A protocol for identifying universal reference genes within a genus based on RNA-Seq data: a case study of poplar stem gene expression.

Real-time quantitative reverse transcription polymerase chain reaction (RT-qPCR) plays a crucial role in relative gene expression analysis, and accurate normalization relies on suitable reference genes (RGs). In this study, a pipeline for identifying candidate RGs from publicly available stem-related RNA-Seq data of different species under various developmental and abiotic stress conditions is presented. DESeq2's median of ratios yielded the smallest coefficient of variance (CV) values in a total of 292 RNA-Seq samples and was therefore chosen as the method for sample normalization.

A Pectate Lyase Gene Plays a Critical Role in Xylem Vascular Development in .

As a major component of the plant primary cell wall, structure changes in pectin may affect the formation of the secondary cell wall and lead to serious consequences on plant growth and development. Pectin-modifying enzymes including pectate lyase-like proteins (PLLs) participate in the remodeling of pectin during organogenesis, especially during fruit ripening. In this study, we used as a model system to identify critical genes that are of particular importance for vascular development.

Expressing a Short Tandem Target Mimic (STTM) of miR164b/e-3p enhances poplar leaf serration by co-regulating the miR164-NAC module.

MicroRNAs (miRNAs) are short non-coding RNAs (21-24 nt) that play important roles in plant growth and development. The miR164 family is highly conserved in plants and the miR164-NAM/ATAF/CUC (NAC) module is validated to regulate leaf and flower development, lateral root initiation and stress response. However, our knowledge of its role in Populus remains limited.

Poplar's Waterlogging Resistance Modeling and Evaluating: Exploring and Perfecting the Feasibility of Machine Learning Methods in Plant Science.

Floods, as one of the most common disasters in the natural environment, have caused huge losses to human life and property. Predicting the flood resistance of poplar can effectively help researchers select seedlings scientifically and resist floods precisely. Using machine learning algorithms, models of poplar's waterlogging tolerance were established and evaluated.

Influence of Switchgrass Genes on Vascular Development.

As a member of the CLAVATA3 (CLV3)/EMBRYO SURROUNDING REGION (CLE) family, the dodecapeptide tracheary element differentiation inhibitory factor (TDIF) has a major impact on vascular development in plants. However, the influence of polymorphisms in the TDIF peptide motif on activity remains poorly understood. The model plant, provides a fast and effective tool for assaying the activity of homologs.

Development of genic SSR marker resources from RNA-seq data in Camellia japonica and their application in the genus Camellia.

Camellia is a genus of flowering plants in the family Theaceae, and several species in this genus have economic importance. Although a great deal of molecular makers has been developed for molecular assisted breeding in genus Camellia in the past decade, the number of simple sequence repeats (SSRs) publicly available for plants in this genus is insufficient. In this study, a total of 28,854 potential SSRs were identified with a frequency of 4.

Molecular and physiological responses in roots of two full-sib poplars uncover mechanisms that contribute to differences in partial submergence tolerance.

Poplar is a major afforestation tree species in flood-prone areas. Here, we compared molecular and physiological responses in the roots of two full-sib poplar clones, LS1 (flood-tolerant) and LS2 (flood-susceptive), subjected to stagnant flooding using transcript and metabolite profiling. LS1 displayed less phenotypic damage and superior leaf gas exchange and plant growth compared with those of LS2.

Construction of a high-density genetic map and its application for leaf shape QTL mapping in poplar.

High-quality and dense genetic maps were constructed, and leaf shape variation was dissected by QTL mapping in poplar. Species in the genus Populus, also known as poplars, are important woody species and considered model plants for perennial trees. High-density genetic maps are valuable genomic resources for population genetics.

RNA-seq based transcriptomic analysis uncovers α-linolenic acid and jasmonic acid biosynthesis pathways respond to cold acclimation in Camellia japonica.

Camellia is a well-known ornamental flower native to Southeast of Asia, including regions such as Japan, Korea and South China. However, most species in the genus Camellia are cold sensitive. To elucidate the cold stress responses in camellia plants, we carried out deep transcriptome sequencing of 'Jiangxue', a cold-tolerant cultivar of Camellia japonica, and approximately 1,006 million clean reads were generated using Illumina sequencing technology.

Effects of fragment traits, burial orientation and nutrient supply on survival and growth in Populus deltoides × P. simonii.

Clonal propagations of shoot or root fragments play pivotal roles in adaptation of clonal trees to environmental heterogeneity, i.e. soil nutrient heterogeneity and burials after disturbance.

[Absorption and metabolism mechanisms of inorganic arsenic in plants: a review].

Arsenic pollution seriously threatens human health and environment safety, being a very prominent environmental issue to be urgently solved in the world. In natural environment and soil systems, arsenic exists in complicated forms, but the plant arsenic poisoning is mainly from As(V) and As (III) exposure. As(V) can be absorbed by plant roots through Pi channel, and reduced rapidly to As(III) by arsenate reductase.