Gene duplication and allelic diversity for adaptation to high soil boron Boron Toxicity 240 mM 67 mM 8 mM Adelaide Boron in South Australian soils Extractable B (mg/kg) 0 • SA soils are of marine origin and shallow 20 40 60 80 100 120 0-10 10-20 • B generally higher in subsoil than the root zone Soil 20-30 Depth 30-40 (cm) 40-50 50-60 60-70 70-80 80-90 90-100 Cartwright et al. (1987) http://www.dwlbc.sa.gov.au/land/soil/ Boron Toxicity Deficiency the predominant issue in northern regions Toxicity http://www.ausgraintech.com/ 16% yield advantage in tolerant lines (233 trials over 12 years) McDonald 2012 Boron toxicity associated with... Root stunting Leaf symptom expression -B +B +B Genetic Variation: Barley • Tolerance primarily based on boron efflux in roots intolerant tolerant intolerant tolerant intolerant tolerant Low boron High boron Barley QTL 4H Clipper (intolerant) X Sahara (tolerant) 6H 2H 3H Jefferies et al., 1999 Barley backcross lines - BT QTL + BT QTL Map Based Cloning rice/br achy barley/ wheat tolerance Trait/ locus barley/ wheat rice/ brachy Candidate 4H tolerance gene: HvBot1 • HvBot1, a borate efflux transporter -anion permeable channel Basis of Allelic Difference: • Bot1 tandemly duplicated in Sahara • Bot1 in Sahara highly expressed Clipper Intolerant Bot1 Sahara Tolerant Bot1 leaf tip root Science 2007 Bot1 Bot1 Bot1 Guttation and boron? 1962 1997 6H tolerance gene: HvNIP2;1 • • • • HvNIP2;1 multifunctional aquaporin: Influx transporter Orthologue of rice silicon transporter Lsi1 Clipper and Sahara proteins are identical Reduced expression allelic basis for tolerance Boric Acid Reduced tissue B is achieved by a combination of transport processes Boron tolerant Boron sensitive B NIP2;1: 6H Bot1: 4H B B Reduced influx B B- B B- Greater efflux B B B Genetic Variation: Wheat 1400 1200 1000 Leaf boron [mg/kg] 800 600 400 200 0 Halberd tolerant Cranbrook intolerant Wheat QTL 7B Cranbrook (intolerant) X Halberd (tolerant) 7D 4A Jefferies et al., 2000 Bo1 region LMA: Late maturity α-amylase Pratylenchus neglectus resistance on 7A Bo1 region O. sativa BEC NAM SBE NSF GMC ABC CHZ CAT GST PPK SPA CRF HMG HY1 UN1 CBE MYB CAL ALS PSY PNH Yellow flour colour B. sylvaticum ABC CHZ NAM SBE NSF GMC CHZ CHZ WAK CHZ CAT Xa21 GST PPK SPA CRF UN2 SEN HMG HY1 CRI UN1 The challenge: Low recombination in Cranbrook x Halberd B. distachyon SBE NSF GMC CHZ CHZ WAK CHZ CAT Xa21 Gene not present in rice GST PPK SPA CRF UN2 SEN HMG HY1 CRI UN1 SP1 CL1 CL2 CBE MYB Gene not present in Brachypodium SRP TS1 TS2 DR1 DR2 LRR RGE Different Res-genes Gene sequence not in any databases 4 Genetic map Cranbrook x Halberd 1 1 CAL RFP Os11 PSY 3 Lr14a Gene not present at all in Langdon (BAC library screen) Lr68 MYB Bo1 region SBE NSF GMC CHZ CAT, GST, PPK, SPA, Gene eventually HMG, CRF, UN2, SEN CBS NIPL identified in an Ae. Tauschii TaBot1L (utilising work of Jan Dvorak et al.) Thorsten Schnurbusch, Margaret Pallotta (Evans Lagudah) BAC Wheat boron transporter 8.8 kb Anion permeable channel 660 aa -85% similar to Barley 4H tolerance Gene HvBot1 -Similar to HvBot1: but not direct orthologue Maria Hrmova, ACPFG EMS mutants • Mutated population in Halberd • Exonic mutant 405A: 1 aa change Low boron Ala-Val High boron 50 Ha 45 40 35 30 25 20 15 EMS-405 10 5 Ha wt mut 0 Ha wt mut -20 0 20 40 60 80 100 Allelic diversity No 7A genome copies RL (mm) Root Growth Boron (mM) Expression A genome, rare allele Absent in most cultivars and A-genome progenitors Identified in a landrace from the Mediterranean Halberd-like * G 4A G61450 (Greek) Higher gene expression high tolerance 25000.0 20000.0 Expression 4A 15000.0 10000.0 - 1 synonomous SNP with Halberd 7B - No evidence of translocation - Dispersed duplication of 7B 5000.0 0.0 7B 7B 7B 4A Allelic distribution in Australia Deficiency the predominant issue in northern regions Toxicity http://www.ausgraintech.com/ Allelic distribution in Australia Advanced breeding lines and released cultivars Mix of southern and northern breeding programs (Australian Grain Technologies) • Indirect selection against tolerance allele in areas of low boron (northern regions) • Boron tolerant genotypes are always boron inefficient under low boron conditions Origins of boron tolerance in wheat Boron toxicity observed Tolerance allele source Hypothesized dispersion Tolerance alleles found Able to follow dispersion from Mediterranean to Australia and South America Boron tolerance appears to be of tetraploid origin - Introgression through the Cretan landrace- Currarwa (20th C)- Halberd Conservation of the tetraploid-derived segment in modern wheats - barrier to recombination - Issue for utilisation of important linked loci, e.g. late maturity alpha-amylase Chromosome 7L A Street Party- everyone welcome Distal 7L: 7A Sr22 , PmG16, Rlnn1, Pch2 7B Rht13, Bo1, LMA, Lr14, Pm5, Yr39, Tan spot, Yfc 7D Sr25, Pch1, Gb3 7E Lr19 , Fhb LMA = Late Maturity Alpha-amylase • Genetic defect- widespread in Australian wheat germplasm • α-amylase mid way in grain development (quality) • Halberd 7BL tolerance locus rare source of non-LMA (desirable form) Often triggered by temp shock Pollination 20 days Phenotype difficult - very slow - no visible difference - not all grains in a spike - Rht genes interfere with trait expression 30 days maturity germination - LMA + LMA Barrero et al 2013 The Boron-LMA problem? • Halberd 7BL non-LMA locus (rare) • desirable in all environments ✓ • Halberd 7BL Boron tolerance • Desirable in southern environments • Undesirable in northern environments ✓ ✗ Problem: low recombination - tetraploid origin (Cretan Landrace) - considerable haplotype conservation Rare recombinant identified: ✓ Bo1 null non LMA X LMA – positional cloning Margie Pallotta Bo1 G1 G2 G3 G4 G5 LMA G6 G7 G8 G9 G10 M1 M2 G11 Rice -absent Brachypodium - absent M1 ? ? M1 ? M2 …....... G11 ? ? ? M2 wheat BAC M T P Odd-Arne Olsen Norway 7B sequencing IWGSC Tolerance mechanisms Wheat vs. barley: • Tolerance arose through divergent evolution of paralogous genes • Transcript level variation a common determinant • Tissue specificity and inducibility differ • In wheat, comparatively broad allelic variation provided adaptation to diverse environments Tolerance mechanisms Wheat: • • • • Recent origin – post-domestication Impact of selection by early farmers Role of duplications Recent importance of landraces in development of locally adapted varieties • Strong allelic selection. Matching alleles to environments is critical Thanks to… Margie Pallotta Julie Hayes Alison Hay Thorsten Schnurbusch Ute Baumann Nick Collins Dave Edwards Andrea Pohlen Anzu Okada Peter Langridge Haydn Kuchel, AGT [email protected]
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