Number of Haplotypes, h 8 Haplotype (gene) diversity, Hd 0.654 Wilds Cultivars Landraces #GeneName CBF14 GeneId HORVU5Hr1G080350 TranscriptId HORVU5Hr1G080350.1 variants_impact_low 1 variants_impact_moderate 4 variants_effect_missense_variant 1 variants_effect_synonymous_variant 4
Number of Haplotypes, h 94 Haplotype (gene) diversity, Hd 0.961 Wilds Cultivars Landraces #GeneName CBF9 GeneId HORVU5Hr1G080230 TranscriptId HORVU5Hr1G080230.1 variants_impact_high 1 variants_impact_low 11 variants_impact_moderate 9 variants_impact_modifier 11 variants_effect_3_prime_utr_variant 5 variants_effect_5_prime_utr_variant 4 variants_effect_downstream_gene_variant 2 variants_effect_missense_variant 9 variants_effect_stop_gained 1 variants_effect_synonymous_variant 11
Gene Trait Barley candidate Complete Significant variants Coordinates Functional annotation Nº exons Captured Total SNPs Morex Version 2016 annotation Type Number D11 Leaf angle MLOC_61008.1 HORVU2Hr1G081650.10 chr2h:592334638-592338706 Cytochrome P450 superfamily protein 9 Partially No start codon 11 Missense 2 Number of Haplotypes, h 9 Haplotype (gene) diversity, Hd 0.535 Tajima s neutrality test -1.39 ns Ka/Ks -6.42 Fst (cultivars vs. landraces) 0.005 Synonimous mutation in exon 5 Thr->Met at 4 codon, WB-496 Arg->Gly in exon 4, WB-467
Geographical distribution of the main haplotypes (geo-referenced landraces only) Hap_1 Hap_2 Hap_3
VARIANT DATA HAS TO BE ROBUST!! Which is the real coverage of the exon capture probes? Map the capture probes and/or BAM files on the genome
VARIANT DATA HAS TO BE ROBUST!! Which is the real coverage of the exon capture probes? There is a serious problem of annotation manually check chr2h Hv_IBSC_PGSB_r1 transcript 185335712 185338937. +. gene_id "HORVU2Hr1G038940"; transcr chr2h Hv_IBSC_PGSB_r1 exon 185335712 185335948. +. gene_id "HORVU2Hr1G038940"; transcr chr2h Hv_IBSC_PGSB_r1 exon 185336040 185336098. +. gene_id "HORVU2Hr1G038940"; transcr chr2h Hv_IBSC_PGSB_r1 exon 185336179 185336234. +. gene_id "HORVU2Hr1G038940"; transcr chr2h Hv_IBSC_PGSB_r1 exon 185336343 185336395. +. gene_id "HORVU2Hr1G038940"; transcr chr2h Hv_IBSC_PGSB_r1 exon 185336536 185338937. +. gene_id "HORVU2Hr1G038940"; transcr chr2h Hv_IBSC_PGSB_r1 5UTR 185335712 185335794. +. gene_id "HORVU2Hr1G038940"; transcr chr2h Hv_IBSC_PGSB_r1 CDS 185335795 185335948. + 0 gene_id "HORVU2Hr1G038940"; transcr chr2h Hv_IBSC_PGSB_r1 CDS 185336040 185336098. + 2 gene_id "HORVU2Hr1G038940"; transcr chr2h Hv_IBSC_PGSB_r1 CDS 185336179 185336234. + 0 gene_id "HORVU2Hr1G038940"; transcr chr2h Hv_IBSC_PGSB_r1 CDS 185336343 185336395. + 1 gene_id "HORVU2Hr1G038940"; transcr chr2h Hv_IBSC_PGSB_r1 CDS 185336536 185336630. + 2 gene_id "HORVU2Hr1G038940"; transcr chr2h Hv_IBSC_PGSB_r1 3UTR 185336631 185338937. +. gene_id "HORVU2Hr1G038940"; transcr
VARIANT DATA HAS TO BE ROBUST!! Which is the real coverage of the exon capture probes? There is a serious problem of annotation manually check How to handle missing data? impute (not always reliable) remove individuals (for example for HvD11 we left with 308 indiviiduals
VARIANT DATA HAS TO BE ROBUST!! Which is the real coverage of the exon capture probes? There is a serious problem of annotation manually check How to handle missing data? impute (not always reliable) remove individuals (for example for HvD11 we left with 308 indiviiduals False heterozygus calls
Gene Trait Barley candidate Complete Significant variants Coordinates Functional annotation Nº exons Captured Total SNPs Morex Version 2016 annotation Type Number PCF6 Leaf size MLOC_63989.1 HORVU5Hr1G103400.1 chr5h:615593077-615596370 TCP family transcription factor 4 1 Partially Yes 35 Missense 10 CDS: 615,593,616-615,594,818, 16 SNPs False heterozygous calls, due to capturing gene paralogs?
Gene PsbR Trait Photosynthesis efficiency Barley candidate Complete Significant variants Coordinates Functional annotation Nº exons Captured Total SNPs Morex Version 2016 annotation Type Number - HORVU2Hr1G038940.2 chr2h:185335712-185338937 Photosystem II 10 kda polypeptide, chloroplastic 5 Partially Yes 17 START lost 1 missense 2 False heterozygous calls, due to capturing gene paralogs? Or cross capturing conserved domains?
VARIANT DATA HAS TO BE ROBUST!! Which is the real coverage of the exon capture probes? There is a serious problem of annotation manually check How to handle missing data? impute (not always reliable) remove individuals (for example for HvD11 we left with 308 indiviiduals False heterozygus calls What about InDels?
M3.3: First year characterization of elite material (M14) D3.4: Characterized elite material, and prospective parents for strategic crosses (to pyramid improved straw without penalizing yield) identified (M24)
Task 3.3 Genetic variation for traits determining biomass and yield in elite material Acc. Nr Acc. Name GH RT Country of origin Characteristics Pedigree WB-004 KW Glacier Winter 2-row United Kingdom fodder KWS Cassia x Retriever WB-006 KW Capella Winter 2-row United Kingdom fodder WB-007 Saffron Winter 2-row United Kingdom fodder Antigua x Tabatha WB-003 KW Cassia Winter 2-row United Kingdom fodder (Eden x Carat) x Saffron WB-028 Nure Winter 2-row Italy fodder (Fior 40 x Alpha) x Baraka WB-010 Meridian Winter 6-row United Kingdom fodder (Ikone x Lomerit) x Fridericus WB-011 Escadre Winter 6-row United Kingdom fodder Esterel x MH93 FV 41 WB-014 Tonic Winter 6-row Germany fodder Leibniz x LP 6-536 WB-023 Fridericus Winter 6-row Germany fodder Carola x LP 6-564 WB-025 Ketos Winter 6-row France fodder (Gotic x Orblonde) x (12813 x 91H595) ITA-01 Atomo Winter 2-row France fodder ITA-02 Cometa Winter 2-row Italy fodder F8PO 202-169 x (Amillis/Fior 2377) ITA-03 Aquirone Winter 2-row Italy fodder Fior 5186 x Naturel ITA-04 Catalina Winter 2-row France fodder ITA-05 Calanque Winter 2-row France fodder ITA-06 Alimini Winter 6-row Italy fodder FIOR 2551 x Federal ITA-07 Atlante Winter 6-row Italy fodder ITA-08 Etincel Winter 6-row France fodder ITA-09 Lutece Winter 6-row France fodder ITA-10 Shangrila Winter 6-row France fodder SPA-01 Pewter Winter 2-row United Kindom malting barley SPA-02 Zoo Winter 6-row Spain Hybrid fodder SPA-03 Kalea Winter 2-row France fodder SPA-04 Meseta Winter 2-row France fodder SPA-05 Hispanic Winter 2-row France fodder SPA-06 Dulcinea Winter 2-row France fodder SPA-07 Graphic Winter 2-row France fodder SPA-08 Cib 333 Winter 2-row Spain fodder SPA-09 Doblona Winter 6-row Spain fodder SPA-10 Mochona 5 Winter 6-row Spain fodder 10 elite cultivars from Whealbi, in both trials 10 elite Italian cultivars, only sown in Italy 10 elite Spanish cultivars, only sown in Spain
ITALY TRIAL: CREA, Fiorenzuola d Arda Sowing date: 02-11-2016 Experimental design: complete randomized block design with three replications Plot size: 1.36 m x 4 m, 300 seeds/m 2 Traits scored up to now: - Date of seedling emergence: all the plots emerged from November 20 to November 24 - Date of onset of tillering: most of the plots started tillering between February 7 and February 15 Plants did not yet start stem elongation
29-12-2016 20-03-2016
SPAIN TRIAL: School of Agronomy, University of Lleida Sowing date:16-11-2016 Experimental design: complete randomized block design with three replications Plot size: 1.2 m x 4m, 300 seeds/m 2 Traits scored up to now: date of emergence date of onset of tillering date of stem elongation (DC 3.1) total biomass, LAI, photosynthesis and SPAD on the last elongated leaf at stem elongation stage From stem elongation radiation interception once a week
The remaining traits will be scored folowing the common protocol developed by Gustavo and Roxana A second year of field trialling will be run in Italy and Spain, plus an extra trial in Polonia (ok for winter lines?)