IBGS 13, Riga 03-07 July 2022
Session 1
Martin Mascher
Inversion in 2H close to CEN, found only in domesticated barleys, probably in Europe.
141 Mb inversion in 7H in Planet. Goes back to Diamant, mutagenesis, originated from Valticky. Also chrom block in 7H than cannot be easily broken
Talks about genepool concept of Harlan.
Expanding the barley pangenome, to circa 80 cultivars
Latest thing. Creation of genus-wide pan genomics, International barley pan-genome consortium created,
HiFi technique (2020) allows access to genomes easily, genus-wide pangenomics accessible
https://pangenome.github.io graphical visualization of pangenomes
Single copy pangenome, a hack for GWAS (ONLY all genes in single copy considered), single copy kmer extracted from SV (PAVSs). Naked gene on 7H found with this technique
Monat et al 2019, frozen diversity
They have resequenced about 1000 barleys, will be published over next 2 years. Also with a genome browser (name?)
Einar B Haraldsson
OBJ: Decipher control of annual vs perennial life history in cereals
First, generate genome of erectifolium, South-american species, Argentina. Unique leaf morphology, leaf rolls up like a cinnamon roll under drought. Potential for WUE. Field experiment in Dusseldorf, C13 discrimination, C:N ratio, large diffs to barley.
Explains sequence construction, 4.5 Gb (vs 5.4 Morex), more sequence statistics…
Explains inversions, rearrangements between species, complete inversion in chrom 3
Transcriptomics at 2 time points, 22 samples, several tissues (6 vegetative, 4 reproductive)
PacBio isoseq, isoseq v3, minimao2? and cupcake…. CodAn, Helixer, etc
ISoSeq Helixer plus annotations with MapMan/Mercator
38322 loci: 28446 protein coding, 140k potential isoforms, 10k non-coding genes
Produced a hybrid with H intercedens (annual?)
Genome assembly of 24 additional species ongoing (PanHordeum Project)
Postdoc position open
Ale Tondelli
Seed color in barley.
Black seed, phytomelanin accumulation, from early dough stage, gets darker as seed fills and matures. Single dom gene in 1HL, BLP1?
Whealbi GWAS, 450 accessions, 440k SNPs, gene found at end of 1H. HvPAP27 gene found. From Chloroplast.
20 pangenome, gene duplicated in black seed accessions? HOR10350, 2 full copies, same scaffold, HOR13821, 2 genes in diff scaffold, one of them partial.
Heterozygous mappings found, same as disease resistance from Carlos, when mapping to Morex
Confirmed by seq depth analysis
Description at protein level
Promoter has several landing sites for ABA, and other regulators
HvPAP27 expression analysis, CAPS assays to discriminate paralogs in semiquantitative PCR.
BMC Plant Biology paper.
Black seed protection to high light or UV? Present in highlands.
Apparently, no nutritional value
Martin Kovacik (Olomouc, Ales Pecinka)
Atlas on gene expression. Focus on grain development, 4 tissues, 5 time points after pollination
Syncytial endosperm has a unique transcriptome.
Endosperm transcriptome is extreme. Loss of transcription going on, many specific genes.
Nice bidimentsional representation of DEG, up and down, along the dates of sampling (for Chesco?). DE genes specific of each date found.
Finding clusters, expression network analysis, summarizing modules of genes, and relating modules to each other. Dimension of seed maturation found. Possible relations, functions and regulators.
BAR bioanalytic resource…..search Nicholas Provart
https://data.nal.usda.gov/dataset/bar-bio-analytic-resource-plant-biology
NF-YB TF specific from aleurone DAP analysis, also DELLA protein GAI, contributes to dormancy and regulates germination in Arabidopsis. Strong expression since syncytial endosperm.
Session 2 Biotic stress, Robert Brueggeman
Brian Steffenson
Optimum temp for barley 18-27 degrees (2017 study)
Stem rust of barley Puccinia graminis. Ug99 virulent on 95% of barleys, rpg4/Rpg5 effective against Ug99 race group.
Temperature affects disease reaction; resistance at 27 degrees erodes rapidly, whereas at 19 is fine. In the field, up to 40% severities in hot summers (in material with resistance)
Work with wild species, mostly spontaneum. It is everywhere in Middle East (very common, not like wild wheats, rather rare), WBDC wild barley diversity collection, ecogeographically diverse, 314 accessions.
OBJ: introducing wild resistance alleles through gene cassette transgenesis, big five against rust disease (Sr45, Sr50, Sr35, Sr22, Sr55/Lr67/Yr46), from different origins. Extreme resistance shown
Xu et al 2021, 2022, GWAS. But GWAS leaves low freq alleles undetected!. Rpg5 detected though linkage mapping, not in GWAS.
AG-RenSeq of Brande Wulff, tested with A tauschii, several genes discovered and cloned. They applied to wild barley and rusts (10 pathotypes, the more the better): 144 seqs related to reactions to 10 races. Rph15 found on 2H, though known before, high value gene.
AG-Renseq shortcomings: dichotomous pattern rarely found (resistance-susceptibility); also, little regulatory seq captures; Only R genes of NLR type found.
International Wild Barley Sequencing Consortium created during pandemics. June 2020, crowdfunding (150k donated), 61 researchers, 35 organizations, 14 countries.
285 wilds sequenced, 10x coverage, 114 million SNps called, mean kmer counts per accessions 1.98x109. Published in September 2022. Data probably earlier. Ines Walde, Axel Himmelbach IPK, involved in seq.
Wilds good for 57 disease resistance datasets. Microelement content, cold hardiness (wilds good for winter Minnesota!!), insect resistance, agronomic, morphologic, everything.
SNP-based vs kmer based GWAS, kmer offers new hits, fewer peaks but encouraging results.
Karl Effert WSU, PhD candidate, very good
Rpt5 cloning, netblotch res, reduces yield and seed quality
P. teres f. maculate and f. teres (netblotch)
Effertz et al 2021, nice graph of res genes in literature (book chapter), 6HL most reported (Rpt5). Coincident with gene SPT1. Could be same or different.
World minicore collection screened for Rpf5, receptor like protein
Transformation at Sainsbury lab in Golden Promise, good results, but not total resistance.
Molly Bergum (Moscou lab)-> Moscou moving to Minnesota this year
Rps8 gene, actually 2 genes. Tilling pop S. Salvi, (Holden et al 2022). Mutants found with loss of resistance, complementation tests done. Resistance recovered when the 2 genes are transformed, only one does not work. What are their functions?
PUR1 and ortholog Xa21, with kinase domains with some diffs.
Xo70 proteins involved in exocytosis, highly expanded family in plants. Involved in receptor-kinase-mediated immunity. Other clades found in grasses (Exo70FX), but lack critical domains, probably undergoing neofunctionalization. Hypothesis on this….
EXO70FX has specialized role in immunity
Pin Yang (recorded)
Bymovirus resistance in barley and wheat
Soil-borne bymoviruses infecting cereals.1970-90s BYMV large effects in Europe and East Asia
Rym4/rym5 (elF4E gene) Stein et al 2005, BYMV BaMMV, are bymoviruses. Also resistance in rym1/rym11…. WYMV y WSSMV, not reported in Spain. Symptoms occur in young leaves in early spring. Late sowing and crop rotation recommended.
Most resistance genes are recessive. rym4/rym5 widely used in winter cereal breeding.
Rym1/11 are allelic
HvelF4E knock out results in resistance, but also in reduced grains per plant, dispensable gene.
In wheat, polyploidy probably buffers effects of recessive genes. They have done triple editing of TaDIL5-1 in wheat (Kan et al New Phytol 2022). Triple mutant more resistant than single or double. No yield penalty of triple mutant, resistant.
Triple editing TaelF4E results in WYMV resistance. Pictures very impressive about plant development in pots with or without virus. Triple mutant is taller and delayed maturity.
PDIL6-1 and elF4E are resistance genes for bymoviruses, and are dispensable.
Session 3……chair, no notes
Sergey Shabala, Eyal Fridman, Agata Daszkowska-Golec, Maitry Paul
Session 4, Wendy Harwood, Kevin Smith
Jochen Kumlehn
Many improvements in gene editing. Things are crystallizing.
Julián García Maldonado
Genomic assisted selection. ICARDA (master IAMZ).
MET proposal, one location strategy first cycle, MET in next cycle. 3 MET strategies, 2 reps, augmented design, genomics assisted sparse testing (from more expensive to cheaper). Last one turns out the best.
Reduced MET with partial replication of genotypes.
Genomic prediction enables MET in early generation, etc
1000 F6 + 6 checks, 96 markers from the 50k chip, well spaced. Includes several QTL. Representative of 50k, gives similar distances as full 50k.
Sparse trial testing 316 genot unrep per location, 24 genot replicated. Some entries replicated within locations, besides the replicated across locations. It is the strategy they are launching now.
4 environments, rather different
Results explained too fast, but apparently they are convinced of carrying on with the genomics assisted sparse testing.
Wendy Harwood
Lawrenson et al Frontiers in Genome Editing. Updated review on gene editing
Agrobacterium and hygromicin to introduce CRISPr in immature embryos, very genotypinc dependent.
Transformation improved with growth regulators (GRF-GIF). In wheat, they can edit almost any genotype. In barley? It does not work the same. Calli did not regenerate. But, using another gene, WOX5, things worked. Also other techniques (PLTP). Wox5 generates too many changes in plants. PLTP plants look better.
KNockout efficiency in 15 diff genes variable, but rather high. Improvement tried with intron-mediated enhancement (Cas9 gene containing multiple introns). Seems to work.
ttHsCas12a?? better than HvCas9 for gene editing.
Cas9 + Cas12, with artificial introns, best results for editing up to 4 genes at a time.
Alan Schulman
Update on NBT policies. Currently under reconsideration in EU, but no new decisions probably until 2024.
Session Barley breeding success stories
Birger Eriksen (Sejet)
Quench in the pedigree of many current important varieties (data from Paul Shaw), 6 of the 8 major cvs in Denmark in the last years. Quench is Sebastian x Drum
Current varieties highly related
Denmark, 4 years of approval for a malting barley, at least grown in 500 ha, stress tests included, strict and regulated process, they must exceed in malting propertied to a set of checks. Few cvs pass.
Success rate in breeding, 0.001%, from 10000 to 10, and then 1 in 10 years succeed… (1.5M€)
Winter wheat and spring barley are the winning combination now in Denmark. Push for cover crops, more yield winter wheat, less input spring barley.
20% barley for malting and food, 80& for feed.
Malting barley now is as productive as feed barley, while malting quality has shown good improvement.
Grain skinning (loose husks) is a problem.
Future: Geen Deal, gools…. Phasing out important fungicides, etc. Yield loss due to no fungicides, loss of circa 10% yield, and increase of CO2 for hectare harvested. Disease resistance has to be improved.
CO2 footprint depends on yield per hectare. Labeling of Global warming potential (GWP) (proposed or in place?). Opportunities for reduction of footprint by improving protein and energy content of wheat and barley. Shows labeling examples.
Voss Fels Nat Plants, increase yield potential, carry over effects for all environments.
Winter barley 2row and 6row are not big, but is part of the future
Alexander Strube, Ackermann
One big headache, IP. Golden or dark age for innovation.
Winter and spring barley breeding (and soy, for crop rotation), part of Saaten Union
Results of survey together with Bill Thomas. Breeder’s exemption most important. Patenting, few people like it.
Fundamental innovations only achievable by subsidized public research!!! It should stay in public research
Patenting prohibitive IP protection. Incompatible with breeder’s exemption. Heavy transaction costs. Global standard for IP protection is good. Exclusivity allows you to refinance innovations. Exemption allows pooling and socializing of breeding progress. Patenting is opposite.
Patent Licensing Platform, the solution? ACLP initiative, on the making. Agricultural crop licensing platform. Simple legal framework. You could use materials carrying patented IP, if there is a commercial use in the end, an standard license agreement about royalties must be signed.
Aclp, eu….SEARCH
PlantBreedingRights+Patents+ACLP, better system tan current. The actual technologies patented, not accessible, though. Only material developed using the patent (for crossing).
Emmanuelle Dyrszka
First hybrid in 2016. Reliable seed production at reasonable cost is essential. Trying to improve full male sterility of female and seed set. Using molecular approaches. Remove partial fertile females by markers, removing lines with bad GS data, etc. Several strategies combined.
Seed set scoring visually in the field. One major focus found by GWAS of >500 females. Now introducing a QTL found into lines with poorer seed set.
Seed set is a quantitative trait. Approach using genomic selection, to capture genes with small effect, accuracy 0.61. Lines with lower seed set predicted than the economic threshold they have calculated are removed.
Undesired fertility restoration in cms found in chr 6H, Rfm1, Rfm3. Several haplotypes found for Rfm3. Some haplotypes related to full sterility, other to full fertility, several to partial fertility. These last haplotypes can be removed by MAS.
Pernille Merete Sarup
Genomic selection in 2rowed spring barley. Nordic Seed
GS allows that now they can select from 2000 lines, instead of 250!
9 years of data, 40k yield plots, 3145 lines, 20 traits, 25 lines per trial, 634 envs.
15K array, with imputation
Huge amount of variance due to additive variation, much more than gxe (Denmark!!!), of other genetic variation. Need high additive variation to be a good crossing parent (no epistasis, for instance).
Predictive ability, much larger with siblings in the TP(0.7), while lower (0.45) for lines without siblings. Still usable, though, because of huge savings for no phenotyping!
How many lines for accurate GS? after 1500 lines in TP, accuracy does not increase
How many lines/years to predict breeding cycles? Same, about 1500 lines
Adding about 100 lines per year to the TP seems enough to keep up with accuracy
GS good for early selection, even better for late predictions of deselected lines. Update TP continuously.
Session Genetics and breeding of biomass
Daniel Miralles
Perspective on barley production in Argentine. European varieties introduced in 90s produced big improvement.
Field experiment, 2 years, 4 reps, with 11 cvs released 1982-2019. Detailed phenotypic evaluation, intercepted radiation during cycle, biomass, RUE, phenology, Yield and components, N in grains and shoots, malting parameters.
Breeding history affects: days to anthesis, longer; gfp unchanged, in days and GDD. Plant height reduced, stem diameter increased. Grain yield increased 69 kg/ha/year, 0.9%/year. Biomass, flat, harvest index increased (from 0.4 to 0.5). Cumulative intercepted radiation increased (due to longer cycle, mostly), no change almost in RUE. Grain number and TKW increased, both. Spikes per m2, no change, grains per spike increased, at least until 2000. Grain protein was not affected, no dilution effect due to grain yield increase. N harvest index, slightly increased.
Lana Shabala, presented by Sergey
KUE and K uptake efficiency. QTLs very minor. Potash price went up from 150 USD per ton in 2003 to 800 USD now
Experiment with 4 K nutrition treatments, 30 genotypes, divided in 3 clusters according to K response. Shoot biomass, bad predictor of KUE. Phloem transport critical.
Microelectrode ion flux measuring (MIFE) technique, combined with FACS (fluorescence activated cell sorting)
Paolo Pesaresi
Happy under the sun 1 (hus1), pale green crops.
Only 25% of sunlight used for phot at top of canopy. Excess may damage plants. At the bottom of canopy, on the contrary, the problem is too much shade (not enough light).
More uniform light penetration would be beneficial, reducing photo-oxidative damage at top of canopy, higher production at high density cultivation, reducing temp at canopy level, with higher reflected shortwave radiation (achievable with pale plants, less chlorophyll).
AGRIVOLTAIC plant REM-TEC, company that produces solar panels compatible with agricultural production interested in this approach.
Mutants in Hortillus and Tillmore, SPAD and Pocketpea used. Reduced chlo content, but high radiation use efficiency and PHOT. hus1 from hortillus, reduced total chlo, increased a/b ratio. PHOT and color maintained along the cycle.
F2 mapping pop, dark and pale, excap, mutation found in 4H, stop codon. Monogenic recessive allele. Protein like an Arabidopsis prot. Function is moving antenna proteins into the chloroplast.
Rotasperti et al 2022
Heterodimer cannot be formed in the mutant, function loss. Plants cultivated in Poland and Spain, very similar to controls. No penalty at standard density.
They then isolated a mutant from TILLMORE. In principle, similar to the hortillus, but sowing it in autumn, the mutant turned yellow and died, probably due to cold. Chloroplasts collapsed. BSA RNA-seq approach to localize the gene. F2 population. Mutation in 7H. Candidate gene XANTHA-H, involved in chlo2 synthesis. The aa substitution was important for the protein-protein interaction domain.
So, not all pale green advantageous under field conditions (Wang et al 2018)
PHOT in hus1 increases because there is less investment in photoprotection. Actually, PHOT in dark adapted leaves is always higher, because there is no need for photoprotection. So, less is more in this case.
Sonia Negrao
Irish whiskey industry booming in Ireland. Interest in impact of terroir, etc, to differentiate their produce.
Waterlogging induces hypoxia in the soil.
Heritage germplasm (old cultivars) largely uncharacterized, may have stress-tolerance features.
Exhibit collection, 365 accesions, 2rowed spring, 3 from Spain, 4 from Italy.
50k genotyped, pop structure 5 groups. Some 6 rows were found, germplasm bank mistakes. Year of release had an impact -> landrace, pre-90, post-90 formed different groups. No geographical diffs.
From 365->230 lines core collection.
Field 2020: 0-2-5-10 days waterlogged. 5 days chosen as best. Very tricky to do and to phenotype, muddy fields!
4 days of irrigation at early tillering, 12h per day of irrigation
Waterlogged flowered later, less biomass, reduced height. Grain protein and Bglucan reduced in waterlogging. Machine learning and artificial intelligence to study lots of drone-image data. Imaging is only possible with UAVs (due to mud), and irrigation elements have to be removed soon, to avoid interference with machine learning.
Session on barley end uses
Henrik Brinch Pedersen
Herz
Dockter
Carlsberg search for raw materials, new ingredients, etc
Specialty barley, sorghum, wheatgrass for the future!
Targeted breeding, NU-LOX3G and 4G barley, with variants of LOX genes, improves beer quality and lowers climate impact (really?)
How to accelerate the process, without GMO?
FIND IT, is their new strategy, and accelerated and traditional trait breeding method, with mutagenesis: Fast identification of nucleotide variants by droplet digital PCR, to find the mutations you want in an efficient way (there is a publication)
TRaitomic platform after Find-it
They have isolated 100 knockout variants of interest, including GW2 (found in from rice)
DELLA mutation in Paustian, earlier, taller, larger grain and spike
Climate targets, increasing robustness of malting barley yield, drought and salt tolerance, keeping quality, getting competitive yields
Crops for the future project, accelerating domestication in sorghum, perfecting wheatgrass for food and brewing; ancient rice and global food security
Leona Leisova-Svobodova
Sponsor presentation, ICARDA
ICARDA, Miguel Sánchez-García
CGIAR, 13 centres
257 barley varieties released since 1979, 50 in the last 10 years
Excellence in Breeding Platform, new in CGIAR: more focused, faster and more efficient
Identification of product profiles, widely grown varieties in a particular area, which can be improved for some characteristic. They co-develop varieties with National Agriculture Research Services (NARS). Now targets grouped into “feed for arid and semiarid”, “feed and forage for favorable”, “food and fodder”, “malt and fodder barley”. Countries and regions grouped in the 4 categories. Same for traits, essential traits identified per megaenvironment.
Crossing block genotyped with 50k. Use PopVar to make simulation progenies. Used for crossing strategies, can calculate yield expectations, but also correlation with malt extract, for instance. Crosses are decided on a combination of traits and correlations among them.
Speed breeding up to F5, then multilocation in F6 (stage 1), using sparse genomic selection approach. Stage 2 multilocation, using alpha lattice. Stage 3, networks f field trials IBYT-ASA or OBYT-FFM.
Up to F5, genomic selection and a little phenotypic. 4 gens/year of speed breeding (capacity of 100.000). Includes disease resistance screening, with mixtures of isolates, NB, scald, etc. They are usually more susceptible in the chamber than in the field. Also NIRS measurements, for B-glucan and Fe content. Crosses with spontaneum provide up to 5% more Fe, and 42% more B-glucan (measured by NIRS)
Multilocation testing needed when 1 loc does not represent all envs. Identify locations that represent target population if environments (TPE). Sparse genomic selection ensures good accuracies compared to carrying out stage 1 in only one location with all genotypes. Also, dispersion protects against catastrophic losses of entire locations, which sometimes happen.
Collaborators in stage 1 in 2021, includes Spain and Portugal (Andalucía).
Stage 2, testing locations specific for some stresses, including disease hotspots. Phenotyping with phenomobile. They have nice location for diseases. Poster 12, disease resistance found, horizontal?
Stage 3. Every year 2 yield trials to more than 25 countries, 22 IBYT-ASA (Arid and semiarid), 22 IBYT-FFM (feed forage malt)
Also have regional networks, like Maghreb-ICARDA barley initiative.
New lines HB1963 and 1964 released in Ethiopia, 48% more grain, and 38% more straw (highly valued by farmers), positive for resilience of crop-livestock farming system. Circular economy incorporated in local value chains, 20% premium price for malt barley grain. 44% more revenues at farm level.
Extensive use of landraces and CWR in the program (31% of stage 1 has LR and CWR). Even lines crossed with bulbosum.
Would it be posible to test ICARDA materials as source of breeding? Registration problems? Previous signed agreement needed? Apparently, they only ask for 1.5%, according to ITPGRFA.
lash&Dash session
Alina Klaus, poster 13
Drought experiments with PEG, root tissue collected, split in regions. Weighted coexpression analyses, combined with DE genes from RNAseq. Network construction for the different root zones. Combination of the two approaches helps to pinpoint candidates.
Kumsal Ecem Colpan, poster 19
High temperature effect on plant growth …. Isolines based on Bowman from Maria; PHYC and PPD1. Both sets of isolines also crossed to each other. Floret fertility in PPD1+PHYC-e, higher than others, because of production of double seeds. PPD1 and PHYC interact, possible epistasis.
Ewa Sybilska, poster 14
Cbp20/cbp80 double mutant under drought, seedling. Part of cap binding complex, involved in miRNA processing, splicing, RNA export, RNA decay. Mutant hypersensitive to ABA during germination, and better tolerance to drought stress. Faster stomatal closure, etc.
Eyal Bdolach poster
B1K collection, chloroplast diversity found with molecular markers. Reciprocal F1 hybrids made, diffs found between reciprocal crosses due to chloroplasts. Cytonuclear multi parent population, 10 parents stress resistance index for CMPP lines.
EA mapping, Chang poster 50
Landraces fdrom Europe, Asia, Africa. Geographical origin inference using deep learning, GEA, PPdH1, FT4 signal in Manhattan plot. They use the geographic info for extracting climate data. 10-fold cross validations for geographical inference, >0.9 accuracy. Associations with temperature seasonality (1626 LR georeferenced); 8338 accessions with geographical data inferred. Chrom 2H, Signal at CEN. Tiene la SBCC.
Laura Paire Naked barley, organic…
Jian, poster 77, IPK, flo.a paired spikelet mutant, extra spikelet and fused glumes, gene HvALOG1, responsible for flo.a, short arm of 6H, 477 kb deletion region on short arm of 6H.
Poster 56. What makes barley itchy? Awn roughness in barley, genes A (Raw1) and B (5H and 7H). The two genes segregating in two populations, F1 crossed, and F2 segregating. Raw 1 controls the size; Raw7HS controls the frequency. Raw1 epistatic to Raw7HS.
Li Guo, U Bonn, poster 75, barley enhanced gravitropic 2. Gravitropism controls guidance of gravity. Shallow roots better for phosphorus, deep roots better for N and water. Mutant egt2-1, enhanced gravitropism. DEG analysis of RNAseq, and Y2H
Mingjiu Li, Genes CMF7, CMF3, causan white stripe y xantha phenotypes respectively. HvClpC1 causes a yellow striped phenotype
Ilyse Putz, HHU Dusseldorf, Life history traits in annual and perennial species of barley. Rains cause soil erosion in bare fields. Perennial agriculture can help, Mosler et al 2021 Front Sust. But breeding for perennial takes very long. Find key genes. H.chilense is perennial. 5 species chosen, 3 ann, 2 perenn. All crossed to produce F1 and some BC; RNAseq.
Maeva Bicard, understanding GEI in spring barley breeding. Unilasalle, Secobra, Kronenbourg, Carlsberg. Determine ecoclimatic factors driving GEI. Build environmental classification based on GEI drivers, and define high-throougput criteria to select for GEI drivers (Understand-Predict-Control). DSSAT, Ceres, 6 cvs 10 ens 2 years, and environ data. Then env classification. Cvs with contrasted response to GEI drivers will be monitored by drones that predict response of contrasting cvs. Poster 81
Barley Genetic Resources workshop
NORDGEN, Jan Svensson
17k barley accessions
Bulbosum introgressions, 176 accessions
Mutants, 9590 Scandinavian mutant collection, with many alleles for single genes represented
991 Bowman NILs
Chlorophyll biosynthesis 373 mutants
Only stable mutants kept (not het.)
Learn from Arabidopsis community for organizing and sharing of resources
Community infrastructure? It is a biological infrastructure
Andrea Visioni, ICARDA
ICARDA new genebank inaugurated in Rabat
30242 barley accessions, 2240 wild relatives, 455 are unique, many characterized phenotypically.
Screening of germplasm with leaf rust, for example, leaf rust in Marchouch. Also Bglucan. FIGS to identify accessions probably carrying adaptive traits. FIGS for winter survival in Minnesota, Stefensson, some lines survived, so FIGS strategy succeeded. Pre-breeding, many crosses with spont to introduce disease resistance. Examples of agronomic traits showing that spont derivated lines are doing well, including yield. Bulbosum introgression lines outyielded the wild line for yield at all locations. PHYSIOTRON facility, fully automated lysimetric system. Also Phenobuggy (developed in connection with company hyphen). AGENT, includes phenotyping genotyping and sharing.
Nils Stein. IPK
Eurisco, barley >21k accessions, largest genebank for crops, barley only second to wheat
PCA with 76k SNPs (Milner)
The barley core collection (Knupffer and van Hintum), 1995, not widely used. Was a vey good compilation of germplasm. It is in IPK, you can order it. Pangenome on the making, 3x 10x 50x (for 1000, 200, 50 accessions) prepublication stage. BPGv2, 50 accessions, wild and cultivated.
Not yet official, Core1000, SSD out of Bridge, not available yet, BPGv1, BPGv2, not available yet, some cannot be delivered by IPK
Gendibar
Icelandic barley
One rainy season: “all the time”. Long growing season. Barley Core Set (1000 genotypes). Ll genotyped with 50k. Also IceBar (breeding material)
Chengdao Li
For 100 years it was not posible to grow barley in Oz, it just did not work. Australian Grains Genebank AGG (double skin freezer design), 2014. 20000 genotypes stored. Project Ozbarley, 400 old varieties and breeding parents, gather datasets and collate using FAIR principles. Cereal Rust Research Centre. Western Crop Genetic Alliance (Joint Research Centre, Chengdao); 6000 accessions from 41 countries, 1000 with low coverage data. 5000 DH lines, 1000 JF Bowman BC lines, RGT Planet mutant pop, Vlamingh mutant pop. Traits: phenology, heat tol, soil abiotic stress tol.
Session 06-07-22, Genetic and database resources: harnessing diversity
Nils Stein
Gap between discovery and user friendly access, and sustainable use
About 70 genomes fully done, public over next months.
Problem for opening genome data to public: generate all the information, annotation, relation across genomes, etc. Not enough resources. TAIR has long term funding. Barley has not.
Past:
Barley Genomics Newsletter, past communication model, still alive in 2020
Next step, Graingenes, main hub for map info
HarvEST, CR-EST, next step, early 2000s
Next, Barlex, to visualize genome, still accessible
Present:
Graingenes still valid, Victoria C. Blake. USDA long term funding (how long?)
EnsemblPlants, MorexV3 available, synteny research possible
IPK Galaxy Blast Suite
JHI, germinate, flapjack, etc, desktop applications
JHI, EoRNA, transcription data
CROPPAL, Perth, proteomics, crop-pal.org , proteins, annotated, includes barley
Project related databases, like BarleyVarDB, no longer available. Difficult to maintain. Send data to permanent repositories
Eurisco, Genesys, to access germplasm, Nordgen
Germinate, for handling large datasets
BRIDGE IPK
BarleyDB in Okayama, K Sato
T3/Barley, triticeae toolbox barley.triticeaetoolbox.org
Databases very distributed, often project-driven. Long-term resources not barley specific
Future:
GWAS catalog, EBI, for humans, mandatory for human research. Graingenes has already included GWAS results. Send GWAS chapter and suppl info
Get used to prepare research and data to be uploaded to databases
FAIR data, findable, accessible, interoperable, reproducible.
The FAIR cookbook, Beier et al….
Plan you research as a resources project. DMP is important.
AGENT, precision collections of 500 barley and 500 wheat, evaluated for agronomic and biotic, a selection for abiotic stress.
Should we develop Graingenes into a new TAIR? If yes, how?
Asis Sherstha
(B Stitch) HHU
Multiparent pop, double round robin, 23 parents , 45 subpops using partial diallel, MARVIN for grain traits, 50k, field trials, grain size characters. Huge genotypic diversity among parents.
Grain traits showed high h2.
mppR package for QTL analysis, special for multiparent. 62 consensus QTL, 13 new QTL, not reported previously. Including proof of concept loci (vrs1, nud).
QTL validation in Lakhan x Georgie, with 2 NILs, crossed, 924 F2 progenies, validated in fine mapping
Comparison of full QTL effect and GP model, GP with GBLUP was always better (30%). QTL effects distributed across all parents, with many positive and negative alleles in each one
Genetic architecture of grain size is complex, more than previously thought. LR have potential to improve these traits, not just for adaptation and stress
POSTER 64
Outmane Bouhial
CGIAR barley breeding toolbox
Assembly of association panels. Specially for developing world, representative of CWANA region
530 mostly spring barleys, CGIAR, elite from all over, and LR.50k, flowering genes, VRN1, PPD1, FT1, CEN, 16 allelic combinations in total.
Genetic subsetting….. 312 entries in public domain, mostly CGIAR and LR.
Cluster, PCA, AMOVA, 6r more polymorphic than 2r, ICARDA most diverse AMOVA of flowering genes indicated mot variation for flowering genes within pops. CEN the most important among pops. All flowering genes associated with pop structure. 16 flowering combinatons AC1-AC16, would be interesting knowing them.
Pop structure with sNMF. Identified pops have common origin and breeding history.
MTK (mean of transformed kinship) measures of kinship pf genotypes in a subset and identifies the most dissimilar set of genotypes
312 (CBBT) do not include some of the more modern, negative side of PC1 (seen in the picture of principal component analysis). But have most subpops and all 16 earliness combinations flowering. They offer it as a collaborative tool. Available in 2023.
Ronja Wonneberger
Comprehensive multi-omics database. OBJ: genomics and transcriptomics 2r springs. 209 selected. UMinn, IPK, JHI, 2 years, field trials, many traits, fertility traits, etc
Available not yet, it will be after the paper (soon)
Transcriptome all 209 accessions, seedling crown and root, developing inflo, preduncle, central spikelet, developing grain 5 days post anthesis.
50k SNP, and RNAse SNP, WGS done, 40M SNPs, after filtering, LD pruning, imputation, 1509447 SNPs. ENA archive
Search preprint
Structure of European 2-rowed spring, PCA differentiates release period. FsT in sliding windows, 5H>0.7, old vs new shift, most of new accessions carry the Barke alleles. Region of 3Mbp shown 50-300Mbp approx. Exactly the same as region in our Molec Ecol paper.
Expression of 800 genes in that region. PCA of expression divides the 2 groups clearly. PCA of genes also done, 2 groups consistently showed diffs, across all tissues. Strongly differentiated across clusters of genotypes. Off expression in old, on expression in new. About 45 genes
Haploblock in a pedigree scheme. Very nice. Six cvs with strange patterns, 3 of them, with diff expression pattern, come from laevigatum.
Global distribution of NEW haplotype, checked in the IPK collection (hap2), mostly in LRs from Mediterranean, including Spain, and Cvs also in Spain (and Europe). Also found in winter and 6row barleys.
New haplotype comprising 5% of barley genome under strong selection in the past 60 years, associated with upregulation of gene expression. Most prevalent in North Africa and Southern Central Europe. Still unclear the reason (disease, leaf rust?). It is definitely the same as the one in Molecular Ecology. Check in databases if it may come from an spontaneum introgression. Article sent to Ronja.
It will be possible to publish papers in Journal of Agronomy, before September 1st.
Agatha Walla (von Korff) HHU
Quest for elusive developmental gene in barley
Shoot architecture, balance between traits, tillers, seeds…negative correlations hamper yield progress.
What are genetic key regulators?
Forward genetics, Nodgen collection of mutants, mnd8,mnd6, mnd1, dwarfs, high tillering. Genes cloned Hibara et al 2021, Mascher et al 2014, Walla et al 2020 (mnd1)
RNAseq in the right tissue and developmental stage. Bowman introgression lines tested. 2 major introgressions, 2H and 7H. In 7H the candidate mutation was found, null mutant due to frameshift. Probably related to histone function and expression downstream. Regulator of meristem transition. Tillers in mnd1 appear along the whole shoot, not just in the two lower nodes, as usual (WT). They found bracteae at the base of spike, and underneath primordia that formed spikelets. Gene expressed in shoot apical meristem.
Further mnd mutants mining found 5 mutants which were not in the 3 main genes. Mnd-like1, mnd-like2. One is Xray, the other natural. Phenotype not as severe as mnd1, tillers only in base of plants.
They found mnd-like mutants were in the same place as for mnd1. But no candidates based on RNA study. WGS for the mutants also did not work. Then biparental mapping in an F2 population. There were 2 introgressions in the region, and a region with no recombination. They found an inversion of 3Mbp in one of the mutants, just upstream of mnd1. In the mnd-like2 they found an insertion in the upstream region of mnd1. Expression of mnd-likes did not go up with time, like the wild. The mutants did not complement
Other mutant mnd7h also had no expression, no diff in coding. Probably also cis variation.
Mnd1 represses vegetative growth, key regulator of many traits. Many cis-regulatory mutations affecting expression. Dosage or spatio-temporal expression patterns probable underlie the nuanced phenotypic traits.
C. Jiang (recorded)
Reference guided tilling by amplicon. Most tilling in EU material
Hatiexi?, landrace NE China. 2row, black, grains and leaves, etc. It is far from East Asia accession in PC Milner. Origin in Middle East. Susceptible to BaYMV, BaMMV. Good for animal feed, high protein.
Mutated with EMS. , 2.8% good germination. They used 2 levels of mutant agent. 8500 M3 seeds. Many phenotypes available.
WGS made to build a reference genome. TILLING platform developed, 3D amplicon-seq.
5184 M2 included in TILLING service. 21 mutants per 1.5 kb !!!
Plant Communications July 2022, publication ready
Session Morphology, phenology, and development, Laura Rossini
Maria von Korff
This is the Udda Lundqvist memorial sponsored talk
Inflorescence development and floral abortion under stress (high T)
Reproductive level particularly sensitive to high temp, reducing seeds per spike
Reference collection of 300 accessions in ICARDA, time ago, many from hot and dry places. 100 accessions LR and elite genotyped 50K. 20-16 degrees control, 28-24 degress stress. Many traits measured in the chamber.
Days to heading, LR from hot env accelerate flowering; elite strongly delay flowering.
Shows correlations of diff vegetative traits with seed number, all positive under control conditions; except fertility. Reproductive traits, positive in control with spikelet number, in high T, fertility was the variable clearly correlated with seed number.
PpdH1 is repressed by ELF3, and PHYC is also involved in response to flowering and hight T. VRN1 also involved, under high T is down regulated, then delayed flowering through FT1.
PPDH1 variant Gly-Trp, effect of the two alleles. Recessive gene, lines flower later in control, in high T they are further delayed (in days); the wild allele actually speeds up development under high T.
Introgression lines to study this. Golden Promise-derived, with introgression of wild PpdH1 from Igri; also Scarlett based, and Bowman based. Same results in the 3 sets. Confirmed results from panel of genotypes, a crossover interaction effect. They studied apex, Waddington scale, because seed number is determined by spikelet initiation and floret abortion.
GP, delay in floret development in high T, GP-fast, acceleration of floret development under high T over control. 1.7 vs 0.9 spikelet primordia per day in GP; 1.6 vs 2.0 in GP-fast (control-high T).
Hight temp affects Inflorescence meristem (IM) size, microscopy, nut not in GP-fast.
Fertility score hugely different between GP and GP-fast. Female or male organs susceptible? Experiments to test this.
Crosses done between ovaries at 28 degress by pollen at 20 degrees, and the opposite. Found that ovary fertility dropped, but pollen dropped much more. But not in GP-fast (GP with Igri dominant PpdH1). Pollen looked shrunk in GP, not in GP-fast.
Molecular changes? RNAseq profiling, at 4 stages: 1.0, 2.0, 3.5, 6.0 Waddington. Still under analysis.
>90% reads mapped to Barke. DE genes found for every genotype and stage. Many more DE genes in GP than in GP-fast. 408 genes related to development AND temperature, 222 annotated, 186 not. Stages drove the clustering of the genes, except GP under heat in 2.0 and 3.5, found cluster of upregulated genes under heat.
Zhong and Kong 2022, SEARCH
FT1 in the leaf TPM of GP-fast much higher AFTER W1.0 than in GP. Downregulated by heat, but not that much.
FT2 is expressed in meristem, down regulated in GP as well, and by heat.
Balance of inducing and repressing genes, FT vs CEN, if you have more CEN you keep the meristem alive. Ratio FT1 in the leave to CEN. Ratio very diff in GP and GP-fast, under heat ratio goes up in GP-fast, down in GP Could explain crossover interaction.
Inflorescence meristem affected by ITN-M/AP2, they analyzed, down regulated by time.
Scarecrow TF and trehalose-6-phosphate synthase, important for sugar status. Both down regulated in GP heat.
MADS34/TaSEP5 and MADS15/BM3 also affected…..
Auxin related genes also tested. Auxin response factor down regulated in GP heat. Validation of hypothesis , HvpPIN1….. expression in IM, Fluorescence reporter lines being developed by Raffaella and Laura.
Hormone homeostasis may be altered. Need to dissect the meristem tissue to search for specific molecular networks.
Started Edgar Damesa-Arevalo, scRNAseq. Molecular Cartography company helps to locate the genes by color in the developing inflorescence, easier than with other methods.
POSTER 18, 67
Higher T effect in experiments with shift, with actually shorter high T treatments.
Ravi Koppolu
Spikelet determinacy for improving grain yield potential.
Rachilla differs between barley-wheat. There is the potential in barley to form more than 1 floret, of having an indeterminate rachilla
Mutants, com1, com2, Int1, Vrs4 central spikeletes transform into a spike like inflor. Rachilla developmental mutants.
Qgene, APETALA2 TF regulated by miRNA172, responsible in wheat for rachilla mutants. Mutants of barley also found (publication of 2021)
Mul2.b mutant, lateral spikelet rachilla elongates to produce up to 3 florets (in a row)
Shows beautiful pictures showing early rachilla development
Data from flo.a x mul2.b cross, indicates they are not allelic
The trait can be treated as quantitative. Studied in pop Morex x mul2.b F2. QTL analysis in F2, 2 large QTLs in 2H and 6H, minor in 3H from Morex! 6H and 2H QTL interact for lateral supernumerary grains, not for central. They are mendelizing the QTLs in lines, to continue with map-based cloning.
New mutant 1 found, nice pictures of rachilla elongation forming new spikes. Rachilla would be like a secondary rachis. Also mutant 2….
Luke Ramsay
Recombination in barley is much lower than in Brachy. Why?
Resource: desynaptic mutants in barley, 15 loci , 24 in Bowman, 3 biparental pops for 15 desynaptic mutants.
Des10 reduces recombination, does not help for breeding. Built a suppressor screen of BW230 desynaptic10, 18000 seeds mutagenized. M2 families in polytunnel and increased for increased fertility. 10 M4 plants with restored fertility
Line with HvRECOQL4 C/T point mutation had highest fertility, in the coding seq. Crossed to WT->FT1, alleles at Mlh3 and RecQL4 tracked, F3 lines with wild type, one mutant or double mutant, 4 classes.
Arrieta et al 2021.
Recomb of recql4 F3 lines was twice than in WT. Double mutant similar to recql4. Mlh3 has much reduced recombination.
They will backcross recql4 into other backgrounds, to see if effect is maintained.
Ivan Acosta
Auxin in production of starch… in pollen maturation.
Pollen matures accumulating starch. Mitosis during maturation forms vegetative cell (energy) and the two sperm cells. Mutant msg39 anthers look normal, pollen seems alive with staining, but seems much lower in starch. Starch accumulation starting around W9 does not occur in the mutant, whereas mitosis occurs normally. The mutant is sterile, has to be maintained with a maintainer line, and inheritance is not Mendelian (16 instead of 25%).
Msg38 encodes an enzyme for auxin biosynthesis (YUCCA). Confirmed by actual measurements of IAA in plants along the time, whereas precursors are accumulated in the mutant. Curiously, at its peak, IAA is quickly degraded into ox-IAA
Protein found only in pollen, after W9. RNAseq, auxin involved in expression of thousands of genes. Studies of diffs clusters, auxin required to boost energy production at W9.25 and 9.35. So, starch was not made in the mutant because it had no energy to do so. Co-expression of genes for energy production and msg38. Auxin is required to increase flux through glycolysis and TCA cycle. The sugars actually reach pollen during its growth, but pollen does not know what to do with them, no energy in the mutant.
Sugar accumulates at W8.75 and W9, inducing a transient boost of auxin synthesis, and a boost of energy genes, High ATP, then starch synthesis.
The msg38 is quite normal. It belongs to a specific subfamily of YUCCAs, and has a specific effect in pollen. Could be a mechanism for sterility in breeding! Cannot be restored by external auxin application, probably because it cannot reach pollen cells.
Vanda B Marosi
Wheat barley transcriptomes comparison. Same growth stage.
Weighted gene correlation network analysis
Mapping to a single transcriptome for each species. Not much diff!
Ortholog analysis: 36k genes vs 108k genes. Orthofinder to find25k orthologs; 11908 single copy orthologs, 1 copy per genome. Used for further analysis
34 coexpression modules in barley, clearly diff by tissues
Looks at overlap of wheat and barley modules, similarities and differences (many)
CONCL: tissue selection was instrumental
Silvio Salvi
Roots.
Mentions Wallace et al, On the road to breeding 4.0. Ann Rev Genet 2018
3 types of roots. Seminal roots (primary or secondary), nodal roots starting from crown, lateral roots starting from other roots
Traits: root/shoot biomass rate. Anchorage to soil, root lodging. RSA (numbers, angles, distribution, etc); anatomical traits (aerenchyma, etc); root hairs; root exudates, Rhizosphere microbiome; nutrient and water absorptions.
fer1, the only barley root architecture mutant in BGNesletter!!!! (fewer root 1), only seminal root available, but seed source was lost. More mutants needed-> TILLING
TILLMore, 3600 lines. POSTER 72, example of forward genetics.
Screening for root phenotypes, rolls, rhizoslides, dirt-rhizotrons….34 mutants found, hypergravitropic, short, wavy, etc.
Enhanced gravitropism 2, PNAS 2021, angle affected in barley and wheat, confirmed with rotation test to ensure ACTIVE gravitropism. Bulked segregation analysis with F2 plants, 5H, only one of the 6 mutations found with a stop codon. Gene edited the gene to have further confirmation. Done. Controls gravitropism of ALL root types. RNAseq of root sections placed it in the meristematic zone, 67 DEG, related to plant cell functions (expansin and peroxudases). EGT2 is close homolog of WEEP2 in peach (shoot gravitropism)
EGT1, PNAS, just accepted. Phenotype similar to EGT2
Possible look for them in OxP????
6H, ask for preprint!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
Natural variation found in Whealbi collection. Haplotypes II and IV showed diff in root angle. Probably affects adaptation. Is independent from auxin.
RNA hybridization indicated location of expression (diff to EGT2)
Type of protein and genes DE related mainly to cell walls.
Are they involved in cellular stiffness? Atomic Force Spectroscopy reveals egt1 cell walls are less stiff.
Konstantinova et al 2021 int J Mol Sci
It seems that the antigravitropic mechanism is cut by the mutants.
Kishner et al 2021 PNAS, Fusi et al 2022 PNAS.
Confirmed in wheat, TILLING in Cadenza, triple mutants for both genes.
Now, it needs to be tested in the field. Also Uauy and Ober (bread and durum wheat)
GWAS, POSTER 51
Rescreen of TILLMORE with CD cases!!! Interesting method. Easy to implement?
Session Baltic and Nordic barley: a regional perspective
Therese Bengtsson
Pre-breeding, N-S, Cont-Maritime, climate constrasts, very long days
Public-Private partnership, why? Climate changes, new pests, food security, small market! Number of programs have been reduced. They depend from the Big 4 companies, which have Nordic and Baltics outside their target. No one else will do the job. Private companies are small.
Pre-breeding is pre-competitive, companies can collaborate. Resources are not enough in companies
Germplasm evaluation and introduction of traits in elite background, HT phenotyping
Funding 50/50 ministry (norden)/private partners. Project leader, Ahmed Jahoor. Boreal, Sejet, Lantmannen, Nordic Seed, Graminor are the private partners; Arric. Univ Iceland. SLU, Luke, and other University as public.
2012-14 screening of adapted material to get linked markers for MAS; materials deposited at Nordgen; screening and crosses using adapted an hidstoric material (MAGIC and biparental pops); phase III, delivery?
Building trust in the beginning was necessary. Each breeder provided 30 lines or cvs, 180 genotypes. Screened for 7 diseases and development traits and yield and straw strength. 9k genotyping and GWAS
KASP markers prepared for the companies to use.
Example: cereal oat cyst nematode, screened by a company. Two markers found on 2H, converted to KASP, already used.
Bengtsson et al 2017, 2 publications. Goransson 2019. QTL for many traits identified.
Phase II 2015-17. 200 genotypes adapted and historic materials, screened at 2 locations for disease and agronomics. MAGICs developed, balanced for row-type, some with 4 some with 8 parents, multiplication in New Zealand. 9 MAGIC and 2 biparental, 83-200 (303 max) lines per pop, DH or SSD.
Phase III. Continue screening, 50k genotyping, disease screening massive, some agronomics (heading, maturity, etc)
Hautsalo et al 2021, TAG 2021, Pops 1-4. Pyramiding of scald resistance.
Studies of early vigor in adapted and historic material, at IPK Lemnatec, EPPN2020. Multitrait GWAS in progress, 250 genotypes (180 from phase I).
Also screened for powdery mildew. Scald and mildew resistance together found.
From Phase III retrieving markers linked to traits, which can be used for MAS.
Many more advantages of project, intangibles and tangibles (picture)
All info shared through INTERNAL website
Alge Leistrumaite
Barley in Lithuania
Mara Bleidere
Barley breeding in Latvia. Interest in roots. Increasing perspective for cultivation of winter barley.
Magnus Goransson
Long days, strong winds, heat sum, only 75% of Scandinavian. Sown end of April.
Traits: maturity in low temp, early heading, straw stability. Icelandic barley is very early. Does it occur at other envs? 17 trials in the PPP for pre-breeding project, and found that earliness is stable over envs. But the 3 early genotypes were too little for GWAS (169 genotypes). Tested in controlled envs. 84 genotpes, 30 hours day, 5 degrees at night, 15 degrees during day, and 15-20 (warm treatment). 9k chip. Heat sum to maturity same in LDC and LDW. Most genotypes severely stressed in SDW. Three early genotypes were very tall, and much more vigorous than LDC and LDW. Most lines delayed heading under short days. Reseq PPD1, ELF3, FT1, CEN, 30 genotypes. Winter CEN gives earliness and yield.
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