Oilseed rape (Brassica napus) resistance to growth of Leptosphaeria maculans in leaves of young plants contributes to quantitative resistance in stems of adult plants

Monitoring the phenology of plant pathogenic fungi: why and how?

Phenology is a key adaptive trait of organisms, shaping biotic interactions in response to the environment. It has emerged as a critical topic with implications for societal and economic concerns due to the effects of climate change on species' phenological patterns. Fungi play essential roles in ecosystems, and plant pathogenic fungi have significant impacts on global food security. However, the phenology of plant pathogenic fungi, which form a huge and diverse clade of organisms, has received limited attention in the literature. This diversity may have limited the use of a common language for comparisons and the integration of phenological data for these taxonomic groups. Here, we delve into the concept of 'phenology' as applied to plant pathogenic fungi and explore the potential drivers of their phenology, including environmental factors and the host plant. We present the PhenoFun scale, a phenological scoring system suitable for use with all fungi and fungus-like plant pathogens. It offers a standardised and common tool for scientists studying the presence, absence, or predominance of a particular phase, the speed of phenological phase succession, and the synchronism shift between pathogenic fungi and their host plants, across a wide range of environments and ecosystems. The application of the concept of 'phenology' to plant pathogenic fungi and the use of a phenological scoring system involves focusing on the interacting processes between the pathogenic fungi, their hosts, and their biological, physical, and chemical environment, occurring during the life cycle of the pathogen. The goal is to deconstruct the processes involved according to a pattern orchestrated by the fungus's phenology. Such an approach will improve our understanding of the ecology and evolution of such organisms, help to understand and anticipate plant disease epidemics and their future evolution, and make it possible to optimise management models, and to encourage the adoption of cropping practices designed from this phenological perspective.

Brassica napus Haploid and Double Haploid Production and Its Latest Applications

Rapeseed is one of the most important oil crops in the world. Increasing demand for oil and limited agronomic capabilities of present-day rapeseed result in the need for rapid development of new, superior cultivars. Double haploid (DH) technology is a fast and convenient approach in plant breeding as well as genetic research. Brassica napus is considered a model species for DH production based on microspore embryogenesis; however, the molecular mechanisms underlying microspore reprogramming are still vague. It is known that morphological changes are accompanied by gene and protein expression patterns, alongside carbohydrate and lipid metabolism. Novel, more efficient methods for DH rapeseed production have been reported. This review covers new findings and advances in Brassica napus DH production as well as the latest reports related to agronomically important traits in molecular studies employing the double haploid rapeseed lines.

Novel gene loci associated with susceptibility or cryptic quantitative resistance to Pyrenopeziza brassicae in Brassica napus

Quantitative disease resistance (QDR) controls the association of the light leaf spot pathogen with Brassica napus; four QDR loci that were in linkage disequilibrium and eight gene expression markers were identified. Quantitative disease resistance (QDR) can provide durable control of pathogens in crops in contrast to resistance (R) gene-mediated resistance which can break down due to pathogen evolution. QDR is therefore a desirable trait in crop improvement, but little is known about the causative genes, and so it is difficult to incorporate into breeding programmes. Light leaf spot, caused by Pyrenopeziza brassicae, is an important disease of oilseed rape (canola, Brassica napus). To identify new QDR gene loci, we used a high-throughput screening pathosystem with P. brassicae on 195 lines of B. napus combined with an association transcriptomics platform. We show that all resistance against P. brassicae was associated with QDR and not R gene-mediated. We used genome-wide association analysis with an improved B. napus population structure to reveal four gene loci significantly (P = 0.0001) associated with QDR in regions showing linkage disequilibrium. On chromosome A09, enhanced resistance was associated with heterozygosity for a cytochrome P450 gene co-localising with a previously described locus for seed glucosinolate content. In addition, eight significant gene expression markers with a false discovery rate of 0.001 were associated with QDR against P. brassicae. For seven of these, expression was positively correlated with resistance, whereas for one, a HXXXD-type acyl-transferase, negative correlation indicated a potential susceptibility gene. The study identifies novel QDR loci for susceptibility and resistance, including novel cryptic QDR genes associated with heterozygosity, that will inform future crop improvement.

Molecular Interactions Between Leptosphaeria maculans and Brassica Species

Canola is an important oilseed crop, providing food, feed, and fuel around the world. However, blackleg disease, caused by the ascomycete Leptosphaeria maculans, causes significant yield losses annually. With the recent advances in genomic technologies, the understanding of the Brassica napus-L. maculans interaction has rapidly increased, with numerous Avr and R genes cloned, setting this system up as a model organism for studying plant-pathogen associations. Although the B. napus-L. maculans interaction follows Flor's gene-for-gene hypothesis for qualitative resistance, it also puts some unique spins on the interaction. This review discusses the current status of the host-pathogen interaction and highlights some of the future gaps that need addressing moving forward.

Genetic dissection of heterotic loci associated with plant weight by Graded pool-seq in heading Chinese cabbage (Brassica rapa)

Four heterotic QTL and a heterozygous segment for plant weight were identified by Graded Pool-Seq, QTL-seq and traditional genetic linkage analysis in heading Chinese cabbage. Heading Chinese cabbage (Brassica rapa L. spp. pekinensis) is a cross-pollinated leafy vegetable with significant heterosis. The use of heterosis is important for breeding high-yield Chinese cabbage hybrids. However, the formation and mechanism of heterosis have not been studied. We dissected the molecular mechanism of heterosis of yield-related traits in Chinese cabbage. An F₁ hybrid with high-parent heterosis of yield-related traits was selected and self-pollinated to generate segregating F₂ populations. QTL-seq, Graded Pool-seq (GPS), and traditional genetic linkage analysis were used to identify four heterotic quantitative trait loci (QTL) for plant weight: qPW1.1, qPW5.1, qPW7.1, and qPW8.1. Traditional genetic linkage analysis over two years showed that qPW8.1, located in marker A08_S45 (18,172,719) and A08_S85 (18,196,752), was mapped to a 23.5 kb genomic region. QTL qPW8.1 explained 8.6% and 23.6% of the phenotypic variation in plant weight and the total numbers of head leaves, respectively, and contained a heterozygous segment that might control the heterosis of plant weight. The qPW1.1 made an 11.7% phenotypic contribution to plant weight. The qPW7.1 was sensitive to environmental influence and explained 10.7% of the phenotypic variance. QTL qPW5.1 had a significant signal and was located in a genetic region near the centromere showing high heterozygosity. The "pseudo-overdominance" and "synergistic allelic" effects from parent line "XJD4" appear to play an important role in heterosis for plant weight in Chinese cabbage. These results provide a basis for an improved understanding of the molecular mechanism of yield-related traits and their heterosis.

Construction of a Quantitative Genomic Map, Identification and Expression Analysis of Candidate Genes for Agronomic and Disease-Related Traits in Brassica napus

Rapeseed is the second most important oil crop in the world. Improving seed yield and seed oil content are the two main highlights of the research. Unfortunately, rapeseed development is frequently affected by different diseases. Extensive research has been made through many years to develop elite cultivars with high oil, high yield, and/or disease resistance. Quantitative trait locus (QTL) analysis has been one of the most important strategies in the genetic deciphering of agronomic characteristics. To comprehend the distribution of these QTLs and to uncover the key regions that could simultaneously control multiple traits, 4,555 QTLs that have been identified during the last 25 years were aligned in one unique map, and a quantitative genomic map which involved 128 traits from 79 populations developed in 12 countries was constructed. The present study revealed 517 regions of overlapping QTLs which harbored 2,744 candidate genes and might affect multiple traits, simultaneously. They could be selected to customize super-rapeseed cultivars. The gene ontology and the interaction network of those candidates revealed genes that highly interacted with the other genes and might have a strong influence on them. The expression and structure of these candidate genes were compared in eight rapeseed accessions and revealed genes of similar structures which were expressed differently. The present study enriches our knowledge of rapeseed genome characteristics and diversity, and it also provided indications for rapeseed molecular breeding improvement in the future.

Comparison of non-subjective relative fungal biomass measurements to quantify the Leptosphaeria maculans-Brassica napus interaction

BACKGROUND

Blackleg disease, caused by the fungal pathogen Leptosphaeria maculans, is a serious threat to canola (Brassica napus) production worldwide. Quantitative resistance to this disease is a highly desirable trait but is difficult to precisely phenotype. Visual scores can be subjective and are prone to assessor bias. Methods to assess variation in quantitative resistance more accurately were developed based on quantifying in planta fungal biomass, including the Wheat Germ Agglutinin Chitin Assay (WAC), qPCR and ddPCR assays.

RESULTS

Disease assays were conducted by inoculating a range of canola cultivars with L. maculans isolates in glasshouse experiments and assessing fungal biomass in cotyledons, petioles and stem tissue harvested at different timepoints post-inoculation. PCR and WAC assay results were well correlated, repeatable across experiments and host tissues, and able to differentiate fungal biomass in different host-isolate treatments. In addition, the ddPCR assay was shown to differentiate between L. maculans isolates.

CONCLUSIONS

The ddPCR assay is more sensitive in detecting pathogens and more adaptable to high-throughput methods by using robotic systems than the WAC assay. Overall, these methods proved accurate and non-subjective, providing alternatives to visual assessments to quantify the L. maculans-B. napus interaction in all plant tissues throughout the progression of the disease in seedlings and mature plants and have potential for fine-scale blackleg resistance phenotyping in canola.

Status and advances in mining for blackleg (Leptosphaeria maculans) quantitative resistance (QR) in oilseed rape (Brassica napus)

KEY MESSAGE

Quantitative resistance (QR) loci discovered through genetic and genomic analyses are abundant in the Brassica napus genome, providing an opportunity for their utilization in enhancing blackleg resistance. Quantitative resistance (QR) has long been utilized to manage blackleg in Brassica napus (canola, oilseed rape), even before major resistance genes (R-genes) were extensively explored in breeding programmes. In contrast to R-gene-mediated qualitative resistance, QR reduces blackleg symptoms rather than completely eliminating the disease. As a polygenic trait, QR is controlled by numerous genes with modest effects, which exerts less pressure on the pathogen to evolve; hence, its effectiveness is more durable compared to R-gene-mediated resistance. Furthermore, combining QR with major R-genes has been shown to enhance resistance against diseases in important crops, including oilseed rape. For these reasons, there has been a renewed interest among breeders in utilizing QR in crop improvement. However, the mechanisms governing QR are largely unknown, limiting its deployment. Advances in genomics are facilitating the dissection of the genetic and molecular underpinnings of QR, resulting in the discovery of several loci and genes that can be potentially deployed to enhance blackleg resistance. Here, we summarize the efforts undertaken to identify blackleg QR loci in oilseed rape using linkage and association analysis. We update the knowledge on the possible mechanisms governing QR and the advances in searching for the underlying genes. Lastly, we lay out strategies to accelerate the genetic improvement of blackleg QR in oilseed rape using improved phenotyping approaches and genomic prediction tools.

Current Status of the Disease-Resistant Gene(s)/QTLs, and Strategies for Improvement in Brassica juncea

Brassica juncea is a major oilseed crop in tropical and subtropical countries, especially in south-east Asia like India, China, Bangladesh, and Pakistan. The widespread cultivation of genetically similar varieties tends to attract fungal pathogens which cause heavy yield losses in the absence of resistant sources. The conventional disease management techniques are often expensive, have limited efficacy, and cause additional harm to the environment. A substantial approach is to identify and use of resistance sources within the Brassica hosts and other non-hosts to ensure sustainable oilseed crop production. In the present review, we discuss six major fungal pathogens of B. juncea: Sclerotinia stem rot (Sclerotinia sclerotiorum), Alternaria blight (Alternaria brassicae), White rust (Albugo candida), Downy mildew (Hyaloperonospora parasitica), Powdery mildew (Erysiphe cruciferarum), and Blackleg (Leptoshaeria maculans). From discussing studies on pathogen prevalence in B. juncea, the review then focuses on highlighting the resistance sources and quantitative trait loci/gene identified so far from Brassicaceae and non-filial sources against these fungal pathogens. The problems in the identification of resistance sources for B. juncea concerning genome complexity in host subpopulation and pathotypes were addressed. Emphasis has been laid on more elaborate and coordinated research to identify and deploy R genes, robust techniques, and research materials. Examples of fully characterized genes conferring resistance have been discussed that can be transformed into B. juncea using advanced genomics tools. Lastly, effective strategies for B. juncea improvement through introgression of novel R genes, development of pre-breeding resistant lines, characterization of pathotypes, and defense-related secondary metabolites have been provided suggesting the plan for the development of resistant B. juncea.

Exploring Mechanisms of Quantitative Resistance to Leptosphaeria maculans (Blackleg) in the Cotyledons of Canola (Brassica napus) Based on Transcriptomic and Microscopic Analyses

Using resistant cultivars is a common approach to managing blackleg of canola/rapeseed caused by Leptosphaeria maculans (Lm). Quantitative resistance (QR), as opposed to major-gene resistance, is of interest because it is generally more durable, due to its multi-genetic basis. However, the mechanisms and genes underlying QR are mostly unknown. In this study, potential QR modes of action in “74-44 BL” was explored. This Canadian canola cultivar showed moderate but consistent race-nonspecific resistance at the cotyledon and adult-plant stages. A susceptible cultivar, “Westar”, was used as a control. After inoculation, the lesions developed more slowly on the cotyledons of 74-44 BL than those of Westar. We used RNA sequencing (-RNA-seq) to identify genes and their functions, putatively related to this resistance, and found that genes involved in programmed cell death (PCD), reactive oxygen species (ROS), signal transduction or intracellular endomembrane transport were most differentially expressed. ROS production was assessed in relation to Lm hyphal growth and lesion size; it occurred beyond the tissue colonized by Lm in 74-44 BL and appeared to trigger rapid cell death, limiting cotyledon colonization by Lm. In contrast, Lm grew more rapidly in Westar, often catching up with the ring of ROS and surpassing lesion boundaries. It appears that QR in 74-44 BL cotyledons is associated with limited colonization by Lm possibly mediated via ROS. The RNA-seq data also showed a link between ROS, signal transduction, and endomembrane vesicle trafficking, as well as PCD in the resistance. These results provide a starting point for a better understanding of the mechanisms behind QR against Lm in canola.