Sunflower Genome Consortium Annual Meeting Nicolas Langlade INRA Toulouse Sunflower Genome Consortium San Diego, January

INRA participation Sunflower Genome Consortium San Diego, January BAC libraries o Preparation CNRGV (H. Bergès, A. Bellec) o BAC-end sequencing LIPM Ultra High Density Genetic map – SFP using Affymetrix microarrays – Genotyping by sequencing – AXIOM map Genome annotation – Transcriptome sequencing – Transcriptome annotation – Genome annotation per se J. Gouzy, S. Carrère, N. Langlade, S. Muños, P. Vincourt

INRA participation Sunflower Genome Consortium San Diego, January BAC libraries Preparation -CNRGV (Centre National de Ressources Génomiques Végétales) H. Bergès, A. Bellec 3 BAC librairies HA412-HO BAC-end sequencing -LIPM J. Gouzy, P. Vincourt, S. Muños, N. Langlade, B. Mayjonade Development of a method to perform high-troughput BAC-end sequencing First experiment: BAC-ends are there but too much contamination

INRA participation Sunflower Genome Consortium San Diego, January Ultra High Density Genetic map – Genotyping SFP using Affymetrix microarrays P. Vincourt, S. Muños, Y. Lippi, N. Langlade, B. Mayjonade – 105 RILs from XRQxPSC8 population – >3000 mkrs – ~6000 cM  Not used

INRA participation Sunflower Genome Consortium San Diego, January Ultra High Density Genetic map – Genotyping by sequencing P. Vincourt, S. Muños, N. Langlade, B. Mayjonade 2 enzymes: PstI and MseI 2 populations: XRQxPSC8 ~192 RILs FUxPAZ2 ~96 RILs Sequencing finished end December 2013 Results expected spring 2014

INRA participation Sunflower Genome Consortium San Diego, January Ultra High Density Genetic map – Genotyping using Affymetrix AXIOM P. Vincourt, S. Muños, N. Langlade, B. Mangin In collaboration with Biogemma and Syngenta 197,914 SNPs mostly in expressed sequences from a small panel of elite lines 2 populations XRQxPSC8 180 RILs FUxPAZ2 87 RILs  35,562 polymorphic between XRQ and PSC8

INRA participation Sunflower Genome Consortium San Diego, January Ultra High Density Genetic map – Genotyping using Affymetrix AXIOM 1.35,562 polymorphic between XRQ and PSC8 + 1,691 Infinium markers from previous map (Cadic et al., 2013) assign the LG 2. Carthagene Number of markers: 31,757 on the 17 LG Total genetic distance of 1,487.7 cM Number of loci: 1,861 = map XRQxPSC8

INRA participation Sunflower Genome Consortium San Diego, January Ultra High Density Genetic map – Genotyping using Affymetrix AXIOM 1.28,529 polymorphic between XRQ and PSC8 + use of AXIOM XRQxPSC8 map to assign the LG 2. Carthagene Number of markers: 17,901 on the 17 LG Total genetic distance of 1,425.3 cM Number of loci: 807 = map FUxPAZ2

INRA participation Sunflower Genome Consortium San Diego, January Ultra High Density Genetic map – Genotyping using Affymetrix AXIOM 1.7,076 markers polymorphic between XRQ and PSC8, and between FU and PAZ2 + use of AXIOM XRQxPSC8 map to assign the LG 2. Carthagene Number of markers: 7,076 on the 17 LG Total genetic distance of 1,471.1 cM Number of loci: 1,113 = map consensus XRQxPSC8 & FUxPAZ2

INRA participation Sunflower Genome Consortium San Diego, January Ultra High Density Genetic map – Genotyping using Affymetrix AXIOM 1.All markers polymorphic between XRQ and PSC8, or between FU and PAZ2 + use of consensus XRQxPSC8 & FUxPAZ2 map as a skeleton 2. Carthagene Number of markers: 45,566 on the 17 LG Total genetic distance of 1, cM Number of loci: 2,711 = final map XRQxPSC8 & FUxPAZ2

INRA participation Sunflower Genome Consortium San Diego, January Ultra High Density Genetic map – Genotyping using Affymetrix AXIOM 1.Final map XRQxPSC8 & FUxPAZ2 2.Context sequences of the 31,757 markers polymorphic between XRQ and PSC8 and mapped 71bp context sequences Collaborative project with Biogemma and Syngenta Available now

INRA participation Sunflower Genome Consortium San Diego, January BAC libraries o Preparation CNRGV (H. Bergès, A. Bellec) o BAC-end sequencing LIPM Ultra High Density Genetic map – SFP using Affymetrix microarrays – Genotyping by sequencing – AXIOM map Genome annotation – Transcriptome sequencing – Transcriptome annotation – Genome annotation per se

INRA participation Sunflower Genome Consortium San Diego, January Transcriptome sequencing – Organ-specific transcriptomes XRQ/B inbred line Webportal

INRA participation Sunflower Genome Consortium San Diego, January Transcriptome sequencing – Suggestion: Range of abiotic stresses on the XRQ/B line: 1.Drought in leaves week old plants 2.Leaves 3.Range of stress intensities 2.Salt stress 1.Plantlets (10 days) 2.Leaves and Roots 3.2 conditions (CTL, NaCl 100 mM) 3.Osmotic stress 1.Plantlets (10 days) 2.Leaves and Roots 3.2 conditions (CTL, NaCl 100 mM) 4.? Cold 1.Plantlets (10 days) 2.Leaves and Roots 3.4 conditions (CTL time 1, 4°C time 1, CTL time 2, 20°C recovery time 2)

INRA participation Sunflower Genome Consortium San Diego, January BAC libraries o Preparation CNRGV (H. Bergès, A. Bellec) o BAC-end sequencing LIPM Ultra High Density Genetic map – SFP using Affymetrix microarrays – Genotyping by sequencing – AXIOM map Genome annotation – Transcriptome sequencing – Transcriptome annotation – Genome annotation per se

Principle of a MAGIC population Bandillo et al. Rice :11 doi: / F1 IM1 IM2 IM2-S1 IM2-S2 IM2-S3 Sunflower Genome Consortium San Diego, January

Sunflower MAGIC population proposal Two populations – Male 400 RILs – Female 400 RILs Wild parents introgressed in cultivated germplasm – 2*5 different Helianthus species and wild H. annuus from UBC germplasm – 6 different B-lines from collaborators – 6 different R-lines from collaborators Sunflower Genome Consortium San Diego, January

Tentative list of the wild material involved 10 wild founders from UBC germplasm W1H.annuusOklahoma FT annuus W2H.annuusModern weedy annuus W3H.annuusUtah annuus (sweep for drought) W4H.annuus? W5H.petiolarisGSD Large seeded W6H.neglectusLarge seeded sand dune W7H.argophyllusShort day W8H.bolanderiNorthern range serpintine W9H.anomalus? W10?? Sunflower Genome Consortium San Diego, January

MAGIC population development W1 X->F1-1 E1 X->IM1-1 E2 x->F1-2 E3 W2 X->F1-3 E2 X->IM1-2 E3 x->F1-4 E4 W3 X->F1-5 E3 X->IM1-3 E4 x->F1-6 E5 W5 X->F1-9 E5 X IM1-5 E6 X->F1-10 E1 … Sunflower Genome Consortium San Diego, January

MAGIC population development W1 X->F1-1 E1 X->IM1-1 E2 x->F1-2 E3 W2 X->F1-3 E2 X->IM1-2 E3 x->F1-4 E4 W3 X->F1-5 E3 X->IM1-3 E4 x->F1-6 E5 W5 X->F1-9 E5 X IM1-5 E6 X->F1-10 E1 … IM2-1 IM2-2 IM2-3 Sunflower Genome Consortium San Diego, January

MAGIC population development W1 X->F1-1 E1 X->IM1-1 E2 x->F1-2 E3 W2 X->F1-3 E2 X->IM1-2 E3 x->F1-4 E4 W3 X->F1-5 E3 X->IM1-3 E4 x->F1-6 E5 W5 X->F1-9 E5 X IM1-5 E6 X->F1-10 E1 … IM2-1 IM2-2 IM2-3 IM1-1 IM1-2IM1-3IM1-4IM1-5 IM1-1 IM2-1 IM2-2 ……… IM1-2 ……… IM1-3 …… IM1-4 … IM1-5 Sunflower Genome Consortium San Diego, January

MAGIC population development W1 X->F1-1 E1 X->IM1-1 E2 x->F1-2 E3 W2 X->F1-3 E2 X->IM1-2 E3 x->F1-4 E4 W3 X->F1-5 E3 X->IM1-3 E4 x->F1-6 E5 W5 X->F1-9 E5 X IM1-5 E6 X->F1-10 E1 … IM2-1 IM2-2 IM2-3 IM2-1-S1-1 IM2-1-S1-2 … IM2-1-S1-20 IM1-1 IM1-2IM1-3IM1-4IM1-5 IM1-1 IM2-1 IM2-2 ……… IM1-2 ……… IM1-3 …… IM1-4 … IM1-5 Sunflower Genome Consortium San Diego, January

W1 X->F1-1 E1 X->IM1-1 E2 x->F1-2 E3 W2 X->F1-3 E2 X->IM1-2 E3 x->F1-4 E4 W3 X->F1-5 E3 X->IM1-3 E4 x->F1-6 E5 W5 X->F1-9 E5 X IM1-5 E6 X->F1-10 E1 … IM2-1 IM2-2 IM2-3 IM2-1-S1-1 IM2-1-S1-2 … IM2-1-S families Each 20 lines  400 lines wilds 6 R-lines Sunflower Genome Consortium San Diego, January