Studies were undertaken to determine Alternaria spp. associated with leaf spot symptoms on canola (Brassica napus) in two cropping seasons (2015, 2016) across southern Australia. Major allergen Alt a1 and plasma membrane ATPase genes were used to identify Alternaria spp. In 2015, 112 isolates of seven Alternaria spp. were obtained, with A. metachromatica predominating. In 2016, 251 isolates of 12 Alternaria spp. were obtained, with A. infectoria predominating. Alternaria spp. isolates were morphologically and phylogenetically identified and studies to determine their pathogenicity on both B. napus (cv. Thunder TT) and B. juncea (cv. Dune) confirmed 10 species (A. alternata, A. arborescens, A. brassicae, A. ethzedia, A. hordeicola, A. infectoria, A. japonica, A. malvae, A. metachromatica and A. tenuissima) as pathogenic on both Brassica species. Alternaria ethzedia, A. hordeicola and A. malvae were recorded for the first time in Australia on any host and the record of A. arborescens was the first for New South Wales (NSW) and South Australia (SA). Other first records included A. infectoria on B. napus in NSW; A. japonica on B. napus in NSW and Western Australia (WA); A. metachromatica on any host in NSW, Victoria (VIC), WA and SA; and A. tenuissima on B. napus in NSW, SA and WA. It is evident that alternaria leaf spot on canola across southern Australia is not solely caused by A. brassicae, but that a range of other Alternaria spp. are also involved to varying degrees, depending upon the year and the geographic locality.

Studies were undertaken under controlled conditions into the effects of different foliage components (cotyledon, first, second and third leaf) at three plant ages (3, 5 and 7 weeks old) on development of Alternaria leaf spot disease, caused by Alternaria japonica or A. brassicae, in canola (Brassica napus cv. Thunder TT) and mustard (B. juncea cv. Dune). Alternaria japonica generally showed percentage disease index (%DI) values similar to A. brassicae across the two Brassica species, different foliage components and plant ages. %DI from either pathogen was greater in older plants than younger plants for the same foliage components in both cultivars. Field studies were then undertaken with canola to compare disease development from A. japonica and A. brassicae across different plant components (leaf, pod and stem) and the consequent adverse impact on seed yield. Alternaria japonica was more severe in terms of leaf area diseased (%LAD 62.6) and stem area diseased (%SAD 69.8) than pod area diseased (%PAD 25.5), whereas A. brassicae was more severe on leaves (%LAD 61.9) than on pods (%PAD 47.4) or stems (%SAD 41.0). Stem disease incidence was greater for A. japonica (%SDI 94.0) than for A. brassicae (%SDI 56.5), but pod disease incidence was greater for A. brassicae (%PDI 93.5) than for A. japonica (%PDI 86.1). For A. japonica, AUDPC values of leaf disease incidence (LDI, 283.5), leaf area diseased (LAD, 253.3) and leaf collapse (LCI, 149.5) resulted in a yield loss of 58.1%, similar to A. brassicae, where AUDPC values of LDI (277.8), LAD (247.2) and LCI (111.0) caused a yield loss of 59.4%. These findings explain observed acceleration of Alternaria leaf spot severity from A. japonica, as from A. brassicae, through the growing season as plants become more susceptible with increasing age, and as more susceptible, later developing leaves become abundant. For the first time, we demonstrate that under conducive field conditions for disease development, A. japonica can cause serious seed-yield losses of a magnitude similar to those occurring with A. brassicae.

Isolates of Hyaloperonospora brassicae inoculated onto cotyledons of 28 diverse Brassicaceae genotypes, 13 from Brassica napus, two from B. juncea, five from B. oleracea, two from Eruca vesicaria, and one each from B. nigra, B. carinata, B. rapa, Crambe abyssinica, Raphanus sativus and R. raphanistrum, showed significant effects (P ≤ 0.001) of isolate, host and their interaction. Host responses ranged from no visible symptom or a hypersensitive response, to systemic spread and abundant pathogen sporulation. Isolates were generally most virulent on their host of origin. Using an octal classification, six host genotypes were identified as suitable host differentials to characterize pathotypes of H. brassicae and distinguished eight distinct pathotypes. There were fewer, but more virulent, pathotypes in 2015–2016 isolates than 2006–2008 pathogen populations, probably explaining the increase in severity of canola downy mildew over the past decade. Phylogenetic relationships determined across 20 H. brassicae isolates collected in 2006–2008 and 88 isolates collected in 2015–2016 showed seven distinct clades, with 70% of 2006–2008 isolates distributed within clade I (bootstrap value (BVs) of 100%) and the remaining 30% in clade V (BVs 83.3%). This is the first study to define phylogenetic relationships of H. brassicae isolates in Australia, setting a benchmark for understanding current and future genetic shifts within pathogen populations; it is also the first to use octal classification to characterize pathotypes of H. brassicae, providing a novel basis for standardizing phenotypic characterization and monitoring of pathotypes on B. napus and some crucifer species in Australia.