L, Yuan L, Yang H (2002) A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science 296(5565):79–92. doi:10.1126/science

    PubMed  CAS  Google Scholar 

  • 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(5):891–898

    PubMed  CAS  Google Scholar 

  • Yuan YX, Zhong SH, Li Q, Zhu ZR, Lou YG, Wang LY, Wang JJ, Wang MY, Li QL, Yang DL, He ZH (2007) Functional analysis of rice NPR1-like genes reveals that OsNPR1/NH1 is the rice orthologue conferring disease resistance with enhanced herbivore susceptibility. Plant Biotechnol 5:313–324

    CAS  Google Scholar 

  • Yuan M, Chu Z, Li X, Xu C, Wang S (2009) Pathogen-induced expressional loss of function is the key factor in race-specific bacterial resistance conferred by a recessive R gene xa13 in rice. Plant Cell Physiol 50(5):947–955

    PubMed  CAS  Google Scholar 

  • Yuan M, Chu Z, Li X, Xu C, Wang S (2010) The bacterial pathogen Xanthomonas oryzae overcomes rice defenses by regulating host copper redistribution. Plant Cell 22(9):3164–3176

    PubMed  CAS  Google Scholar 

  • Yuan T, Li X, Xiao J, Wang S (2011) Characterization of Xanthomonas oryzae-responsive cis-acting element in the promoter of rice race-specific susceptibility gene Xa13. Mol Plant 4(2):300–309

    PubMed  CAS  Google Scholar 

  • Zhang Q (2007) Strategies for developing Green Super Rice. Proc Natl Acad Sci U S A 104(42):16402–16409

    PubMed  CAS  Google Scholar 

  • Zhou B, Liu G, Dolan M, Sakai H, Guodong L, Bellizzi M, Wang GL (2006) The eight amino-acid differences within three leucine-rich repeats between Pi2 and Piz-t resistance proteins determine the resistance specificity. Mol Plant Microbe Interact 19(11):1216–1228

    PubMed  CAS  Google Scholar 

  • Zou JH, Pan XB, Chen ZX, Xu JY, Lu JF, Zhai WX, Zhu LH (2000) Mapping quantitative trait loci controlling sheath blight resistance in two rice cultivars (Oryza sativa L.). Theor Appl Genet 101:569–573

    CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. National Key Lab of Crop Genetic Improvement, Huazhong University, 430070, Wuhan, China

    Wenhao Yan, Zhongmin Han & Yongzhong Xing

Authors
  1. Wenhao Yan
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Zhongmin Han
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Yongzhong Xing
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Yongzhong Xing .

Editor information

Editors and Affiliations

  1. Dept. Agronomy, Iowa State University, Agronomy Hall 1204, Ames, 50011, Iowa, USA

    Thomas Lübberstedt

  2. ICRISAT, Centre of Excellence in Genomics (CEG), Patancheru, 502 324, Andra Pradesh, India

    Rajeev K. Varshney

Rights and permissions

Reprints and permissions

Copyright information

© 2013 Springer Science+Business Media Dordrecht

About this chapter

Cite this chapter

Yan, W., Han, Z., Xing, Y. (2013). Molecular Diagnostics in Rice (Oryza sativa). In: Lübberstedt, T., Varshney, R. (eds) Diagnostics in Plant Breeding. Springer, Dordrecht. https://doi.org/10.1007/978-94-007-5687-8_20

Download citation

Publish with us

Policies and ethics

Search

Navigation