A novel single-base mutation in CaBRI1 confers dwarf phenotype and brassinosteroid accumulation in pepper

Improvement of crop production in controlled environment agriculture through breeding

Controlled environment agriculture (CEA) represents one of the fastest-growing sectors of horticulture. Production in controlled environments ranges from highly controlled indoor environments with 100% artificial lighting (vertical farms or plant factories) to high-tech greenhouses with or without supplemental lighting, to simpler greenhouses and high tunnels. Although food production occurs in the soil inside high tunnels, most CEA operations use various hydroponic systems to meet crop irrigation and fertility needs. The expansion of CEA offers promise as a tool for increasing food production in and near urban systems as these systems do not rely on arable agricultural land. In addition, CEA offers resilience to climate instability by growing inside protective structures. Products harvested from CEA systems tend to be of high quality, both internal and external, and are sought after by consumers. Currently, CEA producers rely on cultivars bred for production in open-field agriculture. Because of high energy and other production costs in CEA, only a limited number of food crops have proven themselves to be profitable to produce. One factor contributing to this situation may be a lack of optimized cultivars. Indoor growing operations offer opportunities for breeding cultivars that are ideal for these systems. To facilitate breeding these specialized cultivars, a wide range of tools are available for plant breeders to help speed this process and increase its efficiency. This review aims to cover breeding opportunities and needs for a wide range of horticultural crops either already being produced in CEA systems or with potential for CEA production. It also reviews many of the tools available to breeders including genomics-informed breeding, marker-assisted selection, precision breeding, high-throughput phenotyping, and potential sources of germplasm suitable for CEA breeding. The availability of published genomes and trait-linked molecular markers should enable rapid progress in the breeding of CEA-specific food crops that will help drive the growth of this industry.

PmLBD3 links auxin and brassinosteroid signalling pathways on dwarfism in Prunus mume

BACKGROUND

Grafting with dwarf rootstock is an efficient method to control plant height in fruit production. However, the molecular mechanism remains unclear. Our previous study showed that plants with Prunus mume (mume) rootstock exhibited a considerable reduction in plant height, internode length, and number of nodes compared with Prunus persica (peach) rootstock. The present study aimed to investigate the mechanism behind the regulation of plant height by mume rootstocks through transcriptomic and metabolomic analyses with two grafting combinations, 'Longyan/Mume' and 'Longyan/Peach'.

RESULTS

There was a significant decrease in brassinolide levels in plants that were grafted onto mume rootstocks. Plant hormone signal transduction and brassinolide production metabolism gene expression also changed significantly. Flavonoid levels, amino acid and fatty acid metabolites, and energy metabolism in dwarf plants decreased. There was a notable upregulation of PmLBD3 gene expression in plant specimens that were subjected to grafting onto mume rootstocks. Auxin signalling cues promoted PmARF3 transcription, which directly controlled this upregulation. Through its binding to PmBAS1 and PmSAUR36a gene promoters, PmLBD3 promoted endogenous brassinolide inactivation and inhibited cell proliferation.

CONCLUSIONS

Auxin signalling and brassinolide levels are linked by PmLBD3. Our findings showed that PmLBD3 is a key transcription factor that regulates the balance of hormones through the auxin and brassinolide signalling pathways and causes dwarf plants in stone fruits.

Molecular Lesions in BRI1 and Its Orthologs in the Plant Kingdom

Brassinosteroids (BRs) are an essential group of plant hormones regulating numerous aspects of plant growth, development, and stress responses. BRI1, along with its co-receptor BAK1, are involved in brassinosteroid sensing and early events in the BR signal transduction cascade. Mutational analysis of a particular gene is a powerful strategy for investigating its biochemical role. Molecular genetic studies, predominantly in Arabidopsis thaliana, but progressively in numerous other plants, have identified many mutants of the BRI1 gene and its orthologs to gain insight into its structure and function. So far, the plant kingdom has identified up to 40 bri1 alleles in Arabidopsis and up to 30 bri1 orthologs in different plants. These alleles exhibit phenotypes that are identical in terms of development and growth. Here, we have summarized bri1 alleles in Arabidopsis and its orthologs present in various plants including monocots and dicots. We have discussed the possible mechanism responsible for the specific allele. Finally, we have briefly debated the importance of these alleles in the research field and the agronomically valuable traits they offer to improve plant varieties.

A 2-bp deletion in the protein kinase domain region of the ERECTA-like receptor kinase gene in cucumber results in short internode phenotype

Cucumber varieties with shortend internodes require less space than regular vining varieties, thus have great significance for germplasm improvement. Here, we found a novel spontaneous cucumber mutant si107 that exhibited short intenodes (si), smaller leaves, fruits, and seeds. The decrease in longitudinal cell length led to the shortened internodes of si107. The genetic analysis revealed a single recessive gene si-2 that was responsible for the mutation. Through multiple lines of evidence, we demonstrated that CsSI is the possible candidate gene for si-2, which encodes an ERECTA leucine-rich repeat receptor-like kinase. The shortened internode in si107 is attributed to a 2-bp deletion in the protein kinase domain region of this gene. The expression of CsSI was higher in the internodes, petioles, and fruit peels of si107 than in the wild type (WT). The transcriptome analysis between the si107 mutant and WT indicated that differentially expressed genes were significantly enriched in the plant hormone signal transduction pathway, in which auxin signal genes comprised the largest group, and all were downregulated in si107. Phytohormone quantitation confirmed that endogenous auxin levels in the stems of si107 were decreased. Our results provide new insights into the molecular mechanisms underlying the internode length control in cucumber.

Genome and transcriptome-based characterization of high energy carbon-ion beam irradiation induced delayed flower senescence mutant in Lotus japonicus

BACKGROUND

Flower longevity is closely related to pollen dispersal and reproductive success in all plants, as well as the commercial value of ornamental plants. Mutants that display variation in flower longevity are useful tools for understanding the mechanisms underlying this trait. Heavy-ion beam irradiation has great potential to improve flower shapes and colors; however, few studies are available on the mutation of flower senescence in leguminous plants.

RESULTS

A mutant (C416) exhibiting blossom duration eight times longer than that of the wild type (WT) was isolated in Lotus japonicus derived from carbon ion beam irradiation. Genetic assays supported that the delayed flower senescence of C416 was a dominant trait controlled by a single gene, which was located between 4,616,611 Mb and 5,331,876 Mb on chromosome III. By using a sorting strategy of multi-sample parallel genome sequencing, candidate genes were narrowed to the gene CUFF.40834, which exhibited high identity to ethylene receptor 1 in other model plants. A physiological assay demonstrated that C416 was insensitive to ethylene precursor. Furthermore, the dynamic changes of phytohormone regulatory network in petals at different developmental stages was compared by using RNA-seq. In brief, the ethylene, jasmonic acid (JA), and salicylic acid (SA) signaling pathways were negatively regulated in C416, whereas the brassinosteroid (BR) and cytokinin signaling pathways were positively regulated, and auxin exhibited dual effects on flower senescence in Lotus japonicus. The abscisic acid (ABA) signaling pathway is positively regulated in C416.

CONCLUSION

So far, C416 might be the first reported mutant carrying a mutation in an endogenous ethylene-related gene in Lotus japonicus, rather than through the introduction of exogenous genes by transgenic techniques. A schematic of the flower senescence of Lotus japonicus from the perspective of the phytohormone regulatory network was provided based on transcriptome profiling of petals at different developmental stages. This study is informative for elucidating the molecular mechanism of delayed flower senescence in C416, and lays a foundation for candidate flower senescence gene identification in Lotus japonicus. It also provides another perspective for the improvement of flower longevity in legume plants by heavy-ion beam.

Large-scale omics data reveal the cooperation of mutation-circRNA-miRNA-target gene network in liver cancer oncogenesis

Aims: Clarifying the initial trigger of the differentially expressed genes in cancers helps researchers understand the cellular system as a whole network. Materials & methods: We retrieve the transcriptome and translatome of tumor and normal tissues from ten liver cancer patients and define differentially expressed genes and tumor-specific mutations. We associate the oncogenesis with the mutations by target prediction and experimental verification. Results: Upregulated genes have tumor-specific mutations in 3'UTRs that abolish the binding of miRNAs. For downregulated genes, their corresponding miRNAs are mutually targeted by two circRNAs, with mutations in base-pairing regions. Transfection experiments support the oncogenic role of these mutations. Conclusions: The tumor-specific mutations serve as the initial trigger of liver cancer. The mutation-circRNA-miRNA-target gene chain is completed.