Fragaria vesca – a model species for climatic adaptation studies Norwegian 21.6. 2016 8th FinnishInternational Rosaceae GenomicsItalian Conference Spanish Tuomas Toivainen Strawberry Research Group Department of Agricultural Sciences Viikki Plant Science Centre University of Helsinki Finland Plant species have adapted to current climate after the last glacial maximum (LGM) Postglacial colonization routes in Europe R4? R3 R1 R2 http://www.gly.uga.edu/railsback/FQS/FQS.html R = refugium Taberlet et al. 1998 • When temperature started to increase after the LGM, plants colonized northern Europe • Plants have adapted warmer climate and and some species have adapted to new climate in the northern Europe • Which genes (alleles) have been under selection in the past? (Footprints of directional selection in local populations) • Which genes underlie current quantitative genetic variation (GWAS) Fragaria vesca ssp. vesca – an excellent model species for climatic adaptation studies Length of growing season (average daily temp. > 5 C) 365 350 300 255 250 200 185 150 98 100 50 0 Portugal (Sintra) Italy (Tenno) Finland Norway (Alta) (Helsinki) Liston et al. 2014 • A wide distrubution in different habitats throughout the Europe (37-71°) • Small genome (211 Mb), suits well to population scale studies • Genetic transformations routinely done, for selected genes allelic effects can be tested F. vesca ssp. vesca TTA1 Phenotypic differentiation along a latitudinal cline across Europe Flowering time !(!( !( !( !(!( !(!( !(!(!( !( !( !( !( !(!( !( !( 35.0 Flowering induction: 12h, 11C, 6 weeks !( !( !( !( !( 32.5 !( (COUNTRY) !( !( !( finland !( !( !( !( !( !( !( !( germany 30.0 iceland italy mean lithuania !( !( !( !(!( !( !( !(!( !( !( !(!(!( !( !( !( !( !( norway !( 27.5 spain !( uk !( 25.0 !( !( !( !( !( !( !( !( !( !( 22.5 !( !( !( !( !( !( !( !( uk !( !( italy spain !( finland !( !( iceland norway lithuania !( !( germany !( !( !(!( !(!(!( 92 genotypes (4 clones of each) !( !( !( !(!( !( !(!( !( !( !( !( !( !( !( !( !( !( • Flowering time correlates with latitude in a mainland (UK and Icelandic samples are exceptions) • Northern populations flower earlier (adaptation to shorter growing season?) • Flowering time differences are likely due to variation in flower induction Diapositive 4 TTA1 in Europe, latitude correlates with day length, mean precipitation and mean temperatures Toivainen, Tuomas A; 16/06/2016 Geographical and genetic structure • Mean read depth 18 130 sequenced accessions • 2 million SNPs !(!( !( !( !(!( !(!( !(!(!( !( !( !( !( !(!( !( !( !( !( !( !( !( !( !( !( !( !( !( !( !( !( !( !( !( !( !( !( !(!( !( !( !(!( !( !( !(!(!( !( !( !( !( !( !( !( !( PC1 (16.7%) PC1 !( !( !( !( !( !( !( !( !( !( !( !( !( !( !( !( !( !( !( !( !( !( !(!( !( !( !(!( !(!(!( !( !( !( !(!( !( !(!( !( !( !( !( !( !( -0.10 -0.05 0.00 0.05 0.10 !( !( !( !( -0.10 -0.05 0.00 0.05 0.10 0.15 • Latitude explains most of the genetic variance PC2 (7.2%) • Central European populations (ITA,GER and UK) cluster together with Iceland (common refugium during LGM?) • Finnish and Lihuanian plants form a clear own genetic cluster(common refugium during LGM) • Norwegian plants can be found from three genetic clusters (moved with humans?) Ancestry 0.0 0.2 0.4 0.6 0.8 1.0 ES-13 ES-18 ES1 ES10 ES11 ES12 ES14 ES15 Spain Italy ES19 ES2 ES20 ES21 ES3 ES4 ES5 ES6 ES7 ES8 ES9 POR2 POR3 IT-3 IT-P18-1 IT-P19-1 IT1 IT10 IT11 IT12 IT13 IT14 IT15 IT16 IT17 IT2 IT4 IT6 IT7 IT8 IT9 GER1 GER10 GER11 GER13 GER (K=6) analysis Admixture GER2 GER3 GER4 GER5 GER6 GER7 GER9 UK1 UK11 UK12 UK UK2 UK3 UK6 UK7 UK9 LIT1 LIT2 LIT LIT3 LIT4 LIT5 LIT6 LIT7 FIN1 FIN10 FIN11 FIN12 FIN13 FIN2 Finland FIN25 FIN28 FIN29 FIN3 FIN39 FIN40 FIN41 FIN5 FIN50 FIN51 FIN53 FIN55 FIN6 FIN7 FIN8 SDfv ICE10 ICE11 ICE12 ICE14 ICE15 Iceland ICE16 ICE17 ICE18 ICE19 ICE1 ICE2 ICE3 ICE4 ICE5 ICE6 ICE7 ICE8 ICE9 NOR11 Tromso NOR1 NOR27 NOR28 NOR29 NOR30 Norway NOR13 NOR14 NOR16 Kåfjord NOR17 NOR1 NOR10 NOR2 Alta NOR3 NOR5 NOR6 NOR7 NOR8 NOR9 NOR18 NOR19 NOR20 NOR21 NOR22 Selection pressure for earlier flowering in spring Detecting directional selection (a hard sweep) Scheinfeldt and Tishkoff 2013 Anderson et al. 2012 Flowering time is advancing e.g. in Boechera stricta • Methods to detect a selective sweep Italy, N=16 Resolution = 10 kbp • Excess of almost fixed new mutations • Linkage disequilibrium • Excess of rare alleles • High population differentiation • Low genetic diversity TFL1 gene as a target of selection? 2 10.37-10.38Mb 0 Tajima D -2 Mb TFL1 gene uncharacterized LOC101294230 0.75 Lowest Tajima’s D and highest Fst at 10.37-10.38Mb Fst 0.25 Mb Indels and SNPs around FvTFL1 Comparison of Italian and Finnish populations • Three almost completely fixed indels were identified in the genomic region containing FvTFL1 • Two indels within 2 kb upstream of FvTFL1 • One indel ~600 bp downstream of FvTFL1 • Five almost completely fixed SNPs were found Fst = 0,97 Fst = 0,92 Fst = 0,92 WT TFL1-RNAi Takeshi Kurokura = INDEL = SNP Takeshi Kurokua Spain VRN1 LOS1 FLX-3 FRI- 5 Italy VRN1 TFL1 FLX-3 Finland FAR1, FHY3 FLX FRI 3 Alta Conclusions • Flowering time correlates with latitude suggesting climatic adaptation • Population structure correlates with latitude • Present genetic clustering might reflect common refugia during the LGM • We have found clear signals of selection, which have likely had a role in climatic adaptation In the future: • Looking other sweeps more closely • GWAS experiment is going on • Do we find associations from selected regions? STRAWBERRY GROUP COLLABORATORS • Timo Hytönen University of Malaga, Spain, David Posé • Paula Elomaa Centro IFAPA Churriana, Spain, José • Marja Rantanen Sánchez-Sevilla • Elli Koskela Fondazione Edmund Mach - IASMA, Italy, Dan Sargent • Samia Samad Agricultural University of Iceland, Jon • Takeshi Kurokura Halsson, Hrannar Hilmarsson • Sonja Kymäläinen Institute of Biotechnology, UH, Petri • Havier Jimenez Auvinen, Lars Paulin, Annina Lyyski Univ. Helsinki, Ari Löytynoja, Jarkko FUNDING Salojärvi • Academy of Finland University of Tromso, Norway, Laura Jaakola Univ. of Reading, UK, Nicholas Battey Bioforsk, Norway, Anita Sonsteby Thank you !.