ADAPTAWHEAT Genetics and physiology of wheat development to flowering: tools to breed for improved adaptation and yield potential

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1 ADAPTAWHEAT Genetics and physiology of wheat development to flowering: tools to breed for improved adaptation and yield potential

2 ADAPTAWHEAT Partners 1 John Innes Centre JIC United Kingdom 2 Universidad de Lleida UdL Spain 3 Institut National de la Recherche Agronomique INRA France 4 Leibniz-Institut fuer Pflanzengenetik und Kulturpflanzenforschung IPK Germany 5 Agricultural Research Institute of the Hungarian Academy of ARI HAS Hungary Sciences 6 KÃ benhavns Universitet UCPH Denmark 7 Vyzkumny Ustav Rostlinne Vyroby CRI Czech Republic 8 Ministry of Education and Science IPBB Kazakhstan 9 Consejo Nacional de Investigaciones Cientificas y Tecnicas CONICET Argentina 10 Centro Internacional de Mejoramiento de Maiz y Trigo Int CIMMYT INT Mexico 11 Commonwealth Scientific and Industrial Research CSIRO Australia Organisation 12 Societe RAGT 2N SAS RAGT 2N France 13 Semillas Batlle SA SB Spain 14 Institut za Ratarstvo i Povrtarstvo IFVCNS Serbia 15 Traitgenetics GmbH TGEN Germany 16 KWS Lochow GmbH KWS-L Germany 17 Limagrain UK Limited LVH UK United Kingdom 18 Arvalis Institut du Vegetal ARVALIS France

3 Diverse heading date Near Isogenic Lines assessed by ADAPTAWHEAT partners in multi site trials and Controlled Environments Precise genetic stocks supplied Agronomic phenotyping Physiological phenotyping

4 Manipulating adaptation while increasing, or at least avoiding decreasing, HI Harvest Index (spike fertility) Spike fertility Spike DW Frost Heat (Drought) Fruiting efficiency Spike DW Anthesis ppd-eps-(vrn) Time to anthesis Adaptation of reproductive growth across the wide range of latitudes in which wheat is grown Spike growth duration Optimising development to lengthening spike growth period Time Anthesis

5 Wheat became a crop species in the fertile crescent Wheat

6 Wild relatives Evolution of wheat Triticum urartu AA Modern cultivars Triticum turgidum AABB Aegilops speltoides BB Ancient landraces Triticum tauschii DD Triticum aestivum AABBDD Triticum spelta AABBDD

7 Flowering time is an important trait in bread wheat influencing adaptation and performance (after Slafer & Rawson, 1994) Light Nitrogen Water High temps Drought Cold temps

8 Short Day Variation in vernalization requirement and photoperiod sensitivity plays a key role in adaptation to mega environments Frozen Winter Spring wheat germination Long Day Wet / cool germination Short Day Winter Winter wheat Long Day Summer flowering Dry/Hot harvest harvest Wet / warm Summer flowering Short Day Short Day Wet / cool Wet / warm Winter Green Revolution Spring wheat flowering Long Day harvest germination Winter Winter wheat Summer Long Day flowering Summer Dry / hot harvest Dry / hot

9 Farming is changing within these environments eg sowing date % crops In September Before 20th Sept Year Source: Defra funded Winter Wheat Pest and Disease Survey

10 Three classical definitions of wheat Vernalization flowering time genes Earlier flowering in response to prolonged cold treatment Photoperiod Response to the length of the day Earliness per se (eps) Response to endogenous signals not influenced by environment

11 Examples of photoperiod response in wheat

12 Ppd-1 is the major gene controlling photoperiod response in wheat and barley

13 Positional cloning of Ppd-H1 in barley revealed the allelic variation underlying photoperiod insensitive alleles from the D and A genomes of bread wheat

14 B genome photoperiod insensitivity is conferred by increased copy number Wild type Chinese Spring (Marquis 2B) DN Alchemy Robigus Paragon Beaver Cappelle-Desprez JIC synthetic Mercia Opata 85 Renan copy number variants Chinese Spring Chinese Spring Tetrasomic 2B Sonora 64 Timstein Chinese Spring Nullisomic 2B Recital Tremie TaqMan copy number estimate 8

15 Adaptive significance of Ppd-D1 in Europe% yield benefit of early flowering Early flowering mutant vs. wild type Ppd-D1 15 C mean July isotherms -1.8 (10) +7.7 (6) 20 C (4) 2D Wheat Worland et al. Euphytica 100: (1996) 25 C

16 Levels of conservation in the molecular control of flowering between the grasses and the model dicot Arabidopsis A B C Arabidopsis PRR7 PRR9 v Rice PRR73(Hd 2) P RR37 P RR59 P RR95 CCA1 L HY OsCCA1 FVE FVE LUX FPA CLF L UX Hd6 FPA LUX ELF4 PRR5 ZTL FLK FIE1 ELF4 ZTL FLK ELF4 P RR3 +GI LD MSI1 LD TOC1 FLD SWN OsTOC1 FLD LUX FY VEL1 LUX FY FIE1 FCA VIN3 FCA MSI1 COP1 VRN1 COP1 SWN ELF3 VRN2 ELF3 VRN5 GI VRN5 OsGI *2 GI Temperate grasses PRR 73 (Ppd1) P RR37 P RR59 P RR95 CCA1 ZTL TOC1 LUX COP1 ELF3 FVE FPA FLK LD FLD FY FCA v FIE1 MSI1 SWN VRN5 CDF1 CDF2 CDF3 CDF5 RFI2 PhyB SPA1 SPA3 SPA4 COP1 PhyA CRY1 CRY2 FKF1 LKP2 ZTL CO mir172 TEM1 TEM2 FRL1 FRL2 FES1 SUF4 FRI +PAF1 e SWR1 HUA2 CO TOE1 LHP1 SMZ +MAF1 ld +HA P3 HA P5 v AGL1 9 AGL24 FLC CDF PhyB SPA COP1 PhyA CRY1a,b CRY2 FKF1 LKP2 ZTL Hd1 HD1 sd +HAP3 HAP5 [Vgt1] sd OsCO3 FRI? [ID1] OsID1 HUA2 LHP1 FKF1 LKP 2 ZTL *1 CDF *1 CO1 CO2 OsMA DS51 PhyB AGL 41 SPA COP1 ld sd Ehd1 Ghd7 ld PhyA CRY1a,b CRY2 CO ld +HA P3 HA P5 TOE1? CO3 ID1 VRN2 FRI? v *3 VRT2 ld VRN1 *4 HUA2 LHP1 clock A, am SVP FD Age mir156 FT + FD SOC1 ELF9 OsMADS22 OsMADS47 OsMADS55 FD [DLF1] + FD Hd3a RFT1 + Gf14c OsMADS50 B m1 B m10 V RT2 sd FT1 (VRN-3) S OC1 FT2 FT3 (Ppd-H2) FD + FD SPL3 FUL AGL17 TFL1 AP1 LFY OsMADS 14 OsRCN OsMADS 15 OsLFY TFL 1 VRN1 LFY Flowering Flowering Flowering

17 Chromosomal locations of flowering time genes in the Triticeae FT4 FT2 GI CO7 Ppd-1/PRR7 CO3 PhyA PhyA CO8 PhyA PhyA CO4 PhyB Ppd-2/FT3 CO ELF3 PhyC Vrn3/FT1 CO1 CO5 CO2 CO6 FT5 Vrn-2 Vrn-1

18 The major determinant of spring and winter type in bread wheat results from variation at Vrn-1 Wheat Vrn Mutant (spring type) is semi-dominant Mutation only known on 7B but gene exists on A, B and D VRN-3 VRN-1 VRN-2 A B D A B D A B D Mutant (spring type) is recessive and is only known in diploids. Probably need mutation of all three homoeologues to see a phenotype in hexaploid wheat. Mutant (spring type) is semi-dominant Mutation of one homoeologue is sufficient to give a spring type.

19 Dominant spring growth habit alleles of Vrn-1 in bread wheat Intact winter allele kb VRN box CArG box ATG STOP A genome Vrn-A1a Vrn-A1b Vrn-A1c B genome Vrn-B1a Vrn-B1b Vrn-B1c D genome Vrn-D1a Vrn-D1b Mutations or deletions Repetitive element Adapted from: Regulation of flowering in temperate cereals A Distelfeld, C Li and J Dubcovsky. Current Opinion in Plant Biology, 12, 1-7, 2009

20 Time to heading Earliness per se Photoperiod/vernalization response Vernalization (days) and/or Photoperiod (hours) Earliness per se aka Intrinsic earliness Narrow sense earliness Basic vegetative period Inherent earliness

21 Variation in earliness per se can reflect differences in phasic development and temperature sensitivity Floral initiation Ear emergence Phases of development Different time of ear emergence but same floral induction Same time of ear emergence but different floral induction Temperature sensitivity Rate of development towards heading 1/days Cappelle Desprez Sunset Temperature ( o C)

22 Ear emergence QTL (eps) in Avalon x Cadenza

23 Using backcrossing to Mendelise heading date QTL

24 SNP and haplotype analysis in hexaploid wheat

25 The wheat 90K array Marker on the array ,0% Functional in hexaploid wheat ,0% Polymorphic in hexaploid wheat (European material) ,5% Functional in durum wheat ,3% Polymorphic in durum wheat MAF between 0.1 and ,4%

26 Norm R SNP assays in wheat detecting all three genomes 2.00 Kukri_c23011_ Norm Theta

27 Norm R Norm R SNP assays in wheat detecting two genomes hexaploid Durum (tetraploid) tplb0024k14_744 Kukri_c23011_ Norm Theta Norm Theta

28 Norm R SNP assay in wheat detecting one genome GENE-0126_ Norm Theta

29 Example for genotype data in wheat varieties for a set of SNP markers in a specific chromosomal region

30 Genetic mapping Hexaploid wheat ITMI population