Identification of genes related to the development of bamboo rhizome bud

Bamboo (Phyllostachys praecox) is one of the largest members of the grass family Poaceae, and is one of the most economically important crops in Asia. However, complete knowledge of bamboo development and its molecular mechanisms is still lacking. In the present study, the differences in anatomical structure among rhizome buds, rhizome shoots, and bamboo shoots were compared, and several genes related to the development of the bamboo rhizome bud were identified. The rice cross-species microarray hybridization showed a total of 318 up-regulated and 339 down-regulated genes, including those involved in regulation and signalling, metabolism, and stress, and also cell wall-related genes, in the bamboo rhizome buds versus the leaves. By referring to the functional dissection of the homologous genes from Arabidopsis and rice, the putative functions of the 52 up-regulated genes in the bamboo rhizome bud were described. Six genes related to the development of the bamboo rhizome bud were further cloned and sequenced. These show 66–90% nucleotide identity and 68–98% amino acid identity with the homologous rice genes. The expression patterns of these genes revealed significant differences in rhizome shoots, rhizome buds, bamboo shoots, leaves, and young florets. Furthermore, in situ hybridization showed that the PpRLK1 gene is expressed in the procambium and is closely related to meristem development of bamboo shoots. The PpHB1 gene is expressed at the tips of bamboo shoots and procambium, and is closely related to rhizome bud formation and procambial development. To our knowledge, this is the first report that uses rice cross-species hybridization to identify genes related to bamboo rhizome bud development, and thereby contributes to the further understanding of the molecular mechanism involved in bamboo rhizome bud development

The complete chloroplast genome of Rhododendron huadingense (Ericaceae)

Rhododendron huadingense is an important horticultural plant that belongs to the Ericaceae family. In this study, the chloroplast genome sequence of R. huadingense is reported. The chloroplast genome of R. huadingense was 198,952 bp in length and had an angiosperm-typical quadripartite structure with a large single-copy (LSC) region of 108,557 bp, a small single-copy (SSC) region of 53 bp, and two inverted repeat regions (IRs) of 45,171 bp. One hundred and thirteen unique genes including 79 protein-coding genes, 30 transfer RNA (tRNA) genes, and four ribosomal RNA (rRNA) genes were identified in the chloroplast genome. Further phylogenetic analysis revealed a close relationship between R. huadingense and R. molle. The complete chloroplast genome of R. huadingense provides valuable genetic information for the phylogeny, varieties breeding and sustainable utilization of this species

A CNN-LSTM-att hybrid model for classification and evaluation of growth status under drought and heat stress in chinese fir (Cunninghamia lanceolata)

Abstract Background Cunninghamia lanceolata (Chinese fir), is one of the most important timber trees in China. With the global warming, to develop new resistant varieties to drought or heat stress has become an essential task for breeders of Chinese fir. However, classification and evaluation of growth status of Chinese fir under drought or heat stress are still labor-intensive and time-consuming. Results In this study, we proposed a CNN-LSTM-att hybrid model for classification of growth status of Chinese fir seedlings under drought and heat stress, respectively. Two RGB image datasets of Chinese fir seedling under drought and heat stress were generated for the first time, and utilized in this study. By comparing four base CNN models with LSTM, the Resnet50-LSTM was identified as the best model in classification of growth status, and LSTM would dramatically improve the classification performance. Moreover, attention mechanism further enhanced performance of Resnet50-LSTM, which was verified by Grad-CAM. By applying the established Resnet50-LSTM-att model, the accuracy rate and recall rate of classification was up to 96.91% and 96.79% for dataset of heat stress, and 96.05% and 95.88% for dataset of drought, respectively. Accordingly, the R2 value and RMSE value for evaluation on growth status under heat stress were 0.957 and 0.067, respectively. And, the R2 value and RMSE value for evaluation on growth status under drought were 0.944 and 0.076, respectively. Conclusion In summary, our proposed model provides an important tool for stress phenotyping in Chinese fir, which will be a great help for selection and breeding new resistant varieties in future

RNA-Seq analysis of differential gene expression in Betula luminifera xylem during the early stages of tension wood formation

Background Betula luminifera H. Winkler, which is widely distributed in southern China, is an economically important broadleaf tree species. However, little genomic information of B. luminifera is available, and little is known about the molecular mechanisms of wood formation in this species. Meanwhile, few efforts have focused on investigating the early transcriptional changes during tension wood formation in woody plants. Results A reference transcriptome dataset was first generated containing 45,700 Unigenes, and 35,135 (76.9%) Unigenes were annotated by a BLAST similarity search against four public databases. Then, based on an anatomical investigation, the global gene expression changes during the early stages of tension wood formation were analyzed. Gene expression profiling showed that a total of 13,273 Unigenes were differentially regulated during the early stages of tension wood formation. Most genes involved in cellulose and lignin biosynthesis were highlighted to reveal their biological importance in tension wood formation. In addition, the transcription levels of many genes involved in the auxin response pathway were significantly changed during the early stages of tension wood formation. Furthermore, 18 TFs co-expressed with key enzymes of cellulose synthesis were identified. Conclusions Our results revealed the transcriptional changes associated with TW formation and identified potential key genes in the regulation of this process. These results will help to dissect the molecular mechanism of wood formation and provide key candidate genes for marker-assisted selection in B. luminifera

The Spatial Shifts and Vulnerability Assessment of Ecological Niches under Climate Change Scenarios for <i>Betula luminifera</i>, a Fast-Growing Precious Tree in China

The spatial shifts and vulnerability assessments of ecological niches for trees will offer fresh perspectives for sustainable development and preservation of forests, particularly within the framework of rapid climate change. Betula luminifera is a fast-growing native timber plantation species in China, but the natural resources have been severely damaged. Here, a comprehensive habitat suitability model (including ten niche-based GIS modeling algorithms) was developed that integrates three types of environmental factors, namely, climatic, soil, and ultraviolet variables, to assess the species contemporary and future distribution of suitable habitats across China. Our results suggest that the habitats of B. luminifera generally occur in subtropical areas (about 1.52 × 106 km2). However, the growth of B. luminifera is profoundly shaped by the nuances of its local environment, the most reasonable niche spaces are only 1.15 × 106 km2 when limiting ecological factors (soil and ultraviolet) are considered, generally considered as the core production region. Furthermore, it is anticipated that species-suitable habitats will decrease by 10 and 8% with climate change in the 2050s and 2070s, respectively. Our study provided a clear understanding of species-suitable habitat distribution and identified the reasons why other niche spaces are unsuitable in the future, which can warn against artificial cultivation and conservation planning

Table_2_Comparative physiological analyses and the genetic basis reveal heat stress responses mechanism among different Betula luminifera populations.XLSX

Betula luminifera is a subtropical fast-growing timber species with high economic value. However, along with global warming, heat stress become one of the main environmental variables that limit the productivity of B. luminifera, and the response of diverse geographic populations to high temperatures is still unclear. In order to offer a comprehensive understanding of the behavior of B. luminifera under heat stress, the physiological responses of six B. luminifera populations (across the core distribution area) were described in this work in an integrated viewpoint. The results showed that a multi-level physiological regulatory network may exist in B. luminifera, the first response was the activity of resistant enzymes [e.g., peroxidase (POD)] at a preliminary stage of 2 h heat stress, and then the proline (osmoregulation substance) content began to increase after 24 h of continuous high-temperature treatment. In addition, photosynthesis was stronlgly affected by heat stress, and the net photosynthetic rate (Pn) showed a downward trend under heat treatment in all six B. luminifera populations. Interestingly, although the physiological change patterns of the six B. luminifera populations were relatively consistent for the same parameter, there were obvious differences among different populations. Comprehensive analysis revealed that the physiological response of Rongshui (RS) was the most stable, and this was the representative B. luminifera population. Illumina RNA-seq analysis was applied to reveal the specific biological process of B. luminifera under heat stress using the RS population, and a total of 116,484 unigenes were obtained. The differentially expressed genes (DEGs) between different time periods under heat stress were enriched in 34 KEGG pathways, and the limonene and pinene degradation pathway was commonly enriched in all pairwise comparisons. Moreover, transcription factors including bHLH (basic helix–loop–helix), MYB, WRKY, and NAC (NAM, ATAF1/2, and CUC2) were identified. In this study, the physiological response and tolerance mechanisms of B. luminifera under high temperature stress were revealed, which can conducive to the basis of B. luminifera selection and resistance assessment for cultivation and breeding.</p

Table_3_Comparative physiological analyses and the genetic basis reveal heat stress responses mechanism among different Betula luminifera populations.XLSX

Betula luminifera is a subtropical fast-growing timber species with high economic value. However, along with global warming, heat stress become one of the main environmental variables that limit the productivity of B. luminifera, and the response of diverse geographic populations to high temperatures is still unclear. In order to offer a comprehensive understanding of the behavior of B. luminifera under heat stress, the physiological responses of six B. luminifera populations (across the core distribution area) were described in this work in an integrated viewpoint. The results showed that a multi-level physiological regulatory network may exist in B. luminifera, the first response was the activity of resistant enzymes [e.g., peroxidase (POD)] at a preliminary stage of 2 h heat stress, and then the proline (osmoregulation substance) content began to increase after 24 h of continuous high-temperature treatment. In addition, photosynthesis was stronlgly affected by heat stress, and the net photosynthetic rate (Pn) showed a downward trend under heat treatment in all six B. luminifera populations. Interestingly, although the physiological change patterns of the six B. luminifera populations were relatively consistent for the same parameter, there were obvious differences among different populations. Comprehensive analysis revealed that the physiological response of Rongshui (RS) was the most stable, and this was the representative B. luminifera population. Illumina RNA-seq analysis was applied to reveal the specific biological process of B. luminifera under heat stress using the RS population, and a total of 116,484 unigenes were obtained. The differentially expressed genes (DEGs) between different time periods under heat stress were enriched in 34 KEGG pathways, and the limonene and pinene degradation pathway was commonly enriched in all pairwise comparisons. Moreover, transcription factors including bHLH (basic helix–loop–helix), MYB, WRKY, and NAC (NAM, ATAF1/2, and CUC2) were identified. In this study, the physiological response and tolerance mechanisms of B. luminifera under high temperature stress were revealed, which can conducive to the basis of B. luminifera selection and resistance assessment for cultivation and breeding.</p

Image_2_Comparative physiological analyses and the genetic basis reveal heat stress responses mechanism among different Betula luminifera populations.TIF

Betula luminifera is a subtropical fast-growing timber species with high economic value. However, along with global warming, heat stress become one of the main environmental variables that limit the productivity of B. luminifera, and the response of diverse geographic populations to high temperatures is still unclear. In order to offer a comprehensive understanding of the behavior of B. luminifera under heat stress, the physiological responses of six B. luminifera populations (across the core distribution area) were described in this work in an integrated viewpoint. The results showed that a multi-level physiological regulatory network may exist in B. luminifera, the first response was the activity of resistant enzymes [e.g., peroxidase (POD)] at a preliminary stage of 2 h heat stress, and then the proline (osmoregulation substance) content began to increase after 24 h of continuous high-temperature treatment. In addition, photosynthesis was stronlgly affected by heat stress, and the net photosynthetic rate (Pn) showed a downward trend under heat treatment in all six B. luminifera populations. Interestingly, although the physiological change patterns of the six B. luminifera populations were relatively consistent for the same parameter, there were obvious differences among different populations. Comprehensive analysis revealed that the physiological response of Rongshui (RS) was the most stable, and this was the representative B. luminifera population. Illumina RNA-seq analysis was applied to reveal the specific biological process of B. luminifera under heat stress using the RS population, and a total of 116,484 unigenes were obtained. The differentially expressed genes (DEGs) between different time periods under heat stress were enriched in 34 KEGG pathways, and the limonene and pinene degradation pathway was commonly enriched in all pairwise comparisons. Moreover, transcription factors including bHLH (basic helix–loop–helix), MYB, WRKY, and NAC (NAM, ATAF1/2, and CUC2) were identified. In this study, the physiological response and tolerance mechanisms of B. luminifera under high temperature stress were revealed, which can conducive to the basis of B. luminifera selection and resistance assessment for cultivation and breeding.</p

Image_3_Comparative physiological analyses and the genetic basis reveal heat stress responses mechanism among different Betula luminifera populations.TIF

Betula luminifera is a subtropical fast-growing timber species with high economic value. However, along with global warming, heat stress become one of the main environmental variables that limit the productivity of B. luminifera, and the response of diverse geographic populations to high temperatures is still unclear. In order to offer a comprehensive understanding of the behavior of B. luminifera under heat stress, the physiological responses of six B. luminifera populations (across the core distribution area) were described in this work in an integrated viewpoint. The results showed that a multi-level physiological regulatory network may exist in B. luminifera, the first response was the activity of resistant enzymes [e.g., peroxidase (POD)] at a preliminary stage of 2 h heat stress, and then the proline (osmoregulation substance) content began to increase after 24 h of continuous high-temperature treatment. In addition, photosynthesis was stronlgly affected by heat stress, and the net photosynthetic rate (Pn) showed a downward trend under heat treatment in all six B. luminifera populations. Interestingly, although the physiological change patterns of the six B. luminifera populations were relatively consistent for the same parameter, there were obvious differences among different populations. Comprehensive analysis revealed that the physiological response of Rongshui (RS) was the most stable, and this was the representative B. luminifera population. Illumina RNA-seq analysis was applied to reveal the specific biological process of B. luminifera under heat stress using the RS population, and a total of 116,484 unigenes were obtained. The differentially expressed genes (DEGs) between different time periods under heat stress were enriched in 34 KEGG pathways, and the limonene and pinene degradation pathway was commonly enriched in all pairwise comparisons. Moreover, transcription factors including bHLH (basic helix–loop–helix), MYB, WRKY, and NAC (NAM, ATAF1/2, and CUC2) were identified. In this study, the physiological response and tolerance mechanisms of B. luminifera under high temperature stress were revealed, which can conducive to the basis of B. luminifera selection and resistance assessment for cultivation and breeding.</p