Identification of differentially expressed genes related to aberrant phenotypes in Brassica oleracea var. botrytis (original) (raw)
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“Aberrant” plants in cauliflower: 1. Phenotype and heredity
Euphytica, 2008
For more than a decade, the number of "aberrant plants" showing various developmental abnormalities in cultivated cauliXowers has dramatically increased, thus hampering the registration of new varieties in some cases. The aberrant phenotype occurred during the cultivation period and in any variety type (pure line or F1 hybrid). The number of aberrant plants increased considerably from 1994 onwards. The rate of aberrant plants observed among F1 hybrids in the Weld was found to vary according to genotype and cultivation area. Besides morphological changes, aberrant phenotypes showed various patterns of evolution, i.e. stable, evolving toward another phenotype or reversing toward normality. Vegetative and seed progenies were obtained in order to investigate the genetic control of these phenotypic variations. Given that the aberrant phenotypes can evolve towards either normality or another abnormality during the life cycle of the plant and that the aberration capacity and/or the "acquired morphological disorder" can be transmitted to the progeny, an epigenetic hypothesis has been proposed for the determinism of this phenomenon.
G3: Genes, Genomes, Genetics, 2023
To improve resolution to small genomic regions and sensitivity to small-effect loci in the identification of genetic factors conferring the enlarged inflorescence and other traits of cauliflower while also expediting further genetic dissection, 104 near-isogenic introgression lines (NIILs) covering 78.56% of the cauliflower genome, were selected from an advanced backcross population using cauliflower [B. oleracea var. botrytis L., mutant for Orange gene (ORG)] as the donor parent and a rapid cycling line (TO1434) as recurrent parent. Subsets of the advanced backcross population and NIILs were planted in the field for eight seasons, finding 141 marker-trait associations for 15 leaf-, stem-and flower-traits. Exemplifying the usefulness of these lines, we delineated the previously-known flower color gene to a 4.5 MB interval on C3; a gene for small plant size to a 3.4 MB region on C8; and a gene for large plant size and flowering time to a 6.1 MB region on C9. This approach unmasked closely linked QTL alleles with opposing effects (on chr. 8), and revealed both alleles with expected phenotypic effects and effects opposite the parental phenotypes. Selected B. oleracea NIILs with short generation time add new value to widely used research and teaching materials.
Expression quantitative trait loci analysis of BAN, F3H and TT19 genes in Brassica napus
2012
Flavonone 3-hydroxylase (F3H), anthocyanidin reductase (ANR) encoded by BANYULS (BAN) gene and glutathione S-transferase encoded by TRANSPARENT TESTA 19 (TT19) gene are three key enzymes in flavonoid pathway, playing important roles in the synthesis and transport of anthocyanin and proanthocyanidin. However, little is known about the expression variations and the regulatory network in Brassica. In this study, we examined their expression levels in seeds of 30 days after flowering (DAF) in F 7 recombinant inbred lines (RILs) derived from a cross between Brassica napus cultivars Youyan2 (black-seeded) and GH06 (yellowseeded), and characterized the locus-level regulatory network related to B. napus BAN, F3H and TT19 genes. Expression quantitative trait loci (eQTL) mapping revealed five, seven and eight eQTLs for BAN, F3H and TT19 genes, respectively. Marker E4M8 was associated with qBAN-8-2 and qTT19-8-2, while marker H022L18-2 was linked with qBAN-16-4 and qF3H-16-6, implying that there might be upstream regulatory genes in E4M8 and H022L18-2 marker flanking regions. In further analysis, we identified four trans-eQTLs (qBAN-16-5, qF3H-16-5, qBAN-16-4 and qF3H-11-2) close to the location of the major QTL controlling yellow-seeded trait of B. napus. The 200-kb flanking sequences of the four eQTL on B. rapa chromosome A09 showed well synteny to B. oleracea genome sequence and partial continuous fragment of chromosome 1 of Arabidopsis genome, suitable for candidate gene predication of eQTLs. Based on gene finding results, seven transcription factors were suggested to be the potential upstream candidate(s) controlling expression variations of BAN, F3H and TT19 genes. These results could provide a new approach for constructing regulatory pathways that contribute to complex traits, such as yellow-seeded trait.
A rich TILLING resource for studying gene function in Brassica rapa
2010
Background: The Brassicaceae family includes the model plant Arabidopsis thaliana as well as a number of agronomically important species such as oilseed crops (in particular Brassica napus, B. juncea and B. rapa) and vegetables (eg. B. rapa and B. oleracea). Separated by only 10-20 million years, Brassica species and Arabidopsis thaliana are closely related, and it is expected that knowledge obtained relating to Arabidopsis growth and development can be translated into Brassicas for crop improvement. Moreover, certain aspects of plant development are sufficiently different between Brassica and Arabidopsis to warrant studies to be carried out directly in the crop species. However, mutating individual genes in the amphidiploid Brassicas such as B. napus and B. juncea may, on the other hand, not give rise to expected phenotypes as the genomes of these species can contain up to six orthologues per single-copy Arabidopsis gene. In order to elucidate and possibly exploit the function of redundant genes for oilseed rape crop improvement, it may therefore be more efficient to study the effects in one of the diploid Brassica species such as B. rapa. Moreover, the ongoing sequencing of the B. rapa genome makes this species a highly attractive model for Brassica research and genetic resource development. Results: Seeds from the diploid Brassica A genome species, B. rapa were treated with ethyl methane sulfonate (EMS) to produce a TILLING (Targeting Induced Local Lesions In Genomes) population for reverse genetics studies. We used the B. rapa genotype, R-o-18, which has a similar developmental ontogeny to an oilseed rape crop. Hence this resource is expected to be well suited for studying traits with relevance to yield and quality of oilseed rape. DNA was isolated from a total of 9,216 M 2 plants and pooled to form the basis of the TILLING platform. Analysis of six genes revealed a high level of mutations with a density of about one per 60 kb. This analysis also demonstrated that screening a 1 kb amplicon in just one third of the population (3072 M 2 plants) will provide an average of 68 mutations and a 97% probability of obtaining a stop-codon mutation resulting in a truncated protein. We furthermore calculated that each plant contains on average~10,000 mutations and due to the large number of plants, it is predicted that mutations in approximately half of the GC base pairs in the genome exist within this population.
Agricultural Sciences in China, 2006
Huayouza 6, a new semi-winter Brassica napus variety with high-yield, good quality, prematurity and extensive adaptability, was derived from the cross between the female parent 8086A and male parent 7-5. Two cDNA-based Arabidopisis microarray were used to analyze gene differential expression in bud of an elite B.napus hybrid Huayouza6 and its parents, in which there were 83 over-expression transcripts and 33 I under-expression transcripts between Huayouza 6 and its female parent 8086A and 94 over-expression transcripts, and 423 under-expression transcripts were demonstrated between Huayouza 6 and its male parent 7-5. Further analysis showed that there were significant number of genes responsible for photosynthesis, and its implication for heterosis was discussed. Northern analysis of phosphoribulokinase coincided with its expression pattern derived from hybridization of Arabidopsis cDNA microarray and B. nupus mRNA, this system of heterologous hybridization analysis should be applicable to other close relatives of Arabidopsis thaliana.
Characterization of Cauliflower OR Mutant Variants
Frontiers in Plant Science, 2020
Cauliflower Orange (Or) mutant is characterized by high level of b-carotene in its curd. Or mutation affects the OR protein that was shown to be involved in the posttranslational control of phytoene synthase (PSY), a major rate-limiting enzyme of carotenoid biosynthesis, and in maintaining PSY proteostasis with the plastid Clp protease system. A transposon integration into the cauliflower wild-type Or gene (BoOR-wt) results in the formation of three differently spliced transcripts. One of them is characterized by insertion (BoOR-Ins), while the other two have exon-skipping deletions (BoOR-Del and BoOR-LD). We investigated the properties of individual BoOR variants and examined their effects on carotenoid accumulation. Using the yeast split-ubiquitin system, we showed that all variants were able to form OR dimers except BoOR-LD. The deletion in BoOR-LD eliminated the first of two adjacent transmembrane domains and was predicted to result in a misplacement of the C-terminal zinc finger domain to the opposite side of membrane, thus preventing OR dimerization. As interaction with PSY is mediated by the N-terminus of BoOR, which remains unaffected after splicing, all BoOR variants including BoOR-LD maintained interactions with PSY. Expression of individual BoOR mutant variants in Arabidopsis revealed that their protein stability varied greatly. While expression of BoOR-Del and BoOR-Ins resulted in increased BoOR protein levels as BoOR-wt, minimal amounts of BoOR-LD protein accumulated. Carotenoid accumulation showed correlated changes in calli of Arabidopsis expressing these variants. Furthermore, we found that OR also functions in E. coli to increase the proportion of native, enzymatically active PSY from plants upon co-expression, but not of bacterial phytoene synthase CrtB. Taken together, these results suggest that OR dimerization is required for OR stability in planta and that the simultaneous presence of PSY interaction-domains in both OR and PSY proteins is required for the holdase function of OR. The more pronounced effect of simultaneous expression of all BoOR variants in cauliflower Or mutant compared with individual overexpression on carotenoid accumulation suggests an enhanced activity with possible formation of various BoOR heterodimers.
DNA Research, 2013
Brassica rapa is an important crop species that produces vegetables, oilseed, and fodder. Although many studies reported quantitative trait loci (QTL) mapping, the genes governing most of its economically important traits are still unknown. In this study, we report QTL mapping for morphological and yield component traits in B. rapa and comparative map alignment between B. rapa, B. napus, B. juncea, and Arabidopsis thaliana to identify candidate genes and conserved QTL blocks between them. A total of 95 QTL were identified in different crucifer blocks of the B. rapa genome. Through synteny analysis with A. thaliana, B. rapa candidate genes and intronic and exonic single nucleotide polymorphisms in the parental lines were detected from whole genome resequenced data, a few of which were validated by mapping them to the QTL regions. Semi-quantitative reverse transcriptase PCR analysis showed differences in the expression levels of a few genes in parental lines. Comparative mapping identified five key major evolutionarily conserved crucifer blocks (R, J, F, E, and W) harbouring QTL for morphological and yield components traits between the A, B, and C subgenomes of B. rapa, B. juncea, and B. napus. The information of the identified candidate genes could be used for breeding B. rapa and other related Brassica species.
International Journal of Molecular Sciences
Despite heterosis contributing to genetic improvements in crops, root growth heterosis in rapeseed plants is poorly understood at the molecular level. The current study was performed to discover key differentially expressed genes (DEGs) related to heterosis in two hybrids with contrasting root growth performance (FO; high hybrid and FV; low hybrid) based on analysis of the root heterosis effect. Based on comparative transcriptomic analysis, we believe that the overdominance at the gene expression level plays a critical role in hybrid roots’ early biomass heterosis. Our findings imply that a considerable increase in up-regulation of gene expression underpins heterosis. In the FO hybrid, high expression of DEGs overdominant in the starch/sucrose and galactose metabolic pathways revealed a link between hybrid vigor and root growth. DEGs linked to auxin, cytokinin, brassinosteroids, ethylene, and abscisic acid were also specified, showing that these hormones may enhance mechanisms of ro...
Planta, 2015
The orange head phenotype of Br - or resulted from a large insertion in carotenoid isomerase (BrCRTISO) . Comparative transcriptome analysis revealed that the mutation affected the expression of abundant transcription factor genes. A new orange trait-specific marker was developed for marker-assisted breeding. Orange head leaves are a desirable quality trait for Chinese cabbage. Our previous fine mapping identified BrCRTISO as the Br-or candidate gene for the orange Chinese cabbage mutant. Here, we examined the BrCRTISO gene from white and orange head Chinese cabbage. While BrCRTISO from the white control plant was able to complement the Arabidopsis Atcrtiso mutant phenotype, Brcrtiso with a large insertion from the orange head Chinese cabbage failed to rescue the Arabidopsis mutant phenotype. The results show that Brcrtiso was non-functional, concomitant with the accumulation of prolycopene in Br-or to yield orange head. Comparative transcriptome analysis by RNA-seq identified 372 d...
PLoS ONE, 2012
The real time quantitative reverse transcription PCR (qRT-PCR) is becoming increasingly important to gain insight into function of genes. Given the increased sensitivity, ease and reproducibility of qRT-PCR, the requirement of suitable reference genes for normalization has become important and stringent. It is now known that the expression of internal control genes in living organism vary considerably during developmental stages and under different experimental conditions. For economically important Brassica crops, only a couple of reference genes are reported till date. In this study, expression stability of 12 candidate reference genes including ACT2, ELFA, GAPDH, TUA, UBQ9 (traditional housekeeping genes), ACP, CAC, SNF, TIPS-41, TMD, TSB and ZNF (new candidate reference genes), in a diverse set of 49 tissue samples representing different developmental stages, stress and hormone treated conditions and cultivars of Brassica juncea has been validated. For the normalization of vegetative stages the ELFA, ACT2, CAC and TIPS-41 combination would be appropriate whereas TIPS-41 along with CAC would be suitable for normalization of reproductive stages. A combination of GAPDH, TUA, TIPS-41 and CAC were identified as the most suitable reference genes for total developmental stages. In various stress and hormone treated samples, UBQ9 and TIPS-41 had the most stable expression. Across five cultivars of B. juncea, the expression of CAC and TIPS-41 did not vary significantly and were identified as the most stably expressed reference genes. This study provides comprehensive information that the new reference genes selected herein performed better than the traditional housekeeping genes. The selection of most suitable reference genes depends on the experimental conditions, and is tissue and cultivar-specific. Further, to attain accuracy in the results more than one reference genes are necessary for normalization.