The Evolutionary History of Wild, Domesticated, and Feral Brassica Oleracea (Brassicaceae)

Brassica oleracea var italica and Their By-Products as Source of Bioactive Compounds and Food Applications in Bakery Products

Broccoli (Brassica oleracea var. italica) is one of the most consumed cruciferous crops in the world, with China and Spain acting as the main producers from outside and within the EU, respectively. Broccoli florets are edible, while the leaves and stalks, discarded in the field and during processing, are by-products. Therefore, the objective of this study was to conduct a comprehensive review of the nutrient and phytochemical composition of broccoli and its by-products, as well as its beneficial effects. In addition, the study highlights the revalorization of broccoli by-products through innovative green technologies and explores their potential use in bakery products for the development of functional foods. The studies suggested that broccoli is characterized by a high content of nutrients and bioactive compounds, including vitamins, fiber, glucosinolates, and phenolic compounds, and their content varied with various parts. This high content of value-added compounds gives broccoli and its various parts beneficial properties, including anti-cancer, anti-inflammatory, antioxidant, antimicrobial, metabolic disorder regulatory, and neuroprotective effects. Furthermore, broccoli and its by-products can play a key role in food applications by improving the nutritional profile of products due to their rich content of bioactive compounds. As a result, it is essential to harness the potential of the broccoli and its by-products that are generated during its processing through an appropriate agro-industrial revalorization, using environmentally friendly techniques.

Genomic variation, environmental adaptation, and feralization in ramie, an ancient fiber crop

Feralization is an important evolutionary process, but the mechanisms behind it remain poorly understood. Here, we use the ancient fiber crop ramie (Boehmeria nivea (L.) Gaudich.) as a model to investigate genomic changes associated with both domestication and feralization. We first produced a chromosome-scale de novo genome assembly of feral ramie and investigated structural variations between feral and domesticated ramie genomes. Next, we gathered 915 accessions from 23 countries, comprising cultivars, major landraces, feral populations, and the wild progenitor. Based on whole-genome resequencing of these accessions, we constructed the most comprehensive ramie genomic variation map to date. Phylogenetic, demographic, and admixture signal detection analyses indicated that feral ramie is of exoferal or exo-endo origin, i.e., descended from hybridization between domesticated ramie and the wild progenitor or ancient landraces. Feral ramie has higher genetic diversity than wild or domesticated ramie, and genomic regions affected by natural selection during feralization differ from those under selection during domestication. Ecological analyses showed that feral and domesticated ramie have similar ecological niches that differ substantially from the niche of the wild progenitor, and three environmental variables are associated with habitat-specific adaptation in feral ramie. These findings advance our understanding of feralization, providing a scientific basis for the excavation of new crop germplasm resources and offering novel insights into the evolution of feralization in nature.

Polyphenols in edible plant leaves: an overview of their occurrence and health properties

Edible plant leaves (EPLs) constitute a major renewable functional plant biomass available all year round, providing an essential source of polyphenols in the global diet. Polyphenols form a large family of antioxidant molecules. They protect against the harmful effects of free radicals, strengthen immunity and stimulate the body's natural defenses thanks to their antibacterial and antiviral functions. This study refers to phenolic compounds from 50 edible plant leaves divided into four categories: green leafy vegetables, underutilized leafy vegetables, leafy spices and leafy drinks. It provides data on the identification, occurrence and pharmacological functions of polyphenols contained in EPLs, and provides a better understanding of trends and gaps in their consumption and study. Certain EPLs, such as moringa (Moringa oleifera Lam.), tea (Camellia sinensis L.) and several leafy spices of the Lamiaceae family, reveal important characteristics and therapeutic potential. The polyphenol composition of EPLs makes them functional plants that offer relevant solutions in the fight against obesity, the management of food insecurity and the prevention of chronic diseases.

Genomic analyses reveal the stepwise domestication and genetic mechanism of curd biogenesis in cauliflower

Cauliflower (Brassica oleracea L. var. botrytis) is a distinctive vegetable that supplies a nutrient-rich edible inflorescence meristem for the human diet. However, the genomic bases of its selective breeding have not been studied extensively. Herein, we present a high-quality reference genome assembly C-8 (V2) and a comprehensive genomic variation map consisting of 971 diverse accessions of cauliflower and its relatives. Genomic selection analysis and deep-mined divergences were used to explore a stepwise domestication process for cauliflower that initially evolved from broccoli (Curd-emergence and Curd-improvement), revealing that three MADS-box genes, CAULIFLOWER1 (CAL1), CAL2 and FRUITFULL (FUL2), could have essential roles during curd formation. Genome-wide association studies identified nine loci significantly associated with morphological and biological characters and demonstrated that a zinc-finger protein (BOB06G135460) positively regulates stem height in cauliflower. This study offers valuable genomic resources for better understanding the genetic bases of curd biogenesis and florescent development in crops.

Persistence of genetically engineered canola populations in the U.S. and the adventitious presence of transgenes in the environment

Feralization of genetically engineered (GE) crops increases the risk that transgenes will become integrated into natural and naturalizing plant populations. A key assumption of the management of GE crops is that populations of escaped plants are short-lived and therefore the risks they pose are limited. However, few populations of escaped crop plants have been tracked over the long term so our understanding of their persistence in ruderal or natural landscapes is limited. We repeated a large-scale road survey of feral GE canola populations in North Dakota, USA, initially conducted in 2010. Our objectives in 2021 were to determine the current distribution of feral canola populations, and to establish the relative frequency of GE and non-GE phenotypes in populations of canola throughout North Dakota. Our results indicate that, although the incidence of feral canola was less in 2021 than 2010, escaped canola populations remain common throughout the state. The prevalence of alternate forms of GE herbicide resistance changed between surveys, and we found an overabundance of non-GE plants compared to the frequency of non-transgenic forms in cultivation. Indirect evidence of persistence includes sampling plants with multiple transgenic traits, and finding populations far from transportation routes. We conclude that feral canola populations expressing transgenic herbicide resistance are established outside of cultivation, that they may be under selection for loss of the transgene, but that they nonetheless pose long-term risks by harboring transgenes in the unmanaged landscape.

A new chromosome-scale genome of wild Brassica oleracea provides insights into the domestication of Brassica crops

The cultivated diploid Brassica oleracea is an important vegetable crop, but the genetic basis of its domestication remains largely unclear in the absence of high-quality reference genomes of wild B. oleracea. Here, we report the first chromosome-level assembly of the wild Brassica oleracea L. W03 genome (total genome size, 630.7 Mb; scaffold N50, 64.6 Mb). Using the newly assembled W03 genome, we constructed a gene-based B. oleracea pangenome and identified 29 744 core genes, 23 306 dispensable genes, and 1896 private genes. We re-sequenced 53 accessions, representing six potential wild B. oleracea progenitor species. The results of the population genomic analysis showed that the wild B. oleracea populations had the highest level of diversity and represents the most closely related population to modern-day horticultural B. oleracea. In addition, the WUSCHEL gene was found to play a decisive role in domestication and to be involved in cauliflower and broccoli curd formation. We also illustrate the loss of disease-resistance genes during selection for domestication. Our results provide new insights into the domestication of B. oleracea and will facilitate the future genetic improvement of Brassica crops.

Chromosome-scale reference genome of broccoli (Brassica oleracea var. italica Plenck) provides insights into glucosinolate biosynthesis

Broccoli (Brassica oleracea var. italica Plenck) is an important vegetable crop, as it is rich in health-beneficial glucosinolates (GSLs). However, the genetic basis of the GSL diversity in Brassicaceae remains unclear. Here we report a chromosome-level genome assembly of broccoli generated using PacBio HiFi reads and Hi-C technology. The final genome assembly is 613.79 Mb in size, with a contig N50 of 14.70 Mb. The GSL profile and content analysis of different B. oleracea varieties, combined with a phylogenetic tree analysis, sequence alignment, and the construction of a 3D model of the methylthioalkylmalate synthase 1 (MAM1) protein, revealed that the gene copy number and amino acid sequence variation both contributed to the diversity of GSL biosynthesis in B. oleracea. The overexpression of BoMAM1 (BolI0108790) in broccoli resulted in high accumulation and a high ratio of C4-GSLs, demonstrating that BoMAM1 is the key enzyme in C4-GSL biosynthesis. These results provide valuable insights for future genetic studies and nutritive component applications of Brassica crops.

Genetic diversity, population structure and marker-trait associations in Indian kale (Brassica oleracea L. gp. acephala) using cross-species microsatellite markers

Kale is known for its exceptional nourishing and functional benefits to human body. However, it is an understudied species from genomic as well as agronomic aspects. It is important to characterize niche kale germplasms around the world to systematically conserve and utilize its genetic variability, especially for commercial traits in the interest of growers, consumers and industry. With this view, genomic and phenotypic characterizations of 62 Kashmiri kale accessions including popular landraces were done to estimate and partition genetic diversity, understand trait relationships, develop population structure and divulge marker-trait associations of economic significance. Sixty-six cross species microsatellite (SSR) markers within Brassica genus amplified 269 alleles in the germplasm. Their polymorphic information content (PIC) ranged from 0.00078 to 0.953 with an average of 0.407. The population structure analysis and neighbour joining tree clustering categorized the germplasm into three sub-populations. AMOVA revealed more within-population variance (67.73 %) than among-populations (32.27 %) variance. The principal component analysis (PCA) involving 24 agronomical traits revealed seven PCs (PC1 to PC7) having Eigen values more than 1, which explained a cumulative variation of 69.21 %. Association mapping with respect to these 24 agronomical traits using mixed linear model and general linear model revealed six overlapping significant marker-trait relationships with five being significant at probability value of 0.001/0.0001. The highly significant associations of two SSRs with economically important traits (siliqua length and seed weight) significantly correlated/related with leaf yield and seed yield were revealed for their possible utilization in marker assisted breeding for higher leaf and seed yields.

Defense strategies and associated phytohormonal regulation in Brassica plants in response to chewing and sap-sucking insects

Plants have evolved distinct defense strategies in response to a diverse range of chewing and sucking insect herbivory. While chewing insect herbivores, exemplified by caterpillars and beetles, cause visible tissue damage and induce jasmonic acid (JA)-mediated defense responses, sucking insects, such as aphids and whiteflies, delicately tap into the phloem sap and elicit salicylic acid (SA)-mediated defense responses. This review aims to highlight the specificity of defense strategies in Brassica plants and associated underlying molecular mechanisms when challenged by herbivorous insects from different feeding guilds (i.e., chewing and sucking insects). To establish such an understanding in Brassica plants, the typical defense responses were categorized into physical, chemical, and metabolic adjustments. Further, the impact of contrasting feeding patterns on Brassica is discussed in context to unique biochemical and molecular modus operandi that governs the resistance against chewing and sucking insect pests. Grasping these interactions is crucial to developing innovative and targeted pest management approaches to ensure ecosystem sustainability and Brassica productivity.

Large-scale gene expression alterations introduced by structural variation drive morphotype diversification in Brassica oleracea

Brassica oleracea, globally cultivated for its vegetable crops, consists of very diverse morphotypes, characterized by specialized enlarged organs as harvested products. This makes B. oleracea an ideal model for studying rapid evolution and domestication. We constructed a B. oleracea pan-genome from 27 high-quality genomes representing all morphotypes and their wild relatives. We identified structural variations (SVs) among these genomes and characterized these in 704 B. oleracea accessions using graph-based genome tools. We show that SVs exert bidirectional effects on the expression of numerous genes, either suppressing through DNA methylation or promoting probably by harboring transcription factor-binding elements. The following examples illustrate the role of SVs modulating gene expression: SVs promoting BoPNY and suppressing BoCKX3 in cauliflower/broccoli, suppressing BoKAN1 and BoACS4 in cabbage and promoting BoMYBtf in ornamental kale. These results provide solid evidence for the role of SVs as dosage regulators of gene expression, driving B. oleracea domestication and diversification.

A graph-based pan-genome of Brassica oleracea provides new insights into its domestication and morphotype diversification

The domestication of Brassica oleracea has resulted in diverse morphological types with distinct patterns of organ development. Here we report a graph-based pan-genome of B. oleracea constructed from high-quality genome assemblies of different morphotypes. The pan-genome harbors over 200 structural variant hotspot regions enriched in auxin- and flowering-related genes. Population genomic analyses revealed that early domestication of B. oleracea focused on leaf or stem development. Gene flows resulting from agricultural practices and variety improvement were detected among different morphotypes. Selective-sweep and pan-genome analyses identified an auxin-responsive small auxin up-regulated RNA gene and a CLAVATA3/ESR-RELATED family gene as crucial players in leaf-stem differentiation during the early stage of B. oleracea domestication and the BoKAN1 gene as instrumental in shaping the leafy heads of cabbage and Brussels sprouts. Our pan-genome and functional analyses further revealed that variations in the BoFLC2 gene play key roles in the divergence of vernalization and flowering characteristics among different morphotypes, and variations in the first intron of BoFLC3 are involved in fine-tuning the flowering process in cauliflower. This study provides a comprehensive understanding of the pan-genome of B. oleracea and sheds light on the domestication and differential organ development of this globally important crop species.

Map-based cloning and functional analysis of a major quantitative trait locus, BolC.Pb9.1, controlling clubroot resistance in a wild Brassica relative (Brassica macrocarpa)

KEY MESSAGE

A causal gene BoUGT76C2, conferring clubroot resistance in wild Brassica oleracea, was identified and functionally characterized. Clubroot is a devastating soil-borne disease caused by the obligate biotrophic pathogen Plasmodiophora brassica (P. brassicae), which poses a great threat to Brassica oleracea (B. oleracea) production. Although several QTLs associated with clubroot resistance (CR) have been mapped in cultivated B. oleracea, none have been cloned in B. oleracea. Previously, we found that the wild B. oleracea B2013 showed high resistance to clubroot. In this study, we constructed populations using B2013 and broccoli line 90196. CR in B2013 is quantitatively inherited, and a major QTL, BolC.Pb9.1, was identified on C09 using QTL-seq and linkage analysis. The BolC.Pb9.1 was finely mapped to a 56 kb genomic region using F2:3 populations. From the target region, the candidate BoUGT76C2 showed nucleotide variations between the parents, and was inducible in response to P. brassicae infection. We generated BoUGT76C2 overexpression lines in the 90196 background, which showed significantly enhanced resistance to P. brassicae compared to the WT line, suggesting that BoUGT76C2 corresponds to the resistance gene BolC.Pb.9.1. This is the first report on the CR gene map-based cloning and functional analysis from wild relatives, which provides a theoretical basis to the understanding of the molecular mechanism of CR, and lays a foundation to improve the CR of cultivated B. oleracea.

Current status of global conservation and characterisation of wild and cultivated Brassicaceae genetic resources

BACKGROUND

The economic importance of the globally distributed Brassicaceae family resides in the large diversity of crops within the family and the substantial variety of agronomic and functional traits they possess. We reviewed the current classifications of crop wild relatives (CWRs) in the Brassicaceae family with the aim of identifying new potential cross-compatible species from a total of 1,242 species using phylogenetic approaches.

RESULTS

In general, cross-compatibility data between wild species and crops, as well as phenotype and genotype characterisation data, were available for major crops but very limited for minor crops, restricting the identification of new potential CWRs. Around 70% of wild Brassicaceae did not have genetic sequence data available in public repositories, and only 40% had chromosome counts published. Using phylogenetic distances, we propose 103 new potential CWRs for this family, which we recommend as priorities for cross-compatibility tests with crops and for phenotypic characterisation, including 71 newly identified CWRs for 10 minor crops. From the total species used in this study, more than half had no records of being in ex situ conservation, and 80% were not assessed for their conservation status or were data deficient (IUCN Red List Assessments).

CONCLUSIONS

Great efforts are needed on ex situ conservation to have accessible material for characterising and evaluating the species for future breeding programmes. We identified the Mediterranean region as one key conservation area for wild Brassicaceae species, with great numbers of endemic and threatened species. Conservation assessments are urgently needed to evaluate most of these wild Brassicaceae.

Plant biology: Phylogenomics of mustards and their relatives

A new nuclear phylogeny for the large family Brassicaceae opens the way for advanced comparative studies of adaptation, development, coevolution, hybridization, and diversification in this crucial group, which is the source for many of the genomic resources now used across the flowering plants.

A natural mutation in the promoter of Ms-cd1 causes dominant male sterility in Brassica oleracea

Male sterility has been used for crop hybrid breeding for a long time. It has contributed greatly to crop yield increase. However, the genetic basis of male sterility has not been fully elucidated. Here, we report map-based cloning of the cabbage (Brassica oleracea) dominant male-sterile gene Ms-cd1 and reveal that it encodes a PHD-finger motif transcription factor. A natural allele Ms-cd1PΔ-597, resulting from a 1-bp deletion in the promoter, confers dominant genic male sterility (DGMS), whereas loss-of-function ms-cd1 mutant shows recessive male sterility. We also show that the ethylene response factor BoERF1L represses the expression of Ms-cd1 by directly binding to its promoter; however, the 1-bp deletion in Ms-cd1PΔ-597 affects the binding. Furthermore, ectopic expression of Ms-cd1PΔ-597 confers DGMS in both dicotyledonous and monocotyledonous plant species. We thus propose that the DGMS system could be useful for breeding hybrids of multiple crop species.

Genome-wide analysis of glutamate receptor gene family in allopolyploid Brassica napus and its diploid progenitors

Ionotropic glutamate receptors are ligand-gated nonselective cation channels that mediate neurotransmission in the central nervous system of animals. Plants possess homologous proteins called glutamate receptor-like channels (GLRs) which are involved in vital physiological processes including seed germination, long-distance signaling, chemotaxis, Ca2+ signaling etc. Till now, a comprehensive genome-wide analysis of the GLR gene family members in different economically important species of Brassica is missing. Considering the origin of allotetraploid Brassica napus from the hybridization between the diploid Brassica oleracea and Brassica rapa, we have identified 11, 27 and 65 GLR genes in B. oleracea, B. rapa and B. napus, respectively showing an expansion of this gene family in B. napus. Chromosomal locations revealed several tandemly duplicated GLR genes in all the three species. Moreover, the gene family expanded in B. napus after allopolyploidization. The phylogenetic analysis showed that the 103 GLRs are classified into three main groups. The exon-intron structures of these genes are not very conserved and showed wide variation in intron numbers. However, protein sequences are much conserved as shown by the presence of ten short amino acid sequence motifs. Predicted cis-acting elements in 1 kb promoters of GLR genes are mainly involved in light, stress and hormone responses. RNA-seq analysis showed that in B. oleracea and B. rapa, some GLRs are more tissue specific than others. In B. napus, some GLRs are downregulated under cold stress, while others are upregulated. In summary, this bioinformatic study of the GLR gene family of the three Brassica species provides evidence for the expansion of this gene family in B. napus and also provided useful information for in-depth studies of their biological functions in Brassica.

Interploidy Introgression Shaped Adaptation during the Origin and Domestication History of Brassica napus

Polyploidy is recurrent across the tree of life and known as an evolutionary driving force in plant diversification and crop domestication. How polyploid plants adapt to various habitats has been a fundamental question that remained largely unanswered. Brassica napus is a major crop cultivated worldwide, resulting from allopolyploidy between unknown accessions of diploid B. rapa and B. oleracea. Here, we used whole-genome resequencing data of accessions representing the majority of morphotypes and ecotypes from the species B. rapa, B. oleracea, and B. napus to investigate the role of polyploidy during domestication. To do so, we first reconstructed the phylogenetic history of B. napus, which supported the hypothesis that the emergence of B. napus derived from the hybridization of European turnip of B. rapa and wild B. oleracea. These analyses also showed that morphotypes of swede and Siberian kale (used as vegetable and fodder) were domesticated before rapeseed (oil crop). We next observed that frequent interploidy introgressions from sympatric diploids were prominent throughout the domestication history of B. napus. Introgressed genomic regions were shown to increase the overall genetic diversity and tend to be localized in regions of high recombination. We detected numerous candidate adaptive introgressed regions and found evidence that some of the genes in these regions contributed to phenotypic diversification and adaptation of different morphotypes. Overall, our results shed light on the origin and domestication of B. napus and demonstrate interploidy introgression as an important mechanism that fuels rapid diversification in polyploid species.

Revealing the secrets of a 2900-year-old clay brick, discovering a time capsule of ancient DNA

The recent development of techniques to sequence ancient DNA has provided valuable insights into the civilisations that came before us. However, the full potential of these methods has yet to be realised. We extracted ancient DNA from a recently exposed fracture surface of a clay brick deriving from the palace of king Ashurnasirpal II (883-859 BCE) in Nimrud, Iraq. We detected 34 unique taxonomic groups of plants. With this research we have made the pioneering discovery that ancient DNA, effectively protected from contamination inside a mass of clay, can successfully be extracted from a 2900-year-old clay brick. We encourage future research into this subject, as the scientific prospects for this approach are substantial, potentially leading to a deeper understanding of ancient and lost civilisations.

Comparative Transcriptome Analysis Points to the Biological Processes of Hybrid Incompatibility between Brassica napus and B. oleracea

Improving Brassica napus via introgression of the genome components from its parental species, B. oleracea and B. rapa, is an important breeding strategy. Interspecific hybridization between B. napus and B. rapa is compatible with high rate of survival ovules, while the hybridization between B. napus and B. oleracea is incompatible with the high occurrence of embryo abortion. To understand the diverse embryo fate in the two interspecific hybridizations, here, the siliques of B. napus pollinated with B. oleracea (AE) and B. rapa (NE) were employed for transcriptome sequencing at 8 and 16 days after pollination. Compared to NE and the parental line of B. napus, more specific differentially expressed genes (DEGs) (1274 and 1698) were obtained in AE and the parental line of B. napus at 8 and 16 days after pollination (DAP). These numbers were 51 and 5.8 times higher than the number of specific DEGs in NE and parental line of B. napus at 8 and 16 DAP, respectively, suggesting more complex transcriptional changes in AE. Most of DEGs in the terms of cell growth and cell wall formation exhibited down-regulated expression patterns (96(down)/131(all) in AE8, 174(down)/235(all) in AE16), while most of DEGs in the processes of photosynthesis, photorespiration, peroxisome, oxidative stress, and systemic acquired resistance exhibited up-regulated expression patterns (222(up)/304(all) in AE8, 214(up)/287(all) in AE16). This is in accordance with a high level of reactive oxygen species (ROS) in the siliques of B. napus pollinated with B. oleracea. Our data suggest that the disorder of plant hormone metabolism, retardation of cell morphogenesis, and the accumulation of ROS may be associated with hybrid incompatibility between B. napus and B. oleracea.

Two domestications for grapes

Glacial cycles and wild adaptations shaped grape domestication and the rise of wine.

Whole-Genome Comparison Reveals Structural Variations behind Heading Leaf Trait in Brassica oleracea

Brassica oleracea displays remarkable morphological variations. It intrigued researchers to study the underlying cause of the enormous diversification of this organism. However, genomic variations in complex heading traits are less known in B. oleracea. Herein, we performed a comparative population genomics analysis to explore structural variations (SVs) responsible for heading trait formation in B. oleracea. Synteny analysis showed that chromosomes C1 and C2 of B. oleracea (CC) shared strong collinearity with A01 and A02 of B. rapa (AA), respectively. Two historical events, whole genome triplication (WGT) of Brassica species and differentiation time between AA and CC genomes, were observed clearly by phylogenetic and Ks analysis. By comparing heading and non-heading populations of B. oleracea genomes, we found extensive SVs during the diversification of the B. oleracea genome. We identified 1205 SVs that have an impact on 545 genes and might be associated with the heading trait of cabbage. Overlapping the genes affected by SVs and the differentially expressed genes identified by RNA-seq analysis, we identified six vital candidate genes that may be related to heading trait formation in cabbage. Further, qRT-PCR experiments also verified that six genes were differentially expressed between heading leaves and non-heading leaves, respectively. Collectively, we used available genomes to conduct a comparison population genome analysis and identify candidate genes for the heading trait of cabbage, which provides insight into the underlying reason for heading trait formation in B. oleracea.

Antioxidant and Antiproliferative Activities of Kale (Brassica oleracea L. Var. acephala DC.) and Wild Cabbage (Brassica incana Ten.) Polyphenolic Extracts

Brassicaceae are rich in healthy phytochemicals that have a positive impact on human health. The aim of this study was to analyze the phenolic compounds and antioxidant and anticancer potential of traditional Croatian kale (Brassica oleracea L. var. acephala DC.) and wild cabbage (Brassica incana Ten.) extracts. The phenolic groups and antioxidant activity were determined by spectrophotometry, selected phenolic compounds (ferulic acid, sinapic acid, salicylic acid, kaempferol, and quercetin) were analyzed by LC-MS/MS, and anticancer potential was evaluated in vitro using HeLa cells. The extracts of both plant species are rich in phenolic compounds and showed significant antioxidant activity at similar levels. LC-MS/MS detected sinapic acid as the most abundant phenolic acid, followed by ferulic acid, while salicylic acid was present at lower concentrations. A comparative analysis showed that wild cabbage contained significantly more sinapic acid, while kale contained more kaempferol and quercetin. Both Brassica extracts at a concentration of 50 µg mL^-1 showed an antiproliferative effect on HeLa cells, while they did not affect the proliferation of normal human skin fibroblasts. Wild cabbage extract also showed an antiproliferative effect on HeLa cells at a lower applied concentration of 10 µg mL^-1 of extracts. The clonogenic analysis also revealed the inhibitory effect of the extracts on HeLa colony growth.

Molecular Markers for Detecting Inflorescence Size of Brassica oleracea L. Crops and B. oleracea Complex Species (n = 9) Useful for Breeding of Broccoli (B. oleracea var. italica) and Cauliflower (B. oleracea var. botrytis)

The gene flow from Brassica oleracea L. wild relatives to B. oleracea vegetable crops have occurred and continue to occur ordinarily in several Mediterranean countries, such as Sicily, representing an important hot spot of diversity for some of them, such as broccoli, cauliflower and kale. For detecting and for exploiting the forgotten alleles lost during the domestication processes of the B. oleracea crops, attention has been pointed to the individuation of specific markers for individuating genotypes characterized by hypertrophic inflorescence traits by the marker assisted selection (MAS) during the first plant growing phases after the crosses between broccoli (B. oleracea var. italica)/cauliflower (B. oleracea var. botrytis) with B. oleracea wild relatives (n = 9), reducing the cultivation and evaluation costs. The desired traits often found in several B. oleracea wild relatives are mainly addressed to improve the plant resistance to biotic and abiotic stresses and to increase the organoleptic, nutritive and nutraceutical traits of the products. One of the targeted traits for broccoli and cauliflower breeding is represented by the inflorescences size as is documented by the domestication processes of these two crops. Based on the previous results achieved, the numerical matrix, obtained utilizing five simple sequence repeats (SSRs), was analyzed to assess the relationship among the main inflorescence characteristics and the allelic variation of the SSRs loci analyzed (BoABI1, BoAP1, BoPLD1, BoTHL1 and PBCGSSRBo39), both for the Brassica oleracea and B. oleracea wild relatives (n = 9) accessions set. The main inflorescence morphometric characteristics, such as weight, height, diameter, shape, inflorescence curvature angle and its stem diameter, were registered before the flower anthesis. We analyzed the correlations among the allelic variation of the SSRs primers utilized and the inflorescence morphometric characteristics to individuate genomic regions stimulating the hypertrophy of the reproductive organ. The relationships found explain the diversity among B. oleracea crops and the B. oleracea complex species (n = 9) for the inflorescence size and structure. The individuated markers allow important time reduction during the breeding programs after crossing wild species for transferring useful biotic and abiotic resistances and organoleptic and nutraceutical traits to the B. oleracea crops by MAS.

Convergence in domesticated fungi used for cheese and dry-cured meat maturation: beneficial traits, genomic mechanisms, and degeneration

Humans have domesticated genetically distant fungi for similar uses, the fermentation of lipid-rich and sugar-rich food to generate attractive aspects, odor and aroma, and to improve shelf life and product safety. Multiple independent domestication events also occurred within species. We review recent evidence of phenotypic convergence during the domestication of fungi for making cheese (Saccharomyces cerevisiae, Penicillium roqueforti, P. camemberti, and Geotrichum candidum) and for dry-cured meat making (P. nalgiovense and P. salamii). Convergence following adaptation to similar ecological niches involved colony aspect (fluffiness and color), lipolysis, proteolysis, volatile compound production, and competitive ability against food spoilers. We review evidence for convergence in genetic diversity loss in domesticated populations and in the degeneration of unused traits, such as toxin production and sexual reproduction. Phenotypic convergence sometimes occurred by similar mechanisms of genomic adaptation, in particular horizontal gene transfers and loss of genes.

Prospects of Feral Crop De Novo Redomestication

Modern agriculture depends on a narrow variety of crop species, leaving global food and nutritional security highly vulnerable to the adverse effects of climate change and population expansion. Crop improvement using conventional and molecular breeding approaches leveraging plant genetic diversity using crop wild relatives (CWRs) has been one approach to address these issues. However, the rapid pace of the global change requires additional innovative solutions to adapt agriculture to meet global needs. Neodomestication-the rapid and targeted introduction of domestication traits using introgression or genome editing of CWRs-is being explored as a supplementary approach. These methods show promise; however, they have so far been limited in efficiency and applicability. We propose expanding the scope of neodomestication beyond truly wild CWRs to include feral crops as a source of genetic diversity for novel crop development, in this case 'redomestication'. Feral crops are plants that have escaped cultivation and evolved independently, typically adapting to their local environments. Thus, feral crops potentially contain valuable adaptive features while retaining some domestication traits. Due to their genetic proximity to crop species, feral crops may be easier targets for de novo domestication (i.e. neodomestication via genome editing techniques). In this review, we explore the potential of de novo redomestication as an application for novel crop development by genome editing of feral crops. This approach to efficiently exploit plant genetic diversity would access an underutilized reservoir of genetic diversity that could prove important in support of global food insecurity in the face of the climate change.

Building a foundation for gene family analysis in Rosaceae genomes with a novel workflow: A case study in Pyrus architecture genes

The rapid development of sequencing technologies has led to a deeper understanding of plant genomes. However, direct experimental evidence connecting genes to important agronomic traits is still lacking in most non-model plants. For instance, the genetic mechanisms underlying plant architecture are poorly understood in pome fruit trees, creating a major hurdle in developing new cultivars with desirable architecture, such as dwarfing rootstocks in European pear (Pyrus communis). An efficient way to identify genetic factors for important traits in non-model organisms can be to transfer knowledge across genomes. However, major obstacles exist, including complex evolutionary histories and variable quality and content of publicly available plant genomes. As researchers aim to link genes to traits of interest, these challenges can impede the transfer of experimental evidence across plant species, namely in the curation of high-quality, high-confidence gene models in an evolutionary context. Here we present a workflow using a collection of bioinformatic tools for the curation of deeply conserved gene families of interest across plant genomes. To study gene families involved in tree architecture in European pear and other rosaceous species, we used our workflow, plus a draft genome assembly and high-quality annotation of a second P. communis cultivar, 'd'Anjou.' Our comparative gene family approach revealed significant issues with the most recent 'Bartlett' genome - primarily thousands of missing genes due to methodological bias. After correcting assembly errors on a global scale in the 'Bartlett' genome, we used our workflow for targeted improvement of our genes of interest in both P. communis genomes, thus laying the groundwork for future functional studies in pear tree architecture. Further, our global gene family classification of 15 genomes across 6 genera provides a valuable and previously unavailable resource for the Rosaceae research community. With it, orthologs and other gene family members can be easily identified across any of the classified genomes. Importantly, our workflow can be easily adopted for any other plant genomes and gene families of interest.

Construction of an SNP fingerprinting database and population genetic analysis of 329 cauliflower cultivars

Cauliflower is one of the most important vegetable crops grown worldwide. However, the lack of genetic diversity information and efficient molecular markers hinders efforts to improve cauliflower. This study aims to construct DNA fingerprints for 329 cauliflower cultivars based on SNP markers and the KASP system. After rigorous filtering, a total of 1662 candidate SNPs were obtained from nearly 17.9 million SNP loci. The mean values of PIC, MAF, heterozygosity and gene diversity of these SNPs were 0.389, 0.419, 0.075, and 0.506, respectively. We developed a program for in silico simulations on 153 core germplasm samples to generate ideal SNP marker sets from the candidates. Finally, 41 highly polymorphic KASP markers were selected and applied to identify 329 cauliflower cultivars, mainly collected from the public market. Furthermore, based on the KASP genotyping data, we performed phylogenetic analysis and population structure analysis of the 329 cultivars. As a result, these cultivars could be classified into three major clusters, and the classification patterns were significantly related to their curd solidity and geographical origin. Finally, fingerprints of the 329 cultivars and 2D barcodes with the genetic information of each sample were generated. The fingerprinting database developed in this study provides a practical tool for identifying the authenticity and purity of cauliflower seeds and valuable genetic information about the current cauliflower cultivars.

The Boechera model system for evolutionary ecology

Model systems in biology expand the research capacity of individuals and the community. Closely related to Arabidopsis, the genus Boechera has emerged as an important ecological model owing to the ability to integrate across molecular, functional, and eco-evolutionary approaches. Boechera species are broadly distributed in relatively undisturbed habitats predominantly in western North America and provide one of the few experimental systems for identification of ecologically important genes through genome-wide association studies and investigations of selection with plants in their native habitats. The ecologically, evolutionarily, and agriculturally important trait of apomixis (asexual reproduction via seeds) is common in the genus, and field experiments suggest that abiotic and biotic environments shape the evolution of sex. To date, population genetic studies have focused on the widespread species B. stricta, detailing population divergence and demographic history. Molecular and ecological studies show that balancing selection maintains genetic variation in ~10% of the genome, and ecological trade-offs contribute to complex trait variation for herbivore resistance, flowering phenology, and drought tolerance. Microbiome analyses have shown that host genotypes influence leaf and root microbiome composition, and the soil microbiome influences flowering phenology and natural selection. Furthermore, Boechera offers numerous opportunities for investigating biological responses to global change. In B. stricta, climate change has induced a shift of >2 weeks in the timing of first flowering since the 1970s, altered patterns of natural selection, generated maladaptation in previously locally-adapted populations, and disrupted life history trade-offs. Here we review resources and results for this eco-evolutionary model system and discuss future research directions.

Genetic dissection of morphological variation in rosette leaves and leafy heads in cabbage (Brassica oleracea var. capitata)

Correlations between morphological traits of cabbage rosette leaves and heads were found. Genome-wide association studies of these traits identified 50 robust quantitative trait loci in multiple years. Half of these loci affect both organs. Cabbage (Brassica oleracea var. capitata) is an economically important vegetable crop cultivated worldwide. Cabbage plants go through four vegetative stages: seedling, rosette, folding and heading. Rosette leaves are the largest leaves of cabbage plants and provide most of the energy needed to produce the leafy head. To understand the relationship and the genetic basis of leaf development and leafy head formation, 308 cabbage accessions were scored for rosette leaf and head traits in three-year field trials. Significant correlations were found between morphological traits of rosette leaves and heads, namely leaf area with the head area, height and width, and leaf width with the head area and head height, when heads were harvested at a fixed number of days after sowing. Fifty robust quantitative trait loci (QTLs) for rosette leaf and head traits distributed over all nine chromosomes were identified with genome-wide association studies. All these 50 loci were identified in multiple years and generally affect multiple traits. Twenty-five of the QTL were associated with both rosette leaf and leafy head traits. We discuss thirteen candidate genes identified in these QTL that are expressed in heading leaves, with an annotation related to auxin and other phytohormones, leaf development, and leaf polarity that likely play a role in leafy head development or rosette leaf expansion.

Investigation of Brassica and its relative genomes in the post-genomics era

The Brassicaceae family includes many economically important crop species, as well as cosmopolitan agricultural weed species. In addition, Arabidopsis thaliana, a member of this family, is used as a molecular model plant species. The genus Brassica is mesopolyploid, and the genus comprises comparatively recently originated tetrapolyploid species. With these characteristics, Brassicas have achieved the commonly accepted status of model organisms for genomic studies. This paper reviews the rapid research progress in the Brassicaceae family from diverse omics studies, including genomics, transcriptomics, epigenomics, and three-dimensional (3D) genomics, with a focus on cultivated crops. The morphological plasticity of Brassicaceae crops is largely due to their highly variable genomes. The origin of several important Brassicaceae crops has been established. Genes or loci domesticated or contributing to important traits are summarized. Epigenetic alterations and 3D structures have been found to play roles in subgenome dominance, either in tetraploid Brassica species or their diploid ancestors. Based on this progress, we propose future directions and prospects for the genomic investigation of Brassicaceae crops.

A cluster of transcripts identifies a transition stage initiating leafy head growth in heading morphotypes of Brassica

Leaf heading is an important and economically valuable horticultural trait in many vegetables. The formation of a leafy head is a specialized leaf morphogenesis characterized by the emergence of the enlarged incurving leaves. However, the transcriptional regulation mechanisms underlying the transition to leaf heading remain unclear. We carried out large-scale time-series transcriptome assays covering the major vegetative growth phases of two headingBrassica crops, Chinese cabbage and cabbage, with the non-heading morphotype Taicai as the control. A regulatory transition stage that initiated the heading process is identified, accompanied by a developmental switch from rosette leaf to heading leaf in Chinese cabbages. This transition did not exist in the non-heading control. Moreover, we reveal that the heading transition stage is also conserved in the cabbage clade. Chinese cabbage acquired through domestication a leafy head independently from the origins of heading in other cabbages; phylogenetics supports that the ancestor of all cabbages is non-heading. The launch of the transition stage is closely associated with the ambient temperature. In addition, examination of the biological activities in the transition stage identified the ethylene pathway as particularly active, and we hypothesize that this pathway was targeted for selection for domestication to form the heading trait specifically in Chinese cabbage. In conclusion, our findings on the transcriptome transition that initiated the leaf heading in Chinese cabbage and cabbage provide a new perspective for future studies of leafy head crops.

Nucleotide Evolution, Domestication Selection, and Genetic Relationships of Chloroplast Genomes in the Economically Important Crop Genus Gossypium

Gossypium hirsutum (upland cotton) is one of the most economically important crops worldwide, which has experienced the long terms of evolution and domestication process from wild species to cultivated accessions. However, nucleotide evolution, domestication selection, and the genetic relationship of cotton species remain largely to be studied. In this study, we used chloroplast genome sequences to determine the evolutionary rate, domestication selection, and genetic relationships of 72 cotton genotypes (36 cultivated cotton accessions, seven semi-wild races of G. hirsutum, and 29 wild species). Evolutionary analysis showed that the cultivated tetraploid cotton genotypes clustered into a single clade, which also formed a larger lineage with the semi-wild races. Substitution rate analysis demonstrated that the rates of nucleotide substitution and indel variation were higher for the wild species than the semi-wild and cultivated tetraploid lineages. Selection pressure analysis showed that the wild species might have experienced greater selection pressure, whereas the cultivated cotton genotypes underwent artificial and domestication selection. Population clustering analysis indicated that the cultivated cotton accessions and semi-wild races have existed the obviously genetic differentiation. The nucleotide diversity was higher in the semi-wild races compared with the cultivated genotypes. In addition, genetic introgression and gene flow occurred between the cultivated tetraploid cotton and semi-wild genotypes, but mainly via historical rather than contemporary gene flow. These results provide novel molecular mechanisms insights into the evolution and domestication of economically important crop cotton species.

Genetic analysis reveals three novel QTLs underpinning a butterfly egg-induced hypersensitive response-like cell death in Brassica rapa

BACKGROUND

Cabbage white butterflies (Pieris spp.) can be severe pests of Brassica crops such as Chinese cabbage, Pak choi (Brassica rapa) or cabbages (B. oleracea). Eggs of Pieris spp. can induce a hypersensitive response-like (HR-like) cell death which reduces egg survival in the wild black mustard (B. nigra). Unravelling the genetic basis of this egg-killing trait in Brassica crops could improve crop resistance to herbivory, reducing major crop losses and pesticides use. Here we investigated the genetic architecture of a HR-like cell death induced by P. brassicae eggs in B. rapa.

RESULTS

A germplasm screening of 56 B. rapa accessions, representing the genetic and geographical diversity of a B. rapa core collection, showed phenotypic variation for cell death. An image-based phenotyping protocol was developed to accurately measure size of HR-like cell death and was then used to identify two accessions that consistently showed weak (R-o-18) or strong cell death response (L58). Screening of 160 RILs derived from these two accessions resulted in three novel QTLs for Pieris brassicae-induced cell death on chromosomes A02 (Pbc1), A03 (Pbc2), and A06 (Pbc3). The three QTLs Pbc1-3 contain cell surface receptors, intracellular receptors and other genes involved in plant immunity processes, such as ROS accumulation and cell death formation. Synteny analysis with A. thaliana suggested that Pbc1 and Pbc2 are novel QTLs associated with this trait, while Pbc3 also contains an ortholog of LecRK-I.1, a gene of A. thaliana previously associated with cell death induced by a P. brassicae egg extract.

CONCLUSIONS

This study provides the first genomic regions associated with the Pieris egg-induced HR-like cell death in a Brassica crop species. It is a step closer towards unravelling the genetic basis of an egg-killing crop resistance trait, paving the way for breeders to further fine-map and validate candidate genes.

Evidence for two domestication lineages supporting a middle-eastern origin for Brassica oleracea crops from diversified kale populations

Brassica oleracea displays enormous phenotypic variation, including vegetables like cabbage, broccoli, cauliflower, kohlrabi, kales etc. Its domestication has not been clarified, despite several genetic studies and investigations of ancient literature. We used 14 152 high-quality SNP markers for population genetic studies and species-tree estimation (treating morphotypes as "species") using SVD-quartets coalescent-modelling of a collection of 912 globally distributed accessions representing ten morphotypes of B. oleracea, wild B. oleracea accessions and nine related C9 Brassica species. Our genealogical tree provided evidence for two domestication lineages, the "leafy head" lineage (LHL) and the "arrested inflorescence" lineage (AIL). It also showed that kales are polyphyletic with regards to B. oleracea morphotypes, which fits ancient literature describing highly diverse kale types at around 400 BC. The SVD-quartets species tree topology showed that different kale clades are sister to either the LHL or the AIL. Cabbages from the middle-east formed the first-branching cabbage-clade, supporting the hypothesis that cabbage domestication started in the middle-east, which is confirmed by archeological evidence and historic writings. We hypothesize that cabbages and cauliflowers stem from kales introduced from Western Europe to the middle-east, possibly transported with the tin-trade routes in the Bronze age, to be re-introduced later into Europe. Cauliflower is the least diverse morphotype showing strong genetic differentiation with other morphotypes except broccoli, suggesting a strong genetic bottleneck. Genetic diversity reduced from landraces to modern hybrids for almost all morphotypes. This comprehensive Brassica C-group germplasm collection provides valuable genetic resources and a sound basis for B. oleracea breeding.

Different Shades of Kale-Approaches to Analyze Kale Variety Interrelations

Brassica oleracea is a vegetable crop with an amazing morphological diversity. Among the various crops derived from B. oleracea, kale has been in the spotlight globally due to its various health-benefitting compounds and many different varieties. Knowledge of the existing genetic diversity is essential for the improved breeding of kale. Here, we analyze the interrelationships, population structures, and genetic diversity of 72 kale and cabbage varieties by extending our previous diversity analysis and evaluating the use of summed potential lengths of shared haplotypes (SPLoSH) as a new method for such analyses. To this end, we made use of the high-density Brassica 60K SNP array, analyzed SNPs included in an available Brassica genetic map, and used these resources to generate and evaluate the information from SPLoSH data. With our results we could consistently differentiate four groups of kale across all analyses: the curly kale varieties, Italian, American, and Russian varieties, as well as wild and cultivated types. The best results were achieved by using SPLoSH information, thus validating the use of this information in improving analyses of interrelations in kale. In conclusion, our definition of kale includes the curly varieties as the kales in a strict sense, regardless of their origin. These results contribute to a better understanding of the huge diversity of kale and its interrelations.