Newly identified miRNAs may contribute to aerenchyma formation in sugarcane roots

Comparative genome-wide characterization of salt responsive micro RNA and their targets through integrated small RNA and de novo transcriptome profiling in sugarcane and its wild relative Erianthus arundinaceus

Soil salinity and saline irrigation water are major constraints in sugarcane affecting the production of cane and sugar yield. To understand the salinity induced responses and to identify novel genomic resources, integrated de novo transcriptome and small RNA sequencing in sugarcane wild relative, Erianthus arundinaceus salt tolerant accession IND 99-907 and salt-sensitive sugarcane genotype Co 97010 were performed. A total of 362 known miRNAs belonging to 62 families and 353 miRNAs belonging to 63 families were abundant in IND 99-907 and Co 97010 respectively. The miRNA families such as miR156, miR160, miR166, miR167, miR169, miR171, miR395, miR399, miR437 and miR5568 were the most abundant with more than ten members in both genotypes. The differential expression analysis of miRNA reveals that 221 known miRNAs belonging to 48 families and 130 known miRNAs belonging to 42 families were differentially expressed in IND 99-907 and Co 97010 respectively. A total of 12,693 and 7982 miRNA targets against the monoploid mosaic genome and a total of 15,031 and 12,152 miRNA targets against the de novo transcriptome were identified for differentially expressed known miRNAs of IND 99-907 and Co 97010 respectively. The gene ontology (GO) enrichment analysis of the miRNA targets revealed that 24, 12 and 14 enriched GO terms (FDR < 0.05) for biological process, molecular function and cellular component respectively. These miRNAs have many targets that associated in regulation of biotic and abiotic stresses. Thus, the genomic resources generated through this study are useful for sugarcane crop improvement through biotechnological and advanced breeding approaches.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-023-03867-7.

Genome-wide identification and characterization of the HD-Zip gene family and expression analysis in response to stress in Rehmannia glutinosa Libosch

The HD-Zip family of transcription factors is unique to the plant kingdom, and play roles in modulation of plant growth and response to environmental stresses. R. glutinosa is an important Chinese medicinal material. Its yield and quality are susceptible to various stresses. The HD-Zip transcription factors is unique to the plant, and roles in modulation of plant growth and response to environmental stresses. However, there is no relevant research on the HD-ZIP of R. glutinosa. In this study, 92 HD-Zip transcription factors were identified in R. glutinosa, and denominated as RgHDZ1-RgHDZ92. Members of RgHDZ were classified into four groups (HD-ZipI-IV) based on the phylogenetic relationship of Arabidopsis HD-Zip proteins, and each group contains 38, 18, 17, and 19 members, respectively. Expression analyses of RgHDZ genes based on transcriptome data showed that the expression of these genes could be induced by the endophytic fungus of R. glutinosa. Additionally, we showed that RgHDZ genes were differentially expressed in response to drought, waterlogging, temperature, and salinity treatments. This study provides important information for different expression patterns of stress-responsive HD-Zip and may contribute to the better understanding of the different responses of plants to biotic and abiotic stresses, and provide a molecular basis for the cultivation of resistant varieties of R. glutinosa.

Stressed to Death: The Role of Transcription Factors in Plant Programmed Cell Death Induced by Abiotic and Biotic Stimuli

Programmed cell death (PCD) is a genetically controlled pathway that plants can use to selectively eliminate redundant or damaged cells. In addition to its fundamental role in plant development, PCD can often be activated as an essential defense response when dealing with biotic and abiotic stresses. For example, localized, tightly controlled PCD can promote plant survival by restricting pathogen growth, driving the development of morphological traits for stress tolerance such as aerenchyma, or triggering systemic pro-survival responses. Relatively little is known about the molecular control of this essential process in plants, especially in comparison to well-described cell death models in animals. However, the networks orchestrating transcriptional regulation of plant PCD are emerging. Transcription factors (TFs) regulate the clusters of stimuli inducible genes and play a fundamental role in plant responses, such as PCD, to abiotic and biotic stresses. Here, we discuss the roles of different classes of transcription factors, including members of NAC, ERF and WRKY families, in cell fate regulation in response to environmental stresses. The role of TFs in stress-induced mitochondrial retrograde signaling is also reviewed in the context of life-and-death decisions of the plant cell and future research directions for further elucidation of TF-mediated control of stress-induced PCD events are proposed. An increased understanding of these complex signaling networks will inform and facilitate future breeding strategies to increase crop tolerance to disease and/or abiotic stresses.