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PMID: 19359285 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't Review

Towards the understanding of complex traits in rice: substantially or superficially?

DNA research : an international journal for rapid publication of reports on genes and genomes ·Vol. 16 ·No. 3 ·2009-06-00 ·Pages 141-54

Yamamoto T, Yonemaru J, Yano M

Abstract

Completion of the genome analysis followed by extensive comprehensive studies on a variety of genes and gene families of rice (Oryza sativa) resulted in rapid accumulation of information concerning the presence of many complex traits that are governed by a number of genes of distinct functions in this most important crop cultivated worldwide. The genetic and molecular biological dissection of many important rice phenotypes has contributed to our understanding of the complex nature of the genetic control with respect to these phenotypes. However, in spite of the considerable advances made in the field, details of genetic control remain largely unsolved, thereby hampering our exploitation of this useful information in the breeding of new rice cultivars. To further strengthen the field application of the genome science data of rice obtained so far, we need to develop more powerful genomics-assisted methods for rice breeding based on information derived from various quantitative trait loci (QTL) and related analyses. In this review, we describe recent progresses and outcomes in rice QTL analyses, problems associated with the application of the technology to rice breeding and their implications for the genetic study of other crops along with future perspectives of the relevant fields.

MeSH Terms
Breeding Crops, Agricultural/genetics Genetic Markers Genetic Variation Genome, Plant Oryza/genetics Quantitative Trait Loci
Chemicals
Genetic Markers
Authors & Affiliations
3 authors, click to expand affiliations / ORCID
Yamamoto Toshio
QTL Genomics Research Center, National Institute of Agrobiological Science, Kannondai 2-1-2, Tsukuba, Ibaraki 305-8602, Japan.
Yonemaru Junichi
Yano Masahiro
References (79)
79 references, click to expand
  1. 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. 2004 Apr 15;18(8):926-36 PMID: 15078816
  2. Advanced backcross QTL analysis in a cross between an elite processing line of tomato and its wild relative L. pimpinellifolium.
    Theor Appl Genet. 1996 Feb;92(2):213-24 PMID: 24166170
  3. Isolation of a rice regeneration quantitative trait loci gene and its application to transformation systems.
    Proc Natl Acad Sci U S A. 2005 Aug 16;102(33):11940-4 PMID: 16091467
  4. QTL x environment interactions in rice. I. heading date and plant height.
    Theor Appl Genet. 2003 Dec;108(1):141-53 PMID: 12961067
  5. Comparative linkage maps of the rice and maize genomes.
    Proc Natl Acad Sci U S A. 1993 Sep 1;90(17):7980-4 PMID: 8103599
  6. Natural variation in Ghd7 is an important regulator of heading date and yield potential in rice.
    Nat Genet. 2008 Jun;40(6):761-7 PMID: 18454147
  7. Homoeologous relationships of rice, wheat and maize chromosomes.
    Mol Gen Genet. 1993 Dec;241(5-6):483-90 PMID: 7903411
  8. Inference of the japonica rice domestication process from the distribution of six functional nucleotide polymorphisms of domestication-related genes in various landraces and modern cultivars.
    Plant Cell Physiol. 2008 Sep;49(9):1283-93 PMID: 18701522
  9. Evolutionary analysis of the Sub1 gene cluster that confers submergence tolerance to domesticated rice.
    Ann Bot. 2009 Jan;103(2):143-50 PMID: 18824474
  10. Comparative analysis of multiple disease resistance in ryegrass and cereal crops.
    Theor Appl Genet. 2008 Aug;117(4):531-43 PMID: 18521564
  11. Genetic dissection and pyramiding of quantitative traits for panicle architecture by using chromosomal segment substitution lines in rice.
    Theor Appl Genet. 2008 Apr;116(6):881-90 PMID: 18274726
  12. Hd3a protein is a mobile flowering signal in rice.
    Science. 2007 May 18;316(5827):1033-6 PMID: 17446351
  13. Rice domestication by reducing shattering.
    Science. 2006 Mar 31;311(5769):1936-9 PMID: 16527928
  14. Genetic architecture of flowering time in maize as inferred from quantitative trait loci meta-analysis and synteny conservation with the rice genome.
    Genetics. 2004 Dec;168(4):2169-85 PMID: 15611184
  15. An SNP caused loss of seed shattering during rice domestication.
    Science. 2006 Jun 2;312(5778):1392-6 PMID: 16614172
  16. Green revolution: a mutant gibberellin-synthesis gene in rice.
    Nature. 2002 Apr 18;416(6882):701-2 PMID: 11961544
  17. Development of submergence-tolerant rice cultivars: the Sub1 locus and beyond.
    Ann Bot. 2009 Jan;103(2):151-60 PMID: 18974101
  18. A marker-assisted backcross approach for developing submergence-tolerant rice cultivars.
    Theor Appl Genet. 2007 Oct;115(6):767-76 PMID: 17657470
  19. Hd1, a major photoperiod sensitivity quantitative trait locus in rice, is closely related to the Arabidopsis flowering time gene CONSTANS.
    Plant Cell. 2000 Dec;12(12):2473-2484 PMID: 11148291
  20. Convergent domestication of cereal crops by independent mutations at corresponding genetic Loci.
    Science. 1995 Sep 22;269(5231):1714-8 PMID: 17821643
  21. Quantitative trait loci mapping and the genetic basis of heterosis in maize and rice.
    Genetics. 2008 Nov;180(3):1707-24 PMID: 18791260
  22. A QTL for rice grain width and weight encodes a previously unknown RING-type E3 ubiquitin ligase.
    Nat Genet. 2007 May;39(5):623-30 PMID: 17417637
  23. Daylength measurements by rice plants in photoperiodic short-day flowering.
    Int Rev Cytol. 2007;256:191-222 PMID: 17241908
  24. Single-locus heterotic effects and dominance by dominance interactions can adequately explain the genetic basis of heterosis in an elite rice hybrid.
    Proc Natl Acad Sci U S A. 2003 Mar 4;100(5):2574-9 PMID: 12604771
  25. Application of a metabolomic method combining one-dimensional and two-dimensional gas chromatography-time-of-flight/mass spectrometry to metabolic phenotyping of natural variants in rice.
    J Chromatogr B Analyt Technol Biomed Life Sci. 2007 Aug;855(1):71-9 PMID: 17556050
  26. Stability of QTLs for rice grain dimension and endosperm chalkiness characteristics across eight environments.
    Theor Appl Genet. 2005 May;110(7):1334-46 PMID: 15809851
  27. Control of a key transition from prostrate to erect growth in rice domestication.
    Nat Genet. 2008 Nov;40(11):1360-4 PMID: 18820699
  28. Identification, isolation and pyramiding of quantitative trait loci for rice breeding.
    Trends Plant Sci. 2006 Jul;11(7):344-50 PMID: 16769240
  29. Gramene: development and integration of trait and gene ontologies for rice.
    Comp Funct Genomics. 2002;3(2):132-6 PMID: 18628886
  30. Overdominant epistatic loci are the primary genetic basis of inbreeding depression and heterosis in rice. I. Biomass and grain yield.
    Genetics. 2001 Aug;158(4):1737-53 PMID: 11514459
  31. QTL detection for eating quality of cooked rice in a population of chromosome segment substitution lines.
    Theor Appl Genet. 2004 Dec;110(1):71-9 PMID: 15551043
  32. Whole genome genotyping technologies on the BeadArray platform.
    Biotechnol J. 2007 Jan;2(1):41-9 PMID: 17225249
  33. Molecular identification of a major quantitative trait locus, qLTG3-1, controlling low-temperature germinability in rice.
    Proc Natl Acad Sci U S A. 2008 Aug 26;105(34):12623-8 PMID: 18719107
  34. Characterization and functional analysis of three wheat genes with homology to the CONSTANS flowering time gene in transgenic rice.
    Plant J. 2003 Oct;36(1):82-93 PMID: 12974813
  35. Comprehensive transcriptome analysis of phytohormone biosynthesis and signaling genes in microspore/pollen and tapetum of rice.
    Plant Cell Physiol. 2008 Oct;49(10):1429-50 PMID: 18718932
  36. Green revolution: preparing for the 21st century.
    Genome. 1999 Aug;42(4):646-55 PMID: 10464789
  37. Quantitative genetics in the age of omics.
    Curr Opin Plant Biol. 2008 Apr;11(2):123-8 PMID: 18325828
  38. Genetic control of flowering time in rice, a short-day plant.
    Plant Physiol. 2001 Dec;127(4):1425-9 PMID: 11743085
  39. Grain yield responses to moisture regimes in a rice population: association among traits and genetic markers.
    Theor Appl Genet. 2005 Dec;112(1):106-13 PMID: 16231161
  40. Importance of epistasis as the genetic basis of heterosis in an elite rice hybrid.
    Proc Natl Acad Sci U S A. 1997 Aug 19;94(17):9226-31 PMID: 11038567
  41. Sequencing of natural strains of Arabidopsis thaliana with short reads.
    Genome Res. 2008 Dec;18(12):2024-33 PMID: 18818371
  42. Vernalization response in perennial ryegrass (Lolium perenne L.) involves orthologues of diploid wheat (Triticum monococcum) VRN1 and rice (Oryza sativa) Hd1.
    Plant Mol Biol. 2006 Mar;60(4):481-94 PMID: 16525886
  43. Genetic control of rice plant architecture under domestication.
    Nat Genet. 2008 Nov;40(11):1365-9 PMID: 18820696
  44. Assessing the importance of genotype x environment interaction for root traits in rice using a mapping population II: conventional QTL analysis.
    Theor Appl Genet. 2006 Sep;113(5):953-64 PMID: 16896715
  45. Identification of quantitative trait loci across recombinant inbred lines and testcross populations for traits of agronomic importance in rice.
    Genetics. 2006 Feb;172(2):1287-300 PMID: 16322522
  46. Genomics: the personal side of genomics.
    Nature. 2007 Oct 4;449(7162):627-30 PMID: 17914399
  47. The evolution of CONSTANS-like gene families in barley, rice, and Arabidopsis.
    Plant Physiol. 2003 Apr;131(4):1855-67 PMID: 12692345
  48. Identifying genetic components controlling fertility in the outcrossing grass species perennial ryegrass (Lolium perenne) by quantitative trait loci analysis and comparative genetics.
    New Phytol. 2008;178(3):559-71 PMID: 18346108
  49. Cytokinin oxidase regulates rice grain production.
    Science. 2005 Jul 29;309(5735):741-5 PMID: 15976269
  50. Overdominant epistatic loci are the primary genetic basis of inbreeding depression and heterosis in rice. II. Grain yield components.
    Genetics. 2001 Aug;158(4):1755-71 PMID: 11514460
  51. Comparative genetics in the grasses.
    Plant Mol Biol. 1997 Sep;35(1-2):3-15 PMID: 9291955
  52. qUVR-10, a major quantitative trait locus for ultraviolet-B resistance in rice, encodes cyclobutane pyrimidine dimer photolyase.
    Genetics. 2005 Dec;171(4):1941-50 PMID: 15965242
  53. Genetic dissection of an elite rice hybrid revealed that heterozygotes are not always advantageous for performance.
    Genetics. 2002 Dec;162(4):1885-95 PMID: 12524357
  54. Mapping QTLs for root morphology of a rice population adapted to rainfed lowland conditions.
    Theor Appl Genet. 2002 Apr;104(5):880-893 PMID: 12582650
  55. Deletion in a gene associated with grain size increased yields during rice domestication.
    Nat Genet. 2008 Aug;40(8):1023-8 PMID: 18604208
  56. Saturation mapping of QTL regions and identification of putative candidate genes for drought tolerance in rice.
    Mol Genet Genomics. 2004 Aug;272(1):35-46 PMID: 15221451
  57. DNA sequencing: bench to bedside and beyond.
    Nucleic Acids Res. 2007;35(18):6227-37 PMID: 17855400
  58. Detection of QTLs with additive effects and additive-by-environment interaction effects on panicle number in rice (Oryza sativa L.) with single-segment substitution lines.
    Theor Appl Genet. 2008 May;116(7):923-31 PMID: 18274724
  59. Development of a wide population of chromosome single-segment substitution lines in the genetic background of an elite cultivar of rice (Oryza sativa L.).
    Genome. 2006 May;49(5):476-84 PMID: 16767172
  60. Mode of inheritance of primary metabolic traits in tomato.
    Plant Cell. 2008 Mar;20(3):509-23 PMID: 18364465
  61. 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. 2001 Jul 3;98(14):7922-7 PMID: 11416158
  62. A maize CONSTANS-like gene, conz1, exhibits distinct diurnal expression patterns in varied photoperiods.
    Planta. 2008 May;227(6):1377-88 PMID: 18301915
  63. A rice quantitative trait locus for salt tolerance encodes a sodium transporter.
    Nat Genet. 2005 Oct;37(10):1141-6 PMID: 16155566
  64. Hd3a, a rice ortholog of the Arabidopsis FT gene, promotes transition to flowering downstream of Hd1 under short-day conditions.
    Plant Cell Physiol. 2002 Oct;43(10):1096-105 PMID: 12407188
  65. QTLs for drought escape and tolerance identified in a set of random introgression lines of rice.
    Theor Appl Genet. 2005 Nov;111(8):1642-50 PMID: 16200414
  66. Yield response to water deficit in an upland rice mapping population: associations among traits and genetic markers.
    Theor Appl Genet. 2004 Oct;109(6):1237-46 PMID: 15490102
  67. EST derived SSR markers for comparative mapping in wheat and rice.
    Mol Genet Genomics. 2004 Jul;271(6):742-51 PMID: 15197579
  68. Next is now: new technologies for sequencing of genomes, transcriptomes, and beyond.
    Curr Opin Plant Biol. 2009 Apr;12(2):107-18 PMID: 19157957
  69. Dominance is the major genetic basis of heterosis in rice as revealed by QTL analysis using molecular markers.
    Genetics. 1995 Jun;140(2):745-54 PMID: 7498751
  70. Epistasis for three grain yield components in rice (Oryza sativa L.).
    Genetics. 1997 Feb;145(2):453-65 PMID: 9071598
  71. 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. 2006 Apr;112(6):1164-71 PMID: 16453132
  72. Dominance, overdominance and epistasis condition the heterosis in two heterotic rice hybrids.
    Genetics. 2008 Nov;180(3):1725-42 PMID: 18791236
  73. Identification of heading date quantitative trait locus Hd6 and characterization of its epistatic interactions with Hd2 in rice using advanced backcross progeny.
    Genetics. 2000 Feb;154(2):885-91 PMID: 10655238
  74. Identification of QTL for growth- and grain yield-related traits in rice across nine locations of Asia.
    Theor Appl Genet. 2003 Aug;107(4):679-90 PMID: 12920521
  75. A high-resolution linkage map of the vicinity of the rice submergence tolerance locus Sub1.
    Mol Gen Genet. 2000 May;263(4):681-9 PMID: 10852491
  76. Identification and linkage mapping of complementary recessive genes causing hybrid breakdown in an intraspecific rice cross.
    Theor Appl Genet. 2007 Jul;115(2):179-86 PMID: 17486310
  77. Sub1A is an ethylene-response-factor-like gene that confers submergence tolerance to rice.
    Nature. 2006 Aug 10;442(7103):705-8 PMID: 16900200
  78. Quantitative trait loci (QTL) analysis for rice grain width and fine mapping of an identified QTL allele gw-5 in a recombination hotspot region on chromosome 5.
    Genetics. 2008 Aug;179(4):2239-52 PMID: 18689882
  79. The map-based sequence of the rice genome.
    Nature. 2005 Aug 11;436(7052):793-800 PMID: 16100779
Article Info
Journal
DNA research : an international journal for rapid publication of reports on genes and genomes
Abbr.
DNA Res
ISSN
1756-1663
DOI
10.1093/dnares/dsp006
Published
2009-06-00
Epub
2009-00-09
Pages
141-54
Language
English
Region
England
NLM ID
9423827
PMCID
PMC2695773
Subset
IM
External Links
PubMed source DOI: 10.1093/dnares/dsp006 PMC Full Text View journal details
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