P. W. J. Taylor

One stop shop: backbones trees for important phytopathogenic genera: I (2014)

Many fungi are pathogenic on plants and cause significant damage in agriculture and forestry. They are also part of the natural ecosystem and may play a role in regulating plant numbers/density. Morphological identification and analysis of plant pathogenic fungi, while important, is often hampered by the scarcity of discriminatory taxonomic characters and the endophytic or inconspicuous nature of these fungi. Molecular (DNA sequence) data for plant pathogenic fungi have emerged as key information for diagnostic and classification studies, although hampered in part by non-standard laboratory practices and analytical methods. To facilitate current and future research, this study provides phylogenetic synopses for 25 groups of plant pathogenic fungi in the Ascomycota, Basidiomycota, Mucormycotina (Fungi), and Oomycota, using recent molecular data, up-to-date names, and the latest taxonomic insights. Lineage-specific laboratory protocols together with advice on their application, as well as general observations, are also provided. We hope to maintain updated backbone trees of these fungal lineages over time and to publish them jointly as new data emerge. Researchers of plant pathogenic fungi not covered by the present study are invited to join this future effort. Bipolaris, Botryosphaeriaceae, Botryosphaeria, Botrytis, Choanephora, Colletotrichum, Curvularia, Diaporthe, Diplodia, Dothiorella, Fusarium, Gilbertella, Lasiodiplodia, Mucor, Neofusicoccum, Pestalotiopsis, Phyllosticta, Phytophthora, Puccinia, Pyrenophora, Pythium, Rhizopus, Stagonosporopsis, Ustilago and Verticillium are dealt with in this paper.

Sensitivity of random amplified polymorphic DNA analysis to detect genetic change in sugarcane during tissue culture

Random amplified polymorphic DNA (RAPD) analysis using 10-mer oligonucleotide primers efficiently differentiated sugarcane cultivars and proved suitable for detecting gross genetic change such as that which can occur in sugarcane subjected to prolonged tissue culture, for example in protoplast-derived callus. However, RAPD analysis was not sufficiently sensitive to detect smaller genetic changes that occur during sugarcane genetic transformation. The length of DNA scored for polymorphism per primer averaged 13.2 kb, or 0.0001% of the typical sugarcane genome size of 1.2 × 107 kb (2C). RAPD analysis of sugarcane plants regenerated from embryogenic callus revealed very few polymorphisms, indicating that gross genetic change is infrequent during this tissue culture procedure, although epigenetic effects result in transient morphological changes in regenerated plants. More sensitive variations on the RAPD technique may increase the practicality of DNA-based screening of regenerated plant lines to reveal somaclonal variants.

Chilli anthracnose disease caused by Colletotrichum species

Anthracnose disease is one of the major economic constraints to chilli production worldwide, especially in tropical and subtropical regions. Accurate taxonomic information is necessary for effective disease control management. In the Colletotrichum patho-system, different Colletotrichum species can be associated with anthracnose of the same host. Little information is known concerning the interactions of the species associated with the chilli anthracnose although several Colletotrichum species have been reported as causal agents of chilli anthracnose disease worldwide. The ambiguous taxonomic status of Colletotrichum species has resulted in inaccurate identification which may cause practical problems in plant breeding and disease management. Although the management and control of anthracnose disease are still being extensively researched, commercial cultivars of Capsicum annuum that are resistant to the pathogens that cause chilli anthracnose have not yet been developed. This paper reviews the causal agents of chilli anthracnose, the disease cycle, conventional methods in identification of the pathogen and molecular approaches that have been used for the identification of Colletotrichum species. Pathogenetic variation and population structure of the causal agents of chilli anthracnose along with the current taxonomic status of Colletotrichum species are discussed. Future developments leading to the disease management strategies are suggested.

Establishment of embryogenic callus and high protoplast yielding suspension cultures of sugarcane (Saccharum spp. hybrids)

For 18 sugarcane cultivars, four distinct callus types developed on leaf explant tissue cultured on modified MS medium, but only Type 3 (embryogenic) and Type 4 (organogenic) were capable of plant regeneration. Cell suspension cultures were initiated from embryogenic callus incubated in a liquid medium. In stage one the callus adapted to the liquid medium. In stage two a heterogeneous cell suspension culture formed in 14 cultivars after five to eight weeks of culture. In stage three a homogeneous cell suspension culture was developed in six cultivars after 10 to 14 weeks by selective subculturing to increase the proportion of actively dividing cells from the heterogeneous cell suspension culture. Plants were regenerated from cell aggregates in heterogeneous cell suspension cultures for up to 148 days of culture but plants could not be regenerated from homogeneous cell suspension cultures. High yields of protoplasts were obtained from homogeneous cell suspension cultures (3.4 to 5.2 × 106 protoplasts per gram fresh weight of cells [gfwt-1]) compared to heterogeneous cell suspension cultures (0.1 × 106 protoplasts gfwt-1). Higher yields of protoplasts were obtained from homogeneous cell suspension cultures for cultivars Q63 and Q96 after regenerating callus from the cell suspension cultures, then recycling this callus to liquid medium (S-cell suspension cultures). This process increased protoplast yield to 9.4 × 106 protoplasts gfwt-1. Protoplasts isolated from S-cell suspension cultures were regenerated to callus and recycled to produce SP-cell suspension cultures yielding 6.4 to 13.2 × 106 protoplasts gfwt-1. This recycling of callus to produce S-cell suspension cultures allowed protoplasts to be isolated for the first time from cell lines of cultivars Q110 and Q138.

Genetics of resistance to ascochyta blight (Ascochyta lentis) of lentil and the identification of closely linked RAPD markers

Abstract Foliar resistance to Ascochyta lentis is controlled at a single major locus by a dominant gene (AbR1) in the lentil accession ILL5588 (cv ‘Northfield’). Flanking RAPD markers that are closely linked to the resistance locus in coupling phase were identified by bulked segregant analysis. Out of 261 decanucleotide primers screened 7 produced a polymorphic marker that segregated with the resistance locus, and all markers were found to exist within a single linkage group. Five of the seven RAPD markers were within 30 cM of the resistance locus. Log likelihood analysis for detecting QTL associated with the foliar resistance revealed that a single narrow peak accounted for almost 90% of the variance of resistance between the bulks. Preliminary mapping in an F3 population revealed that the closest flanking markers were approximately 6 and 14 centiMorgans (cM) away from the resistance locus. These markers should be useful for the discrimination of resistant germplasm through marker-assisted selection in future breeding programmes and represent the first essential step towards the map-based cloning of this resistance gene.

Bacterial colonization and biofilm development on minimally processed vegetables

Bacterial biofilms have been observed and reported on food and food‐processing surfaces and can contribute to increased risks for product quality and food safety. The colonization of fruit and vegetables by pectynolitic bacteria like Pseudonomas fluorescens attributable to conditions such as soft rot, can also manifest as biofilms. A developed biofilm structure can provide a protective environment for pathogens such as Listeria monocytogenes reducing the effectiveness of sanitisers and other inhibitory agents. Understanding the colonization of bacteria on leaf surfaces is essential to the development of a better understanding of the leaf ecology of vegetable products. Studies of microbial colonization of leaf surfaces have been conducted using SEM and more recently using confocal microsocpy techniques. In the current study, a Leica TCS NT laser scanning confocal microscope was used to investigate biofilm formation using vital fluorescence staining on intact vegetable leaves. Reflection contrast and fluorescence three‐dimensional imaging successfully delineated bacterial and biofilm morphology without disturbing the bacterial or leaf surface structure. The results demonstrate the presence and development of biofilm on the surface of lettuce. The biofilms appeared to originate on the cuticle in distinct micro‐environments such as in the natural depression of the stomata, or in the intercellular junction. Bacteria also adhered to and developed biofilm colonies within an hour of contact and with clean stainless steel surfaces. Our study investigates the progression of biofilm formation from leaf colonization, and will assist in characterising the critical mechanisms of plant/host interaction and facilitate the development of improved preservation, sanitising and packaging strategies for minimally processed vegetable products.

Pathotypes of Colletotrichum capsici, the Causal Agent of Chili Anthracnose, in Thailand

Eleven isolates of Colletotrichum capsici were screened on nine chili genotypes derived from four cultivated species of Capsicum: Capsicum annuum, C. baccatum, C. chinense, and C. frutescens. Host reactions were assessed 9 days after inoculation by microinjection of spores into the pericarp of red fruit. A set of disease scales, with 0 to 9 scores, were developed for anthracnose infection of each Capsicum sp. based on percent lesion size in relation to fruit size, appearance of necrotic or water-soaked tissue, and presence of acervuli. Three pathotypes, PCc1, PCc2, and PCc3, were identified according to differential qualitative infection of fruit of C. chinense genotypes PBC932 and C04714. PCc1 was the most virulent pathotype, infecting all genotypes of C. annuum, C. chinense, and C. frutescens, whereas PCc3 was the least virulent pathotype, infecting only the genotypes C. annuum and C. frutescens. Quantitative infection occurred in all chili genotypes except for genotypes of C. baccatum, where no infection occurred, demonstrating various levels of aggressiveness of isolates within pathotypes.

Prospecting for sources of resistance to ascochyta blight in wild Cicer species

A collection of 114 Cicer accessions including 95 wild Cicer accessions from four different species (C. bijugum K. H. Rech., C. echinospermum P. H. Davis, C. pinnatifidum Jaub. & Sp. and C. reticulatum Ladiz.) was screened in glasshouse trials for resistance to ascochyta blight (caused by Ascochyta rabiei (Pass.) Lab.). Resistance was identified in accessions from all four wild Cicer species. There was variation for resistance within accessions of C. echinospermum, C. pinnatifidum and C. reticulatum, with only C. bijugum containing accessions in which all plants were completely resistant. Resistant accessions from C. echinospermum and C. reticulatum may offer accessible sources of resistance because fully fertile hybrids with cultivated chickpea can be readily obtained.

Diversity analysis and species identification in Lens using PCR generated markers

Using random amplified polymorphic DNA (RAPD) analysis we assessed the genetic relationships between 16 accessions and cultivars of lentil (Lens culinaris ssp. culinaris) in the Australian lentil breeding program. All lines exhibited polymorphism with a maximum dissimilarity value of 0.36. This indicated a limited degree of genetic variation. Polymerase chain reaction (PCR) with primers based on the flanking regions of the 5S rRNA gene from Pisum sativum amplified the non-translated spacer (NTS) region from within the 5S rRNA gene of Lens. Three distinct amplification banding patterns differentiated between restricted genomic DNA of Lens spp. L. culinaris ssp. culinaris and L. culinaris ssp. orientalis shared similar markers of two distinctly different NTS sizes. L. nigricans and L. odemensis shared the same amplification pattern of a single sized NTS region. However, L. ervoides contained two separate sizes of NTS, distinct from other Lens species. In an effort to widen the genetic base of cultivated lentil, these species-specific molecular markers may be used to follow potential introgression between species.

Developmental changes of sinigrin and glucoraphanin in three Brassica species (Brassica nigra, Brassica juncea and Brassica oleracea var. italica)

Hydrolysis products of sinigrin (2-propenylglucosinolate) and glucoraphanin (4-methylsulphinylbutylglucosinolate) have been shown to protect against the development of cancers. However, there was limited information available on the variation of these two glucosinolates throughout the plant cycle. The objective of this study was to evaluate sinigrin and glucoraphanin levels within Brassica plants during development. Sinigrin concentration in B. juncea and B. nigra decreased from seedling to early flowering stage, increased in the late flowering stage and then decreased again during seed maturation. The lowest concentration of sinigrin occurred at the early flowering stage except in one genotype of B. juncea (PI 179858). Sinigrin concentration also increased in maturing seeds while the concentration in pods decreased. The concentration of glucoraphanin in B. oleracea var. italica decreased from the start of seed germination to the flowering stages. The lowest concentration was also found at the flowering stage. A higher concentration of glucoraphanin was detected in the green broccoli heads and flower heads than in other reproductive tissues. However, the highest content of glucoraphanin occurred at the green head stage and then declined as flowering was initiated. These results have shown that green and brown seeds of mustards contained the highest concentration of sinigrin while the highest concentration of glucoraphanin occurred in young broccoli seedlings and seeds. This information should be useful for the development of those compounds as nutraceuticals.