Facing New Climate Change Scenarios By QTLome andPangenome Analysis of the Global Durum GenomicResources (GDGR)

The Breeding of new varieties can be boosted by leveraging genomics tools applied to germplasm collections. With this aim, UNIBO and partners assembleda golden-standard cv. Svevo Durum wheat genome reference and a comprehensive Global Durum Genomic Resources (GDGR), including: the Global DurumPanel (GDP: 1,033 cultivars) and the Tetraploid Global Collection (TGC: 1,856 tetraploid wheats) and INNOVAR durum wheat panel (modern Europeanvarieties, 250 genotypes). Resources were genotyped with the Illumina 90K wheat SNP Array, and 40 selected representatives of diversity were sequencedand assembled based on PACBIO Hi-Fi. The GDGR was evaluated in a field trial network for: (i) phenology, yield components and quality traits, (ii) responsewheat diseases such as the Soil-borne Cereal Mosaic Virus (SBCMV), Septoria tritici blotch (STB) and rusts. An extensive haplotype analysis was performedon the GDGR panel to trace by identity-by descent (IBD) chromosomic regions inherited from breeding founders to modern varieties. The analysis showedthat chromosomic regions from Southern Europe, North America, CIMMYT and ICARDA founders were clearly inherited to modern genotypes, representing amosaic of IBD regions from breeding founders. Herein, we present two case studies where a combination of phenotyping, genotyping, RNAseq and long-range PACBIO sequencing techniques was used to analyse SBCMV resistance/susceptibility and spike fertility with the tetraploid wheat pangenome. SBCMVresistance is regulated by a major QTL on chr. 2B named QSbm.ubo-2BS = Sbm2 (R =60%), recently fine mapped to a 1.5 Mb region where 21 KASP®markers were designed defining Sbm2 resistant/susceptible haplotypes. The region showed a clear enrichment for disease-response related genes (such asprotein kinases and NBS-LRRs) confirmed by RNAseq analysis. Comparing the Sbm2 region of Svevo cultivar (resistant) to different susceptible genotypes(Simeto, Kronos and Altar84), a 1.1 Mb deletion was identified in the fined mapped interval, removing all candidate resistance genes, and leading to SBCMV. susceptibility. Similarly, we identified a locus for grain number increase (GNI) carried by the CIMMYT founder AltarC84, contributing to the +/+ haplotype and phenotype (+0.54 grain per spikelet), directly associated to a 1.5 kb deletion in the QTL region. As to conclusion, the combination of haplotype and QTLome characterization, allele mining and pangenome analysis helps to better describe germplasm collections and specific case study of interest to select key haplotypes and markers aiming at defining new resilient varieties to evolving climate change scenarios. The GDGR provides unprecedented opportunities to more effectively leverage the tetraploid wheat diversity also for a more effective hexaploid wheat breeding. Aknowledgements. PANWHEATGRAIN (PRIN-2020), AGRITECH, Agritech National Research Center, European Union Next-GenerationEU (PIANO NAZIONALE DI RIPRESA E RESILIENZA (PNRR) – MISSIONE 4 COMPONENTE 2, INVESTIMENTO 1.4), Canadian Tetraploid Pan Genomics, National Projects supporting the Svevo Durum Wheat Genome Sequencing Consortium, the Tetraploid Wheat Pangenome Consortium and the development of the GDGR, “PLAN’EAT” - Food systems transformation towards healthy and sustainable dietary behaviour and “WHEAT SECURITY”, H2020 FP7 “INNOVAR” - Next generation variety testing for improved cropping on European farmland and by “CerealMed”- Enhancing diversity in Mediterranean cereal farming systems project, funded by PRIMA2019.