Plant Direct最新文献

{"title":"Chromosome Numbers and Reproductive Life Cycles in Green Plants: A Phylotranscriptomic Perspective.","authors":"Rijan R Dhakal, Alex Harkess, Paul G Wolf","doi":"10.1002/pld3.70044","DOIUrl":"10.1002/pld3.70044","url":null,"abstract":"<p><p>The strong correlation between reproductive life cycle type and chromosome numbers in green plants has been a long-standing mystery in evolutionary biology. Within green plants, the derived condition of heterosporous reproduction has emerged from the ancestral condition of homospory in disparate locations on the phylogenetic tree at least 11 times, of which three lineages are extant. In all green plant lineages where heterospory has emerged, there has been a significant downsizing in chromosome numbers. This dynamic has been investigated without clear answers for many decades. In this study, we combine known ideas from existing literature with novel methods, tools, and data to generate fresh insights into an old question. Using gene family evolution models and selection analyses, we identified gene families that have undergone significant expansion, contraction, or selection in heterosporous lineages. Alongside lineage-specific genomic changes, our results revealed shared genomic changes/trends among heterosporous lineages. We found expansions in gene families related to developmental regulation, signaling pathways, and stress responses across heterosporous groups. Notably, the MATE efflux family showed consistent expansion and evidence of selection in heterosporous lineages, suggesting a potentially conserved role in heterospory evolution. These findings could provide novel avenues to investigate and probe the underlying mechanism that may underpin the association between heterospory and genomic changes. The general importance of chromosome numbers, structure, and sizes in cellular biology notwithstanding, the association between the emergence of heterosporous reproduction and chromosome number reduction/genome downsizing is not fully understood. It remains unclear why there exists an association between aspects of biology at such disparate levels as reproductive life cycles and chromosome numbers/genome size. Exploring and answering this conundrum of evolutionary biology can add to our broader understanding of life sciences and of biology at different levels. Applying the novel tools and methods emerging from ongoing progress in biotechnology and computational sciences presents an opportunity to make new inroads into this long-standing question.</p>","PeriodicalId":20230,"journal":{"name":"Plant Direct","volume":"9 1","pages":"e70044"},"PeriodicalIF":2.3,"publicationDate":"2025-01-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11758355/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143047269","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The Significant Effects of Threshold Selection for Advancing Nitrogen Use Efficiency in Whole Genome of Bread Wheat.","authors":"Mohammad Bahman Sadeqi, Agim Ballvora, Said Dadshani, Md Nurealam Siddiqui, Mohammad Kamruzzaman, Ahossi Patrice Koua, Jens Léon","doi":"10.1002/pld3.70036","DOIUrl":"10.1002/pld3.70036","url":null,"abstract":"<p><p>Currently in wheat breeding, genome wide association studies (GWAS) have successfully revealed the genetic basis of complex traits such as nitrogen use efficiency (NUE) and its biological processes. In the GWAS model, thresholding is common strategy to indicate deviation of expected range of <i>p</i>-<i>value</i>(s), and it can be used to find the distribution of true positive associations under or over of test statistics. Therefore, the threshold plays a critical role to identify reliable and significant associations in wide genome, while the proportion of false positive results is relatively low. The problem of multiple comparisons arises when a statistical analysis involves multiple simultaneous statistical tests, each of them has the potential to be a discovery. There are several ways to address this problem, including the family-wise error rate and false discovery rate (FDR), raw and adjusted <i>p</i>-<i>value</i>(s), consideration of threshold coherence and consonance, and the properties of proportional hypothesis tests in the threshold definition. We encountered some limitations in the definition of FDR threshold, particularly in the upper bounds of linear and nonlinear approaches. We emphasize that empirical null distributions based on permutation test can be useful when the assumption of linear or parametric FDR approaches do not hold. Nevertheless, we believe that it is necessary to utilize modern statistical optimization techniques to evaluate the stability and performance of our results and to select significant FDR threshold. By incorporating the neural network algorithm, it is possible to improve the reliability of FDR threshold and increase the probability of identifying true genetic associations while minimizing the risk of false positives in GWAS results.</p>","PeriodicalId":20230,"journal":{"name":"Plant Direct","volume":"9 1","pages":"e70036"},"PeriodicalIF":2.3,"publicationDate":"2025-01-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11750810/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143024444","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Arabidopsis 3-Deoxy-d-<i>Arabino</i>-Heptulosonate 7-Phosphate (DAHP) Synthases of the Shikimate Pathway Display Both Manganese- and Cobalt-Dependent Activities.","authors":"Ryo Yokoyama, Hiroshi A Maeda","doi":"10.1002/pld3.70037","DOIUrl":"10.1002/pld3.70037","url":null,"abstract":"<p><p>The plant shikimate pathway directs a significant portion of photosynthetically assimilated carbon into the downstream biosynthetic pathways of aromatic amino acids (AAA) and aromatic natural products. 3-Deoxy-d-<i>arabino</i>-heptulosonate 7-phosphate (DAHP) synthase (hereafter DHS) catalyzes the first step of the shikimate pathway, playing a critical role in controlling the carbon flux from central carbon metabolism into the AAA biosynthesis. Previous biochemical studies suggested the presence of manganese- and cobalt-dependent DHS enzymes (DHS-Mn and DHS-Co, respectively) in various plant species. Unlike well-studied DHS-Mn, however, the identity of DHS-Co is still unknown. Here, we show that all three DHS isoforms of <i>Arabidopsis thaliana</i> exhibit both DHS-Mn and DHS-Co activities in vitro. A phylogenetic analysis of various DHS orthologs and related sequences showed that Arabidopsis 3-deoxy-D-<i>manno</i>-octulosonate-8-phosphate synthase (KDOPS) proteins were closely related to microbial Type I DHSs. Despite their sequence similarity, these Arabidopsis KDOPS proteins showed no DHS activity. Meanwhile, optimization of the DHS assay conditions led to the successful detection of DHS-Co activity from Arabidopsis DHS recombinant proteins. Compared with DHS-Mn, DHS-Co activity displayed the same redox dependency but distinct optimal pH and cofactor sensitivity. Our work provides biochemical evidence that the DHS isoforms of Arabidopsis possess DHS-Co activity.</p>","PeriodicalId":20230,"journal":{"name":"Plant Direct","volume":"9 1","pages":"e70037"},"PeriodicalIF":2.3,"publicationDate":"2025-01-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11750804/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143024429","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genome-Wide Analysis of the <i>APETALA2/Ethylene-Responsive Factor</i> Gene Family in <i>Carthamus tinctorius L</i>.","authors":"Zheng-Wei Tan, Dan-Dan Lu, Yong-Liang Yu, Lei Li, Lan-Jie Xu, Wei Dong, Chun-Ming Li, Qing Yang, Hui-Zhen Liang","doi":"10.1002/pld3.70032","DOIUrl":"https://doi.org/10.1002/pld3.70032","url":null,"abstract":"<p><p>The <i>APETALA2/ethylene-responsive factor (AP2/ERF)</i> superfamily represents a class of transcription factors involved in plant growth, development, and stress responses. <i>Carthamus tinctorius L</i>., also known as safflower, is an important plant whose flowers contain carthamin, an expensive aromatic pigment with various medicinal and flavoring properties. This study aimed to elucidate the roles of these transcription factors in plant growth, metabolic regulation, and environmental adaptation in safflower, providing foundational information and theoretical support for genetic improvement and stress resilience research in this crop. In this study, we identified and characterized the <i>AP2/ERF</i> family genes in safflower through a comprehensive genomic analysis. A total of 127 <i>AP2/ERF</i> genes were identified and clustered into seven groups and 14 subgroups based on phylogenetic analysis. Multiple sequence alignment revealed that the basic region and two helical structures were highly conserved in most AP2/ERF proteins. <i>Cis</i>-acting elements in the promoters of the <i>AP2/ERF</i> genes were analyzed, and a degree of safflower specificity was observed among different safflower species. Tissue-specific expression analysis showed that 23, 21, 15, and 9 genes were most abundantly expressed in the roots, leaves, flowers, and buds, respectively, while only eight genes were highly expressed in all tissues examined. These results indicate that the <i>AP2/ERF</i> family genes in safflower are diverse and complex, with distinct expression patterns for different genes in different safflower species. The findings provide important fundamental data for in-depth studies of the growth, development, and stress response mechanisms in safflower.</p>","PeriodicalId":20230,"journal":{"name":"Plant Direct","volume":"9 1","pages":"e70032"},"PeriodicalIF":2.3,"publicationDate":"2025-01-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11736709/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143010338","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Chloroplast Vesiculation and Induced <i>Chloroplast Vesiculation</i> and <i>Senescence-Associated Gene 12</i> Expression During Tomato Flower Pedicel Abscission.","authors":"Magda Tušek Žnidarič, Maja Zagorščak, Živa Ramšak, Katja Stare, Marko Chersicola, Maruša Pompe Novak, Aleš Kladnik, Marina Dermastia","doi":"10.1002/pld3.70035","DOIUrl":"10.1002/pld3.70035","url":null,"abstract":"<p><p>Abscission is a tightly regulated process in which plants shed unnecessary, infected, damaged, or aging organs, as well as ripe fruits, through predetermined abscission zones in response to developmental, hormonal, and environmental signals. Despite its importance, the underlying mechanisms remain incompletely understood. This study highlights the deleterious effects of abscission on chloroplast ultrastructure in the cells of the tomato flower pedicel abscission zone, revealing spatiotemporal differential gene expression and key transcriptional networks involved in chloroplast vesiculation during abscission. Significant changes in chloroplast structure and vesicle formation were observed 8 and 14 h after abscission induction, coinciding with the differential expression of vesiculation-related genes, particularly with upregulation of <i>Senescence-Associated Gene 12</i> (<i>SAG12</i>) and <i>Chloroplast Vesiculation</i> (<i>CV</i>). This suggests a possible vesicle transport of chloroplast degrading material for recycling by autophagy-independent senescence-associated vacuoles (SAVs) and CV-containing vesicles (CCVs). Ethylene signaling appears to be involved in the regulation of these processes, as treatment with a competitive inhibitor of ethylene action, 1-methylcyclopropene, delayed vesiculation, reduced the expression of <i>SAG12</i>, and increased expression of <i>Curvature Thylakoid 1A</i> (<i>CURT1A</i>). In addition, chloroplast vesiculation during abscission was associated with differential expression of photosynthesis-related genes, particularly those involved in light reactions, underscoring the possible functional impact of the observed structural changes. This work provides new insights into the molecular and ultrastructural mechanisms underlying abscission and offers potential new targets for agricultural or biotechnological applications.</p>","PeriodicalId":20230,"journal":{"name":"Plant Direct","volume":"9 1","pages":"e70035"},"PeriodicalIF":2.3,"publicationDate":"2025-01-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11710935/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142953796","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Modification of Gene Expression Involved in Alkaloid Production in Opium Poppy by VIGS Combined With Pretreatment of Macerozyme Enzyme.","authors":"Deniz Ece Özcan, Deniz Köm, Ozan Doğan, Semiha Erişen, Selma Onarici","doi":"10.1002/pld3.70034","DOIUrl":"10.1002/pld3.70034","url":null,"abstract":"<p><p><i>Papaver somniferum</i> L., a medicinal plant renowned for its pharmaceutical alkaloids, has captivated scientific interest due to its rich secondary metabolite profile. This study explores a novel approach to manipulating alkaloid biosynthesis pathways by integrating virus-induced gene silencing (VIGS) with macerozyme enzyme pretreatment. Targeting key genes in the benzylisoquinoline alkaloid (BIA) pathway (<i>CODM</i>, <i>T6ODM</i>, <i>COR</i>, <i>DIOX2</i>), the research aimed to elucidate the transformative potential of enzymatic preconditioning in somatic embryo cultures. To address the cell wall barrier, a known limitation in genetic manipulation, macerozyme pretreatment was employed, significantly enhancing gene silencing efficacy. Quantitative reverse transcription PCR analyses revealed significant alterations in gene expression profiles with macerozyme pretreatment, whereas no changes were observed in its absence. The T6ODM + DIOX combination was the most effective, reducing <i>CODM</i>, <i>T6ODM</i>, and <i>DIOX2</i> expression by 72%, 65%, and 60%, respectively. Conversely, <i>T6ODM</i> expression increased by up to 107% in the CODM treatment. Notably, <i>COR</i> expression displayed dual regulatory dynamics, with suppression (47% decrease in T6ODM + DIOX) and enhancement (49% increase in CODM+DIOX) observed under different conditions. These findings underscore the complex interplay of gene regulation in the morphine biosynthesis pathway. This study highlights the critical role of macerozyme enzymatic pretreatment in overcoming cell wall barriers, enabling effective VIGS applications in somatic suspension cultures. The combination of VIGS and enzymatic pretreatment provides a robust platform for targeted metabolic engineering, offering insights into the regulation of morphine biosynthesis and paving the way for advancements in pharmaceutical alkaloid production and functional genomics in medicinal plants.</p>","PeriodicalId":20230,"journal":{"name":"Plant Direct","volume":"9 1","pages":"e70034"},"PeriodicalIF":2.3,"publicationDate":"2025-01-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11706800/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142953798","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Transcriptomics of long-term, low oxygen storage coupled with ethylene signaling interference suggests neofunctionalization of hypoxia response pathways in apple (<i>Malus domestica</i>).","authors":"John A Hadish, Heidi L Hargarten, Huiting Zhang, James P Mattheis, Stephen P Ficklin, Loren A Honaas","doi":"10.1002/pld3.70025","DOIUrl":"10.1002/pld3.70025","url":null,"abstract":"<p><p>Research on how plants respond to hypoxia has concentrated on model organisms where tissues can only survive hypoxic conditions for a few hours to a few days. In contrast, hypoxic conditions are used commercially as a method to prolong the shelf life of <i>Malus domestica</i> (apple) fruit for up to a year of storage without substantial changes in fruit quality, not to mention a lack of tissue death. This ability of apples to withstand protracted hypoxic conditions is an interesting adaptation that has had limited molecular investigation despite its economic importance. Here, we investigate the long-term apple hypoxia response using a time-course RNA-seq analysis of several postharvest storage conditions. We use phylogenetics, differential expression, and regulatory networks to identify genes that regulate and are regulated by the hypoxia response. We identify potential neofunctionalization of core-hypoxia response genes in apples, including novel regulation of group VII ethylene response factor (ERF VII) and plant cysteine oxidase (PCO) family members.</p>","PeriodicalId":20230,"journal":{"name":"Plant Direct","volume":"8 12","pages":"e70025"},"PeriodicalIF":2.3,"publicationDate":"2024-12-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11660084/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142876904","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Synthesis of β-Alanine From Isoleucine and Propionate Catabolism via Aminotransferases.","authors":"Margo H Goldfarb, Joseph Boesel, Kai C Wilczewski-Shirai, Peter Reinhart, Trenton Scherger, Chloe Webb, Morgan Newlun, Kerry A Rouhier","doi":"10.1002/pld3.70030","DOIUrl":"10.1002/pld3.70030","url":null,"abstract":"<p><p>In plants, the nonproteinogenic amino acid β-alanine plays a role in response to hypoxia, flooding, drought, heat, and heavy metal stress conditions. It is also a key intermediate in the synthesis of essential molecules including vitamin B5 and coenzyme A (CoA) through the condensation reaction with pantoate. While the syntheses of pantoate, vitamin B5, and CoA appear to be conserved across plants and bacteria, the synthesis of β-alanine is not. Bacteria and fungi use aspartate, whereas plants can use uracil, spermidine, or propionate to synthesize β-alanine. Given that these three precursors can be formed from the metabolism of glutamine, arginine, isoleucine, and valine, the synthesis of β-alanine could be linked to numerous pathways. Studies of valine catabolism in <i>Arabidopsis</i> suggested that some branched-chain amino acids could in fact serve as precursors for the synthesis of β-alanine. Using GC-MS and isotopically labeled isoleucine and propionate, we linked their metabolism to the synthesis of β-alanine via a proposed transamination of malonate semialdehyde. We then identified three aminotransferases that each catalyzed this final reversible transamination reaction. These results affirm our hypothesis that isoleucine metabolism is also linked to the synthesis of β-alanine via the transamination of metabolic intermediates.</p>","PeriodicalId":20230,"journal":{"name":"Plant Direct","volume":"8 12","pages":"e70030"},"PeriodicalIF":2.3,"publicationDate":"2024-12-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11655180/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142865317","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A bHLH Transcription Factor Confers Salinity Stress Tolerance in <i>Betula platyphylla</i>.","authors":"Qilong Fang, Di Wu, Hu Sun, Luyao Wang, Yuping Liu, Wenfeng Mei, Huiyan Guo","doi":"10.1002/pld3.70029","DOIUrl":"10.1002/pld3.70029","url":null,"abstract":"<p><p>Basic helix-loop-helix (bHLH) proteins comprise a large family of transcription factors that are involved in plant growth and development, as well as responses to various types of environmental stress. <i>Betula platyphylla</i> (birch) is a pioneer tree species in secondary forest that plays a key role in maintaining ecosystem stability and forest regeneration, but few bHLHs involved in abiotic stress responses have been unveiled in birch. In this study, nine BpbHLH TFs related to stress responses in the birch genome were identified. Quantitative real-time polymerase chain reaction (RT-PCR) analysis indicated that the expression of these TFs can be induced by salt stress, and the expression of <i>BpbHLH1</i> was higher than that of other <i>BpbHLH</i> genes. Particle bombardment analysis revealed that BpbHLH1 was localized to the nucleus. Yeast transformation found that BpbHLH1 has transcriptional activation activity. We generated <i>BpbHLH1</i>-overexpressing and silencing transgenic birch plants and subjected them to salt stress analysis. <i>BpbHLH1</i> can enhance the salt tolerance of birch plants by increasing the reactive oxygen species scavenging ability and inhibiting cell death. Yeast one-hybrid, ß-glucuronidase, and chromatin immunoprecipitation assays revealed that BpbHLH1 can regulate the expression of target genes involved in stress resistance by binding to the E-box-1, E-box-2 and G-box elements in their promoters. The results of this study enhanced our understanding of the salt tolerance conferred by BpbHLH TFs in <i>B. platyphylla</i> and identified useful genes for the breeding of novel birch germplasm.</p>","PeriodicalId":20230,"journal":{"name":"Plant Direct","volume":"8 12","pages":"e70029"},"PeriodicalIF":2.3,"publicationDate":"2024-12-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11651711/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142847559","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Combined Physiological and Transcriptomic Analysis Reveals Key Regulatory Networks and Potential Hub Genes Controlling Chilling Tolerance During Soybean Germination.","authors":"Jianguo Xie, Yuhong Zheng, Guang Li, Wei Zhang, Fanfan Meng, Xuhong Fan, Xingmiao Sun, Yunfeng Zhang, Mingliang Wang, Qingshan Chen, Shuming Wang, Hongwei Jiang","doi":"10.1002/pld3.70027","DOIUrl":"10.1002/pld3.70027","url":null,"abstract":"<p><p>Chilling is an important limiting factor for seed germination of soybean (<i>Glycine max</i> [L.] Merr.). To reveal the regulatory mechanism of chilling tolerance during the soybean germination stage, based on previous studies, the chilling tolerance line R48 and chilling sensitive line R89 in chromosome segment substitution lines were selected for physiological index determination and transcriptome sequencing. It was found that reactive oxygen species (ROS) scavenging system related enzymes, ROS, and osmotic regulators were significantly different between the two lines. Gene Ontology enrichment and Kyoto Encyclopedia of Genes and Genomes enrichment were performed on the differentially expressed genes obtained by transcriptome sequencing. It was found that terms or pathways related to flavonoids, unsaturated fatty acids, and abscisic acid were highly enriched. In addition, weighted gene coexpression network analysis (WGCNA) method was used to analyze the physiological index data and transcriptome sequencing data. Four main coexpression modules significantly related to physiological indicators were obtained, and the hub genes in each module were screened according to eigengene-based connectivity value. Haplotype analysis of important candidate genes using soybean germplasm resources showed that there were significant differences in germination indexes between different major haplotypes of <i>Glyma.17G163200</i>. Based on the results of enrichment analysis and WGCNA, the regulation model of low temperature tolerance during soybean germination was preliminarily drawn. This study will provide theoretical guidance for analyzing the molecular regulation mechanism of cold tolerance in soybean germination stage.</p>","PeriodicalId":20230,"journal":{"name":"Plant Direct","volume":"8 12","pages":"e70027"},"PeriodicalIF":2.3,"publicationDate":"2024-12-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11651713/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142847489","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}