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ABSTRACTS BOOK (Appendix) EAPR 2014 Brussels 19th Triennial Conference of the European Association for Potato Research 6 to 11 July 2014 ABSTRACTS BOOK (appendix) Proceedings of the Conference Full texts of abstracts submitted as ORAL or POSTER presentations ____________________________________________________________ USB Keys are sponsored by Cofabel and John Deere ______________________________________________________________________ EAPR 2014 Brussels 19th Triennial Conference of the European Association for Potato Research 6 to 11 July 2014 ABSTRACTS BOOK (appendix supplied as digital version) Proceedings of the Conference Full texts of abstracts submitted as ORAL or POSTER presentation Editors: Jean-Pierre GOFFART, Jean-Louis ROLOT (CRA-W, Belgium) Kürt DEMEULEMEESTER (INAGRO, Belgium) Marc GOEMINNE (PCA, Belgium) Texts of ABSTRACTS submitted as ORAL or POSTER Abstracts assigned to ORAL sessions (scientific parallel sessions or workshops) are ordered from 1 to 131 bis, and grouped into thematic parallel scientific sessions as scheduled in the detailed scientific program of the Abstracts book. ORAL PRESENTATIONS Session 1 – Genomics (1) (abs. 1 to 6) Session 14 – Genomics (2) (abs. 74 to 79) Session 2 – Fungi/Bacteria (abs. 7 to 12) Session 15 – Biological control (abs. 80 to 85) Session 3 – Global food security (abs. 13 to 18) Session 16 – Agronomy (1) (abs. 86 to 91) Session 4 – Sustainable production (abs. 19 to 24) Session 17 – Nematodes (abs. 92 to 97) Session 5 – Breeding (1) LB (abs. 25 to 29) Session 18 – Physiology (2) (abs. 98 to 102) Session 6 - Post-Harvest/Storage (abs. 30 to 34) Session 19 – Breeding (3)/Ph.(abs. 103 to 108) Session 7 – Tuber quality/Nutrition (abs. 35 to 39) Session 20 – Bacteria /Pests (abs. 109 to 114) Session 8 – Socio-economics (abs. 40 to 44) Session 21 – Agronomy (2) (abs. 115 to 120) Session 9 – Breeding (2) (abs. 45 to 50) Session 22 – Seeds potato (abs. 121 to 126) Session 10 – Late Blight (abs. 51 to 56) Session 11 – Physiology (1) (abs. 57 to 62) Workshop 2 – Precision Agriculture Session 12 – PVY (1) (abs. 63 to 68) (abs. 129, 130, 131, 131bis) Session 13 – PVY (2) (abs. 69 to 73) Workshop 6 - Nematodes (abs. 126bis, 127, 128) Abstracts assigned to POSTER sessions are ordered from 132 to 304, and grouped into scientific topics. POSTER PRESENTATIONS Genomics (abst. 132 to 151) Diseases (abst. 263 to 266) Breeding (abst. 152 to 177) Biological control (abst. 267 to 271) Phenotyping (abst. 178 to 188) Weeds (abst. 272 to 273) Seed potato production (abst. 189 to 201) Post-Harvest and storage (abst. 274 to 278) Agronomy (abst. 202 to 211) Tuber quality (abst. 279 to 288) Physiology (abst. 212 to 222) Potato and Global food security (abst. 289 to 291) Late blight (abst. 223 to 229) Sustainable potato production (abst. 292 to 297) Bacteria (abst. 230 to 242) Socio-economics of the potato (abst. 298) Nematodes (abst. 243 to 248) Organic potato production (abst. 299 to 300) Fungi (abst. 249 to 250) From Research to practice (abst. 301 to 302) Pests (abst. 251 to 252) Ongoing new research projects (abst. 303 to 304) Viruses (abst. 253 to 262) ORAL PRESENTATIONS (Parallel scientific sessions and Workshops) Abstracts 1 to 131bis Session 1 (OP) - GENOMICS (1) 1 APPLICATION OF GENOTYPING-BY-SEQUENCING FOR IDENTIFYING SNP VARIATION AND PERFORMING GENOME-WIDE ASSOCIATION STUDIES IN A TETRAPLOID POTATO ASSOCIATION PANEL S. Sharma 1, M. Bayer 2, K. McClean 1, K. McKenzie 3, S. Daniels 4, F. Dale 1, 5, G. Bryan 1 1 The James Hutton Institute - Cell and Molecular Sciences, Dundee, UNITED KINGDOM 2 The James Hutton Institute - Information and Computational Sciences, Dundee, UNITED KINGDOM 3 Biomathematics and Statistics Scotland, Dundee, UNITED KINGDOM 4 Cygnet PB Ltd, Cambridge, UNITED KINGDOM 5 Mylnefield Research Services Ltd, Dundee, UNITED KINGDOM Sequencing of the potato genome has opened up new vistas for potato genetics and breeding. Further conversion of the sequenced genome into well-structured, oriented and annotated chromosome-scale pseudomolecules has made potato more amenable to modern genomic approaches such as sequenced- based genotyping. Genome-wide association studies (GWAS) are feasible and are gaining importance for studying the genetics of natural variation and traits of agricultural importance. GWAS offers significant advantages, such as increased mapping resolution, increased numbers of segregating traits, and greater allelic diversity than traditional mapping using bi-parental crosses. For a robust GWAS analysis, presence of high-throughput and marker-dense genotyping platforms are preferable. Previously, GWAS has been applied to potato using both more traditional (e.g. SSRs and AFLPs) as well as contemporary, sequence- based (e.g. SNPs) marker types. We are exploiting the latest high-throughput Next Generation Sequencing (NGS) technologies for performing GWAS in potato by employing a ‘Genotyping-by- Sequencing’ (GBS) approach. GBS offers advantages of simultaneous genotyping as well marker discovery and alleviates issues arising from factors such as ascertainment bias. Our Association Panel comprises 350 diverse autotetraploid potato cultivars which have been Illumina-sequenced at a reduced complexity level coupled with indexed sample multiplexing. The panel has also been genotyped using the SolCAP 8k Infinium array for the initial assessment of population stratification and Linkage Disequilibrium (LD). The selected germplasm has been phenotyped in two environments over two growing seasons. Potato, a highly heterozygous and tetraploid crop, brings many challenges for the downstream analysis of GBS data as well as GWAS analysis. Insights from these efforts will be presented. 2 A COMPLEX DISEASE RESISTANCE LOCUS ON POTATO AND TOMATO CHROMOSOME 4 EXHIBITS A CONSERVED STRUCTURE DISPLAYING DIFFERENT RATES OF EVOLUTION IN DIFFERENT LINEAGES D. Milbourne 1, M. Destefanis 1, I. Nagy 1, G.J. Bryan 2, K. McLean 2, I. Hein 2, P.W. Jones 3, D. Griffin 1 1 Teagasc, Crops, Environment and Land Use Programme, Carlow, IRELAND 2 Cell and Molecular Sciences, The James Hutton Institute, Dundee, UNITED KINGDOM 3 University College Cork, Cork, IRELAND Introduction In plant genomes, NB-LRR based resistance (R) genes tend to occur as clusters of variable size in a relatively small number of regions. The R-gene sequences mostly differentiate by accumulating point mutations and gene conversion events. Potato and tomato chromosome 4 harbours a syntenic R-gene locus (known as the R2 locus in potato) that has mainly been examined in central American/Mexican wild potato species on the basis of its contribution to resistance to late blight, caused by the oomycete pathogen Phytophthora infestans. Evidence to date indicates the occurrence of a fast evolutionary mode characterized by gene conversion events at the locus in these genotypes. The recent sequencing of the potato and tomato genomes has afforded the opportunity to examine the evolutionary mode of this locus in a different lineage, of South American origin, where co-evolution with diverse and aggressive isolates of the late blight pathogen may not have been as significant a driving force. Methods and Results A physical map of the R2 locus (representative of the Group Phureja lineage) was developed for three S. tuberosum genotypes and used to identify the tomato syntenic sequence. Functional annotation of the locus revealed the presence of numerous resistance gene homologs (RGHs) belonging to the R2 gene family (R2GHs) organized into several discrete clusters, three of which were conserved across S. tuberosum and tomato. The locus has expanded in S. tuberosum Group Phureja and footprints of recent duplication events can be identified between five sets of potato paralogs. Phylogenetic analysis showed clear orthologous relationships between S. tuberosum Group Phureja R2GHs but not in R2GHs cloned from Solanum wild species. This study confirmed that, in contrast to the wild species R2GHs, which have evolved through extensive sequence exchanges between paralogs, gene conversion was not a major force for differentiation in S. tuberosum Group Phureja R2GHs, and orthologous relationships have been maintained via a slow accumulation of point mutations in these genotypes. In addition, as well as the expected level of positive selection in the LRR regions, members of the R2 gene family from both lineages share significant levels of positive selection in codons at the 5’ end. Discussion Comparative analysis reveals a conserved tripartite structure at the R2 locus predating speciation of potato and tomato. S. tuberosum Group Phureja and S. lycopersicum R2GHs evolved mostly through duplication and deletion events, followed by gradual accumulation of mutations. This slow evolutionary rate unequivocally delineated the orthologous relationships between R2GHs in S. tuberosum genotypes. Conversely, the numerous gene conversion events detected in R2GHs from Solanum wild species conceal mutual orthologous relationships. Conclusions We conclude that different selective forces shaped the evolution of the R2 locus and that co-evolution with a pathogen steered selection on different evolutionary paths. 3 ALLELE-SPECIFIC MOLECULAR MARKERS FOR THE POTATO’S DISEASE RESISTANCE GENES VIA NEXT GENERATION SEQUENCING F. Trognitz 1, K. Muders 2, B. Truberg 2, H. Junghans 2, T. Schmidt 3, C. Prakash 4, A. von Haeseler 4, B. Trognitz 1 1 Austrian Institute of Technology, Tulln, AUSTRIA 2 NORIKA GmbH, Gross Luesewitz, GERMANY 3 Technical University Dresden, Dresden, GERMANY 4 Center for Integrative Bioinformatics,
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