The selection of elite bud-sports is an important breeding approach in horticulture. We discovered and evaluated a thornless pummelo bud-sport (TL) that grew more vigorously and was more tolerant to ...Huanglongbing (HLB) than the thorny wild type (W). To reveal the underlying molecular mechanisms, we carried out whole-genome sequencing of W, and transcriptome comparisons of W, TL, and partially recovered thorny “mutants” (T). The results showed W, TL, and T varied in gene expression, allelic expression, and alternative splicing. Most genes/pathways with significantly altered expression in TL compared to W remained similarly altered in T. Pathway and gene ontology enrichment analysis revealed that the expression of multiple pathways, including photosynthesis and cell wall biosynthesis, was altered among the three genotypes. Remarkably, two polar auxin transporter genes, PIN7 and LAX3, were expressed at a significantly lower level in TL than in both W and T, implying alternation of polar auxin transport in TL may be responsible for the vigorous growth and thornless phenotype. Furthermore, 131 and 68 plant defense-related genes were significantly upregulated and downregulated, respectively, in TL and T compared with W. These genes may be involved in enhanced salicylic acid (SA) dependent defense and repression of defense inducing callose deposition and programmed cell death. Overall, these results indicated that the phenotype changes of the TL bud-sport were associated with tremendous transcriptome alterations, providing new clues and targets for breeding and gene editing for citrus improvement.
Impatiens downy mildew (IDM) is a devastating disease to garden impatiens. A good understanding of IDM resistance in New Guinea impatiens is essential for improving garden impatiens resistance to ...this disease. The present study was conducted to sequence, assemble, annotate and compare the leaf transcriptomes of two impatiens cultivars differing in resistance to IDM, reveal sequence polymorphisms and identify candidate genes for IDM resistance. RNA-Seq was performed on cultivars Super Elfin
XP Pink (SEP) and SunPatiens
Compact Royal Magenta (SPR). De novo assembly of obtained sequence reads resulted in 121,497 unigenes with an average length of 1156 nucleotides and N50 length of 1778 nucleotides. Searching the non-redundant protein and non-redundant nucleotide, Swiss-Prot, Kyoto Encyclopedia of Genes and Genomes and Clusters of Orthologous Groups and Gene Ontology databases, resulted in annotation of 57.7% to 73.6% of the unigenes. Fifteen unigenes were highly similar to disease resistance genes and more abundant in the IDM-resistant cultivar than in the susceptible cultivar. A total of 22,484 simple sequence repeats (SSRs) and 245,936 and 120,073 single nucleotide polymorphisms (SNPs) were identified from SPR and SEP respectively. The assembled transcripts and unigenes, identified disease resistance genes and SSRs and SNPs sites will be a valuable resource for improving impatiens and its IDM resistance.
Blackberries have gained considerable attention due to their high antioxidant content and potential health benefits. This study compared the metabolite profiles of six blackberry cultivars and ...investigated their biological activities. The metabolites extracted from blackberries were analyzed using metabolomics, and their biological activities and mechanisms were confirmed using in vitro models and network pharmacology. Among the cultivars examined, "Kiowa" ripe berries exhibited the highest antioxidant and anti-inflammatory activities. These effects were primarily attributed to the accumulation of flavonoids (quercitrin and luteolin) and anthocyanin (cyanidin 3-
-glucoside) in the phenylpropanoid pathway. Furthermore, our research identified 13 blackberry metabolites that interacted with 31 genes, including AKT1, CASP3, JUN, MAPK8, NOS3, NQO1, and HMOX1 which play roles in reducing oxidative stress, protecting cells from damage, and suppressing inflammation. These findings suggest that blackberry metabolites, such as quercitrin, luteolin, and cyanidin 3-
-glucoside, may exert therapeutic effects by modulating specific genes and pathways associated with antioxidant and anti-inflammatory responses. This research is promising not only for plant breeders but also for those interested in harnessing the health-promoting properties of blackberries.
Developing CRISPR/Cas9-mediated non-transgenic mutants in asexually propagated perennial crop plants is challenging but highly desirable. Here, we report a highly useful method using an ...Agrobacterium-mediated transient CRISPR/Cas9 gene expression system to create non-transgenic mutant plants without the need for sexual segregation. We have also developed a rapid, cost-effective, and high-throughput mutant screening protocol based on Illumina sequencing followed by high-resolution melting (HRM) analysis. Using tetraploid tobacco as a model species and the phytoene desaturase (PDS) gene as a target, we successfully created and expediently identified mutant plants, which were verified as tetra-allelic mutants. We produced pds mutant shoots at a rate of 47.5% from tobacco leaf explants, without the use of antibiotic selection. Among these pds plants, 17.2% were confirmed to be non-transgenic, for an overall non-transgenic mutation rate of 8.2%. Our method is reliable and effective in creating non-transgenic mutant plants without the need to segregate out transgenes through sexual reproduction. This method should be applicable to many economically important, heterozygous, perennial crop species that are more difficult to regenerate.
RNA sequencing has been widely used to profile genome-wide gene expression and identify candidate genes controlling disease resistance and other important traits in plants. Gerbera daisy is one of ...the most important flowers in the global floricultural trade, and powdery mildew (PM) is the most important disease of gerbera. Genetic improvement of gerbera PM resistance has become a crucial goal in gerbera breeding. A better understanding of the genetic control of gerbera resistance to PM can expedite the development of PM-resistant cultivars.
The objectives of this study were to identify gerbera genotypes with contrasting phenotypes in PM resistance and sequence and analyze their leaf transcriptomes to identify disease resistance and susceptibility genes differentially expressed and associated with PM resistance. An additional objective was to identify SNPs and SSRs for use in future genetic studies. We identified two gerbera genotypes, UFGE 4033 and 06-245-03, that were resistant and susceptible to PM, respectively. De novo assembly of their leaf transcriptomes using four complementary pipelines resulted in 145,348 transcripts with a N50 of 1124 bp, of which 67,312 transcripts contained open reading frames and 48,268 were expressed in both genotypes. A total of 494 transcripts were likely involved in disease resistance, and 17 and 24 transcripts were up- and down-regulated, respectively, in UFGE 4033 compared to 06-245-03. These gerbera disease resistance transcripts were most similar to the NBS-LRR class of plant resistance genes conferring resistance to various pathogens in plants. Four disease susceptibility transcripts (MLO-like) were expressed only or highly expressed in 06-245-03, offering excellent candidate targets for gene editing for PM resistance in gerbera. A total of 449,897 SNPs and 19,393 SSRs were revealed in the gerbera transcriptomes, which can be a valuable resource for developing new molecular markers.
This study represents the first transcriptomic analysis of gerbera PM resistance, a highly important yet complex trait in a globally important floral crop. The differentially expressed disease resistance and susceptibility transcripts identified provide excellent targets for development of molecular markers and genetic maps, cloning of disease resistance genes, or targeted mutagenesis of disease susceptibility genes for PM resistance in gerbera.
The discovery of triploids in caladium has raised strong interest in their use in cultivar development. For triploid production, tetraploids must first be generated from elite breeding material ...without the introduction of deleterious alleles like has been seen with chemical agents like colchicine and 2,4-D. To meet this new demand, virus eradicated, meristem-tip caladium cultures were grown on auxin-free media and used for generation and evaluation of new somaclonal variants. Over 12,000 micropropagated caladiums were visually screened ex vitro for sports varying from the wild-type phenotype. Eight variants from four cultivars were discovered and characterized for morphological, cytological, and molecular changes. Genome duplication occurred in seven of the variants with an average nuclear DNA content of 18.76 pg·2C−1. The tetraploid variant of cultivar ‘White Wing’ had eight more chromosomes (2n = 4x = 68) than the other tetraploids and exactly double that of its wildtype. All other diploids had the expected 2n = 2x = 30 chromosomes and tetraploids recorded 2n = 4x = 60. Tetraploids had 19% rounder leaves and 44% thicker leaves than the diploids in the study. Tetraploids also had a 49% and 31% increase in stomata length and width, respectively. Molecular marker analysis only revealed two polymorphisms with both occurring in the 'White Wing' variant. Few changes in molecular marker banding could indicate that the tetraploids discovered have a clean duplication of the genome and might effectively be used for new triploid cultivar development.
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