Functional mechanisms of drought tolerance in maize

Transcription

1 Functional mechanisms of drought tolerance in maize Nepolean Thirunavukkarasu Division of Genetics Indian Agricultural Research Institute New Delhi

2 Mt Importance of Maize in India Area: Production: Productivity: Current 8.55 m ha m t 2.54 t/ha Y2050 Rosegrant et al % 1% 1% 25% 12% 12% Maize Utilization Pattern in India How to improve productivity? Better cultivars Better cultural practices Stress tolerance

3 IPCC weather report for The Palmer Drought Severity Index

4 % yield reduction Yield loss-water stress Critical stage Tasseling Silking Blister stage Milk stage Soft dough Hard dough Emergence Pollination Maturity

5 Phenotyping for Drought Drought nursery, Summer 2011, 2012 o88 genotypes/maturity group = 264 genotypes oalpha lattice design 1 Phenotyping owell-irrigated control oflowering stage stress Locations 1. IARI, New Delhi 2. ANGRAU, Hyderabad 3. Maize Research Station, Karimnagar 3 2

6 Genotyping 240 genotypes was genotyped by genomewide SNPs using Illumina Infinium assay. ~56,000 SNPs covering entire maize genome. 240 x = 13.4 million SNPs LD Heatmaps Chromosome 3 Chromosome 8

7 > 5 MAF LD decay Per se LD pattern = 0 MAF > 5 MAF > 10 MAF Chromosome LD decay (Kb) r r Mean high (r 2 > 0.8) Intermediate (0.4 < r 2 < 0.8) Low (r 2 < 0.4)

8 Population stratification Cross validation Principal components G1 G2 G3 + G4

9 Model effect - ASI, Hyderabad K Mixed model for BLUPs: 3 location 2 year 2 treatment 3 maturity group R: GenAbel 1. G + P + Kinship + MDS + FDR 2. G + P + Kinship + MDS + Pop structure + FDR R: GAPIT 3. G + P + Kinship + PCA + FDR 4. G + P + Kinship + PCA + Pop Structure + FDR K + PCA Anthesis- Silking Interval, Across data K + PCA + Structure

10 P value heat map of significant SNPs SNP Chr. Position (Mb) ASI Ear Length Ear girth Kernel/Row Kernel Row/cob 100 K wt Grain yield P value

11 Chromosome 5 Gene model IARI Hyderabad Karimnagar Mean M1 M2 M3 M4 Grain Yield Drought responsive genes Other genes MYB transcription factor ERF-Ethylene responsive factor SBP- Transcription Factor

12 Functional roles of candidate SNPs associated with drought tolerance Drought-tolerant genes NAC, flavin monooxygenase, V-type PPase H + pump Molecular mechanisms Drought Tolerance Trait expression

13 Expression of Transcriptomes HKI PC3 HKI1532 (Tolerant) PC3 (Sensitive) HKI 1532 PC3

14 HKI1532 Co-expression map 544 microarray samples PC genes 1139 genes 174 drought-related genes 75 unique to HKI1532 ohsp-coding gene was co-expressed with 19 DEGs omyb coexpressed with 50 DEGs oerf coexpressed 84 DEGs

15 Drought-responsive genes of HKI1532 Cluster 3: Phtosynthesis Cluster 2: Signalling and phosphoprotein cascade genes Cluster 1: Stomatal closure (NAC, WRKY, ERF, AP2, MYB, SBP, C2H2, and NF-YB) Cluster 1 Cluster 2 Cluster 3 Cluster 4 Cluster 5 Cluster 6 Cluster 7 Cluster 8 Cluster 9 Cluster 10 Cluster 11 Up-regulated DEGs 0-10 Fold Change > Fold Change > Fold Change >1000 Fold Change Down-regulated DEGs 0-10 Fold Change > Fold Change > Fold Change >1000 Fold Change

16 Functional relationship of genes Drought Stress Sensors TFs MAPK, G-Protein, Phosphoinosides, PPFGS-II, Calmodulin, Calcium Kinases Ethylene, ABA, Jasmonate, Brassinosteroid synthesizing gene Stomatal Closure G3PD, Chl-AB binding protein, ATP synthase, RuBisCo, PAK, PS-I & II, F 1-6-biophosphate, Glycolate Oxidase ROS OPR AAA ATPase, LEA, HSPs, Chaperonin, PDI Protein folding CIP Protease, Subtilisin Like Protease, HSP, MAPK, Cysteine protease1 Protein degradation JA Synthesis Cell wall Loosening Expansin, XET, NAC, Auxin, FMO Cystein Protease, Phospholipase A/D, TPA, LOX Hydrolysis SqMO, PSS, CYT450, PAP, ACP Synthase, ACP COA Ligase Synthesis SAM, Glutamine Synthetase, Polyamine Oxidase Polyamine Metabolism PLP dependent enzyme, AspAT, AlaAT Amino acid Metabolism Amylase, Invertase, Hexokinase Starch duration Sucrose Synthase, Starch synthase, AGP small/large subunit Sucrose Synthesis Glutathiane S- transferase, WRKY, GDP mannase, ADH, Catalase, Superoxide dismutase Protein folding and elimination of damaged & misfolded protein Root growth at apical region Lipid Molecules Protect cell Membrane by stabilizing membrane composition Soluble sugar & Sucrose concentration increases Detoxification MtN3, Sugar Acts as signaling in transporters, ABC Sucrose Initiate sugar related A. Maintenance of photosynthesis initiating stress and other metabolic response transporters, acts as stress responsive Auxin Transporters Osmolyte pathways B. Maintenance of water balance C. ROS scavenging WRKY, NA+/H+ antiporter, LEA, TIP, AWPM-14. Vacular Protein Decrease water potential & helps in water absorbance Osmoregulation

17 Comparative co-expression maps Maize Rice Wheat 544 samples, 1810 genes 1531 samples, 2539 genes 901 samples, 3438 genes

18 bhlh-regulate ABA, signalling, jasmonate pathway C2H2-Stomatal closure, ABA pathway, regulation of transcription NAC-Stomatal closure, embryo/flower/root development, cell wall ERF-Transcription regulator WRKY-ABA signalling, jasmonate, embryogenesis, signalling bhlh C2H2 NAC ERF WRKY bhlh C2H2 Comparative gene regulation ERF bhlh Maize Rice Wheat ERF NAC 17 families WRKY 494 genes C2H2 NAC WRKY 17 families 287 genes 17 families 449 genes

19 Role of mirnas in gene regulation 42 target mrnas expressed differentially under drought were regulated by 13 mirnas families. Single mirna was controlling multiple mrna targets mirna Target mrna Interaction Prediction Expression of mirnas and their targets MiRNA Target mrna Function HKI1532 (Tolerant) mirna mrna PC3 (Sensitive) mirna mrna zma-mir 159e-3p m MYB TF Down Up Up Down zma-mir 164h-5p m NAC TF Down Up Up Down zma-mir 166a-3p m ERF TF Down Up Up Down

20 Summary Genes/SNPs responsible for important biological functions Photosynthesis Osmoregulation ROS scavenging Metabolic processes Selected founder lines Shuffling/combining the alleles Selection of genotypes with better allele/gene compositions

21 Acknowledgements Donors National Agricultural Innovation Project Network Project on Functional Genomics, ICAR Collaborators Firoz Hossain Sumalini Shobarani Sreelatha Research Fellows/Technicians Rajesh Kumar Kaliyugam Rinku Sharma Kanika Sweta Swati Rita Kumari Namratha

22 THANK YOU