Genetic architecture of factors underlying partial resistance to Alternaria leaf blight in carrot

Challenges and Opportunities in the Sustainable Improvement of Carrot Production

From an agricultural perspective, carrots are a significant tap root vegetable crop in the Apiaceae family because of their nutritional value, health advantages, and economic importance. The edible part of a carrot, known as the storage root, contains various beneficial compounds, such as carotenoids, anthocyanins, dietary fiber, vitamins, and other nutrients. It has a crucial role in human nutrition as a significant vegetable and raw material in the nutraceutical, food, and pharmaceutical industries. The cultivation of carrot fields is susceptible to a wide range of biotic and abiotic hazards, which can significantly damage the plants' health and decrease yield and quality. Scientific research mostly focuses on important biotic stressors, including pests, such as nematodes and carrot flies, as well as diseases, such as cavity spots, crown or cottony rot, black rot, and leaf blight, caused by bacteria, fungi, and oomycetes. The emerging challenges in the field include gaining a comprehensive understanding of the interaction between hosts and pathogens in the carrot-pathogen system, identifying the elements that contribute to disease development, expanding knowledge of systemic treatments, exploring host resistance mechanisms, developing integrated control programs, and enhancing resistance through breeding approaches. In fact, the primary carrot-growing regions in tropical and subtropical climates are experiencing abiotic pressures, such as drought, salinity, and heat stress, which limit carrot production. This review provides an extensive, up-to-date overview of the literature on biotic and abiotic factors for enhanced and sustainable carrot production, considering the use of different technologies for the shelf-life extension of carrots. Therefore, it addresses the current issues in the carrot production chain, opening new perspectives for the exploration of carrots both as a food commodity and as a source of natural compounds.

Co-Localization of Resistance and Metabolic Quantitative Trait Loci on Carrot Genome Reveals Fungitoxic Terpenes and Related Candidate Genes Associated with the Resistance to Alternaria dauci

Alternaria leaf blight, caused by the fungus Alternaria dauci, is the most damaging foliar disease of carrot. Some carrot genotypes exhibit partial resistance to this pathogen and resistance Quantitative Trait Loci (rQTL) have been identified. Co-localization of metabolic QTL and rQTL identified camphene, α-pinene, α-bisabolene, β-cubebene, caryophyllene, germacrene D and α-humulene as terpenes potentially involved in carrot resistance against ALB. By combining genomic and transcriptomic analyses, we identified, under the co-localization regions, terpene-related genes which are differentially expressed between a resistant and a susceptible carrot genotype. These genes include five terpene synthases and twenty transcription factors. In addition, significant mycelial growth inhibition was observed in the presence of α-humulene and caryophyllene.

Crop management system and carrot genotype affect endophyte composition and Alternaria dauci suppression

Managing pests in carrot production is challenging. Endophytic microbes have been demonstrated to improve the health and productivity of many crops, but factors affecting endophyte dynamics in carrot is still not well understood. The goal of this study was to determine how crop management system and carrot genotype interact to affect the composition and potential of endophytes to mitigate disease caused by Alternaria dauci, an important carrot pathogen. Twenty-eight unique isolates were collected from the taproots of nine diverse genotypes of carrot grown in a long-term trial comparing organic and conventional management. Antagonistic activity was quantified using an in vitro assay, and potential for individual isolates to mitigate disease was evaluated in greenhouse trials using two carrot cultivars. Results confirm that carrot taproots are colonized by an abundant and diverse assortment of bacteria and fungi representing at least distinct 13 genera. Soils in the organic system had greater total organic matter, microbial biomass and activity than the conventional system and endophyte composition in taproots grown in this system were more abundant and diverse, and had greater antagonistic activity. Carrot genotype also affected endophyte abundance as well as potential for individual isolates to affect seed germination, seedling growth and tolerance to A. dauci. The benefits of endophytes on carrot growth were greatest when plants were subject to A. dauci stress, highlighting the importance of environmental conditions in the functional role of endophytes. Results of this study provide evidence that endophytes can play an important role in improving carrot performance and mediating resistance to A. dauci, and it may someday be possible to select for these beneficial plant-microbial relationships in carrot breeding programs. Implementing soil-building practices commonly used in organic farming systems has potential to promote these beneficial relationships and improve the health and productivity of carrot crops.

Link between carrot leaf secondary metabolites and resistance to Alternaria dauci

Alternaria Leaf Blight (ALB), caused by the fungus Alternaria dauci, is the most damaging foliar disease affecting carrots (Daucus carota). In order to identify compounds potentially linked to the resistance to A. dauci, we have used a combination of targeted and non-targeted metabolomics to compare the leaf metabolome of four carrot genotypes with different resistance levels. Targeted analyses were focused on terpene volatiles, while total leaf methanolic extracts were subjected to non-targeted analyses using liquid chromatography couple to high-resolution mass spectrometry. Differences in the accumulation of major metabolites were highlighted among genotypes and some of these metabolites were identified as potentially involved in resistance or susceptibility. A bulk segregant analysis on F3 progenies obtained from a cross between one of the resistant genotypes and a susceptible one, confirmed or refuted the hypothesis that the metabolites differentially accumulated by these two parents could be linked to resistance.

QTL mapping of carrot resistance to leaf blight with connected populations: stability across years and consequences for breeding

Combining biparental and multiparental connected population analyses was useful for the identification of 11 QTLs in two new genetic backgrounds of carrot resistance to Alternaria dauci and for breeding recommendations. Leaf blight due to the fungus Alternaria dauci is the major carrot foliar disease worldwide. Some resistance QTLs have been previously identified in one population, but the evaluation of additional genetic backgrounds with higher level of resistance would give opportunities for breeders to combine them by pyramiding. For this purpose, two segregating populations were evaluated twice across 4 years in the same environment (1) to compare the efficiency of the single vs. the connected populations approach for characterizing the new sources of carrot resistance to Alternaria dauci; (2) to evaluate the stability of QTLs over the years; and (3) to give recommendations to breeders for marker-assisted selection. Single and connected analyses were complementary; their combination allowed the detection of 11 QTLs. Connected analyses allowed the identification of common and specific QTLs among the two populations and the most favorable allele at each QTL. Important contrasts between allelic effects were observed with four and five most favorable alleles coming from the two resistant parental lines, whereas two other favorable alleles came from the susceptible parental line. While four QTLs were consistent across years, seven were detected within a single year. The heritabilities for both populations PC2 and PC3 were high (75 and 78%, respectively), suggesting that the resistance of carrot to A. dauci was little affected by these environmental conditions, but the instability of QTL over years may be due to changing environmental conditions. The complementarity between these parental lines in terms of interesting allelic combinations is also discussed.