Transcriptome profile analysis of Indian mustard (Brassica juncea L.) during seed germination reveals the drought stress-induced genes associated with energy, hormone, and phenylpropanoid pathways.

Indian mustard (Brassica juncea L. Czern and Coss) is an important oil and vegetable crop frequently affected by seasonal drought stress during seed germination, which retards plant growth and causes yield loss considerably. However, the gene networks regulating responses to drought stress in leafy Indian mustard remain elusive. Here, we elucidated the underlying gene networks and pathways of drought response in leafy Indian mustard using next-generation transcriptomic techniques. Phenotypic analysis showed that the drought-tolerant leafy Indian mustard cv. 'WeiLiang' (WL) had a higher germination rate, antioxidant capacity, and better growth performance than the drought-sensitive cv. 'ShuiDong' (SD). Transcriptome analysis identified differentially expressed genes (DEGs) in both cultivars under drought stress during four germination time points (i.e., 0, 12, 24, and 36 h); most of which were classified as drought-responsive, seed germination, and dormancy-related genes. In the Kyoto Encyclopedia of Genes and Genome (KEGG) analyses, three main pathways (i.e., starch and sucrose metabolism, phenylpropanoid biosynthesis, and plant hormone signal transduction) were unveiled involved in response to drought stress during seed germination. Furthermore, Weighted Gene Co-expression Network Analysis (WGCNA) identified several hub genes (novel.12726, novel.1856, BjuB027900, BjuA003402, BjuA021578, BjuA005565, BjuB006596, novel.12977, and BjuA033308) associated with seed germination and drought stress in leafy Indian mustard. Taken together, these findings deepen our understanding of the gene networks for drought responses during seed germination in leafy Indian mustard and provide potential target genes for the genetic improvement of drought tolerance in this crop.

E. urophylla × E. grandis high-quality genome and comparative genomics provide insights on evolution and diversification of eucalyptus.

BACKGROUND: Eucalyptus urophylla × Eucalyptus grandis, an economically important forest tree, provides important raw material for energy and reduces damage to native forests. However, the absence of a high-quality E. urophylla × E. grandis reference genome has significantly hindered its evolution and genetic analysis. RESULTS: We successfully presented a high-quality reference genome of E. urophylla × E. grandis (545.75 Mb; scaffold N50, 51.62 Mb) using a combination of the Illumina, PacBio HiFi, and Hi-C sequencing platforms. A total of 34,502 genes and 58.56% of the repetitive sequences in this genome were annotated. Using genome evolution analyses, we identified a recent whole-genome duplication (WGD) event in E. urophylla × E. grandis. We further found that gene families associated with starch and sucrose metabolism, flavonoid biosynthesis, and plant-pathogen interaction were significantly expanded in E. urophylla × E. grandis. Moreover, comparative genomic and evolutionary analyses showed large structural variations among the different chromosomes of the 34 Eucalyptus accessions, which were divided into six clades. CONCLUSIONS: Overall, our findings provide a valuable resource for expanding our understanding of the E. urophylla × E. grandis genome evolution, genetic improvement, and its comparative biology.

A banana transcriptional repressor MaAP2a participates in fruit starch degradation during postharvest ripening.

Fruit postharvest ripening is a crucial course for many fruits with significant conversion of biosubstance, which forms an intricate regulatory network. Ethylene facilitates the ripening process in banana with a remarkable change of fruit starch, but the mechanism adjusting the expression of starch degradation-related enzyme genes is incompletely discovered. Here, we describe a banana APETALA2 transcription factor (MaAP2a) identified as a transcriptional repressor with its powerful transcriptional inhibitory activity. The transcriptional level of MaAP2a gradually decreased with the transition of banana fruit ripening, suggesting a passive role of MaAP2a in banana fruit ripening. Moreover, MaAP2a is a classic nucleoprotein and encompasses transcriptional repressor domain (EAR, LxLxLx). More specifically, protein-DNA interaction assays found that MaAP2a repressed the expression of 15 starch degradation-related genes comprising MaGWD1, MaPWD1, MaSEX4, MaLSF1, MaBAM1-MaBAM3, MaAMY2B/2C/3A/3C, MaMEX1/2, and MapGlcT2-1/2-2 via binding to the GCC-box or AT-rich motif of their promoters. Overall, these results reveal an original MaAP2a-mediated negative regulatory network involved in banana postharvest starch breakdown, which advances our cognition on banana fruit ripening and offers additional reference values for banana varietal improvement.

Efficient genetic transformation method for Eucalyptus genome editing.

Plantation forestry of Eucalyptus urophylla × Eucalyptus grandis supplies high-quality raw material for pulp, paper, wood, and energy and thereby reduces the pressures on native forests and their associated biodiversity. Nevertheless, owing to the heterozygosity of the E. urophylla × E. grandis genetic background, germplasm improvement by crossbreeding tends to be inefficient. As an alternative approach, genetic engineering of Eucalyptus can be used to effectively improve germplasm resources. From a strategic standpoint, increasing the plantation productivity and wood quality by transgenic technology has become increasingly important for forest industry. In this study, we established a fluorescence labelling method using CRISPR/Cas9 technology to obtain positive transformed progenies. The positive transformed progenies were easily obtained from the genetically modified population via fluorescence screening. This system can be used as a plant genome site-specific editing tool and may be useful for improving Eucalyptus genetic resources.

Physiological parameters and differential expression analysis of N-phenyl-N'-[6-(2-chlorobenzothiazol)-yl] urea-induced callus of Eucalyptus urophylla × Eucalyptus grandis.

In this study, we analyzed differences in the enzyme activities and transcriptomes of embryogenic and non-embryogenic calli to gain insights for improving the success of tissue culture-based breeding. A total of 2,856 differentially expressed genes (DEGs; 1,632 up-regulated and 1,224 down-regulated) were identified based on RNA sequencing and verified by reverse transcription quantitative polymerase chain reaction. Gene set enrichment analysis revealed that many of the up-regulated DEGs in embryogenic callus were enriched in the photosynthesis processes. Furthermore, the enzyme activity, hormone content, and cytokinin oxidase/dehydrogenase (CKX) gene expression analyses were found to be consistent with the transcriptome results. Cytokinin biosynthesis in N-phenyl-N'-[6-(2-chlorobenzothiazol)-yl] urea (PBU)-induced embryogenic callus increased owing to CKX repression. Measurement of endogenous hormones by high-performance liquid chromatography revealed that, compared with non-embryogenic callus, in embryogenic callus, the indole-3-acetic acid, abscisic acid and trans-zeatin riboside content had significantly higher values of 129.7, 127.8 and 78.9 ng/g, respectively. Collectively, the findings of this study will provide a foundation for elucidating the molecular mechanisms underlying embryogenic callus differentiation and can potentially contribute to developing procedures aimed at enhancing the success of callus-based plant regeneration.

Repurposing of Anthocyanin Biosynthesis for Plant Transformation and Genome Editing.

CRISPR/Cas9 gene editing technology has been very effective in editing genes in many plant species including rice. Here we further improve the current CRISPR/Cas9 gene editing technology in both efficiency and time needed for isolation of transgene-free and target gene-edited plants. We coupled the CRISPR/Cas9 cassette with a unit that activates anthocyanin biosynthesis, providing a visible marker for detecting the presence of transgenes. The anthocyanin-marker assisted CRISPR (AAC) technology enables us to identify transgenic events even at calli stage, to select transformants with elevated Cas9 expression, and to identify transgene-free plants in the field. We used the AAC technology to edit LAZY1 and G1 and successfully generated many transgene-free and target gene-edited plants at T1 generation. The AAC technology greatly reduced the labor, time, and costs needed for editing target genes in rice.

Correction to: An efficient transgene-free DNA-editing system for Arabidopsis using a fluorescent marker.

The article An efficient transgene-free DNA-editing system for Arabidopsis using a fluorescent marker, written by Lejun Ouyang . Mingsai Ma and Limei Li, was originally published electronically on the publisher's internet portal (currently SpringerLink) on 03 December 2019 with open access. With the author(s)' decision to step back from Open Choice, the copyright of the article changed on 18 December 2019 to © Springer Nature B.V. 2019 and the article is forthwith distributed under the terms of copyright. The original article has been corrected.

An efficient transgene-free DNA-editing system for Arabidopsis using a fluorescent marker.

OBJECTIVE: To obtain transgene-free progeny by constructing a DNA editing system with a fluorescent screening marker gene and two pairs of single-guide RNAs to simultaneously recognize two different sites in the target gene encoding Arabidopsis microRNA(miR)160A RESULTS: The T1 seeds with red fluorescence were easily identified and were selected to verify that the proportion of miR160A knockout mutants reached approximately 50%. Seeds with no fluorescence in the T2 generation were selected and screened for homozygous mutants. In the T2 generation plants, the Cas9 fragment was not detected by polymerase chain reaction. The traits of the homozygous mutants were stably inherited by the T2 population. CONCLUSIONS: A highly efficient DNA-editing construct was successfully developed and can be used as a plant genome site-specific editing tool that may be useful for improving plant genetic resources.

Hypolipidaemic effects and mechanisms of the main component of Opuntia dillenii Haw. polysaccharides in high-fat emulsion-induced hyperlipidaemic rats.

The antihyperlipidaemic effects of ODP-Ia, one of the main components of Opuntia dillenii Haw. polysaccharides, were studied. Gavage administration of ODP-Ia was observed to significantly decrease serum lipid levels and to increase serum high-density lipoprotein cholesterol level in hyperlipidaemic rats. Similar suppressive patterns were also seen in hepatic total cholesterol and triglyceride levels. Moreover, the ODP-Ia administration significantly increased serum lecithin:cholesterol acyltransferase activity, increased the production of serum NO, inhibited hepatic HMG-CoA reductase activity, augmented serum and hepatic superoxide dismutase activities and decreased the serum and hepatic malondialdehyde contents in hyperlipidaemic rats. In addition, a histopathological examination revealed that ODP-Ia administration significantly suppressed inflammatory cell infiltration and the expression of VCAM-1. Together, these results indicate that ODP-Ia is a potential natural product for the treatment of hyperlipidaemia-related diseases by improving antioxidant levels, modulating the activities of enzymes involved in cholesterol metabolism, promoting the production of NO and suppressing the expression of VCAM-1, thereby suppressing lipid accumulation and inflammatory cell infiltration.

Efficient Regeneration of Eucalyptus urophylla x Eucalyptus grandis from Stem Segment

The aim of the present study was to establish an efficient regeneration system for the hybrid E. urophylla x E. grandis by means of organogenesis. Stem segments from seedlings were used as explants and cultured in a modified Murashige and Skoog medium (MS), supplemented with 13.2 µM N-phenyl-N'-[6-(2-chlorobenzothiazol)-yl] urea (PBU) and 0.285 µM indole-3-acetic acid (IAA). PBU was a useful growth regulator. After cultivating for 5 d, 96% explants formed callus. After 30 d, the calli obtained were transferred to MS medium containing different combinations of 6-benzyladenine (BA) and naphthalene acetic acid (NAA). Compared with other growth regulator combinations, PBU stimulated more vigorous calli and restrained browning. In addition, a large percentage (91.3%) of the calli induced by PBU showed adventitious buds formation. Shoot elongation was then stimulated on half-strength MS mineral salts medium supplemented with 6.6 µM PBU and 0.285 µM IAA for 20 d. For rooting, the elongated shoots were cultivated on root induction medium containing 2.46 µM indole-3-butyric acid (IBA). Plantlets were then successfully transplanted to a greenhouse. This procedure represented an efficient way of E. urophylla x E. grandis plant regeneration.