title: Three genetic systems controlling growth, development and productivity of rice (Oryza sativa L.): a reevaluation of the 'Green Revolution'.
abstract: The Green Revolution (GR-I) included worldwide adoption of semi-dwarf rice cultivars (SRCs) with mutant alleles at GA20ox2 or SD1 encoding gibberellin 20-oxidase. Two series of experiments were conducted to characterize the pleiotropic effects of SD1 and its relationships with large numbers of QTLs affecting rice growth, development and productivity. The pleiotropic effects of SD1 in the IR64 genetic background for increased height, root length/mass and grain weight, and for reduced spikelet fertility and delayed heading were first demonstrated using large populations derived from near isogenic IR64 lines of SD1. In the second set of experiments, QTLs controlling nine growth and yield traits were characterized using a new molecular quantitative genetics model and the phenotypic data of the well-known IR64/Azucena DH population evaluated across 11 environments, which revealed three genetic systems: the SD1-mediated, SD1-repressed and SD1-independent pathways that control rice growth, development and productivity. The SD1-mediated system comprised 43 functional genetic units (FGUs) controlled by GA. The SD1-repressed system was the alternative one comprising 38 FGUs that were only expressed in the mutant sd1 backgrounds. The SD1-independent one comprised 64 FGUs that were independent of SD1. GR-I resulted from the overall differences between the former two systems in the three aspects: (1) trait/environment-specific contributions; (2) distribution of favorable alleles for increased productivity in the parents; and (3) different responses to (fertilizer) inputs. Our results suggest that at 71.4 % of the detected loci, a QTL resulted from the difference between a functional allele and a loss-of-function mutant, whereas at the remaining 28.6 % of loci, from two functional alleles with differentiated effects. Our results suggest two general strategies to achieve GR-II (1) by further exploiting the genetic potential of the SD1-repressed and SD1-independent pathways and (2) by restoring the SD1-mediated pathways, or 'back to the nature' to fully exploit the genetic diversity of those loci in the SD1-mediated pathways which are virtually inaccessible to most rice-breeding programs worldwide that are exclusively based on sd1.
authors: Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
authors: Fan
authors: F
authors: Zhang
authors: Yun-Zhu
authors: YZ
authors: Jiang
authors: Si-Bin
authors: SB
authors: Yu
authors: J
authors: J
authors: Ali
authors: A H
authors: AH
authors: Paterson
authors: G S
authors: GS
authors: Khush
authors: Jian-Long
authors: JL
authors: Xu
authors: Yong-Ming
authors: YM
authors: Gao
authors: Bin-Ying
authors: BY
authors: Fu
authors: R
authors: R
authors: Lafitte
authors: Zhi-Kang
authors: ZK
authors: Li
mesh_terms: D000383:Agriculture / Q000266:history / Q000379:methods*; D000704:Analysis of Variance; D001947:Breeding / Q000379:methods; D002874:Chromosome Mapping; D004777:Environment; D058685:Genetic Pleiotropy / Q000235:genetics*; D005838:Genotype; D049673:History, 20th Century; D016014:Linear Models; D006899:Mixed Function Oxygenases / Q000235:genetics; D008957:Models, Genetic; D012275:Oryza / Q000235:genetics* / Q000254:growth & development*; D010641:Phenotype; D040641:Quantitative Trait Loci / Q000235:genetics*
chemical_list: D006899:Mixed Function Oxygenases; C089210:gibberellin, 2-oxoglutarate-oxygen oxidoreductase (20-hydroxylating, oxidizing)
references: Theor Appl Genet. 2002 Aug;105(2-3):248-257
references: 12582526
references: Trends Plant Sci. 2000 Dec;5(12):523-30
references: 11120474
references: Plant Physiol. 2011 Aug;156(4):1905-20
references: 21693671
references: Theor Appl Genet. 2006 Feb;112(4):648-56
references: 16331475
references: Proc Natl Acad Sci U S A. 1999 May 25;96(11):5952-9
references: 10339523
references: Proc Natl Acad Sci U S A. 2002 Jun 25;99(13):9043-8
references: 12077303
references: J Exp Bot. 2010 Oct;61(15):4145-56
references: 20660496
references: Plant Physiol. 2004 Apr;134(4):1642-53
references: 15075394
references: Theor Appl Genet. 2003 Dec;108(1):141-53
references: 12961067
references: Genetics. 1994 Apr;136(4):1457-68
references: 8013918
references: Annu Rev Plant Biol. 2008;59:225-51
references: 18173378
references: PLoS One. 2011 Jan 20;6(1):e14541
references: 21283795
references: Theor Appl Genet. 1994 Sep;89(1):54-9
references: 24177769
references: Proc Natl Acad Sci U S A. 2011 Jul 5;108(27):10931-2
references: 21693643
references: Nature. 2002 Apr 18;416(6882):701-2
references: 11961544
references: Proc Natl Acad Sci U S A. 2011 Jul 5;108(27):11034-9
references: 21646530
references: DNA Res. 2002 Feb 28;9(1):11-7
references: 11939564
references: Nat Rev Genet. 2001 Oct;2(10):815-22
references: 11584298
references: Trends Genet. 2003 Jan;19(1):5-9
references: 12493241
references: Biotechnol Adv. 2012 Sep-Oct;30(5):1059-70
references: 21888963
references: Proc Natl Acad Sci U S A. 2007 Oct 16;104(42):16402-9
references: 17923667
references: Trends Plant Sci. 2008 Apr;13(4):192-9
references: 18337155
references: Nat Commun. 2010 Nov 30;1:132
references: 21119645
references: Cell. 2006 Aug 11;126(3):467-75
references: 16901781
references: Science. 1997 Jul 25;277(5325):504-9
references: 20662149
references: Plant Mol Biol. 1994 Dec;26(5):1529-55
references: 7858203
references: J Exp Bot. 2007;58(2):169-75
references: 16997901
references: Science. 2003 May 2;300(5620):758-62
references: 12730592