From basic research to crop improvement Dirk Inze VIB-UGent Center for Plant Systems Biology Oct 2017
The Great Challenge By 2050 70% more food on the same land area Growing world population Climate change - Sustainability Oct 2017 Dirk Inze VIB Center for Plant Systems Biology
Plant size and plant organ size are major determinants for yield Genotype X Environment Plant organ size is remarkably constant Oct 2017 Dirk Inze VIB Center for Plant Systems Biology
Leaves as model to study plant organ growth Arabidopsis 1,000,000,000 square km leaf on earth Oct 2017 Maize Dirk Inze VIB Center for Plant Systems Biology
> 60 leaf growth promoting genes identified and their mechanism studied Wild-type Leaf series AVP1 BRI1 GA20-OX Size is determined by. Number of cells. Size of cells GRF5 5 examples
Leaf size is a quantitative trait: how to measure leaf growth with high precision and throughput? Phenotyping platforms Image processing Data analysis and visualization Increased throughput by multi-level automation Oct 2017 Dirk Inze VIB Center for Plant Systems Biology
Automated phenotyping @ www.wiwam.be Oct 2017 Dirk Inze VIB Center for Plant Systems Biology
Cellular processes governing organ size in Arabidopsis Number of cells recruited at the shoot apical meristem to become part of the leaf primordium 24 days DA1; SAMBA; STRUWELPETER Oct 2017 Dirk Inze VIB Center for Plant Systems Biology
Cellular processes governing organ size in Arabidopsis Cell proliferation Duration to complete a round of cell division 24 days APC10; CDC27a; FBX92; GIFs; AIP10; ABAP1 Oct 2017 Dirk Inze VIB Center for Plant Systems Biology
Cellular processes governing organ size in Arabidopsis 24 days Transition from cell division to cell expansion ANT; AIL; ARGOS; AVP1; BRI1; BB/EOD1; CYCD3; DA1; DA2; DELLA; EBP1; ERF5/ERF6; GA20Ox; GIFs (AN3); GRF3; GRF5; JAW (mri396); KLUH; MED25; NGATHA; OBP4; TCP4; UBP15 Oct 2017 Dirk Inze VIB Center for Plant Systems Biology
Cellular processes governing organ size in Arabidopsis Only cell expansion and cellular differentiation 24 days ARF2; ARL1; CCS52a; EXPANSINS; EBP1; GA20OX; DELLA; OBP4; RPT2; SAUR19; SAUR36; TOR; ZHD5 Oct 2017 Dirk Inze VIB Center for Plant Systems Biology
Cellular processes governing organ size in Arabidopsis Activity of the meristemoids (only in dicots) KIX 8/KIX9; PEAPOD; SAP 24 days Oct 2017 Dirk Inze VIB Center for Plant Systems Biology
From individual genes to networks
Growth regulatory modules: leaf initiation
Growth regulatory modules: cell cycle
Growth regulatory modules: early cell division
Mutation in DA1 enhances organ growth and abolishes DA1 peptidase activity WT Transgenic WT Transgenic ICE61 Yeg-1 An-1 Cvi-0 Ler-0 Sha Col-0 Blh-1 ICE153 ICE138 ICE97 Ey15-2 C24 ICE163 Oy-0 ICE75 Most accessions visibly responded by changing their growth Oct 2017 Dirk Inze VIB Center for Plant Systems Biology
Translation to crops Wild-type DA1 R358K Maize Xie et al., 2017 Plant Biotech Journal Brassica Wang et al., 2017 Wild-type versus DA1 mutant
Growth regulatory modules: transition cell division to cell expansion
Complex molecular machines: SWI/SNF chromatin remodeling complex Oct 2017 Dirk Inze VIB Center for Plant Systems Biology
SWI/SNF chromatin remodeling complex: larger organs (leaves, seeds, ) Oct 2017 Brassica (collaboration with Javier Palatnik) Dirk Inze VIB Center for Plant Systems Biology
Increased seed yield in rice Li et al., 2016
LER (mm/h) GA20-OX enhances the speed of growth 4.5 4 3.5 3 2.5 2 1.5 1 0.5 0 0 2 4 6 8 10 12 14 days after leaf 4 appearance WT UBI-L::GA20OX Overexpression of GA20-OX 33.1 % larger leaves Oct 2017 Dirk Inze VIB Center for Plant Systems Biology
LER (mm/h) PLA1 extends the duration of growth 3.5 3 2.5 2 1.5 1 0.5 0 0 2 4 6 8 10 12 14 days after leaf 4 appearance WT GA2OX::KLUH Ectopic expression of PLASTOCHRON 1A (PLA1A) 15.5% larger leaves Oct 2017 Dirk Inze VIB Center for Plant Systems Biology
Field trials in Belgium and Iowa Hybrids Two years Two locations 88,000 plants/ha Oct 2017 Dirk Inze VIB Center for Plant Systems Biology
Increased seed yield in PLA1 hybrids Line 1 Non-transgenic Transgenic Line 2 Non-transgenic Transgenic 7-14% more kernels per row 6-16% larger seeds 17-27% larger cobs 18-27% higher cob dry weight PLA1A (KLUH)-mediated growth regulatory mechanisms conserved in different organs Oct 2017 Dirk Inze VIB Center for Plant Systems Biology
Growth regulatory modules: cell expansion
Growth regulatory modules: meristemoids
Inactivating PEAPOD pathway triggers enhanced growth and yield Specific for dicots BIG SEEDS1 is the Medicago PEAPOD orthologue (Ge et al., 2016) Oct 2017 Dirk Inze VIB Center for Plant Systems Biology
Inactivating PEAPOD in soybean enhances seed yield Naito et al. 2017
BIG LEAF of poplar encodes a SAP Yordanov et al., 2017 Oct 2017 Dirk Inze VIB Center for Plant Systems Biology
Many growth promoting genes act additively or synergistically to further promote growth In 80% of pair wise combinations of 13 leaf growth enhancing genes, additive or synergistic effects on leaf size were found Oct 2017 Dirk Inze VIB Center for Plant Systems Biology
Triple gene combinations: da1-1 eod1-2 samba DA1: ubiquitin receptor/peptidase (dominant negative) EOD1-2: E3-ligase ubiquinating DA1 SAMBA: interactor and inhibitor of APC/C complex
LER (mm/h) The combination of GA20-OX and PLA1 affects both the speed and also the duration of growth 4.5 4 3.5 3 2.5 2 1.5 1 0.5 0 0 2 4 6 8 10 12 14 days after leaf 4 appearance WT combination Additive effects on growth by combined overexpression of GA20-OX and PLA1A 50.0 % larger leaves Oct 2017 Dirk Inze VIB Center for Plant Systems Biology
From knowledge to crop improvement Knowledge-based Basic Research Numerous in-house growth-related datasets in Arabidopsis and maize Emphasis on mode of action research Strong bioinformatics and systems biology expertise In-house maize transformation pipeline: highly efficient genome editing In-house automated phenotyping platform for maize plants grown to full maturity (PHENOVISION) Expertise with transgenic field trials Oct 2017 Dirk Inze VIB Center for Plant Systems Biology
Phenovision 400 plants up to 2.5m height 4 different watering regimes RGB Thermal Hyperspectral (200 # wavelengths)
Maize RGB imaging 3D model Multi view RGB imaging Growth and development o shoot height o shoot width o shoot volume o shoot bounding volume o total leaf surface area o stem diameter o stem length o leaf number o leaf angle Time (days after plant emergence)
Hyperspectral imaging Two top-view cameras capture light reflected by plant VIS-NIR (400 1000 nm) SWIR (1000-2500 nm) => complete reflectance spectrum for every pixel at 3 & 6 nm steps soil drying period soil water deficit well-watered
Stacked transgenes in PHENOVISION Wild-type PLA1 GA20-ox GA20-ox X PLA1 Well watered conditions Oct 2017 Dirk Inze VIB Center for Plant Systems Biology
Mild drought stress in Phenovision Well-watered Mild Drought Time (days after plant emergence)
Stacked transgenes in PHENOVISION increases final leaf length under mild drought Wild-type PLA1 GA20-ox GA20-ox X PLA1 Mild drought conditions Oct 2017 Dirk Inze VIB Center for Plant Systems Biology
Stacked transgenes in PHENOVISION Increased biomass productivity The PLA1 X GA20 ox transgenics under mild drought are even larger that the wild type plants under well watered conditions Field trials planned for 2018 in Belgium and Missouri(USA) Oct 2017 Dirk Inze VIB Center for Plant Systems Biology
Cycling of knowledge from lab to field to lab allows faster learning Subtle phenotypes Sensor technology Organ growth Genes Pathways Regulation Phenotyping Automated, high-throughput phenotyping in Greenhouse Field Germplasm Environment Ultimate Goal: Yield Climate Resilience Precision breeding Genome editing
The Great Challenge By 2050 70% more food on the same land area Oct 2017 Dirk Inze VIB Center for Plant Systems Biology
Thank you Dirk Inze VIB-UGent Center for Plant Systems Biology Oct 2017