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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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8

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