Trait physiology and crop modelling to link phenotypic complexity to underlying genetic systems

New tools derived from advances in molecular biology have not been widely adopted in plant breeding because of the inability to connect information at gene level to the phenotype in a manner that is useful for selection. We explore whether a crop growth and development modelling framework can link phenotype complexity to underlying genetic systems in a way that strengthens molecular breeding strategies. We use gene-to-phenotype simulation studies on sorghum to consider the value to marker-assisted selection of intrinsically stable QTLs that might be generated by physiological dissection of complex traits. The consequences on grain yield of genetic variation in four key adaptive traits – phenology, osmotic adjustment, transpiration efficiency, and staygreen – were simulated for a diverse set of environments by placing the known extent of genetic variation in the context of the physiological determinants framework of a crop growth and development model. It was assumed that the three to five genes associated with each trait, had two alleles per locus acting in an additive manner. The effects on average simulated yield, generated by differing combinations of positive alleles for the traits incorporated, varied with environment type. The full matrix of simulated phenotypes, which consisted of 547 location-season combinations and 4235 genotypic expression states, was analysed for genetic and environmental effects. The analysis was conducted in stages with gradually increased understanding of gene-to-phenotype relationships, which would arise from physiological dissection and modelling. It was found that environmental characterisation and physiological knowledge helped to explain and unravel gene and environment context dependencies. We simulated a marker-assisted selection (MAS) breeding strategy based on the analyses of gene effects. When marker scores were allocated based on the contribution of gene effects to yield in a single environment, there was a wide divergence in rate of yield gain over all environments with breeding cycle depending on the environment chosen for the QTL analysis. It was suggested that knowledge resulting from trait physiology and modelling would overcome this dependency by identifying stable QTLs. The improved predictive power would increase the utility of the QTLs in MAS. Developing and implementing this gene-to-phenotype capability in crop improvement requires enhanced attention to phenotyping, ecophysiological modelling, and validation studies to test the stability of candidate QTLs.

Italian wild hop (Humulus lupulus L.): from biodiversity evaluation to varietal selection

Hop (Humulus lupulus L.) is a dioecius perennial plant. The cultivation is specific for female plants, used mainly for brewing and pharmacology. Female inflorescence, known as cone or strobili, contains bitter acids, essential oil and polyphenols. Commercial hop cultivation provides better results in regions between 45 and 55 degrees north or south in latitude, an area that also includes the northern part of Italy, where hop is endemic. Despite several studies have been conducted on the characterization of wild hops biodiversity in the U.S.A. and Europe, a lack in literature concerning the description of Italian wild hops genetic variability is still present. The increasing request of hop varieties improved in important traits, like diseases, resistance and valuable aroma profile, is bringing the hop industry. Moreover, Italian agricultural sector needs new impulse to be competitive in the market. In this view, Italian wild hop biodiversity is a resource, useful for the obtaining of Italian hop varieties, characterized by peculiar aromatic traits and more adaptable to Mediterranean climate, making their cultivation more sustainable. Based on this consideration, the present Ph.D. thesis deals with the evaluation of the Italian hop biodiversity, through the characterization of the wild samples under different point of view. The project started with the recovery of wild hop samples in different areas of north of Italy to consitue a collection field, where 11 commercial cultivars of US and European origin were grown, to have a complete vision of the hop panorama. Ph.D. project followed different research lines, the results of each one contributed to completly characterize the northern Italian hop wild biodiversity: • the morphological description showed a high phenological variability (Study 1); • the genetic characterization confirmed the rich biodiversity of the Italian population and showed a significant genetic distance between Italian genotypes and the commercial cultivars, taken in consideration (Study 2); • the need of an early sex discrimination method leads to an improvement of a genetic marker, developing a more efficient marker (Study 3); • a complete morphologic, genetic and chemical analysis of plants gave results to select the most promising genotypes (Study 4); • the comparison between the performance of wild hops and commercial cultivars in the same collection field indicated that some wild genotypes had a higher environment adaptability (Study 5); • the evaluation of the terroir, obtained comparing commercial cultivars in the collection field and the same genotypes purchased in the market, showed the influence of the northern Italian environment on the aromatic profile (Study 5); • a new analytical method for the revelation of bioactive metabolites and a simple extraction procedure were developed (Study 6). In conclusion, the Ph.D. thesis, contains the first characterization of Italian wild hop, made under field condition. The present study: i) permits to obtain a complete and significative description of the genotypes; ii) allows the identification of the most promising wild Italian genotypes; iii) allows the identification of commercial cultivars more adaptable the northern Italian climate.