Resumen de Assessment of genomic and high-through put phenotyping tools in a diversity panel of mediterranean landraces and cultivars for wheat breeding under rainfed environments
Bread wheat (Triticum aestivum L.) is the main crop cultivated around the world, but climate change will significantly affect its production, with special impact in the Mediterranean basin. The ultimate purpose of this PhD thesis is to provide scientific knowledge and useful tools for the development of the next generation of superior bread wheat varieties resilient to the increased drought expected in the next decades as consequence of climate change. To achieve this objective, the existence of genetic, phenotypic and/or geographic structures in the germplasm collections was explored and quantitative trait loci (QTLs) controlling traits related to terminal drought resistance using a genome wide association study (GWAS) were identified. The MED6WHEAT IRTA-panel, with 170 landraces from 24 Mediterranean countries and 184 to modern varieties cultivated in 19 countries in the region, was characterized with more than 10K single nucleotide polymorphism (SNP) markers. A clear geographical pattern was found for the landraces, with three subpopulations (SPs) representing the western, northern, and eastern Mediterranean, whereas the modern cultivars were structured according to the breeding programmes operating in the region: CIMMYT/ICARDA, France/Italy, and Balkan/eastern European countries. Landraces were used to investigate their seminal root system architecture (RSA) adapted to rainfed Mediterranean conditions. Those from northern Mediterranean countries showed the highest number of seminal roots with a root angle not statistically different from the western Mediterranean ones, whereas eastern Mediterranean landraces showed the lowest number of roots but the widest angle, the longest shoots, and the lowest seed weight. A GWAS detected marker-trait associations (MTAs) linked to root-related traits and 31 candidate genes related to RSA traits, seed size, root development and abiotic stress tolerance were found within 15 QTL hotspots. The whole panel was evaluated on a two-year field trial using high-throughput phenotyping (HTP) technologies with the aim to predict agronomic traits. The best estimation of LAI was achieved through the modified triangular vegetation index (MTVI2), and ground-based RGB vegetation indices (VIs) showed better predictions of agronomic traits. The predictive value of the models developed for modern genotypes increased when the data of more than one growing season were aggregated to build them. Results based on a three consecutive year study found significant differences for agronomic traits between subpopulations, pointing out the division of the whole set into landraces and modern cultivars. Modern SPs showed higher values of grain yield and components, harvest index and biomass and longer grain filling duration than landrace SPs, which were taller. The highest grain yield was observed for modern cultivars from France and Italy. A GWAS identified 2579 markers associated with agronomic and VIs–related traits that were simplified to 11 QTL hotspots. In silico analysis of candidate genes detected 12 differentially expressed genes (DEG) upregulated under abiotic stress within 6 QTL hotspots. Among them, five genes were previously reported to be involved in abiotic stress tolerance. Overall, these results proved that Mediterranean wheat landraces are a valuable source of variability to introgress new alleles for desirable traits in the breeding programs in the Mediterranean Basin. The use of remote sensing technology is an efficient and rapid tool for the assessment of agronomic traits. Finally, GWAS have resulted a useful approach for the identification of genomic regions controlling important traits in the bread wheat Mediterranean germplasm.
