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Identifying genes for changes in root architecture under water stress

Identifying genes for changes in root architecture under water stress. Georgia Davis University of Missouri. www.rootgenomics.org. Overview. Root architecture QTLs vp mutants Root transcriptome map. Quantitative. Qualitative. One gene Discrete distribution. Several - many genes

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Identifying genes for changes in root architecture under water stress

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  1. Identifying genes for changes in root architecture under water stress Georgia Davis University of Missouri www.rootgenomics.org

  2. Overview • Root architecture QTLs • vp mutants • Root transcriptome map

  3. Quantitative Qualitative • One gene • Discrete distribution • Several - many genes • Continuous distribution

  4. Quantitative Trait Mapping • Population segregating for the trait • Molecular markers to create a linkage map • Trait measurements • Enough replication to get a good idea of genotype vs. environmental differences

  5. Playing the Numbers • A QTL of 15 cM contains 450 - 900 loci in maize. • QTL size is reduced by increasing recombination (ex. random intermating, larger sample of individuals) and to some degree by mapping additional genetic markers.

  6. Gene 1 Mp313E Va35 1 2 3 4 5 6 Lo Hi Int. Hi Lo Int. Lo Int. Gene 2 Lo Hi Int. Hi Lo Int. Lo Int. Molecular mapping DNA fingerprint • Compare the DNA fingerprint with trait value. • Look for bands on fingerprint associated with high value and those associated with low value.

  7. QTL Mapping • Using Intermated B73 x Mo17 (IBM) population to map root architecture under well-watered and water-stress conditions. • Studying the IBM 94 reduced the number of candidate genes per cM to 14.3. • The IBM genetic map is linked to the physical map and anchored sequence information allowing us to identify genes not found on the genetic map. Mike Gerau, undergraduate

  8. Root Architecture QTL • Measured under well-watered and water-stressed conditions: • primary root length • root branching • root mass • seminal root number • shoot mass • leaf relative water content

  9. Analysis • Mean values for ww, ws and the response (ww-ws)/ww were used for QTL analysis against 643 markers spaced <10 cm apart on the genetic map.

  10. 1 2 3 4 5 6 7 8 9 10 ww ws resp ww ws resp Primary root length Seminal root # Branching Leaf # Root mass Leaf RWC Shoot mass 58 Root Architecture QTL

  11. vp5 pds1 rt1 d10 d12 la1 hsf1 knox sod3 gst rab15 rab28 Candidate Genes

  12. Endogenous ABA accumulation is required for root growth maintenance under water deficits (Saab et al., 1990; 1992; Sharp et al., 1994)

  13. phytoene phytofluene z-carotene neurosporene lycopene d-,g-carotene a-,b-carotene *possible oxidativecleavage steps in planta; reactions catalyzed by NCED (9-cis-epoxycarotenoid dioxygenase) zeaxanthin antheraxanthin all-trans-violaxanthin vp5 (maize) fluridone (FLU) 9-cis-violaxanthin all-trans-neoxanthin 9’-cis-neoxanthin * vp14 (maize) * Xanthoxin ABA-aldehyde ABA Modified from Taylor et al. (2000) J Exp Bot 51: 1563-74

  14. ROOT TIP ABA CONTENT (ng g-1 H2O) Sharp et al. (1994) J Exp Bot 45: 1743-51 118 ± 18 21 ± 5 96 ± 29

  15. vp mutants • viviparous (vp) mutants have defects in carotenoid and/or ABA biosynthesis. • Six vp mutants: vp5, vp5-DR3076, vp8, vp9, vp10 and vp12 • WW and WS • Same measurments as QTL. Ryan Dierking, undergraduate

  16. phytoene phytofluene z-carotene neurosporene lycopene d-,g-carotene a-,b-carotene zeaxanthin antheraxanthin all-trans-violaxanthin vp5 (maize) fluridone (FLU) vp10 9-cis-violaxanthin vp9 all-trans-neoxanthin 9’-cis-neoxanthin vp14 (maize) xanthoxin ABA-aldehyde ABA vp8 Modified from Taylor et al. (2000) J Exp Bot 51: 1563-74

  17. vp5-DR mutant Mean difference between well-watered and water-stressed treatments. * = significant at  = 0.5.

  18. vp8 mutant Mean difference between well-watered and water-stressed treatments. * = significant at  = 0.5.

  19. phytoene phytofluene z-carotene neurosporene lycopene d-,g-carotene a-,b-carotene zeaxanthin antheraxanthin all-trans-violaxanthin vp5 (maize) fluridone (FLU) vp10 9-cis-violaxanthin vp9 all-trans-neoxanthin 9’-cis-neoxanthin vp14 (maize) xanthoxin ABA-aldehyde ABA vp8 Modified from Taylor et al. (2000) J Exp Bot 51: 1563-74

  20. Root transcriptome map • 8000 root unigenes based on EST sequencing of clones from ww and ws root segments. • Goal: Use laboratory and computational methods to identify map locations. • Future: Align the map information with relevant mutant and QTL information.

  21. Root transcriptome map • Three strategies: • Wet-lab genetic mapping or physical mapping by BAC pools. (300) • E-mapping by identity with previously mapped probe. (~1700 genes) • E-mapping by sequence alignment to complete BAC or BAC end sequence. (in progress)

  22. Root transcriptome map 1L • Built on IBM neighbors framework • Red are core markers • Blue are newly mapped • Black are prior mapped • Can add kinematic information

  23. Mike Gerau Doug Davis Theresa Musket Hector Sanchez Steve Schroeder Bill Spollen Ryan Dierking Nicole Grweizowzciak Matt Meyer Dustin Partney Kristen Leach Dana Woodruff Acknowledgements

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