Populus euphratica is mainly distributed in desert environments with dry and hot climate in summer and cold in winter. Compared with other poplars, P. euphratica is more resistant to salt stress. It is critical to investigate the transcriptome and molecular basis of salt tolerance in order to uncover stress-related genes. In this study, salt-tolerant treatment of P. euphratica resulted in an increase in osmo-regulatory substances and recovery of antioxidant enzymes. To improve the mining efficiency of candidate genes, the analysis combining both the transcriptome WGCNA and the former GWAS results was selected, and a range of key regulatory factors with salt resistance were found. The PeERF1 gene was highly connected in the turquoise modules with significant differences in salt stress traits, and the expression levels were significantly different in each treatment. For further functional verification of PeERF1, we obtained stable overexpression and dominant suppression transgenic lines by transforming into Populus alba × Populusglandulosa. The growth and physiological characteristics of the PeERF1 overexpressed plants were better than that of the wild type under salt stress. Transcriptome analysis of leaves of transgenic lines and WT revealed that highly enriched GO terms in DEGs were associated with stress responses, including abiotic stimuli responses, chemical responses, and oxidative stress responses. The result is helpful for in-depth analysis of the salt tolerance mechanism of poplar. This work provides important genes for poplar breeding with salt tolerance.

The plant leaf, the main organ of photosynthesis, is an important regulator of growth. To explore the difference between leaf size of Populusdeltoides ‘Danhong’ (Pd) and Populus simonii ‘Tongliao1’ (Ps), we investigated the leaf length, leaf width, leaf thickness, leaf area, leaf mass per area (LMA), and cell size of leaves from two genotypes and profiled the transcriptome-wide gene expression patterns through RNA sequencing. Our results show that the leaf area of Pd was significantly larger than that of Ps, but the epidermal cell area was significantly smaller than that of Ps. The difference of leaf size was caused by cell numbers. Transcriptome analysis also revealed that genes related to chromosome replication and DNA repair were highly expressed in Pd, while genes such as the EXPANSIN (EXPA) family which promoted cell expansion were highly expressed in Ps. Further, we revealed that the growth-regulating factors (GRFs) played a key role in the difference of leaf size between two genotypes through regulation of cell proliferation. These data provide a valuable resource for understanding the leaf development of the Populus genus.

The adventitious root (AR) is the basis for successful propagation by plant cuttings and tissue culture and is essential for maintaining the positive traits of a variety. Members of the amino acid/auxin permease (AAAP) gene family play indispensable roles in various plant metabolisms and have few studies on root growth and amino acid transport. In this study, with a systematic bioinformatics analysis of the Populus AAAP family, 83 PtrAAAPs were identified from Populus trichocarpa and grouped into 8 subfamilies. Subsequently, chromosomal distribution, genetic structure, cis-elements analysis, and expression pattern analysis of the AAAP family were performed and the potential gene AAAP21 regulating root development was screened by combining the results of RNA-Seq and QTL mapping. PsAAAP21 was proven as promoting root development by enhancing AR formation. Differentially expressed genes (DEGs) from RNA-seq results of overexpressing lines were enriched to multiple amino acid-related pathways, and the amino acid treatment to transgenic lines indicated that PsAAAP21 regulated amino acid transport, including tyrosine, methionine, and arginine. Analysis of the AAAP gene family provided a theoretical basis for uncovering the functions of AAAP genes. The identification of PsAAAP21 on root promotion and amino acid transport in Populus will help with breeding new woody plant species with strong rooting ability.

The basic helix-loop-helix (bHLH) family of transcription factors is one of the largest and oldest transcription factor families in plants. Members of the bHLH family regulate various growth and metabolic processes in plants. We used quantitative trait locus (QTL) mapping and transcriptome sequencing (RNA-seq) to identify PRE1 as a candidate bHLH transcription factor associated with root dry weight (RDW) in poplar. PRE1 was highly expressed in the roots and xylem, and was responsive to gibberellin, salicylic acid, drought, and salt stress. We cloned the PRE1 homolog from Populus simonii 'Tongliao1', referred to as PsPRE1, and transformed it into 84K poplar (Populus alba × Populus glandulosa). The overexpression of PsPRE1 in 84K poplar increased adventitious root development, fresh weight, total root number, and maximum root length. Poplar lines overexpressing PsPRE1 also exhibited enhanced salt tolerance while retaining a normal growth phenotype in the presence of salt stress. Catalase (CAT) activity in the PsPRE1 overexpression lines was higher than that of the wild-type, which may play a role in detoxifying stress-induced hydrogen peroxide production. An RNA-seq analysis of the PsPRE1 overexpression line revealed several differentially expressed genes (DEGs) involved in or related to auxin-, gibberellin-, and salicylic acid pathways, which indicates that the regulation of root development in poplar by PsPRE1 may involve multiple hormones.

Light is an important environmental factor for plant growth, and in higher plants, phytochrome A (phyA) is the predominant far-red photoreceptor, involved in various photoresponses. The FAR1/FHY3 transcription factor family, derived from transposases, is able to regulate plant development in response to multiple photosensitizers phytochrome. In total, 51 PtrFRSs were identified in the poplar genome, and were divided into 4 subfamilies. Among them, 47 PtrFRSs are located on 17 chromosomes. Upstream cis-acting elements of the PtrFRS genes were classified into three categories: growth and metabolism, stress and hormone, and the hormone and stress categories contained most of the cis-acting elements. Analysis of the regulatory networks and expression patterns showed that most PtrFRSs responded to changes in light intensity and were involved in the regulation of phytochromes. In this study, 51 PtrFRSs were identified and comprehensively bioinformatically analyzed, and preliminary functional analysis and prediction of PtrFRSs was carried out.

Salt is an important environmental stress factor, which seriously affects the growth, development and distribution of plants. Chlorophyllase plays an important role in stress response. Nevertheless, little is known about the physiological and molecular mechanism of chlorophyll (Chlase, CLH) genes in plants. We cloned PeCLH2 from Populus euphratica and found that PeCLH2 was differentially expressed in different tissues, especially in the leaves of P. euphratica. To further study the role of PeCLH2 in salt tolerance, PeCLH2 overexpression and RNA interference transgenic lines were established in Populus alba × Populus glandulosa and used for salt stress treatment and physiologic indexes studies. Overexpressing lines significantly improved tolerance to salt treatment and reduced reactive oxygen species production. RNA interference lines showed the opposite. Transcriptome analysis was performed on leaves of control and transgenic lines under normal growth conditions and salt stress to predict genes regulated during salt stress. This provides a basis for elucidating the molecular regulation mechanism of PeCLH2 in response to salt stress and improving the tolerance of poplar under salt stress.