using gramene to help in molecular breeding noel yap & the ...codominant markers for pita &...
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Using Gramene to Help in Molecular Breeding
Using Gramene to Help in Molecular Breeding
Noel Yap & The Gramene TeamNoel Yap & The Gramene Team
Phenotype - Genotype
DNA DNA -- RNA RNA -- ProteinProtein
GENEGENE (Open Reading Frame)(Open Reading Frame)
Messenger RNAMessenger RNA
ProteinProtein
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Blast resistance mediated by Pi-ta
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Resistant to M. grisea race IB-49 (isolate ZN52). Resistant to M. grisea race IC-17 (isolate ZN57).
Pita
Phenotype
Long grain length; early maturityDescription
Bonnet 73/CI 9722//Starbonnet/Tetep/3/Lebonnet
Parents
KatyGermplasm name
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R S
Jia et al 2002. Crop Sci 42:2145
Dominant markers forPita resistance gene
TCAGGTTGAAGATGCATAGCYL102
CAATGCCGAGTCTGCAAAGGYL100Pi-ta403
CTACCAACAAGTTCATCAAAYL87
AGCAGGTTATAAGCTAGGCCYL155Pi-ta1042
ATGACACCCTGCGATGCAAYL154
CAACAATTTAATCATACACGYL153Pi-ta440
SequencePrimerLocus
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Codominant markers for Pita & pita
CTACCAACAAGTTCATCAAAYL87
CAATGCCGAGTCTGCAAAGGYL183pi-ta
CTACCAACAAGTTCATCAAAYL87
AGCAGGTTATAAGCTAGGCCYL155Pi-ta1042
SequencePrimerLocus
Jia et al, 2004. Phytopathology 94:296
Pi-ta1042
pi-ta
R R R R R R R R RS S S S S S S S S
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Heading QTL Hd1 & Hd3
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Map-based cloning of Hd1 QTL• Hd1 is allelic to Se1 – a major gene controlling
photoperiod sensitivity (PS).• R1679 and P130 –RFLP markers were used to detect
DNA recombination events between Hd1 and markers.• Fine scale and high resolution mapping
Yano et al
Hd1
Se1
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Hd1 sequence and allelic variation.Yano et al. 2000. Plant Cell 12:2473
M. Yano, et al. 1997. TAG 95:1025L. Monna, et al. 2002. TAG 104:772
Hd3
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Hd3a promotes transition to flowering by Hd1 under short-day conditionsKojima et al. 2002. Plant Cell Phys 43:1096
Hd3
Hd1
Epistatic interaction between QTL Hd1 and Hd3Lin et al. 2000. Theor Appl Genet 101:1021
Fig. Morphology of Fig. Morphology of wildwild--type and dwf7type and dwf7--1 plants1 plants
((ChoeChoe et al., The Plant et al., The Plant Cell, Vol.11, 207Cell, Vol.11, 207--221)221)
Flower Development Pathways
Hd1
Hd3a
aesrg.tamu.edu/image
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Sasanishiki-sd1 Sasanishiki Taichung65 IR8 (sd1)
Green Revolution Gene in Rice, sd1
--- Comparison of phenotypes between mutant and phenotype
Sasaki et al. 2002. Nature 416: 701-702.
Monna et al. 2002. DNA Research 9: 11-17
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Wild-type phenotype---Nipponbare, Taichung 65, etc
Same sd1 phenotype
383-bp deletionDee-geo-woo-gen
IR8
ggg10gtgGly(94)ValJikkoku
ctc10ttcLeu(266)PheCalrose76
gac10cacAsp(349)His
Reimei
Sasaki et al. 2002. Nature 416: 701-702.
Phenotype ≠ Genotype
250 250 bpbp
500 500 bpbp
750 750 bpbp1000 1000 bpbp
IR64IR64 IR8IR8
LemontLemontNipponNippon--barebare
O. O. rufipogonrufipogon
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IR64
With sd1 gene
Nipponbare
Without sd1 gene
Milyang 23
With sd1 gene
Phenotype ≠ Genotype
Yield QTL yld2.1Yield QTL yld2.1
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yld2.1Xiao et al, 1996. Genes from wild rice improve yield. Nature 384:223.
V/64
V20BO.
rufip
ogon
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Xiao et al., 1996Nature 384:223
Septiningsih et al., 2003TAG 107:1419
Thomsom et al., 2004TAG 107:479
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Find markers in the rice genome
GR TIGR Assm IRGSP Seq 2005
www.gramene.org
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The Gramene Team
Not pictured:Doreen WareEd BucklerSteve SchmidtLiya RenKiran RatnapuWill SpoonerShuly AvrahamChengzhi Liang