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Molecular markers and genomics: interfacing pre-breeding and commercial wheat breeding

Molecular markers and genomics: interfacing pre-breeding and commercial wheat breeding. Dr Michael Francki Manager- Biotechnology Plant and Animal Genome XVI Town and Country Hotel, San Diego, CA 12 January 2008. Pre-breeding and commercial breeding.

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Molecular markers and genomics: interfacing pre-breeding and commercial wheat breeding

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  1. Molecular markers and genomics: interfacing pre-breeding and commercial wheat breeding Dr Michael Francki Manager- Biotechnology Plant and Animal Genome XVI Town and Country Hotel, San Diego, CA 12 January 2008

  2. Pre-breeding and commercial breeding

  3. Target traits for pre-breeding of spring wheat in Western Australia Disease: Stagonospora nodorum (leaf and glume resistance) New sources of rust resistance Abiotic Stress: Salt tolerance- exploitation of wild relatives Grain quality: Genetic analysis and QTL in adapted germplasm: Flour (b*) colour, milling yield, water absorption, non-null4A GBSS FSV Adaptation: Allelic determinants of Ppd and Vrn genes for adaptation of Australian wheat to major grain production zones

  4. Leaf blotch Glume blotch S. nodorum- QTL mapping Adult plant resistance from spring and winter wheat sources Polygenic control- independent flag leaf and glume resistance QTL and flanking markers identified Flag Leaf: chromosome2DL (Shankar et al, in press) Flag Leaf: chromosome 2AL (unpublished) Glume: chromosome 2DL (Uphaus et al, 2007. Crop Sci 47:1813) Glume: chromosome 4BL (Shankar et al, in press) Phenotyping in multiple locations (local environments, USA and Australia) Each QTL accounts for 10-38% of total phenotypic variation Heritability: 0.77-0.81

  5. S. nodorum- Adoption through germplasm development • Donor Parent • leaf (2DL) and glume (4BL) resistance from spring wheat 6HRWSN125 • glume (2DL) resistance from winter wheat P91193D1 • Choice of recurrent parents • Stage 3&4 crossbreds and released varieties- hard, soft and noodle classes with acceptable quality standards • Minimal standards for rust resistance • Marker polymorphism flanking QTL • Same Rht1 and Rht2 alleles • Background resistance to S. nodorum • Backcrossing and marker screening • Generate BC1F2 (spring wheat donor) and BC2F2 lines (winter wheat donor) • SSR screening at each generation using Multiplex Ready Technology™ (MRT™)

  6. 2040 assays 6888 assays BC1F2 selections from 6 populations 63 lines with leaf QTL 107 lines with glume QTL 11 lines with leaf and glume QTL BC1F2 phenotyping commencing in 2008 BC2F2 selections from 8 populations ongoing X X S. nodorum- MAS using MRT 14 populations developed: 350-400 BC1F2 andBC2F2 progeny/population Selection of heterozygous lines for QTL at BC1F1/ BC2F1 using single SSR Selection of homozygous lines for QTL at BC1F2/ BC2F2 using flanking SSRs

  7. 1DL.1RS Gabo T6-1 49-7 CS 0c 4 4 0c 4 Novel stem rust resistance (SrR) SrR+ identified on chromosome 1RS from ‘Imperial’ rye in 1DL.1RS translocation (notSr31) Linkage between secalin and rust resistance broken in 1DS recombinants T6-1: SrR+ Sec-1- T49-7: SrR- Sec-1+ pAS1 + Rye DNA probe Rye DNA probe Small introgression Rye DNA probe Rye DNA probe

  8. SrR+Sec-1- WAWHT2046 SrR+Sec-1- BC1F1 individuals BC1F1 individuals parents for recurrent backcrossing Deployment of SrR • Deployment in Western Australian wheat germplasm • PCR marker, AW2-5, developed for tracking rye segment • Deploying SrR on rye segment in WA adapted germplasm • 5 BC4F2 populations using hard, soft and noodle varieties as recurrent parents • Selection at each backcross generation using AW2-5 • Grain quality evaluation at BC4F3 to confirm no quality defects

  9. Wheatgrass chromatin 524-568 Salt tolerance from wild relatives • Na+ exclusion from tall wheatgrass introgressed into wheat • Homoeologous group 3 substitution lines account for ~50% of Na+ exlcusion (Mullan et al 2007 MGG 277:199) • Induce homoeologous recombination with wheat • Marker development (EST-SSR) for tracking small wheatgrass segments (Mullan et al 2005, Genome 48:811) • Classify karyotypes according to different introgressed segments (Mullan et al, unpublished)

  10. Salt tolerance-comparative genomics and candidate genes Functional genes for Na+ transport in Arabidopsis SOS1, NHX1, NHX5, AVP1, AVP2, HKT1, LCT1 Comparative genomics to identify orthologs in wheat and wheatgrass using rice as a bridging species

  11. Gene expression of SOS1 and HKT1 in 3E substitution lines +/- 200 mM Na Cl Complex interaction of other genes from wheat and wheatgrass for low Na+ accumulation Salt tolerance- gene location and expression Chromosomal assignment of wheat and wheatgrass orthologs forSOS1, NHX1, NHX5, AVP1, AVP2, HKT1, LCT1

  12. Rust resistance Salt tolerance Stagonospora resistance Summary

  13. Acknowledgments DAFWA Esther Walker Steve Brown Ghader Mirzaghaderi Allison Crawford Manisha Shankar Hossein Golzar Rob Loughman Intergrain Pty Ltd Robin Wilson Iain Barclay Robyn McLean Chris Moore Purdue University Jim Uphaus Herb Ohm The University of Western Australia Daniel Mullan Tim Colmer University of Adelaide Ian Dundas Ratna Anugrahwati Ken Shepherd Dawn Verling Matt Hayden

  14. Thankyou………..

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