Understanding the genetic and physiology controls of 'crumbly' fruit in red raspberry (Rubus idaeus)

Abstract

‘Crumbly’ fruit is a generic term to indicate a phenomenon affecting raspberry (Rubus idaeus) and causing the formation of misshapen fruits characterised, in general, by very large drupelets but drastically reduced in number. The imperfect adhesion between these abnormal drupelets causes the fruit to crumble when is picked up and hence the name ‘crumbly’ fruit. Symptoms vary in degree, with very severe forms, genetically determined and here defined as Crumbly Fruit Condition (CFC), to more variable and environmental related phenotypes here defined as Malformed Fruit Disorder (MFD). ‘Crumbly’ fruit can cause high yield losses and in particular MFD, studied in this thesis, due to its unpredictable expression across different seasons is becoming a serious threat for the raspberry industry. Early studies stated that ‘‘crumbly’ fruit is an indication of a partial failure in one or more physiological processes concerned with fruit development’. The aim of this project was to study, in red raspberry, the physiology and the molecular processes behind fruit development to help control or eradicate the phenomenon. ‘Crumbly’ fruit phenotypic data, over many seasons, from a population of Latham x Glen Moy were re-analysed on a new Genotype by Sequencing (GbS) high density linkage map. The analysis identified a new ‘crumbly’ quantitative trait locus (QTL) on linkage group 3 (LG3) and confirmed the two previously identified QTL on LG1 and LG3. From the same population, transcriptomic analysis, via RNA microarray experiments identified genes differently expressed, some of which mapped inside the ‘crumbly’ QTLs. The study of the function of these differently expressed genes showed how impairments in processes related to pollen formation, pollen tube elongation and its interaction with the ovule might be responsible for the occurrence of this phenomenon. Target phytohormones analyses on artificially induced ‘crumbly’ fruits at two different stages (i.e. green and red berry) and in two different parts (i.e. drupelet and receptacle) showed statistically significant differences in abscisic acid (ABA) and in gibberellin A1 (GA1) levels, respectively in receptacle at green stage and in drupelet at red stage. These findings indicated the important role played by ABA and GA1 in ‘crumbly’ fruit and in particular of ABA, as confirmed by the significant difference in the expression levels of numerous genes abscisic acid related (e.g. activated in response to ABA or related to its metabolism, biosynthesis and signalling pathway) found in the transcriptomic analysis.