Figure - available from: Plant Biotechnology Journal
This content is subject to copyright. Terms and conditions apply.
Waterfall plot of the Sclerotinia resistance‐linked QTL qLR10‐3 (SWUC177 ‐ BoGMS1032). Gene order is determined by position in the reference assembly.
Source publication
Brassica oleracea is an important agricultural species encompassing many vegetable crops including cabbage, cauliflower, broccoli and kale, however it can be susceptible to a variety of fungal diseases such as clubroot, blackleg, leaf spot, and downy mildew. Resistance to these diseases is meditated by specific disease resistance genes‐analogs (RGA...
Similar publications
Key message
About 10% of cultivars possessed superior resistance to four fungal diseases and association mapping for multiple disease resistance identified loci which are not detected by analyzing individual disease resistances.
Abstract
Multiple disease resistance (MDR) aims for cultivars that are resistant to more than one disease which is an im...
Citations
... These work against pathogens with a biotrophic or latent phase by either directly or indirectly recognizing pathogen effector molecules and eliciting a hypersensitive cell death response. NBS-LRR genes are typically diverse in natural plant populations, showing numerous presence/absence polymorphisms (Bayer et al., 2019;Tirnaz et al., 2020). Given their major positive impacts on disease resistance, a In response to this question, it was initially suggested that some R genes create a fitness penalty in the absence of pathogens. ...
In plants, growth and defence are controlled by many molecular pathways that are antagonistic to one another. This results in a ‘growth‐defence trade‐off’, where plants temporarily reduce growth in response to pests or diseases. Due to this antagonism, genetic variants that improve resistance often reduce growth and vice versa. Therefore, in natural populations, the most disease resistant individuals are often the slowest growing. In crops, slow growth may translate into a yield penalty, but resistance is essential for protecting yield in the presence of disease. Therefore, plant breeders must balance these traits to ensure optimal yield potential and yield stability. In crops, both qualitative and quantitative disease resistance are often linked with genetic variants that cause yield penalties, but this is not always the case. Furthermore, both crop yield and disease resistance are complex traits influenced by many aspects of the plant's physiology, morphology and environment, and the relationship between the molecular growth‐defence trade‐off and disease resistance‐yield antagonism is not well‐understood. In this article, we highlight research from the last 2 years on the molecular mechanistic basis of the antagonism between defence and growth. We then discuss the interaction between disease resistance and crop yield from a breeding perspective, outlining the complexity and nuances of this relationship and where research can aid practical methods for simultaneous improvement of yield potential and disease resistance.
... After that, plenty of studies have delved into the plant pan-genomes of diverse species, such as poplar (Zhang et al., 2019), Brachypodium distachyon (Gordon et al., 2017), Brassica oleracea (Golicz et al., 2016), Brassica napus (Hurgobin et al., 2018), pepper (Ou et al., 2018), Medicago (Zhou et al., 2017), rice (Zhao et al., 2018), soybean (Li et al., 2014), hexaploid bread wheat (Montenegro et al., 2017), tomato (Gao et al., 2019), and sunflower (Hübner et al., 2019). These plant pangenomics studies are pivotal in pinpointing key novel non-reference genes or sequences related to processes like signaling (Golicz et al., 2016), defense mechanisms (Gordon et al., 2017), resistance pathways (Bayer et al., 2019), important agricultural traits (Gao et al., 2019), and heterosis (Zhang et al., 2016). ...
... The pan-genome study proves effective for plant genomic studies because it aims to encompass all genomic diversity of a certain species, which is important for the deep understanding of evolution and providing more novel genomic targets for breeding. It aids in identifying crucial novel non-reference genes or sequences associated with signaling (Golicz et al., 2016), defense mechanisms (Gordon et al., 2017), resistance pathways (Bayer et al., 2019), vital agricultural attributes (Gao et al., 2019), and heterosis (Zhang et al., 2016). Currently, three strategies based on next-generation sequencing short-reads are utilized for constructing the plant pan-genome, they can be summarized as iterative individual, iterative pooling, and map-to-pan. ...
Pan-genome studies are important for understanding plant evolution and guiding the breeding of crops by containing all genomic diversity of a certain species. Three short-read-based strategies for plant pan-genome construction include iterative individual, iteration pooling, and map-to-pan. Their performance is very different under various conditions, while comprehensive evaluations have yet to be conducted nowadays. Here, we evaluate the performance of these three pan-genome construction strategies for plants under different sequencing depths and sample sizes. Also, we indicate the influence of length and repeat content percentage of novel sequences on three pan-genome construction strategies. Besides, we compare the computational resource consumption among the three strategies. Our findings indicate that map-to-pan has the greatest recall but the lowest precision. In contrast, both two iterative strategies have superior precision but lower recall. Factors of sample numbers, novel sequence length, and the percentage of novel sequences’ repeat content adversely affect the performance of all three strategies. Increased sequencing depth improves map-to-pan’s performance, while not affecting the other two iterative strategies. For computational resource consumption, map-to-pan demands considerably more than the other two iterative strategies. Overall, the iterative strategy, especially the iterative pooling strategy, is optimal when the sequencing depth is less than 20X. Map-to-pan is preferable when the sequencing depth exceeds 20X despite its higher computational resource consumption.
... 71), it may become possible to model molecular interactions and design targeted interventions to respond to rapidly evolving pathogens 72 . Pangenomes may also tell us about the evolutionary origins and patterns of structural variation in other types of resistance genes 73 and similarly complex loci where duplication is common, such as metabolic gene clusters 74 or storage proteins 75 . ...
Plant genome sequences catalogue genes and the genetic elements that regulate their expression. Such inventories further research aims as diverse as mapping the molecular basis of trait diversity in domesticated plants or inquiries into the origin of evolutionary innovations in flowering plants millions of years ago. The transformative technological progress of DNA sequencing in the past two decades has enabled researchers to sequence ever more genomes with greater ease. Pangenomes - complete sequences of multiple individuals of a species or higher taxonomic unit - have now entered the geneticists' toolkit. The genomes of crop plants and their wild relatives are being studied with translational applications in breeding in mind. But pangenomes are applicable also in ecological and evolutionary studies, as they help classify and monitor biodiversity across the tree of life, deepen our understanding of how plant species diverged and show how plants adapt to changing environments or new selection pressures exerted by human beings.
... The Brassicaceae family encompasses over 372 genera and 4060 species, with considerable significance in terms of agronomy, science, aesthetics, and economics (Bayer et al. 2018). Among these species, Brassica oleracea var. ...
The ornamental kale, scientifically known as Brassica oleracea var. acephala, stands out as an attractive plant admired for its vibrant leaves that grace the winter season. Notably, the hybrid KTOK-28-1 × KTOK-40-1 demonstrated the highest embryogenesis rate, yielding 56.12 embryos per Petri dish. This efficiency largely hinges on the characteristics of the donor plants used. Through flow cytometry analysis, approximately 61% of spontaneous doubled haploids (DH) were identified. These individuals exhibited normal flower development and successfully produced seeds when subjected to bud pollination. The compatibility index values exhibited variation among different DH lines, ranging from 1.0 to 13.12. This diversity is promising for the development of superior hybrids. Noteworthy among the DHs were KTDH-52, KTDH-56, and KTDH-57, exhibiting suitability for various horticultural traits. The emergence of these novel DH lines suggests their potential contribution to future breeding programs aimed at producing superior-quality hybrids. Crop Breeding and Applied Biotechnology 24(2): e46742423, 2024 Brazilian Society of Plant Breeding. Printed in Brazil http://dx.
... juncea, B. napus and B. carinata) (Schranz et al., 2006). The Brassicaceae family comprises more than 372 genera and about 4060 species, many of which are economically important species (Bayer et al., 2019). The Brassica genus is also the economically most important genus within the tribe Brassicaceae, consisting of 37 different species. ...
Plant breeding has had a tremendous influence on crop improvement. However, due to dwindling germplasm resources, identification of variability for incorporation into new cultivars is becoming more difficult. Therefore, there has been recourse to alternative approaches including mutagenesis, tissue culture and genetic transformation to aid breeding programs. Development and application of molecular markers derived from genes, commonly called genic markers or sometimes functional markers, is gaining momentum in plant genetics and breeding. Presently, marker discovery, genotyping and molecular breeding practices would be routine in crop improvement in many crop species including Brassica. Molecular markers are known as particularly effective and reliable tools for the characterization of genome architectures and the investigation of gene polymorphisms in cabbage also. Cabbage breeding, genomics and their applications have been discussed in detailed in this review article.
... The authors reported both genes for resistance to biotic (e.g., blackleg disease, caused by Leptosphaeria maculans; clubroot, caused by Plasmodiophora brassicae; and stem rot, caused by Sclerotinia sclerotiorum) and abiotic (e.g., heat, drought, cold, and salinity) stresses. They highlighted a study on pan-genomics of B. oleracea, which identified many candidate genes for disease resistance in wild species B. macrocarpa [138]. Recently, the clubroot-resistant gene CRd from Chinese cabbage was transferred to canola through interspecific hybridization [139]. ...
Embryo rescue (ER) techniques are among the oldest and most successful in vitro tissue culture protocols used with plant species. ER refers to a series of methods that promote the development of an immature or lethal embryo into a viable plant. Intraspecific, interspecific, or intergeneric crosses allow the introgression of important alleles of agricultural interest from wild species, such as resistance or tolerance to abiotic and biotic stresses or morphological traits in crops. However, pre-zygotic and post-zygotic reproductive barriers often present challenges in achieving successful hybridization. Pre-zygotic barriers manifest as incompatibility reactions that hinder pollen germination, pollen tube growth, or penetration into the ovule occurring in various tissues, such as the stigma, style, or ovary. To overcome these barriers, several strategies are employed, including cut-style or graft-on-style techniques, the utilization of mixed pollen from distinct species, placenta pollination, and in vitro ovule pollination. On the other hand, post-zygotic barriers act at different tissues and stages ranging from early embryo development to the subsequent growth and reproduction of the offspring. Many crosses among different genera result in embryo abortion due to the failure of endosperm development. In such cases, ER techniques are needed to rescue these hybrids. ER holds great promise for not only facilitating successful crosses but also for obtaining haploids, doubled haploids, and manipulating the ploidy levels for chromosome engineering by monosomic and disomic addition as well substitution lines. Furthermore, ER can be used to shorten the reproductive cycle and for the propagation of rare plants. Additionally, it has been repeatedly used to study the stages of embryonic development, especially in embryo-lethal mutants. The most widely used ER procedure is the culture of immature embryos taken and placed directly on culture media. In certain cases, the in vitro culture of ovule, ovaries or placentas enables the successful development of young embryos from the zygote stage to maturity.
... There have been several studies that identify NLRs, RLKs and RLPs in Brassicaceae species and investigate their distribution and variation; however, none of these have focused on TM-CCs (Alamery et al., 2018;Bayer et al., 2019;Mun et al., 2009;Tirnaz et al., 2020;Yang et al., 2020;Zhang, Shao, et al., 2016). In this study, we carried out a species-wide in-silico prediction of TM-CCs among different domesticated and wild members of the Brassicaceae family. ...
... Our results revealed variation in the number of TM-CCs among different species of this family, which is consistent with findings on the distribution of NLRs, RLKs and RLPs in Brassicaceae species (Alamery et al., 2018;Bayer et al., 2019;Mun et al., 2009;Tirnaz et al., 2020;Yang et al., 2020;Zhang, Shao, et al., 2016) and in other plant genera like Fragaria (Zhong et al., 2018), Oryza and ...
The Brassicaceae family is composed of a broad range of species, including the economically important crops from Brassica , Raphanus , Camelina and Sinapis genera. The production of Brassicaceae species, particularly the crop members, is threatened by major diseases. However, the impact of diseases can be minimized or even negated by improving disease resistance. Transmembrane‐coiled‐coil (TM‐CC) genes are a type of resistance gene analogue (RGA) that have been proven to play specific roles in resistance to several diseases. Here, TM‐CCs have been predicted in 27 genomes from Brassicaceae genera including Arabidopsis , Arabis , Barbarea , Boechera , Brassica , Camelina , Capsella , Cardamine , Eutrema , Leavenworthia , Lepidium , Raphanus , Sinapis , Sisymbrium , Schrenkiella and Thlaspi . The number of TM‐CCs varies throughout the studied genomes, as well as between genera, diploids and polyploids, and Brassica genomes and subgenomes. In total, 6788 TM‐CCs were identified, with 708 of them predicted with signalling function, 172 colocalized with previously known disease resistance regions and 70 phylogenetically related to cloned resistance genes, indicating the possible functional involvement of TM‐CCs in resistance. This study provides a resource for the identification of functional Brassicaceae TM‐CCs along with their clustering and duplication patterns and provides a benchmark for further studies investigating TM‐CCs.
... With the advancement of next-generation sequencing and computational analysis, genome-wide distribution scans of RGAs have become common-place (Bayer et al., 2019;Tirnaz et al., 2020). In the Brassica genus alone, more than 30 species, including both cultivated species and wild relatives, have been analysed for their RGA content, resulting in the identification of more than 30 000 RGAs (Bayer et al., 2019;Dolatabadian et al., 2020;Fu et al., 2019;Hofberger et al., 2014;Tirnaz et al., 2020;Yang et al., 2021;Zhang et al., 2016). ...
... With the advancement of next-generation sequencing and computational analysis, genome-wide distribution scans of RGAs have become common-place (Bayer et al., 2019;Tirnaz et al., 2020). In the Brassica genus alone, more than 30 species, including both cultivated species and wild relatives, have been analysed for their RGA content, resulting in the identification of more than 30 000 RGAs (Bayer et al., 2019;Dolatabadian et al., 2020;Fu et al., 2019;Hofberger et al., 2014;Tirnaz et al., 2020;Yang et al., 2021;Zhang et al., 2016). Of these RGAs, at least 600 were predicted in B. rapa (Alamery et al., 2018;Hofberger et al., 2014;Yang et al., 2021;Zhang et al., 2016). ...
... While RGAs are abundant in most crop genomes, not all are detected due to the limited genomic information captured by a single reference genome (Bayer et al., 2019;Golicz et al., 2020). Thus, in recent years, there has been a shift from developing single reference genomes towards constructing pangenomes that encompass the full genomic landscape of a species (Golicz et al., 2016;Hu et al., 2021;Hurgobin et al., 2018;Montenegro et al., 2017;Rijzaani et al., 2021;Zhao et al., 2020). ...
Brassica rapa is grown worldwide as economically important vegetable and oilseed crop. However, its production is challenged by yield-limiting pathogens. The sustainable control of these pathogens mainly relies on the deployment of genetic resistance primarily driven by resistance gene analogues (RGAs). While several studies have identified RGAs in B. rapa, these were mainly based on a single genome reference and do not represent the full range of RGA diversity in B. rapa. In this study, we utilized the B. rapa pangenome, constructed from 71 lines encompassing 12 morphotypes, to describe a comprehensive repertoire of RGAs in B. rapa. We show that 309 RGAs were affected by presence-absence variation (PAV) and 223 RGAs were missing from the reference genome. The transmembrane leucine-rich repeat (TM-LRR) RGA class had more core gene types than variable genes, while the opposite was observed for nucleotide-binding site leucine-rich repeats (NLRs). Comparative analysis with the B. napus pangenome revealed significant RGA conservation (93%) between the two species. We identified 138 candidate RGAs located within known B. rapa disease resistance QTL, of which the majority were under negative selection. Using blackleg gene homologues, we demonstrated how these genes in B. napus were derived from B. rapa. This further clarifies the genetic relationship of these loci, which may be useful in narrowing-down candidate blackleg resistance genes. This study provides a novel genomic resource towards the identification of candidate genes for breeding disease resistance in B. rapa and its relatives.
... Fuentes et al. (2019) found the stress response genes were enriched on the rice genomic regions with frequent SVs. Bayer et al. (2019) and Dolatabadian et al. (2020) revealed that disease-resistance genes show diverse SV patterns among different Brassica accessions which seems to be a common feature of plant pangenomes. Pan-genomes are becoming necessary to identify the SVs through constructing multiple reference-quality genome assemblies via identifying loci with variants represented by alternative sequences. ...
... These abovementioned results indicate SVs indeed were involved the expression of some genes in the ER-related pathways contributing to heat tolerance. Although SVs have been identified to be responsive to environmental stress and defence response (Fuentes et al. 2019;Bayer et al. 2019 andDolatabadian et al. 2020), the SVs underlying heat tolerance were not detaily characterized in these studies. Yan et al. (2023) revealed the SVs potentially particicpate in important processes in the ER system, extending our understanding of roles of SVs underlying heat tolerance. ...
Global warming adversely affects crop production worldwide. Massive efforts have been undertaken to study mechanisms regulating heat tolerance in plants. However, the roles of structural variations (SVs) in heat stress tolerance remain unclear. In a recent article, Yan et al. (Nat Genet 1–12, 2023) constructed the first pan-genome of pearl millet ( Pennisetum glaucum ) and identified key SVs linked to genes involved in regulating plant tolerance to heat stress for an important crop with a superior ability to thrive in extremely hot and arid climates. Through multi-omics analyses integrating by pan-genomics, comparative genomics, transcriptomics, population genetics and and molecular biological technologies, they found RWP-RK transcription factors cooperating with endoplasmic reticulum-related genes play key roles in heat tolerance in pearl millet. The results in this paper provided novel insights to advance the understanding of the genetic and genomic basis of heat tolerance and an exceptional resource for molecular breeding to improve heat tolerance in pearl millet and other crops.
... Requirements for diverse adaptation in wild species increase gene and allele diversity in populations, much of which is lost during selection for specific crop traits, including yield, resistance to pathogens, tolerance to abiotic stresses, and quality traits. Host plant resistance genes have undergone intense selection during breeding because they have either strong beneficial effects when providing resistance to relevant pathogens or potential negative impacts when associated with reduced crop performance [65,66], including taste and nutrition. There can also be trade-offs between these, including for selection against bitterness, which makes fruits more palatable to not only human consumers, but also other herbivores. ...
Mutations with deleterious consequences in nature may be conditionally deleterious in crop plants. That is, while some genetic variants may reduce fitness under wild conditions and be subject to purifying selection, they can be under positive selection in domesticates. Such deleterious alleles can be plant breeding targets, particularly for complex traits. The difficulty of distinguishing favorable from unfavorable variants reduces the power of selection, while favorable trait variation and heterosis may be attributable to deleterious alleles. Here, we review the roles of deleterious mutations in crop breeding and discuss how they can be used as a new avenue for crop improvement with emerging genomic tools, including HapMaps and pangenome analysis, aiding the identification, removal, or exploitation of deleterious mutations.
