Towards a high and sustainable biomass production: the Salix molecular breeding activities program (SAMBA)

Transcription

1 Towards a high and sustainable biomass production: the Salix molecular breeding activities program (SAMBA) Ann Christin Rönnberg-Wästljung*, Berit Samils, Nils-Erik Nordh, Jan Stenlid & Martin Weih *Dept. of Plant Biology Swedish University of Agricultural Sciences, Uppsala Contact: anki.wastljung@slu.se

2 Pre-breeding research molecular markers as selection tools Breeding program at Lantmännen ek.för. Pre-breeding research Genetics Resistance Growth Molecular markers in important genes SAMBA homepage:

3 Approaches to study the genetic background Mapping of QTLs Mapping populations Identify a region in the genome (QTL) - Ghelardini et al BMC Plant Biol - Berlin et al Molecular Breeding - Pucholt et al Heredity - Höglund et al Arthropod-Plant Interactions Mapping of genes Natural population Thousands of SNP-markers across the genome from GBS Association to specific genes Development of markers for Salix breeding - Berlin et al Tree Genetics & Genomes. - Hallingbäck et al GCB, Bioenergy

4 QTL-mapping in contrasting environments Sweden Italy, irrigated non irrigated Aims: - finding genomic regions for regulation of biomass and phenology traits as well as for plasticity of these traits as a first step towards MAS - studying similarities and differences across contrasting environments S 1 mapping population: S. viminalis x (S. viminalis x S. schwerinii) x Rational: - S. schwerinii has been used as a resistance donor (rust) in most Salix varieties - breeding goal to develop varieties for northern and southern Europe x Orm Björn x 463 individuals Genetic linkage map: 696 markers 4.4 cm between markers Berlin et al BMC Genomics 11: 129

5 QTL-mapping in contrasting environments Pustnäs, Sweden established 2008 Cavallermaggiore, Italy established 2012 One field experiments in Pustnäs, Sweden Two in Cavallermaggiore, Italy (irrigated, non irrigated) 463 genotypes Complete randomized block design, 6 blocks Phenology traits; bud burst, leaf senescens, 2010, 2013, 2014 Biomass traits; # shoots, weight, diameters, 2010, 2013, 2014 Plasticity traits; difference in standardized trait values between contrasts Photos: Berit Samils - Ghelardini et al BMC Plant Biol - Berlin et al. submitted

6 P: Pu-NI P: Pu-IRR FW14 FW10 MeanD13 Nsh10 LS10 Nsh14 Nsh14 FW10 FW14 SumBA09 Nsh14 Nsh10 P: Pu-NI P: Pu-IRR MeanD13 P: IRR-NI MenD13 P: Pu-NI MeanD13 P: Pu-IRR MeanD13 P: Pu-NI P: Pu-IRR SumBA14 SumBA14 MeanD13 Nsh14 Nsh14 II QTL-mapping in contrasting environments Results Common biomass QTL across all environments, but few XIX Biomass QTL for Cavallermaggiore (Ca) cluster separately to Pustnäs (Pu) XVII Phenology QTL cluster together across environment Plasticity QTL often cluster together with trait QTL for Cavallermaggiore Leaf senescence Bud burst No shoots Diameters Fresh weight Filled, Pu, Sweden Striped, Ca, irr, Italy Plasticity Unfilled, Ca, non irr, Italy

7 P: Pu-NI P: Pu-IRR FW14 FW10 MeanD13 Nsh10 LS10 Nsh14 Nsh14 FW10 FW14 SumBA09 Nsh14 Nsh10 P: Pu-NI P: Pu-IRR P: Pu-NI MeanD13 P: Pu-IRR MeanD13 SumBA14 MeanD13 P: IRR-NI MenD13 P: Pu-NI P: Pu-IRR SumBA14 MeanD13 Nsh14 Nsh14 II QTL-mapping in contrasting environments Results Common biomass QTL across all environments, but few XIX Biomass QTL for Cavallermaggiore (Ca) cluster separately to Pustnäs (Pu) XVII Phenology QTL cluster together across environment Plasticity QTL often cluster together with trait QTL for Cavallermaggiore Bud burst Leaf senescence No shoots Diameters Fresh weight Filled, Pu, Sweden Striped, Ca, irr, Italy Plasticity Unfilled, Ca, non irr, Italy

8 Bud burst P: Pu-NI P: Pu-IRR FW14 FW10 MeanD13 Nsh14 Nsh14 Nsh10 LS10 Diameter Diameter QTL-mapping in contrasting environments - effect of S. schwerinii Sweden & Italy Italy Sweden Results II Large difference between alleles in the hybrid male parent Björn vi m schw vi m schw vi m schw S. schwerinii alleles give large effects Phenology: S. schwerinii gives effects in the same direction independent of environment Bud burst Leaf senescence No shoots Diameters Fresh weight Plasticity Filled, Pu, Sweden Striped, Ca, irr, Italy Unfilled, Ca, non irr, Italy Biomass: S. schwerinii gives effects in different direction depending on climate (Sweden - Italy) Markers can be used to select for or against S. schwerinii alleles

9 Plots of estimated clonal biomass production between contrasting climate and water environments Pustnäs Cavallermaggiore-IRR Björn Correlation : 0.25 ( ) G x E interaction when contrasting climates Cavallermaggiore-NI Separate breeding for different climates Correlation : 0.72 ( ) Björn Cavallermaggiore-NI

10 D143 D178 90_CZ 86_CZ S226_CZ 54_CZ 58_CZ 76_CZ 79_CZ CZ_vim3 65_CZ 98_PL 37_CZ 34_CZ 30_CZ S294_CZ 06_CZ 09_CZ 19_CZ P _PL 126_PL 123_PL 105_PL 107_PL 33_RU IA155 IA153 IA113 IA104 IA102 IA101 IA145 IA138 IA142 IA Sko3 BJ Skarp Kniv SA_31 SA_32 SA_45 SA_67 23_Wye_UK 14_Wye_UK 11_Sev_UK 02_Sev_UK Bel47 Bel38 T QTL mapping vs. Association mapping x Crosses x Study population Map 0,0 X-1b 0,6 SB493 9,5 X_4_sa 11,3 A33.b.4 17,6 SB53 34,4 LA37.b.1 35,3 L30gr ,7 L24gr ,1 SB488 40,4 X_DT_28_sa X_6_sa 44,7 P1132f 49,3 Ph2 50,4 L27gr.443f 60,7 L1gr ,6 X-3 70,5 L24b ,9 X_15_sa 75,0 L13y ,5 X-4 94,5 X_17om_sa 100,6 X_27_sa 103,0 L11b ,7 X_18_sa 118,9 X-19_sa 119,7 R_79_sa R_48_sa 119,9 R_56_sa 126,7 L22gr.168f 133,5 SB ,7 X-21_sa 142,3 L3gr.227f Collection effort Study population Structure Series4 Series3 Series2 Series1 Controlled crosses, pedigree known Usually requires construction of a linkage map Very limited genetic diversity Significant associations (QTLs) may be relevant only to the particular cross Natural or diverse population with unknown pedigree. Requires estimation of hidden population structure and coancestry Considerable genetic diversity Significant assocations may be relevant in a wider context

11 Association-mapping in Central and Southern Sweden Aims: - finding important genes for regulation of biomass and phenology traits MAS - studying similarities and differences across contrasting environments Material and field experiments Population of 320 unique accessions of Salix viminalis collected by SLU, RRes and Lantmännen, SWseed Origins: UK, Sweden, Belgium, Western Russia, Czech Republic, Germany, Poland Field trials established in May 2009, extensively measured Two field trails in Sweden, 6 clonal replicates for each accession and trial Rational: - S. viminalis is extensively used in breeding of Salix for Europe Genotyping by sequencing (GBS): ~ markers across the genome - Berlin et al Tree Genetics & Genomes. - Hallingbäck et al GCB, Bioenergy

12 Association mapping 30 0'0"W 20 0'0"W 10 0'0"W 0 0'0" 20 0'0"E 50 0'0"E 80 0'0"E 100 0'0"E 110 0'0"E 120 0'0"E 130 0'0"E 50 0'0"N 50 0'0"N 40 0'0"N 40 0'0"N 20 0'0"E 30 0'0"E 40 0'0"E 50 0'0"E 60 0'0"E 70 0'0"E 80 0'0"E Swedish cluster W European cluster E European cluster Russian cluster - Berlin et al Tree Genetics & Genomes.

13 Preliminary results markers from GBS. Salix purpurea as reference genome (L. Smart) Pustnäs, bud burst 2010 Pustnäs, leaf senescence Chromosome Chromosome Pustnäs, mean diameter 2016 Svalöv, mean diameter Chromosome Chromosome

14 Conclusions QTL studies genetic markers for Salix schwerinii alleles QTL studies breeding for separate climates Association mapping genetic markers of more general use for S. viminalis

15 Acknowledgements Earlier members of SAMBA: Sara von Arnold, Sofia Berlin Kolm, Luisa Ghelardini, Tom Martin, Henrik Hallingbäck; Plant Biology, SLU Lorenzo Bonosi, Friderike Beyer; Plant Production Ecology, SLU Christer Björkman, Johan Stenberg, Adriana Puentes, Karin Eklund; Ecology, SLU Gabriele Engkvist; Lantmännen ek.för. Collaborations outside SAMBA: Pascal Pucholt; Plant Biology, SLU Ulf Lagercrantz; UU Anna Schnürer; Microbiology, SLU Ewa Mellerowicz; UPSC Steve Hanley, Rothamsted Research, UK Angela Karp, Rothamsted Research, UK Larry Smart, Cornell Unv. USA Funding and support: