Understanding the genetic architecture of adventitious root and related shoot traits will facilitate the cultivation of superior genotypes. In this study, we measured 12 adventitious root and related shoot traits of 434 F₁ genotypes originating from Populus deltoides ‘Danhong’ × Populus simonii ‘Tongliao1’ and conducted an integrative analysis of quantitative trait locus (QTL) mapping and RNA-Seq data to dissect their genetic architecture and regulatory genes. Extensive segregation, high repeatability, and significant correlation relationship were detected for the investigated traits. A total of 150 QTLs were associated with adventitious root traits, explaining 3.1–6.1% of phenotypic variation (PVE); while 83 QTLs were associated with shoot traits, explaining 3.1–19.8% of PVE. Twenty-five QTL clusters and 40 QTL hotspots were identified for the investigated traits. Ten QTL clusters were overlapped in both adventitious root traits and related shoot traits. Transcriptome analysis identified 10,172 differentially expressed genes (DEGs) among two parents, three fine rooting and three poor-rooting genotypes, 143 of which were physically located within the QTL intervals. K-means cluster and weighted gene co-expression network analysis showed that PtAAAP19 (Potri.004G111400) encoding amino acid transport protein was tightly associated with adventitious roots and highly expressed in fine-rooting genotypes. Compare with ‘Danhong’, 153 bp deletion in the coding sequence of PtAAAP19 in ‘Tongliao1’ gave rise to lack one transmembrane domain, which might cause the variation of adventitious roots. Taken together, this study deciphered the genetic basis of adventitious root and related shoot traits and provided potential function genes for genetic improvement of poplar breeding.

Heat shock transcription factors (Hsfs) play an important role in response to high temperatures by binding to the promoter of the heat shock protein gene to promote its expression. As an important ornamental plant, the rose often encounters heat stress during the flowering process. However, there are few studies on the Hsf family in roses (Rosa. chinensis). In the current study, 19 Hsf genes were identified from R. chinensis and grouped into three main subfamilies (A, B, and C) according to their structural characteristics and phylogenetic analysis. The expression patterns of RcHsf genes were detected in different tissues by quantitative real-time PCR. The RcHsf genes exhibited distinct expression patterns at high temperatures, with RcHsf17 having the highest expression level. RcHsf17 was localized in the nucleus and had transcriptional activity. The overexpression of RcHsf17 increased thermotolerance in Arabidopsis, suggesting the potential role of RcHsf17 in the regulation of the high-temperature response. In addition, RcHsf17 overexpressed in Arabidopsis could enhance the response of transgenic Arabidopsis to methyl jasmonate. Collectively, this study identified and screened RcHsfs in response to high temperatures in roses, providing new insights into the functional divergence of RcHsfs and a basis for screening new varieties of rose.

Drought is a major environmental constraint to plant growth, development and productivity. Compared with most willows that are generally susceptible to drought, the desert willow Salix psammophila has extraordinary adaptation to drought stress. However, its molecular basis of drought tolerance is still largely unknown. During polyethylene glycol 6000 (PEG 6000)-simulated drought stress, we found that the osmotic adjustment substances were accumulated and the antioxidant enzyme activities were enhanced in S. psammophila roots. A total of 8172 differentially expressed genes were identified in roots of S. psammophila through RNA-Sequencing. Based on K-means clustering, their expression patterns were classified into nine clusters, which were enriched in several stress-related processes including transcriptional regulation, response to various stresses, cell death, etc. Moreover, 672 transcription factors from 45 gene families were differentially expressed under drought stress. Furthermore, a weighted gene co-expression network was constructed, and eight genes were identified as hub genes. We demonstrated the function of two hub genes, magnesium-dependent phosphatase 1 (SpMDP1) and SpWRKY33, through overexpression in Arabidopsis thaliana. Overexpression of the two hub genes enhanced the drought tolerance in transgenic plants, suggesting that the identification of candidate drought tolerance genes in this study was highly efficient and credible. Our study analyzed the physiological and molecular responses to drought stress in S. psammophila, and these results contribute to dissect the mechanism of drought tolerance of S. psammophila and facilitate identification of critical genes involved in drought tolerance for willow breeding.

In plants, the R2R3-MYB transcription factors are one of the largest MYB gene families. These MYB transcription factors are very important for regulating plant growth and development. RcMYB114, RcbHLH, and RcWD40 promote anthocyanin accumulation by forming the MBW (MYB-bHLH-WD40) complex and determine the rose flower’s color. RcMYB114 genomic sequences differ between the red petal and white varieties. Two non-synonymous substitutions were found in the open reading frame. It leads to a change in amino acids. Here, the anthocyanin content showed that there was no anthocyanin in white petals, while the anthocyanin content in red petals increased firstly at stage 2, decreased slightly at stage 4, and then increased again at stage 5. The spatiotemporal expression pattern analysis showed that RcMYB114 was not expressed in all petals and tissues of white petals at different flower development stages. In red petal varieties, RcMYB114 was highly expressed in petals, followed by styles, and not expressed in stems, young leaves, and stage 1 of flower development. However, RcMYB114 has the highest expression level at the blooming stage. The RcMYB114 sequence contains 9 SNPs in the coding region, 7 of which were synonymous substitutions that had no effect on the translation product and 2 of which were non-synonymous substitutions that resulted in amino acid alteration at positions 116 and 195, respectively. The RcMYB114 gene in red rose was named RcMYB114a, and in white rose was RcMYB114b. RcMYB114c was mutated into leucine via artificial mutation; it was valine at position 116 of RcMYB114a, and Glycine mutated into Arginine at position 195 of RcMYB114a was RcMYB114d. RcMYB114b was the double mutation at positions 116 and 195 of RcMYB114a. The results of yeast two-hybrid experiments showed that RcMYB114a and its missense mutations RcMYB114b, RcMYB114c, and RcMYB114d could both interact with RcbHLH and RcWD40 to form the MYB-bHLH-WD40 complex. A transient transformation experiment in tobacco confirmed that RcMYB114a and its missense mutations RcMYB114b, RcMYB114c, and RcMYB114d could significantly promote the high expression of related structural genes in tobacco, together with the RcbHLH gene, which led to the accumulation of anthocyanins and produced the red color of the leaves. The RcMYB114a gene and its missense mutations RcMYB114b, RcMYB114c, and RcMYB114d interacted with the RcbHLH gene and significantly regulated the accumulation of anthocyanins. The two non-synonymous mutations of RcMYB114 do not affect the function of the gene itself, but the content of the anthocyanins accumulated was different. This study should provide clues and references for further research on the molecular mechanism underlying the determination of rose petal color.

Scent is the key character of the horticultural ornamental plant rose, and benzenoid–phenylpropanoid compounds are the main source of scent. However, the underlying biosynthesis mechanism of these benzenoid–phenylpropanoid scent metabolites during Rosa flowering is poorly understood. In this study, the volatile metabolome and transcriptome conjoint analysis was conducted on the six stages petals of the variety ‘Lanxing’ to investigate the synthesis of benzenoid–phenylpropanoid metabolites. A total of 25 benzenoid–phenylpropanoid volatile compounds were identified, of which eugenol possessed the highest content. Meanwhile, transcriptome analysis produced 87.9 million clean reads and 22,004 differentially expressed genes (DEGs). Group pairwise comparison of gene ontology (GO) and Kyoto encyclopedia of genes and genomes (KEGG) enrichment analysis found DEGs were enriched into phenylpropanoid compound synthesis related pathway. Weighted gene co-expression network analysis (WGCNA) found a MEgreenyellow gene module (650 DEGs) correlated with phenylpropanoid compounds. Based on the eugenol content variation and gene spatio-temporal expression, a key candidate gene RcEGS32 related to the synthesis of eugenol was identified. Co-expression network analysis found that five transcription factors, RcMYB1, RcBES1, RcERF2, RcbHLH1, and RcTUB, may act as regulators in the eugenol synthesis process by directly binding to RcEGS32 or forming a complex unit. This study provided key insights into the formation of the scent substance eugenol during flowering, offering a valuable volatile metabolome and transcriptome resource for the future target trait-related gene discovery of roses.