Forestry research最新文献_第4页

Transcriptome analysis reveals genes associated with the bitter-sweet trait of apricot kernels. 转录组分析揭示了与杏核苦甜性状相关的基因。

Forestry research Pub Date : 2024-02-29 eCollection Date: 2024-01-01 DOI: 10.48130/forres-0024-0004

Yu Zhang, Wenquan Bao, Ta-Na Wuyun, Mengzhen Huang, Chen Chen, Dun Ao, Rong Yang, Haiguang Huang, Lin Wang

{"title":"Transcriptome analysis reveals genes associated with the bitter-sweet trait of apricot kernels.","authors":"Yu Zhang, Wenquan Bao, Ta-Na Wuyun, Mengzhen Huang, Chen Chen, Dun Ao, Rong Yang, Haiguang Huang, Lin Wang","doi":"10.48130/forres-0024-0004","DOIUrl":"https://doi.org/10.48130/forres-0024-0004","url":null,"abstract":"Prunasin and amygdalin are important factors that influence the kernel taste of apricots, however, the regulatory mechanisms underlying this are unclear. In this study, we analyzed the phenotype and transcriptome of kernels during development in Prunus sibirica (bitter kernels) and Prunus armeniaca × Prunus sibirica (kernel consumption apricot, sweet kernels). Prunasin and amygdalin content was significantly higher in bitter kernels compared with that in sweet kernels. Prunasin content exhibited a decreasing trend in both bitter and sweet kernels. The fastest decline was observed in bitter and sweet kernels during S3-S4 (82.21%) and S2-S3 (59.65%), respectively. The amygdalin content in the bitter kernels exhibited the fastest increase between 45-60 d after flowering, and reached a peak at 6.22% on 60 d after flowering. In contrast, the peak in sweet kernels occurred at 60 d after flowering, with a much lower content of 0.18%. Transcriptome analysis revealed 6,942 differentially expressed genes (DEGs), with a subset of 38 DEGs specifically enriched in the cyanoamino acid metabolic pathway. Among these, the ten candidate genes, including CYP79, CYP71, UGT1, AH, and PH, were identified as crucial in regulating prunasin and amygdalin metabolism. Furthermore, a weighted gene co-expression network analysis (WGCNA) unveiled two modules that exhibited significant correlation with prunasin and amygdalin content. Five DEGs were located at the center of the co-expression network, and were identified as hub genes, with four positively regulating prunasin content and one negatively regulating amygdalin content. Our results provide novel insights into the molecular-level regulation of the apricot kernel taste.","PeriodicalId":520285,"journal":{"name":"Forestry research","volume":"4 ","pages":"e007"},"PeriodicalIF":0.0,"publicationDate":"2024-02-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11524293/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142635611","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Involvement of 5mC DNA demethylation via 5-aza-2'-deoxycytidine in regulating gene expression during early somatic embryo development in white spruce (Picea glauca). 通过 5-aza-2'-deoxycytidine 使 5mC DNA 去甲基化参与调节白云杉早期体细胞胚胎发育过程中的基因表达。

Forestry research Pub Date : 2023-12-26 eCollection Date: 2023-01-01 DOI: 10.48130/fr-0023-0030

Ying Gao, Xiaoyi Chen, Chengbi Liu, Huanhuan Zhao, Fengbin Dai, Jian Zhao, Jinfeng Zhang, Lisheng Kong

{"title":"Involvement of 5mC DNA demethylation via 5-aza-2'-deoxycytidine in regulating gene expression during early somatic embryo development in white spruce (Picea glauca).","authors":"Ying Gao, Xiaoyi Chen, Chengbi Liu, Huanhuan Zhao, Fengbin Dai, Jian Zhao, Jinfeng Zhang, Lisheng Kong","doi":"10.48130/fr-0023-0030","DOIUrl":"https://doi.org/10.48130/fr-0023-0030","url":null,"abstract":"DNA methylation plays a crucial role in the development of somatic embryos (SEs) through the regulation of gene expression. To examine the impact of DNA methylation on gene expression during early SE development in Picea glauca, the demethylation reagent 5-aza-dC (5-aza-2'-deoxycytidine) was employed to modify DNA methylation regions and levels during the pre-maturation stage of somatic embryogenesis. The application of 2.0 µM 5-aza-dC did not induce toxicity to SEs in early development. Following treatment, the global DNA methylation level decreased significantly on the 7th day of pre-maturation and the 1st week of maturation. Methylated DNA immunoprecipitation (MeDIP) sequencing revealed that differentially methylated regions, as analyzed through Gene Ontology (GO), were related to plant development and reproduction and that they were hypomethylated on the 3rd day but hypermethylated on the 7th day in 5-aza-dC-treated embryogenic tissues. These findings indicate that 5-aza-dC treatment positively impacts early SE development, which was inhibited following 7 d of treatment. The expression of MSH7, JMJ14, and CalS10 was associated with DNA methylation, epigenetic regulation, and somatic embryogenesis. Further analysis of methylated regions revealed that the expression profiles of MSH7, JMJ14, and CalS10 were correlated with altered DNA methylation, suggesting DNA methylation at 5 mC may play a role in controlling the expression of these genes and regulating the early development of SEs in P. glauca. This study offers new insights into the regulation of somatic embryogenesis in conifers.","PeriodicalId":520285,"journal":{"name":"Forestry research","volume":"3 ","pages":"30"},"PeriodicalIF":0.0,"publicationDate":"2023-12-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11543301/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142635536","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Genome-wide discovery of CBL genes in Nitraria tangutorum Bobr. and functional analysis of NtCBL1-1 under drought and salt stress. Nitraria tangutorum Bobr.中 CBL 基因的全基因组发现以及 NtCBL1-1 在干旱和盐胁迫下的功能分析。

Forestry research Pub Date : 2023-12-22 eCollection Date: 2023-01-01 DOI: 10.48130/FR-2023-0028

Liming Zhu, Jingxiang Wu, Mengjuan Li, Hao Fang, Jingbo Zhang, Yuchang Chen, Jinhui Chen, Tielong Cheng

{"title":"Genome-wide discovery of CBL genes in Nitraria tangutorum Bobr. and functional analysis of NtCBL1-1 under drought and salt stress.","authors":"Liming Zhu, Jingxiang Wu, Mengjuan Li, Hao Fang, Jingbo Zhang, Yuchang Chen, Jinhui Chen, Tielong Cheng","doi":"10.48130/FR-2023-0028","DOIUrl":"https://doi.org/10.48130/FR-2023-0028","url":null,"abstract":"Calcineurin B-like (CBL) proteins are a class of important Ca2+ receptors that play key roles in plant stress response. CBLs have been shown to participate in responses to abiotic stresses such as drought, salt, and cold in many plant species, including Arabidopsis and rice. However, little is known about their potential functions in the desert halophyte Nitraria tangutorum. Here, we have identified 11 CBL genes distributed across six chromosomes of N. tangutorum and categorized them into four groups through phylogenetic analysis. Synteny analysis showed that they have strong collinear relationships and have undergone purifying selection during their evolution. NtCBL promoter regions contain a variety of cis-acting elements related to hormone and environmental stress responses. Real-time quantitative PCR showed that the expression of NtCBLs differed significantly among various tissues and was upregulated by salt and drought stress. We chose NtCBL1-1 for an in-depth functional characterization and observed that transgenic Arabidopsis plants expressing NtCBL1-1 exhibited increased tolerance to both drought and salt stress. Compared to wild-type Arabidopsis, transgenic lines showed higher germination rates, slower chlorophyll degradation, more soluble proteins, and reduced accumulation of the oxidative stress marker malondialdehyde. These findings indicate that NtCBL1-1 plays a significant role in responding to drought and salt stress, laying the foundation for further investigations into the functional mechanisms of NtCBL genes in N. tangutorum.","PeriodicalId":520285,"journal":{"name":"Forestry research","volume":"3 ","pages":"28"},"PeriodicalIF":0.0,"publicationDate":"2023-12-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11524306/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142635530","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Breeding polyploid Populus: progress and perspective. 多倍体杨树育种：进展与展望。

Forestry research Pub Date : 2022-03-31 eCollection Date: 2022-01-01 DOI: 10.48130/FR-2022-0004

Xiangyang Kang, Hairong Wei

{"title":"Breeding polyploid Populus: progress and perspective.","authors":"Xiangyang Kang, Hairong Wei","doi":"10.48130/FR-2022-0004","DOIUrl":"https://doi.org/10.48130/FR-2022-0004","url":null,"abstract":"Populus is a genus of 25-30 species of deciduous flowering plants in the family Salicaceae, which are primarily planted in short-rotation planations for producing timber, pulpwood, wooden products as well as bioenergy feedstock; they are also widely planted in agricultural fields and along roadsides as shelter forest belts for windbreak, decoration, and reduction of pollutants and noise. Moreover, their fast-growth and good adaptation to marginal lands enable them to provide some critical ecosystem services at various phytoremediation sites for land restoration and reclaimation. Thanks to their important roles, breeding for fast growing poplar trees has been one of the most important objectives for nearly a century. One of the most demonstrated, documented achievements in this aspect is polyploid breeding, especially triploid breeding. This paper critically reviews the various techniques used in inducing triploid plants, including natural 2n formation, artificial induction of 2n male and female gemmates through chemical or physical treatments, trait characterization of the triploid and tetraploid breeding populations, unveiling the molecular mechanisms underpinning the significantly improved traits, and identification and selection of the best triploid progenies. This review also recapitulated the challenges and strategies facing the future of triploid breeding in Populus, including amelioration of 2n gamete induction techniques and efficiency, selection of the best parents and identification of the best progrenies, utilization of the huge amount of genomic, transcriptomic, proteomic, metabolomic, and other omics data for selecting parents for improving target traits.","PeriodicalId":520285,"journal":{"name":"Forestry research","volume":"2 ","pages":"4"},"PeriodicalIF":0.0,"publicationDate":"2022-03-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11524227/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142635528","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Case study of a rhizosphere microbiome assay on a bamboo rhizome with excessive shoots. 对笋过多的竹子根茎进行根瘤微生物组测定的案例研究。

Forestry research Pub Date : 2021-06-24 eCollection Date: 2021-01-01 DOI: 10.48130/FR-2021-0010

Fuqiang Cui, Yifan Yang, Mengyuan Ye, Wei Wei, Wenqian Huang, Ying Wu, Xi Jiao, Xiaoxue Ye, Shutong Zhou, Zhubing Hu, Yinhai Zhang, Renyi Gui, Wenwu Wu, Kim Yrjälä, Kirk Overmyer, Shenkui Liu

{"title":"Case study of a rhizosphere microbiome assay on a bamboo rhizome with excessive shoots.","authors":"Fuqiang Cui, Yifan Yang, Mengyuan Ye, Wei Wei, Wenqian Huang, Ying Wu, Xi Jiao, Xiaoxue Ye, Shutong Zhou, Zhubing Hu, Yinhai Zhang, Renyi Gui, Wenwu Wu, Kim Yrjälä, Kirk Overmyer, Shenkui Liu","doi":"10.48130/FR-2021-0010","DOIUrl":"https://doi.org/10.48130/FR-2021-0010","url":null,"abstract":"Young moso bamboo shoots are a popular seasonal food and an important source of income for farmers, with value for cultivation estimated at $30,000 per hectare. Bamboo also has great environmental importance and its unique physiology is of scientific interest. A rare and valuable phenomenon has recently appeared where a large number of adjacent buds within a single moso bamboo rhizome have grown into shoots. Although of practical importance for the production of edible shoots, such occurrences have not been scientifically studied, due to their rarity. Analysis of collected reports from enhanced shoot production events in China showed no evidence that enhanced shoot development was heritable. We report the analysis of the rhizosphere microbiome from a rhizome with 18 shoots, compared to rhizomes having one or no shoots as controls. The community of prokaryotes, but not fungi, correlated with the shoot number. Burkholderia was the most abundant genus, which was negatively correlated with rhizome shoot number, while Clostridia and Ktedonobacteria were positively correlated. Two Burkholderia strains were isolated and their plant-growth promoting activity was tested. The isolated Burkholderia strains attenuated the growth of bamboo seedlings. These data provide the first study on excessive shoot development in bamboo, which will facilitate hypothesis building for future studies.","PeriodicalId":520285,"journal":{"name":"Forestry research","volume":"1 ","pages":"10"},"PeriodicalIF":0.0,"publicationDate":"2021-06-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11524271/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142635519","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

HB-PLS: A statistical method for identifying biological process or pathway regulators by integrating Huber loss and Berhu penalty with partial least squares regression. HB-PLS：一种通过将 Huber 损失和 Berhu 惩罚与偏最小二乘法回归相结合来识别生物过程或途径调节器的统计方法。

Forestry research Pub Date : 2021-03-30 eCollection Date: 2021-01-01 DOI: 10.48130/FR-2021-0006

Wenping Deng, Kui Zhang, Cheng He, Sanzhen Liu, Hairong Wei

{"title":"HB-PLS: A statistical method for identifying biological process or pathway regulators by integrating Huber loss and Berhu penalty with partial least squares regression.","authors":"Wenping Deng, Kui Zhang, Cheng He, Sanzhen Liu, Hairong Wei","doi":"10.48130/FR-2021-0006","DOIUrl":"https://doi.org/10.48130/FR-2021-0006","url":null,"abstract":"Gene expression data features high dimensionality, multicollinearity, and non-Gaussian distribution noise, posing hurdles for identification of true regulatory genes controlling a biological process or pathway. In this study, we integrated the Huber loss function and the Berhu penalty (HB) into partial least squares (PLS) framework to deal with the high dimension and multicollinearity property of gene expression data, and developed a new method called HB-PLS regression to model the relationships between regulatory genes and pathway genes. To solve the Huber-Berhu optimization problem, an accelerated proximal gradient descent algorithm with at least 10 times faster than the general convex optimization solver (CVX), was developed. Application of HB-PLS to recognize pathway regulators of lignin biosynthesis and photosynthesis in Arabidopsis thaliana led to the identification of many known positive pathway regulators that had previously been experimentally validated. As compared to sparse partial least squares (SPLS) regression, an efficient method for variable selection and dimension reduction in handling multicollinearity, HB-PLS has higher efficacy in identifying more positive known regulators, a much higher but slightly less sensitivity/(1-specificity) in ranking the true positive known regulators to the top of the output regulatory gene lists for the two aforementioned pathways. In addition, each method could identify some unique regulators that cannot be identified by the other methods. Our results showed that the overall performance of HB-PLS slightly exceeds that of SPLS but both methods are instrumental for identifying real pathway regulators from high-throughput gene expression data, suggesting that integration of statistics, machine leaning and convex optimization can result in a method with high efficacy and is worth further exploration.","PeriodicalId":520285,"journal":{"name":"Forestry research","volume":"1 ","pages":"6"},"PeriodicalIF":0.0,"publicationDate":"2021-03-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11524267/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142635523","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0