Comparative phylogenetic analysis of CBL reveals the gene family evolution and functional divergence in Saccharum spontaneum

Characterization and expression profiles of the B-box gene family during plant growth and under low-nitrogen stress in Saccharum

BACKGROUND

B-box (BBX) zinc-finger transcription factors play crucial roles in plant growth, development, and abiotic stress responses. Nevertheless, little information is available on sugarcane (Saccharum spp.) BBX genes and their expression profiles.

RESULTS

In the present study, we characterized 25 SsBBX genes in the Saccharum spontaneum genome database. The phylogenetic relationships, gene structures, and expression patterns of these genes during plant growth and under low-nitrogen conditions were systematically analyzed. The SsBBXs were divided into five groups based on phylogenetic analysis. The evolutionary analysis further revealed that whole-genome duplications or segmental duplications were the main driving force for the expansion of the SsBBX gene family. The expression data suggested that many BBX genes (e.g., SsBBX1 and SsBBX13) may be helpful in both plant growth and low-nitrogen stress tolerance.

CONCLUSIONS

The results of this study offer new evolutionary insight into the BBX family members in how sugarcane grows and responds to stress, which will facilitate their utilization in cultivated sugarcane breeding.

Genome-Wide Identification and Expression Analysis of the 4-Coumarate: CoA Ligase Gene Family in Solanum tuberosum

4-coumarate: CoA ligase (4CL) is not only involved in the biosynthetic processes of flavonoids and lignin in plants but is also closely related to plant tolerance to abiotic stress. UV irradiation can activate the expression of 4CL genes in plants, and the expression of 4CL genes changed significantly in response to different phytohormone treatments. Although the 4CL gene has been cloned in potatoes, there have been fewer related studies of the 4CL gene family on the potato genome-wide scale. In this study, a total of 10 potato 4CL genes were identified in the potato whole genome. Through multiple sequence alignment, phylogenetic analysis as well as gene structure analysis indicated that the potato 4CL gene family could be divided into two subgroups. Combined with promoter cis-acting element analysis, transcriptome data, and RT-qPCR results indicated that potato 4CL gene family was involved in potato response to white light, UV irradiation, ABA treatment, MeJA treatment, and PEG simulated drought stress. Abiotic stresses such as UV, ABA, MeJA, and PEG could promote the up-regulated expression of St4CL6 and St4CL8 but inhibits the expression of St4CL5. The above results will increase our understanding of the evolution and expression regulation of the potato 4CL gene family and provide reference value for further research on the molecular biological mechanism of 4CL participating in response to diverse environmental signals in potatoes.

Genome-Wide Analysis of SQUAMOSA-Promoter-Binding Protein-like Family in Flowering Pleioblastus pygmaeus

SQUAMOSA Promoter-Binding Protein-Like (SPL) family is well-known for playing an important role in plant growth and development, specifically in the reproductive process. Bamboo plants have special reproductive characteristics with a prolonged vegetative phase and uncertain flowering time. However, the underlying functions of SPL genes in reproductive growth are undisclosed in bamboo plants. In the study, a total of 28 SPLs were screened from an ornamental dwarf bamboo species, Pleioblastus pygmaeus. Phylogenetic analysis indicates that 183 SPLs from eight plant species can be classified into nine subfamilies, and the 28 PpSPLs are distributed among eight subfamilies. Homologous analysis shows that as many as 32 pairs of homologous genes were found between P. pygmaeus and rice, and 83 pairs were found between P. pygmaeus and Moso bamboo, whose Ka/Ks values are all <1. MiRNA target prediction reveals that 13 out of the 28 PpSPLs have recognition sites complementary to miRNA156. To screen the SPLs involved in the reproductive growth of bamboo plants, the mRNA abundance of the 28 PpSPLs was profiled in the different tissues of flowering P. pygmaeus and non-flowering plants by RNA-Seq. Moreover, the relative expression level of eight PpSPLs is significantly higher in flowering P. pygmaeus than that in non-flowering plants, which was also validated by RT-qPCR. Combined with phylogenetic analysis and homologous analysis, the eight significant, differentially expressed PpSPLs were identified to be associated with the reproductive process and flower organ development. Among them, there are four potential miRNA156-targeting PpSPLs involved in the flowering process. Of significant interest in the study is the identification of 28 SPLs and the exploration of four key flowering-related SPLs from P. pygmaeus, which provides a theoretic basis for revealing the underlying functions of SPLs in the reproductive growth of bamboo plants.

Genome-wide characterization and expression analysis of the growth-regulating factor family in Saccharum

BACKGROUND

Growth regulating factors (GRFs) are transcription factors that regulate diverse biological and physiological processes in plants, including growth, development, and abiotic stress. Although GRF family genes have been studied in a variety of plant species, knowledge about the identification and expression patterns of GRFs in sugarcane (Saccharum spp.) is still lacking.

RESULTS

In the present study, a comprehensive analysis was conducted in the genome of wild sugarcane (Saccharum spontaneum) and 10 SsGRF genes were identified and characterized. The phylogenetic relationship, gene structure, and expression profiling of these genes were analyzed entirely under both regular growth and low-nitrogen stress conditions. Phylogenetic analysis suggested that the 10 SsGRF members were categorized into six clusters. Gene structure analysis indicated that the SsGRF members in the same group were greatly conserved. Expression profiling demonstrated that most SsGRF genes were extremely expressed in immature tissues, implying their critical roles in sugarcane growth and development. Expression analysis based on transcriptome data and real-time quantitative PCR verification revealed that GRF1 and GRF3 were distinctly differentially expressed in response to low-nitrogen stress, which meant that they were additional participated in sugarcane stress tolerance.

CONCLUSION

Our study provides a scientific basis for the potential functional prediction of SsGRF and will be further scrutinized by examining their regulatory network in sugarcane development and abiotic stress response, and ultimately facilitating their application in cultivated sugarcane breeding.

Isolation of the 3β-HSD promoter from Digitalis ferruginea subsp. ferruginea and its functional characterization in Arabidopsis thaliana

BACKGROUND

Although members of the SDR gene family (short chain dehydrogenase) are distributed in kingdom of life, they have diverse roles in stress tolerance mechanism or secondary metabolite biosynthesis. Nevertheless, their precise roles in gene expression or regulation under stress are yet to be understood.

METHODS

As a case study, we isolated, sequenced and functionally characterized the 3β-HSD promoter from Digitalis ferruginea subsp. ferruginea in Arabidopsis thaliana.

RESULTS

The promoter fragment contained light and stress response elements such as Box-4, G-Box, TCT-motif, LAMP element, ABRE, ARE, WUN-motif, MYB, MYC, W box, STRE and Box S. The functional analysis of the 3β-HSD promoter in transgenic Arabidopsis seedlings showed that the promoter was expressed in cotyledon and root elongation zone in 2 days' seedlings. However, this expression was extended to hypocotyl and complete root in 6 days' seedlings. In 20 days-old seedlings, promoter expression was distributed to the whole seedling including hydathodes aperture, vascular bundle, shoot apical meristem, trichomes, midrib, leaf primordia, hypocotyl and xylem tissues. Further, expression of the promoter was enhanced or remained stable under the different abiotic stress conditions like osmotic, heat, cold, cadmium or low pH. In addition, the promoter also showed response to methyl jasmonate (MeJA) application. The expression could not be induced in wounded cotyledon most likely due to lack of interacting elements in the promoter fragment.

CONCLUSIONS

Taken together, the 3β-HSD promoter could be a candidate for the development of transgenic plants especially under changing environmental conditions.

A soybean EF-Tu family protein GmEF8, an interactor of GmCBL1, enhances drought and heat tolerance in transgenic Arabidopsis and soybean

A soybean elongation factor Tu family (EF-Tu) protein, GmEF8, was determined to interact with GmCBL1, and GmEF8 expression was found to be induced by various abiotic stresses such as drought and heat. An ortholog of GmEF8 was identified in Arabidopsis, a T-DNA knockout line for which exhibited hypersensitivity to drought and heat stresses. Complementation with GmEF8 rescued the sensitivity of the Arabidopsis mutant to drought and heat stresses, and GmEF8 overexpression conferred drought and heat tolerance to transgenic Arabidopsis plants. In soybean, plants with GmEF8-overexpressing hairy roots (OE-GmEF8) exhibited enhanced drought and heat tolerance and had higher proline levels compared to plants with RNAi GmEF8-knockdown hairy roots (MR-GmEF8) and control hairy roots (EV). A number of drought-responsive genes, such as GmRD22 and GmP5CS, were induced in the OE-GmEF8 line compared to MR-GmEF8 and EV under normal growth conditions. These results suggest that GmEF8 has a positive role in regulating drought and heat stresses in Arabidopsis and soybean. This study reveals a potential role of the soybean GmEF8 gene in response to abiotic stresses, providing a foundation for further investigation into the complexities of stress signal transduction pathways.