title: Haplotype dictionary for the Rht-1 loci in wheat.
abstract: The introduction of Reduced height (Rht)-B1b and Rht-D1b into bread wheat (Triticum aestivum) varieties was a key component of the 'green revolution' and today these alleles are the primary sources of semi-dwarfism in wheat. The Rht-1 loci encode DELLA proteins, which are transcription factors that affect plant growth and stress tolerance. In bread wheat, Rht-D1b and Rht-B1b influence resistance to the disease Fusarium Head Blight. To identify Rht-1 variants, locus specific primers were developed and used to sequence the entire open reading frame (ORF) and 1.7 kb of the 5' and 0.5 kb of the 3' flanking regions of Rht-A1 (Rht-A1+f), Rht-B1 (Rht-B1+f), and Rht-D1 (Rht-D1+f) in bread wheat (36 sequences from each genome) and tetraploid and diploid wheat (TDW) (one to three sequences from each genome). Among the bread wheat accessions, the Rht-A1+f and Rht-D1+f sequences contained relatively low genetic diversity and few haplotypes relative to the Rht-B1+f sequences. The TDW accessions were relatively rich in genetic diversity and contained the majority of the polymorphic sites. Novel polymorphisms, relative to 'Chinese Spring', discovered among the accessions include 160 and 197 bp insertions 5' of Rht-B1 and a frameshift in the Rht-B1 ORF. Quantitative real-time PCR using shoot and leaf tissue from 5-day-old seedlings of genotypes lacking or containing the 5' insertions revealed no major effect on Rht-B1 transcript accumulation. This research provides insights into the genetic diversity present at the Rht-1 loci in modern bread wheat and in relation to ancestral wheat accessions.
authors.affiliation: National Institute of Agricultural Botany, Huntingdon Rd, Cambridge, CB3 0LE, UK. edwilhelm@yahoo.com
authors.forename: Edward P
authors.initials: EP
authors.lastname: Wilhelm
authors.forename: Ian J
authors.initials: IJ
authors.lastname: Mackay
authors.forename: Robert J
authors.initials: RJ
authors.lastname: Saville
authors.forename: Andrey V
authors.initials: AV
authors.lastname: Korolev
authors.forename: Francois
authors.initials: F
authors.lastname: Balfourier
authors.forename: Andy J
authors.initials: AJ
authors.lastname: Greenland
authors.forename: Margaret I
authors.initials: MI
authors.lastname: Boulton
authors.forename: Wayne
authors.initials: W
authors.lastname: Powell
mesh_terms: D019295:Computational Biology; D006239:Haplotypes; D010940:Plant Proteins / Q000235:genetics*; D016133:Polymerase Chain Reaction; D040641:Quantitative Trait Loci; D014908:Triticum / Q000235:genetics*
chemical_list: D010940:Plant Proteins; C120413:RHT-D1A protein, Triticum aestivum
references.citation: J Genet Genomics. 2007 Jul;34(7):623-33
references.pmid: 17643948
references.citation: New Phytol. 2012 Oct;196(1):282-291
references.pmid: 22849513
references.citation: Trends Genet. 2008 Jan;24(1):24-32
references.pmid: 18054117
references.citation: Science. 2006 Jan 6;311(5757):91-4
references.pmid: 16400150
references.citation: J Exp Bot. 2009;60(4):1085-92
references.pmid: 19043067
references.citation: Genetics. 1983 Oct;105(2):437-60
references.pmid: 6628982
references.citation: G3 (Bethesda). 2012 Mar;2(3):407-19
references.pmid: 22413094
references.citation: Theor Appl Genet. 2013 May;126(5):1321-36
references.pmid: 23381809
references.citation: Nat Genet. 2011 Feb;43(2):169-72
references.pmid: 21217754
references.citation: Nucleic Acids Res. 2001 May 1;29(9):e45
references.pmid: 11328886
references.citation: Annu Rev Genet. 2004;38:37-59
references.pmid: 15568971
references.citation: Genome. 2006 Sep;49(9):1131-9
references.pmid: 17110993
references.citation: Bioinformatics. 2005 May 1;21(9):2128-9
references.pmid: 15705655
references.citation: Mol Biol Evol. 2007 Jul;24(7):1506-17
references.pmid: 17443011
references.citation: Theor Appl Genet. 2012 Dec;125(8):1751-65
references.pmid: 22926291
references.citation: Plant Cell. 2002 Jan;14(1):57-70
references.pmid: 11826299
references.citation: Theor Appl Genet. 2008 Feb;116(3):439-53
references.pmid: 18060539
references.citation: Theor Appl Genet. 2008 Aug;117(3):321-31
references.pmid: 18488187
references.citation: J Exp Bot. 2012 Feb;63(3):1271-83
references.pmid: 22090435
references.citation: Bioinformatics. 2007 Nov 1;23(21):2947-8
references.pmid: 17846036
references.citation: Genome Biol. 2002 Jun 18;3(7):RESEARCH0034
references.pmid: 12184808
references.citation: Theor Appl Genet. 2009 Feb;118(4):695-702
references.pmid: 19034409
references.citation: Genome. 2009 Dec;52(12):993-1000
references.pmid: 19953127
references.citation: Bioinformatics. 2009 Jun 1;25(11):1451-2
references.pmid: 19346325
references.citation: Plant Cell. 2001 May;13(5):999-1010
references.pmid: 11340177
references.citation: Proc Natl Acad Sci U S A. 2007 Oct 2;104(40):15953-8
references.pmid: 17898165
references.citation: Nat Genet. 2001 Jul;28(3):286-9
references.pmid: 11431702
references.citation: Trends Genet. 2003 Jan;19(1):5-9
references.pmid: 12493241
references.citation: Funct Integr Genomics. 2012 Aug;12(3):489-500
references.pmid: 22592657
references.citation: Theor Appl Genet. 2007 May;114(7):1265-75
references.pmid: 17318494
references.citation: Nucleic Acids Res. 2001 Sep 1;29(17):E88-8
references.pmid: 11522844
references.citation: Mol Plant Pathol. 2008 Mar;9(2):157-69
references.pmid: 18705849
references.citation: Nature. 1999 Jul 15;400(6741):256-61
references.pmid: 10421366
references.citation: Plant Physiol. 2011 Dec;157(4):1820-31
references.pmid: 22013218
references.citation: Genetics. 2004 Jun;167(2):941-7
references.pmid: 15238542
references.citation: Plant Physiol. 2011 Dec;157(4):2120-30
references.pmid: 22010107
references.citation: Theor Appl Genet. 2007 Sep;115(5):617-25
references.pmid: 17607557
references.citation: Theor Appl Genet. 2008 May;116(8):1145-53
references.pmid: 18347773
references.citation: Plant Mol Biol. 2004 Mar;54(4):519-32
references.pmid: 15316287
references.citation: Plant J. 2003 Jul;35(1):104-15
references.pmid: 12834406
references.citation: Plant Physiol. 2002 May;129(1):181-90
references.pmid: 12011349
references.citation: New Phytol. 2011 Jan;189(2):449-58
references.pmid: 21039562
references.citation: Genetics. 2005 Sep;171(1):323-32
references.pmid: 15996988
references.citation: Proc Natl Acad Sci U S A. 2002 Jun 11;99(12):8133-8
references.pmid: 12060759
references.citation: Plant Physiol. 2009 Dec;151(4):2133-44
references.pmid: 19828671
references.citation: Theor Appl Genet. 2002 Nov;105(6-7):1038-1042
references.pmid: 12582931