Comparative analysis of the carrot miRNAome in response to salt stress.

Soil salinity adversely affects the yield and quality of crops, including carrot. During salt stress, plant growth and development are impaired by restricted water uptake and ion cytotoxicity, leading to nutrient imbalance and oxidative burst. However, the molecular mechanisms of the carrot plant response to salt stress remain unclear. The occurrence and expression of miRNAs that are potentially involved in the regulation of carrot tolerance to salinity stress were investigated. The results of small RNA sequencing revealed that salt-sensitive (DH1) and salt-tolerant (DLBA) carrot varieties had different miRNA expression profiles. A total of 95 miRNAs were identified, including 71 novel miRNAs, of which 30 and 23 were unique to DH1 and DLBA, respectively. The comparison of NGS and qPCR results allowed identification of two conserved and five novel miRNA involved in carrot response to salt stress, and which differentiated the salt-tolerant and salt-sensitive varieties. Degradome analysis supported by in silico-based predictions and followed by expression analysis of exemplary target genes pointed at genes related to proline, glutathione, and glutamate metabolism pathways as potential miRNA targets involved in salt tolerance, and indicated that the regulation of osmoprotection and antioxidant protection, earlier identified as being more efficient in the tolerant variety, may be controlled by miRNAs. Furthermore, potential miRNA target genes involved in chloroplast protection, signal transduction and the synthesis and modification of cell wall components were indicated in plants growing in saline soil.

Population genomics identifies genetic signatures of carrot domestication and improvement and uncovers the origin of high-carotenoid orange carrots.

Here an improved carrot reference genome and resequencing of 630 carrot accessions were used to investigate carrot domestication and improvement. The study demonstrated that carrot was domesticated during the Early Middle Ages in the region spanning western Asia to central Asia, and orange carrot was selected during the Renaissance period, probably in western Europe. A progressive reduction of genetic diversity accompanied this process. Genes controlling circadian clock/flowering and carotenoid accumulation were under selection during domestication and improvement. Three recessive genes, at the REC, Or and Y2 quantitative trait loci, were essential to select for the high α- and ß-carotene orange phenotype. All three genes control high α- and ß-carotene accumulation through molecular mechanisms that regulate the interactions between the carotenoid biosynthetic pathway, the photosynthetic system and chloroplast biogenesis. Overall, this study elucidated carrot domestication and breeding history and carotenoid genetics at a molecular level.

The Retinoblastoma-related gene RBL901 can trigger drought response actions in potato.

KEY MESSAGE: This study provided new insights into response of potato to drought stress.

Transcriptomic and metabolic studies on the role of inorganic and organic iodine compounds in lettuce plants.

Iodine (I) is considered a beneficial element or even micronutrient for plants. The aim of this study was to determine the molecular and physiological processes of uptake, transport, and metabolism of I applied to lettuce plants. KIO3, KIO3 + salicylic acid, 5-iodosalicylic acid and 3,5-diiodosalicylic acid were applied. RNA-sequencing was executed using 18 cDNA libraries constructed separately for leaves and roots from KIO3, SA and control plants. De novo transcriptome assembly generated 1937.76 million sequence reads resulting in 27,163 transcripts with N50 of 1638 bp. 329 differentially expressed genes (DEGs) in roots were detected after application of KIO3, out of which 252 genes were up-regulated, and 77 were down-regulated. In leaves, 9 genes revealed differential expression pattern. DEGs analysis indicated its involvement in such metabolic pathways and processes as: chloride transmembrane transport, phenylpropanoid metabolism, positive regulation of defense response and leaf abscission, and also ubiquinone and other terpenoid-quinone biosynthesis, protein processing in endoplasmic reticulum, circadian rhythm including flowering induction as well as a putative PDTHA (i.e. Plant Derived Thyroid Hormone Analogs) metabolic pathway. qRT-PCR of selected genes suggested their participation in the transport and metabolism of iodine compounds, biosynthesis of primary and secondary metabolites, PDTHA pathway and flowering induction.

Influencing Factors of Bidens pilosa L. Hyperaccumulating Cadmium Explored by the Real-Time Uptake of Cd2+ Influx around Root Apexes under Different Exogenous Nutrient Ion Levels.

Though Bidens pilosa L. has been confirmed to be a potential Cd hyperaccumulator, the accumulation mechanism is not yet clear. The dynamic and real-time uptake of Cd2+ influx by B. pilosa root apexes was determined using non-invasive micro-test technology (NMT), which partly explored the influencing factors of the Cd hyperaccumulation mechanism under the conditions of different exogenous nutrient ions. The results indicated that Cd2+ influxes at 300 µm around the root tips decreased under Cd treatments with 16 mM Ca2+, 8 mM Mg2+, 0.5 mM Fe2+, 8 mM SO42- or 18 mM K+ compared to single Cd treatments. The Cd treatments with a high concentration of nutrient ions showed an antagonistic effect on Cd2+ uptake. However, Cd treatments with 1 mM Ca2+, 0.5 mM Mg2+, 0.5 mM SO42- or 2 mM K+ had no effect on the Cd2+ influxes as compared with single Cd treatments. It is worth noting that the Cd treatment with 0.05 mM Fe2+ markedly increased Cd2+ influxes. The addition of 0.05 mM Fe2+ exhibited a synergistic effect on Cd uptake, which could be low concentration Fe2+ rarely involved in blocking Cd2+ influx and often forming an oxide membrane on the root surface to help the Cd uptake by B. pilosa. The results also showed that Cd treatments with high concentration of nutrient ions significantly increased the concentrations of chlorophyll and carotenoid in leaves and the root vigor of B. pilosa relative to single Cd treatments. Our research provides novel perspectives with respect to Cd uptake dynamic characteristics by B. pilosa roots under different exogenous nutrient ion levels, and shows that the addition of 0.05 mM Fe2+ could promote the phytoremediation efficiency for B. pilosa.

The effects of salinity and pH variation on hyperaccumulator Bidens pilosa L. accumulating cadmium with dynamic and real-time uptake of Cd2+ influx around its root apexes.

Bidens pilosa L. has been confirmed to be a potential Cd hyperaccumulator by some researchers, but the dynamic and real-time uptake of Cd2+ influx by B. pilosa root apexes was a conundrum up to now. The aim of our study was to investigate the effects of salinity and pH variations on the characteristics of Cd2+ influx around the root apexes of B. pilosa. The tested seedlings of B. pilosa were obtained by sand culture experiments in a greenhouse after 1 month from germination, and the Cd2+ influxes from the root apex of B. pilosa under Cd treatments with different salinity and pH levels were determined with application of non-invasive micro-test technology (NMT). The results showed that Cd2+ influxes at 300 µm from the root tips decreased under Cd treatments with 5 mM and 10 mM NaCl, as compared to Cd stress alone. However, Cd treatments with 2.5 mM NaCl had little effect on the net Cd2+ influxes, as compared to Cd treatments alone. Importantly, Cd treatments at pH = 4.0 markedly increased Cd2+ influxes in roots, and Cd treatment at pH = 7.0 had no significant effect on the net Cd2+ influxes compared to Cd treatments at pH = 5.5. Results also showed that Cd treatments with 10 mM NaCl significantly decreased concentrations of chlorophyll (Chl) a and b in leaves and root vigor of B. pilosa relative to Cd treatments alone, while there were no significant differences between Cd treatments with 2.5 mM NaCl and Cd treatments alone. But root vigor was inhibited significantly under Cd treatments with 5 mM and 10 mM NaCl. A significant increase of root vigor was observed in Cd treatments at pH = 4.0, as compared to pH = 5.5. The Cd treatments with high and medium concentrations of NaCl inhibited the uptake of Cd by B. pilosa roots and affected the Chl and root vigor further. But the Cd treatments at pH = 4.0 could promote the Cd uptake and root vigor. Our results revealed the uptake mechanisms of B. pilosa as a potential phytoremediator under different salinity and pH levels combined with Cd contamination and provided a new idea for screening ideal hyperaccumulator and constructing evaluation system.

Cadmium phytoextraction efficiency of hyperaccumulator as affected by harvest stage in three continuous years.

Phytoremediation which mainly using hyperaccumulator is a very popular and environmental-friendly clean method. Long term continuous test is very important due to its low remediation efficiency in a growth period. Cd hyperaccumulator Rorippa globosa (Turcz.) Thell. Was used to explore the effect of two remediation modes (harvests at flowering and maturity stages) on the continuous remediation efficiency in a 3-year experiment using pot experiment with real Cd contaminated soil. The results showed that the biomass in maturity-harvest treatments was 1.12 times of that in flowering-harvest treatments due to the short vegetation time. Shoot Cd concentrations in the flowering-harvest treatments were on average 15.4% lower compared to the maturity-harvest treatments either. However, the Cd phytoextraction efficiency (PE) in the flowering-harvest treatments was 13.8% higher compared to the harvests at the maturity stage due to the growth cycle of R. globosa harvested at the flowering was 34.5% of shorter compared to those in the maturity harvest treatments. After three consecutive years of R. globosa phytoextraction, the concentration of extractable Cd decreased on average by 28.7% and corresponding PEs lower either. It was suggested that cultivation modes of R. globosa and low-accumulation crop rotation, or three times flowering harvests of R. globosa per year seemed to be a good choice in practical solution.

A review of strategies used to identify transposition events in plant genomes.

Transposable elements (TEs) were initially considered redundant and dubbed 'junk DNA'. However, more recently they were recognized as an essential element of genome plasticity. In nature, they frequently become active upon exposition of the host to stress conditions. Even though most transposition events are neutral or even deleterious, occasionally they may happen to be beneficial, resulting in genetic novelty providing better fitness to the host. Hence, TE mobilization may promote adaptability and, in the long run, act as a significant evolutionary force. There are many examples of TE insertions resulting in increased tolerance to stresses or in novel features of crops which are appealing to the consumer. Possibly, TE-driven de novo variability could be utilized for crop improvement. However, in order to systematically study the mechanisms of TE/host interactions, it is necessary to have suitable tools to globally monitor any ongoing TE mobilization. With the development of novel potent technologies, new high-throughput strategies for studying TE dynamics are emerging. Here, we present currently available methods applied to monitor the activity of TEs in plants. We divide them on the basis of their operational principles, the position of target molecules in the process of transposition and their ability to capture real cases of actively transposing elements. Their possible theoretical and practical drawbacks are also discussed. Finally, conceivable strategies and combinations of methods resulting in an improved performance are proposed.

Understanding the Role of PIN Auxin Carrier Genes under Biotic and Abiotic Stresses in Olea europaea L.

The PIN-FORMED (PIN) proteins represent the most important polar auxin transporters in plants. Here, we characterized the PIN gene family in two olive genotypes, the Olea europaea subsp. europaea var. sylvestris and the var. europaea (cv. 'Farga'). Twelve and 17 PIN genes were identified for vars. sylvestris and europaea, respectively, being distributed across 6 subfamilies. Genes encoding canonical OePINs consist of six exons, while genes encoding non-canonical OePINs are composed of five exons, with implications at protein specificities and functionality. A copia-LTR retrotransposon located in intron 4 of OePIN2b of var. europaea and the exaptation of partial sequences of that element as exons of the OePIN2b of var. sylvestris reveals such kind of event as a driving force in the olive PIN evolution. RNA-seq data showed that members from the subfamilies 1, 2, and 3 responded to abiotic and biotic stress factors. Co-expression of OePINs with genes involved in stress signaling and oxidative stress homeostasis were identified. This study highlights the importance of PIN genes on stress responses, contributing for a holistic understanding of the role of auxins in plants.

Mechanism exploration of Solanum nigrum L. hyperaccumulating Cd compared to Zn from the perspective of metabolic pathways based on differentially expressed proteins using iTRAQ.

It is challenging to determine the mechanism involved in only Cd hyperaccumulation by Solanum nigrum L. owing to the uniqueness of the process. Isobaric tags for relative and absolute quantitation (iTRAQ) were used to explore the mechanism by which S. nigrum hyperaccumulates Cd by comparing the differentially expressed proteins (DEPs) for Cd and Zn accumulation (non-Zn hyperaccumulator). Based on the comparison between the DEPs associated with Cd and Zn accumulation, the relative metabolic pathways reflected by 17 co-intersecting specific proteins associated with Cd and Zn accumulation included phagosome, aminoacyl-tRNA biosynthesis, and carbon metabolism. Apart from the 17 co-intersecting specific proteins, the conjoint metabolic pathways reported by 21 co-intersecting specific proteins associated with Cd accumulation and 30 co-intersecting specific proteins associated with Zn accumulation, the most differentially expressed metabolic pathways might cause Cd TF (Translocation factor)> 1 and Zn TF< 1, including protein export, ribosome, amino sugar, and nucleotide sugar metabolism. The determined DEPs were verified using qRT-PCR with the four key proteins M1CW30, A0A3Q7H652, A0A0V0IFB9, and A0A0V0IAC4. The plasma membrane H+-ATPase protein was identified using western blotting. Some physiological indices for protein-related differences indirectly confirmed the above results. These results are crucial to further explore the mechanisms involved in Cd hyperaccumulation.