Screening techniques and sources of resistance to root diseases in cool season food legumes

Summary Soil-borne fungal diseases are among the most important factors, limiting the yield of grain legumes in many countries worldwide. Root rot, caused by Aphanomyces euteiches, Rhizoctonia solani, Fusarium solani and wilt, caused by several formae speciales of Fusarium oxysporum are the most destructive soil-borne diseases of pea, chickpea, lentil, fababean and lupin. The most effective control of these diseases is achieved through the use of resistant varieties. In this paper, recent advances in conventional and innovative screening methods for disease resistance are presented. Many grain legume accessions, which are maintained in national and international germplasm collections, have been evaluated for disease resistance and numerous resistant varieties have been released following incorporation of identified resistance genes from these sources. Recent identification of molecular markers tightly linked to resistance genes has greatly enhanced breeding programs by making marker assisted selection (MAS) possible and allowing the development of varieties with multiple disease resistance. Progress in the understanding of the biology of soil-borne fungal pathogens of grain legumes is also reviewed with particular reference to the genetic structure of their populations, diagnosis and host–pathogen interaction.     

Regional and varietal differences in the risk of wheat seed infection by fungal species associated with fusarium head blight in Italy

The incidence of seed infection by fungal species pertinent to the fusarium head blight complex was monitored from 1999 to 2002 in two soft and three durum wheat cultivars grown across the northern, central and southern production zones of Italy, in order to characterize the species composition at the seed level. The main species recovered were Fusarium graminearum, F. poae and Microdochium nivale. There was a marked influence of production zone on seed infection incidence for both durum and soft wheat cultivars, with incidence of infection generally decreasing from the northern to the southern zone. Incidence of seed infection by different species of Fusarium was twice to four times higher in durum compared with the soft wheat cultivars in the study. There were no significant differences in terms of seed infection incidence between the two soft wheat cultivars, but the durum cultivars differed in their levels of seed infection for some of the pathogens. The results demonstrated that the durum cultivars were more at risk of seed infection by pathogens associated with fusarium head blight, and that wheat grown in northern Italy is at higher risk of seed infection by these species.     

Community structure of the Fusarium complex on wheat seed in Italy

The objective was to quantitatively document the pathogen community associated with the Fusarium head blight complex in Italian wheat. The observational study was prompted by increased concerns about mycotoxin contamination coupled with a surge in organically grown wheat. During the three-year survey (2004 to 2006) in three geopolitically defined zones (north, centre, south), seedborne pathogens associated with Fusarium head blight in organic bread and durum wheat were assayed by the freezing blotter method and identified to species based on morphological features. The four most abundant species overall, in order from highest to lowest, were Fusarium poae, Microdochium nivale, F. verticillioides and F. graminearum. Environment was more influential than wheat cultivar in determining the variances in seed infestation counts. Counts of infested seeds were higher (and more variable) in the north and centre zones than in the south zone. The odds of observing any seed infestation was significantly higher in both the north and centre zones (compared with the south zone) for F. avenaceum, F. graminearum, F. poae, and M. nivale in durum wheat. There was a significant nonlinear relationship between seed infestation prevalence and incidence, with evident separation of species along the prevalence-incidence curve. Species co occurrence was observed, but associations shifted with wheat type, over years, and among zones. F. poae was not positively associated with any other species.     

Genetic variability of Fusarium fujikuroi populations associated with bakanae of rice in Italy

The heterothallic ascomycete Fusarium fujikuroi (teleomorph: Gibberella fujikuroi) is the causal agent of bakanae of rice, a disease of increasing economic importance in the major rice‐producing areas in the world and a serious threat for Italian rice cultivation. A few studies have characterized F. fujikuroi isolates in America and the Philippines but no data are available on the genetic structure of Italian pathogen populations. Microsatellite SSRs are useful tools to study the intraspecific diversity at population level. In this study, 19 polymorphic SSRs have been identified and applied to characterize the genetic variation of 334 isolates of F. fujikuroi coming from eight Italian rice‐growing areas. A high degree of diversity at haplotype level has emerged: in the eight populations, 107 unique haplotypes were scored. Analysis of molecular variance (amova ) showed that 98% of genetic variability occurred within F. fujikuroi Italian populations, as confirmed by the allelic Shannon index ranging from 0.56 to 1.06. The presence of a 1:1 ratio of mating type alleles in six out of eight of the Italian fungal populations suggests a potential for sexual reproduction in the field. However, the high fraction of clonality (43%), confirmed by neighbour‐joining clustering analysis, and the high level of linkage disequilibrium observed, indicates that reproduction of F. fujikuroi is mostly clonal in Italy. All data suggest that the observed genetic variability was probably mediated by human activity and transmission by rice seeds.     

Ascochyta blight of chickpea in Australia: identification, pathogenicity and mating type

The aetiology of blight of chickpea in South Australia was studied following sporadic disease outbreaks over several years that had been tentatively identified as Phoma blight. Nine fungal isolates from diseased chickpeas were tested for pathogenicity in the glasshouse, of which two caused symptoms resembling those of Ascochyta blight. The two aggressive isolates were identified as Ascochyta rabiei based on morphological characteristics of cultures and RAPD analysis. This was further confirmed by successful mating to international standard isolates, which showed that the two Australian isolates were MAT1-1. These isolates are accessioned as DAR 71767 and DAR 71768, New South Wales Agriculture, Australia. This is the first time that A. rabiei has been positively identified in commercial chickpeas in the southern hemisphere. The pathogen was found (in 1992) in only one of 59 seed samples harvested throughout Australia between 1992 and 1996 and tested using International Seed Testing Association methods. The teleomorph has not been found in Australia and results to date suggest that only one mating type is present. This suggests that quarantine restrictions on imported chickpea seed should be retained to prevent the introduction of the opposite mating type.     

Genetic structure of Italian populations of Pyrenochaeta lycopersici,the causal agent of corky root rot of tomato

Pyrenochaeta lycopersici is the causal agent of corky root rot, which is a serious disease worldwide that attacks the roots of tomato. A total of 139 isolates were sampled from eight locations in Italy and Israel and assigned to two molecular types (type 1 and type 2) based on internal transcribed spacer (ITS) sequences. These isolates were genotyped using amplified fragment length polymorphisms (AFLPs) to decipher the population structure. Based on this population structure analysis, three groups of P. lycopersici were identified. One group correlated to ITS type 1, while the other two correlated to ITS type 2. amova indicated high genetic divergence (F_ST = 0·40) between the Italian types 1 and 2. These data support the view that the two ITS types represent significant evolutionary entities, although there might be incomplete lineage sorting present. Some isolates of different ITS type were observed to have very similar multilocus AFLP profiles, and some genotypes were intermediate between the two ITS types. This suggests that parasexual hybridization between the two types has had a significant role in shaping the population structure of P. lycopersici. Finally, the average divergence among the populations within the ITS types was very high (F_SC = 0·710, P < 10^?5), probably due to strong genetic drift and founder effects combined with restricted migration.     

Detection of Single‐feature Polymorphisms (SFPs) between two tomato varieties and their application in defining the introgressions of resistance loci

The objectives of the study were to (i) demonstrate that the hybridization data from microarrays can yield information on sequence variation between two inbred lines, an introgression line ‘Mogeor’ and its genetic background ‘Moneymaker’; (ii) characterize, by means of the identified SFPs, the introgressed genomic segments of ‘Mogeor’, carrying resistance genes; and (iii) deliver a set of genetically anchored SFPs potentially useful for breeding. In this work, the GeSNP software was used to identify SFPs in tomato using Affymetrix data from a previous experiment. Sequencing of 12 putative polymorphism‐containing amplicons yielded a SFP probe set validation rate of 90%. In total, 92 Gene Models putatively harbouring SFPs were identified, distributed as following: 61 Gene Models on chromosome 9, and one to eight on the remaining tomato chromosomes apart from chromosomes 7, 8 and 12. Newly discovered SFPs from microarray data can thus provide not only useful information for definition of introgressed genomic regions, but also identification of candidate genes and new markers for MAS.