SNP ANALYSIS FOR DROUGHT-RELATED CANDIDATE GENES IN A GERMPLASM COLLECTION AND A TILLING POPULATION OF ITALIAN RICE

Rice is the most important food crop in the world, representing the main source of caloric intake for more than one third of the world’s population. Although a great part of the global rice production comes from the developing countries such as China, India, Indonesia and Bangladesh, northern Italy plays a relevant role in terms of rice production providing about 50% of the total European paddy rice production. Due to the nature of the area devoted to rice growth, characterized by large availability of water and an efficient water distribution net, rice in Italy developed in the last two centuries as a water demanding crop, completing its growth cycle under submersion. However in the last decades also these regions experienced a reduction in water availability, with consequences on production and quality. The development of new varieties able to cope with water scarcity is therefore becoming of utmost importance for a sustainable rice cultivation in Italy. This study aims at identifying new alleles with added value for the improvement of drought resistance in Italian rice. The EMS-induced genetic variability in drought-related candidate genes was then explored in a TILLING population developed in the Italian rice variety Volano. The Volano TILLING platform was validated through the screening of three relevant target genes. A mutation density of 1/374 kb was estimated, proving the effectiveness of this approach for targeted rice crop improvement of Italian germplasm. The collection, currently consisting of 1860 mutant lines that are being enlarged with new mutagenized lines, represents an interesting source of variation exploitable in terms of response to drought stress and directly of use for targeted breeding programs. The mutant lines identified, affecting genes shown to be involved in plant drought escape and avoidance strategies, not only are relevant for Volano breeding programs, but represent a powerful genetic material in view of breeding for drought improvement in Italian rice. The second part of the work aimed at understanding the genetic determinants of root system architecture in the Italian rice germplasm, considering the profound implications of root development on the ability of the plant to cope with water deficits. The first Genome-Wide Association study on root traits was then performed on a germplasm collection including local accessions representing the genetic diversity of rice cultivated in Italy and a set of foreign varieties from temperate areas adapted to Italian climatic conditions. Whole genome genotyping was performed at Cornell University using the GBS (Genotyping-by-Sequencing) approach, a novel NGS strategy previously applied with success to maize and barley that uses libraries based on reducing genome complexity by methylation-sensitive restriction enzymes. In parallel, a thorough phenotypic screening for root morphological features was performed under controlled greenhouse conditions using a novel root phenotyping method that combines an optimized plant growing system (plastic cylindrical baskets coupled with PVC pipes) with an efficient imaging analysis (WinRHIZO image analysis software). The results of genome-wide association analyses performed on a first set of root phenotypic traits were very encouraging. All the detected significant associations were co-localizing with root QTLs previously identified in bi-parental mapping populations. Moreover, four of the detected regions co-localized with drought-avoidance QTLs, strongly supporting the hypothesis of their possible involvement in plant ability to cope with water scarcity. This work provides an initial study paving the way towards improvement of Italian rice varieties in terms of drought resistance.