title: Allelic effects on starch structure and properties of six starch biosynthetic genes in a rice recombinant inbred line population.
abstract: BACKGROUND
  The genetic diversity of six starch biosynthetic genes (Wx, SSI, SSIIa, SBEI, SBEIIa and SBEIIb) in indica and japonica rices opens an opportunity to produce a new variety with more favourable grain starch quality. However, there is limited information about the effects of these six gene allele combinations on starch structure and properties. A recombinant inbred line population from a cross between indica and japonica varieties offers opportunities to combine specific alleles of the six genes.
  
  
  RESULTS
  The allelic (indica vs japonica) effects of six starch biosynthetic genes on starch structure, functional properties, and abundance of granule bound proteins in rice grains were investigated in a common genetic background using a recombinant inbred line population. The indica Wx (Wxi) allele played a major role while indica SSI (SSIi), japonica SSIIa (SSIIaj) and indica SBEI (SBEIi) alleles had minor roles on the increase of amylose content. SSIIaj and japonica SBEIIb (SBEIIbj) alleles had a major and a minor role on high ratio of ∑DP ≤ 10 to ∑DP ≤ 24 fractions (RCL10/24), respectively. Both major alleles (Wxi and SSIIaj) reduced peak viscosity (PV), onset, peak and end gelatinization temperatures (GTs) of amylopectin, and increased amylose-lipid complex dissociation enthalpy compared with their counterpart-alleles, respectively. SBEIIai and SBEIIbj decreased PV, whereas SSIi and SBEIIbj decreased FV. SBEIi reduced setback viscosity and gelatinization enthalpy. RCL10/24 of chain length distribution in amylopectin is negatively correlated with PV and BD of paste property and GTs of thermal properties. We also report RILs with superior starch properties combining Wxi, SSIj, SSIIaj, SBEIi and SBEIIbj alleles. Additionally, a clear relation is drawn to starch biosynthetic gene alleles, starch structure, properties, and abundance of granule bound starch biosynthetic enzymes inside starch granules.
  
  
  CONCLUSIONS
  Rice Wxi and SSIIaj alleles play major roles, while SSIi, SBEIi, SBEIIai and SBEIIbj alleles have minor roles in the determination of starch properties between indica and japonica rice through starch structural modification. The combination of these alleles is a key factor for starch quality improvement in rice breeding programs. RCL10/24 value is critical for starch structure and property determination.
authors.affiliation: CSIRO Agriculture Flagship, GPO Box 1600, Canberra, ACT 2601 Australia ; College of Medicine, Biology and Environment, Australian National University, Canberra, ACT 0200 Australia.
authors.forename: Jixun
authors.initials: J
authors.lastname: Luo
authors.affiliation: CSIRO Agriculture Flagship, GPO Box 1600, Canberra, ACT 2601 Australia.
authors.forename: Stephen A
authors.initials: SA
authors.lastname: Jobling
authors.affiliation: College of Medicine, Biology and Environment, Australian National University, Canberra, ACT 0200 Australia.
authors.forename: Anthony
authors.initials: A
authors.lastname: Millar
authors.affiliation: CSIRO Agriculture Flagship, GPO Box 1600, Canberra, ACT 2601 Australia ; International Rice Research Institute, Maligaya, Muñoz, Nueva Ecija Philippines.
authors.forename: Matthew K
authors.initials: MK
authors.lastname: Morell
authors.affiliation: CSIRO Agriculture Flagship, GPO Box 1600, Canberra, ACT 2601 Australia.
authors.forename: Zhongyi
authors.initials: Z
authors.lastname: Li
keywords: DSC; RVA; Rice; Starch; Starch branching enzymes; Starch property; Starch synthases
references.citation: Nat Commun. 2011 Sep 13;2:467
references.pmid: 21915109
references.citation: J Exp Bot. 2004 Oct;55(406):2131-45
references.pmid: 15361536
references.citation: Funct Plant Biol. 2007 Jun;34(5):431-438
references.pmid: 32689370
references.citation: J Integr Plant Biol. 2011 Sep;53(9):756-65
references.pmid: 21711449
references.citation: Theor Appl Genet. 2008 Feb;116(3):335-42
references.pmid: 17989953
references.citation: Plant J. 2001 Mar;25(5):475-86
references.pmid: 11309138
references.citation: J Exp Bot. 2008;59(12):3395-406
references.pmid: 18653693
references.citation: J Proteomics. 2012 Jan 4;75(3):993-1003
references.pmid: 22062158
references.citation: Curr Opin Biotechnol. 2008 Apr;19(2):160-5
references.pmid: 18400487
references.citation: Theor Appl Genet. 2003 Nov;107(8):1433-41
references.pmid: 14513216
references.citation: Plant Cell Physiol. 2010 May;51(5):776-94
references.pmid: 20305271
references.citation: Plant Physiol. 2003 Nov;133(3):1111-21
references.pmid: 14526120
references.citation: Biochem Biophys Res Commun. 1962 Oct 31;9:297-300
references.pmid: 13938053
references.citation: Plant J. 1998 May;14(4):459-65
references.pmid: 9670561
references.citation: Plant Mol Biol. 2005 May;58(2):213-27
references.pmid: 16027975
references.citation: Plant J. 2003 Apr;34(2):173-85
references.pmid: 12694593
references.citation: Cell. 1983 Nov;35(1):225-33
references.pmid: 6313224
references.citation: Funct Plant Biol. 2005 Sep;32(9):763-768
references.pmid: 32689173
references.citation: Plant Cell. 1998 Mar;10(3):399-412
references.pmid: 9501113
references.citation: Plant Mol Biol. 1996 Mar;30(6):1223-32
references.pmid: 8704131
references.citation: Sci Rep. 2012;2:557
references.pmid: 22870386
references.citation: J Exp Bot. 2011 Oct;62(14):4927-41
references.pmid: 21791436
references.citation: Electrophoresis. 1996 Apr;17(4):681-6
references.pmid: 8738327
references.citation: J Agric Food Chem. 2006 Nov 29;54(24):9234-40
references.pmid: 17117815
references.citation: Plant J. 1995 Apr;7(4):613-22
references.pmid: 7742858
references.citation: New Phytol. 2011 Jan;189(2):593-601
references.pmid: 20946420
references.citation: Theor Appl Genet. 2005 Oct;111(6):1072-9
references.pmid: 16172895
references.citation: Theor Appl Genet. 1984 Aug;68(5):467-73
references.pmid: 24257739
references.citation: Cell. 1983 Nov;35(1):235-42
references.pmid: 6313225
references.citation: Funct Plant Biol. 2004 Aug;31(7):671-684
references.pmid: 32688938
references.citation: Plant Physiol. 2006 Mar;140(3):1070-84
references.pmid: 16443699
references.citation: Plant Physiol. 2001 Oct;127(2):459-72
references.pmid: 11598221
references.citation: Theor Appl Genet. 2006 Nov;113(7):1171-83
references.pmid: 16850313
references.citation: Plant Physiol. 2007 Aug;144(4):2009-23
references.pmid: 17586688
references.citation: Plant Physiol. 1999 Oct;121(2):399-410
references.pmid: 10517831
references.citation: Plant Cell Physiol. 2001 Apr;42(4):349-57
references.pmid: 11333304
references.citation: Proc Natl Acad Sci U S A. 2009 Dec 22;106(51):21760-5
references.pmid: 20018713
references.citation: Biomacromolecules. 2006 Mar;7(3):866-76
references.pmid: 16529425
references.citation: Biochem Genet. 1974 Feb;11(2):83-96
references.pmid: 4824506
references.citation: J Exp Bot. 2011 Oct;62(14):5217-31
references.pmid: 21813797
references.citation: Mol Biol Evol. 1998 Aug;15(8):978-87
references.pmid: 9718725
references.citation: Funct Plant Biol. 2002 Aug;29(9):1121-1124
references.pmid: 32689564
references.citation: DNA Res. 2000 Apr 28;7(2):93-101
references.pmid: 10819324
references.citation: Plant Biotechnol J. 2011 Dec;9(9):1074-85
references.pmid: 21645201
references.citation: Biomacromolecules. 2005 Jul-Aug;6(4):2260-70
references.pmid: 16004470