How to generate new tools and methods for improving algal bioresources and the domestication of seaweed species? . Final conference: European Seaweed industry – current status and future perspectives 2012 DONOSTIA/SAN SEBASTIAN Philippe POTIN and Idealg WP leaders Nori farming in Japan 1921 Nori farming in Japan 1990 A reality in western countries Chondrus crispus flowering (NS, (NS Canada, Canada ASP) Hana-Tsunomata™ when translated from Japanese means "Flower Chondrus". Other common references to Hana-Tsunomata™ sea vegetables include Hananori™ ("Flower seaweed"), Cultivated Chondrus Kaede-nori Chondrus, Kaede nori ("Maple seaweed") and Hana-sakura-sou ("Cherry blossom sea plant"). 2011--2010 2011 Seaweed biotechnology and bioresources A national 1010-year large integrative project to merge algal genomics with mariculture, biotechnology and chemistry. chemistry. 1: Control of algal life cycles Dr Kathleen Drew-Baker 1: Control of algal life cycles L i i digitata Laminaria di it t life cycle and farming lif l df i 2: Domestication Decrease in branching and increase in seed size were also selected for during g corn domestication Image credit Nicolle Rager Fuller, National Science Foundation 2: Domestication An example of a domesticated brown l f d i db seaweed : Undaria pinnatifida p f 3. Towards genetic breeding Advances iin genetic Ad ti ttechnologies h l i should h ld contribute to improved seaweeds •Marker assisted selection •Genome-wide association studies •Recombinant DNA technology and transgenic plants , except in closed systems Photo credit: IRRI 3. Towards genetic breeding M k assisted Marker i t d selection l ti (MAS) Phenotype: physical expression of traits Genotype: sequence of all the genes in a genome Photo credit LemnaTec; Anderson, L.K., Lai, A., Stack, S.M., Rizzon, C. and Gaut, B.S. (2006). Uneven distribution of expressed sequence tag loci on maize pachytene chromosomes. Genome Research. 16: 115-122. 3. Towards genetic breeding M k assisted Marker i t d selection l ti (MAS) Selecting for DNA markers is faster than selecting for phenotype Phenotype: physical expression of traits Genotype: sequence of all the genes in a genome Photo credit LemnaTec; Anderson, L.K., Lai, A., Stack, S.M., Rizzon, C. and Gaut, B.S. (2006). Uneven distribution of expressed sequence tag loci on maize pachytene chromosomes. Genome Research. 16: 115-122. Microsatellite markers to estimate genetic diversity in L. digitata Population 1 Low g genetic diversity y Population 2 Forte diversité g génétique q Each line corresponds p to an individual: 189 189 187 187 24 individuals were studied in population 1 e 185 183 185 183 They are all sharing the same genotype Th diversity The di it is i minimum i i Homozygote individual 183/183 Individu homozygote Individu hétérozygote 189/189 183/189 Courtesy M. Valero Microsatellite markers to estimate genetic diversity in L. digitata Population 1 Low g genetic diversity y Population 2 High g genetic g diversity y 189 189 187 187 185 185 183 183 Homozygote individual 183/183 189/189 High genetic differentiation between populations (sharing very few genes in common) Courtesy M. Valero Brown algal genomics The Ectocarpus genome (200 Mb) project J.-M. J M Cock GENOME SEQUENCING : 3,000,000 reads (10X, shotgun) cDNA SEQUENCING : 100,000 reads (full-length cDNAs) P. Rouzé / Y. van der Peer J. M. Cock, Roscoff - STRAIN SELECTION - BIOLOGICAL MATERIAL - LIBRARIES + Es Genome Consortium - LIBRARIES - SEQUENCING - ASSEMBLY - AUTOMATIC ANNOTATION - EXPERT ANNOTATION Cock JM et al. (74 authors) Nature. 2010 Jun 3; 465:617-21 and more than 20 papers during the two last years. years. Brown algal genomics Large‐scale genome assembly using a genetic map New Phytologist (2010) doi: 10.1111/j.1469-8137.2010.03273.x Red seaweed genomes The Chondrus The Chondrus genome project Jonas Collén é Catherine Boyen The Porphyra The Porphyra genome projects Ulva genome John h Bothwell FSU Jena The Ulva ggenome p project j 150 Mbpp Towards Genome-Wide Assoc. Survey Phenotype Phenotypeanalysis analysis Genome-wide methods make it possible to identify genes associated with complex traits, like yield or disease resistance Gene discovery Genotype analysis Association analysis QTL mapping population of Ectocarpus Gametophytes (n) Ec568 Ec32 meiosis Sporophyte (2n) segregating progeny (…) ( ) (…) Genotyping / Phenotyping Gametophytes ( ) (n) Parthenosporophytes h t (n) Courtesy P. Boudry Ifremer QTL mapping population of Ectocarpus Genotyping: - 400 microsatellites / 60 ind. : already available ! - 40 additional individuals - SNP markers on the basis of genomes sequences Phenotyping: - fitness fitness-related related traits: survival to low salinity, growth - gene expression : eQTL - other traits of interest… polysaccharides ? Expected pec ed ou outputs: pu s: - genetic architecture of observed variation of traits - comparative mapping of QTLs between sexes, - comparative mapping of QTLs between ploidy levels Courtesy P. Boudry Ifremer Some anticipated outputs - Large genetic resources for successful cultivation operations. -Reliable methods for the genotyping and the chemical phenotyping p yp g of valuable strains strains.. - Anticipation of the impact of large scale cultivation of seaweeds on the genetic diversity of natural populations using genetic markers - Essential tools for molecular breeding of the most valuable strains or hybrids. - Merging population genomics and classical and quantitative genetics in seaweed aquaculture -AE European concerted t d effort ff t iis required i d to t increase genetic resources and genomics input! Thank you P t Partnership hi IDEALG • • • 12 Academics 5 Private companies 1 Technical center (staff >100) www.idealg.ueb.eu Towards GWAS This approach Thi h allows ll h hundreds d d off genes with small effects to be identified In maize, grain yields are correlated with leaf angle and size. A genomewide association survey (GWAS) revealed hundreds of singlenucleotide polymorphisms (SNPs) associated with these traits, providing invaluable information for breeders. Reprinted by permission from Macmillan Publishers Ltd. Tian, F., Bradbury, P.J., Brown, P.J., Hung, H., Sun, Q., Flint-Garcia, S., Rocheford, T.R., McMullen, M.D., Holland, J.B., and Buckler, E.S. (2011). Genome-wide association study of leaf architecture in the maize nested association mapping population. Nat Genet 43: 159-162. Towards GWAS GWAS reveals SNPs that contribute to disease resistance Similar studies have led to the identification of genes contributing to other agronomically important p traits including drought tolerance Reprinted by permission from Macmillan Publishers Ltd Kump, K.L., Bradbury, P.J., Wisser, R.J., Buckler, E.S., Belcher, A.R., Oropeza-Rosas, M.A., Zwonitzer, J.C., Kresovich, S., McMullen, M.D., Ware, D., Balint-Kurti, P.J., and Holland, J.B. (2011). Genome-wide association study of quantitative resistance to southern leaf blight in the maize nested association mapping population. Nat Genet 43: 163-168.