Plant Science最新文献

{"title":"Differential regulation of the “phytoglobin-nitric oxide respiration” in Medicago truncatula roots and nodules submitted to flooding","authors":"Chaïma Chammakhi ,&nbsp;Marie Pacoud ,&nbsp;Alexandre Boscari ,&nbsp;Antoine Berger ,&nbsp;Haythem Mhadhbi ,&nbsp;Imène Gharbi ,&nbsp;Renaud Brouquisse","doi":"10.1016/j.plantsci.2025.112393","DOIUrl":"10.1016/j.plantsci.2025.112393","url":null,"abstract":"<div><div>Flooding induces hypoxia in plant tissues, impacting various physiological and biochemical processes. This study investigates the adaptive response of the roots and nitrogen-fixing nodules of <em>Medicago truncatula</em> in symbiosis with <em>Sinorhizobium meliloti</em> under short-term hypoxia caused by flooding. Four-week-old plants were subjected to flooding for 1–4 days. Physiological parameters as well as the expression of the senescence marker gene <em>MtCP6</em> remained unchanged after 4 days of flooding, indicating no senescence onset. Hypoxia was evident from the first day, as indicated by the upregulation of hypoxia marker genes (<em>MtADH</em>, <em>MtPDC, MtAlaAT, MtERF73</em>). Nitrogen-fixing capacity was unaffected after 1 day but markedly decreased after 4 days, while energy state (ATP/ADP ratio) significantly decreased from 1 day and was more affected in nodules than in roots. Nitric oxide (NO) production increased in roots but decreased in nodules after prolonged flooding. Nitrate reductase (NR) activity and expression of genes associated with Phytoglobin-NO (Pgb-NO) respiration (<em>MtNR1, MtNR2, MtPgb1.1</em>) were upregulated, suggesting a role in maintaining energy metabolism under hypoxia, but the use of <em>M. truncatula nr1</em> and <em>nr2</em> mutants, impaired in nitrite production, indicated the involvement of these two genes in ATP regeneration during initial flooding response. The addition of sodium nitroprusside or tungstate revealed that Pgb-NO respiration contributes significantly to ATP regeneration in both roots and nodules under flooding. Altogether, these results highlight the importance of NR1 and Pgb1.1 in the hypoxic response of legume root systems and show that nodules are more sensitive than roots to hypoxia.</div></div>","PeriodicalId":20273,"journal":{"name":"Plant Science","volume":"352 ","pages":"Article 112393"},"PeriodicalIF":4.2,"publicationDate":"2025-01-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143010342","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Molecular mechanisms of cold stress response in cotton: Transcriptional reprogramming and genetic strategies for tolerance","authors":"Washu Dev ,&nbsp;Fahmida Sultana ,&nbsp;Hongge Li ,&nbsp;Daowu Hu ,&nbsp;Zhen Peng ,&nbsp;Shoupu He ,&nbsp;Haobo Zhang ,&nbsp;Muhammad Waqas ,&nbsp;Xiaoli Geng ,&nbsp;Xiongming Du","doi":"10.1016/j.plantsci.2025.112390","DOIUrl":"10.1016/j.plantsci.2025.112390","url":null,"abstract":"<div><div>Cold stress has a huge impact on the growth and development of cotton, presenting a significant challenge to its productivity. Comprehending the complex molecular mechanisms that control the reaction to CS is necessary for developing tactics to improve cold tolerance in cotton. This review paper explores how cotton responds to cold stress by regulating gene expression, focusing on both activating and repressing specific genes. We investigate the essential roles that transcription factors and regulatory elements have in responding to cold stress and controlling gene expression to counteract the negative impacts of low temperatures. Through a comprehensive examination of new publications, we clarify the intricacies of transcriptional reprogramming induced by cold stress, emphasizing the connections between different regulatory elements and signaling pathways. Additionally, we investigate the consecutive effects of cold stress on cotton yield, highlighting the physiological and developmental disturbances resulting from extended periods of low temperatures. The knowledge obtained from this assessment allows for a more profound comprehension of the molecular mechanisms that regulate cold stress responses, suggesting potential paths for future research to enhance cold tolerance in cotton by utilizing targeted genetic modifications and biotechnological interventions.</div></div>","PeriodicalId":20273,"journal":{"name":"Plant Science","volume":"352 ","pages":"Article 112390"},"PeriodicalIF":4.2,"publicationDate":"2025-01-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143010345","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Transcription factors PHR1 and PHR1-like 1 regulate ABA-mediated inhibition of seed germination and stomatal opening in Arabidopsis","authors":"Huiying Chen ,&nbsp;Jia Du ,&nbsp;Yifan Wang ,&nbsp;Kexin Chao ,&nbsp;Zitong Wang ,&nbsp;Shahid Ali ,&nbsp;Houqing Zeng","doi":"10.1016/j.plantsci.2025.112389","DOIUrl":"10.1016/j.plantsci.2025.112389","url":null,"abstract":"<div><div>Low phosphate (LP) availability significantly impacts crop yield and quality. PHOSPHATE STARVATION RESPONSE1 (PHR1) along with PHR1-like 1 (PHL1) act as a key transcriptional regulator in a plant's adaptive response to LP conditions. Abscisic acid (ABA) plays an important role in how plants respond to environmental stresses like salinity and drought. However, the involvement of PHR1 and PHL1 in ABA response and signalling mechanisms remains to be fully understood. Our findings reveal that <em>PHR1</em> and <em>PHR1</em>/<em>PHL1</em> knockout mutations enhance the responsiveness of seed germination, early seedling growth, and stomatal opening to ABA in <em>Arabidopsis</em>. Furthermore, these mutations increase sensitivity to combined LP and ABA stress. In contrast, overexpression of <em>PHR1</em> or <em>PHL1</em> reduces this sensitivity in <em>Arabidopsis</em>. Knockout mutations of <em>PHR1</em> and <em>PHR1</em>/<em>PHL1</em> also increase sensitivity to salt and osmotic stresses, as well as to combined LP and salinity/osmotic stress, while overexpression of <em>PHR1</em> or <em>PHL1</em> reduces their sensitivity in seed germination and early seedling development. Knockout mutations of <em>SPX1</em> and <em>SPX2</em>, negative regulators of PHR1 and PHL1, decrease sensitivity to ABA and salt/osmotic stresses in <em>Arabidopsis</em>. A group of genes related to ABA metabolism and signalling is significantly affected by the knockout or overexpression of <em>PHR1</em> and <em>PHL1</em>, with a large proportion of these genes containing PHR1 binding site (P1BS) in their promoters. Moreover, the ABA-sensitive phenotype of <em>phr1</em> or <em>phr1 phl1</em> mutants can be rescued by PHR1 homologs from chlorophyte algae, liverwort and rice, suggesting their conserved roles in ABA signalling. These results indicate that PHR1 and its homologs negatively regulate plant responses to ABA in seed germination and stomatal aperture. This study provides new insights into the interplay between Pi homeostasis, abiotic stress and ABA signaling. Moderately increasing the expression of <em>PHR1</em> or its homologs in crops could be a potential strategy to enhance plant resistance to combined LP and osmotic stress.</div></div>","PeriodicalId":20273,"journal":{"name":"Plant Science","volume":"352 ","pages":"Article 112389"},"PeriodicalIF":4.2,"publicationDate":"2025-01-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143010340","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The TIFY transcription factor ZmJAZ13 enhances plant tolerance to drought and salt stress by interacting with ZmbHLH161 and ZmA0A1D6GLB9","authors":"Shipeng Zhang ,&nbsp;Dengyu Zheng ,&nbsp;Yuqi Gao ,&nbsp;Meng She ,&nbsp;Zhongyi Wu ,&nbsp;Yuncai Lu ,&nbsp;Zhongbao Zhang","doi":"10.1016/j.plantsci.2025.112388","DOIUrl":"10.1016/j.plantsci.2025.112388","url":null,"abstract":"<div><div>The JAZ protein family, serving as a key negative regulator in the jasmonic acid signaling pathway, interacts with transcription factors to play an essential role in plant growth, development, and stress responses. However, minimal research has focused on the role of JAZ transcription factors in regulating the growth, development, and stress responses of maize. In this study, we cloned the JAZ gene <em>ZmJAZ13</em> from maize (<em>Zea mays</em> L.) and conducted a preliminary analysis of its biological function. <em>ZmJAZ13</em> was highly expressed in maize immature embryos and was induced by abiotic stress and plant hormone treatments. Y2H and BiFC assays revealed interactions between <em>ZmJAZ13</em> and <em>ZmbHLH161</em>, as well as <em>ZmA0A1D6GLB9</em>. Heterologous expression of <em>ZmJAZ13</em> in <em>Arabidopsis</em> significantly enhanced plant tolerance to drought and salt stress, increased chlorophyll content, decreased malondialdehyde content, and enhanced peroxidase activity. Under abiotic stress, heterologous expression of <em>ZmJAZ13</em> in <em>Arabidopsis</em> upregulated the expression levels of stress-related genes (<em>RD22</em>, <em>RD29-A</em>). Together, these results suggested that <em>ZmJAZ13</em> may respond to abiotic stress, providing a foundation for further investigation into the mechanism of action of <em>ZmJAZ13</em> in maize.</div></div>","PeriodicalId":20273,"journal":{"name":"Plant Science","volume":"352 ","pages":"Article 112388"},"PeriodicalIF":4.2,"publicationDate":"2025-01-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143010339","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"GhWRKY207 improves drought tolerance through promoting the expression of GhCSD3 and GhFSD2 in Gossypium hirsutum","authors":"Gaofeng Zhang ,&nbsp;Weichao Li ,&nbsp;Tong Han ,&nbsp;Tianyi Huang ,&nbsp;Lirong Sun ,&nbsp;Fushun Hao","doi":"10.1016/j.plantsci.2025.112392","DOIUrl":"10.1016/j.plantsci.2025.112392","url":null,"abstract":"<div><div>Tryptophan-arginine-lysine-tyrosine (WRKY) transcription factors are essential regulators of drought tolerance in multiple plants. However, whether and how GhWRKY207 modulates cotton response to drought stress is unclear. In this study, we determined that <em>GhWRKY207</em> expression was high in leaves and induced by drought stress. The gene encoded a nuclear protein that had transcriptional activation activity. Silencing <em>GhWRKY207</em> by virus-induced gene silencing (VIGS) caused significant reduction in drought tolerance of cotton plants. Consistently, overexpression of <em>GhWRKY207</em> in <em>Arabidopsis thaliana</em> wild type (WT) plants clearly enhanced their drought tolerance. Moreover, <em>GhWRKY207</em> VIGS plants had notably increased malondialdehyde (MDA) contents, electrolyte leakage percentages and O₂^{<strong>·−</strong>} accumulation rates whereas <em>GhWRKY207</em> overexpression lines showed markedly decreased levels of the three parameters compared to their corresponding controls under water deficit conditions. Additionally, GhWRKY207 enhanced superoxide dismutase (SOD) activity by directly activating the expression of <em>GhCu/Zn-SOD3</em> (<em>GhCSD3</em>) and <em>GhFe-SOD2</em> (<em>GhFSD2</em>) genes. Silencing <em>GhCSD3</em> or <em>GhFSD2</em> also markedly reduced drought tolerance of cotton plants. Taken together, these results suggest that GhWRKY207 positively regulates drought tolerance by inducing the expression of <em>GhCSD3</em> and <em>GhFSD2</em> in <em>Gossypium hirsutum</em>.</div></div>","PeriodicalId":20273,"journal":{"name":"Plant Science","volume":"352 ","pages":"Article 112392"},"PeriodicalIF":4.2,"publicationDate":"2025-01-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142984356","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Effects of reactive oxygen species on fruit ripening and postharvest fruit quality","authors":"Wenying Wei,&nbsp;Zesheng Liu,&nbsp;Xuejuan Pan,&nbsp;Tingyue Yang,&nbsp;Caiting An,&nbsp;Yuanhui Wang,&nbsp;Long Li,&nbsp;Weibiao Liao,&nbsp;Chunlei Wang","doi":"10.1016/j.plantsci.2025.112391","DOIUrl":"10.1016/j.plantsci.2025.112391","url":null,"abstract":"<div><div>Reactive oxygen species (ROS) serve as important signaling molecule, involved in numerous biological processes, particularly in the physiological changes associated with fruit ripening and postharvest handing. This review explores ROS key role in plant fruit ripening and postharvest quality. The mechanism of ROS production and degradation in maintaining ROS homeostasis are analyzed in detail. Fruit ripening is a complex and highly coordinated process involving physiological and biochemical changes. Studies have observed that the content of ROS, mainly hydrogen peroxide (H₂O₂), dynamically changes in various types of fruits during ripening. Furthermore, ROS have significant effects on fruit softening, color change, and other ripening processes. In addition, in the postharvest stage, the abnormal accumulation of ROS isclosely related to the decline in fruit quality and the occurrence of decay browning, which seriously affects the market value and shelf life of fruit. Overall, this review demonstrates the crucial role of ROS in regulating the ripening process and postharvest quality of fruit.</div></div>","PeriodicalId":20273,"journal":{"name":"Plant Science","volume":"352 ","pages":"Article 112391"},"PeriodicalIF":4.2,"publicationDate":"2025-01-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142979739","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Rice THIN CULM 4 (TC4) modulates culm strength by regulating morphology, structure, and development","authors":"Ran Zhou ,&nbsp;Chenbo Huang ,&nbsp;Xiaoxia Wen ,&nbsp;Zhihao Sun ,&nbsp;Wei Dong ,&nbsp;Yuyu Chen ,&nbsp;Nuan Huang ,&nbsp;Han Zhang ,&nbsp;Haihan Su ,&nbsp;Yanhui Li ,&nbsp;Zequn Peng ,&nbsp;Yingxin Zhang ,&nbsp;Liyong Cao ,&nbsp;Shihua Cheng ,&nbsp;Xiaodeng Zhan ,&nbsp;Lianping Sun ,&nbsp;Daibo Chen","doi":"10.1016/j.plantsci.2024.112375","DOIUrl":"10.1016/j.plantsci.2024.112375","url":null,"abstract":"<div><div>Culm strength is crucial for rice growth, nutrition transportation, and structural resilience, which are essential for lodging resistance and stable production. In this study, we identified a rice thin culm mutant <em>tc4</em>, characterized by thinner culms and thicker cavity walls, resulting in weakened culm mechanical strength. Using map-based cloning, the candidate gene was isolated, and complementation and CRISPR/Cas9 experiments confirmed that a single nucleotide substitution in <em>TC4</em> is responsible for the thin and brittle culm phenotype. <em>TC4</em>, a homolog of the <em>FLORICAULA/LEAFY</em> gene, localizes to the nucleus and cytoplasm. Further research revealed that <em>TC4</em> regulates culm development by influencing plant hormones and sugar transport. This research not only advances our understanding of rice culm regulation, but also provides valuable insights for breeding lodging-resistant rice varieties.</div></div>","PeriodicalId":20273,"journal":{"name":"Plant Science","volume":"352 ","pages":"Article 112375"},"PeriodicalIF":4.2,"publicationDate":"2025-01-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142971938","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"3,4-dimethylpyrazole phosphate (DMPP) may negate the expected stimulation of elevated atmospheric CO2 and warming on fertilizer-N loss","authors":"Wenjie Zhang ,&nbsp;Lin Zhao ,&nbsp;Ting Zhang ,&nbsp;Mengyun Shi ,&nbsp;Dianjun Lu ,&nbsp;Shuai Wang ,&nbsp;Jia Zhang ,&nbsp;Wei Jiang ,&nbsp;Meng Wei","doi":"10.1016/j.plantsci.2025.112386","DOIUrl":"10.1016/j.plantsci.2025.112386","url":null,"abstract":"<div><div>People have accepted the clear fact that elevated CO₂ (eCO₂) and climate warming are happening, but sustainable agricultural systems are still struggling to adapt. 3,4-dimethyl-1H-pyrazol phosphate (DMPP) is currently recognized as a highly effective strategy for reducing nitrogen (N) loss and related environmental impacts. There is still uncertainty, however, whether DMPP could contribute to building climate-resilient ecosystems in a future climate scenario with co-elevated CO₂ and temperature. Thus, this study evaluated the responses of plant N derived from soil or fertilizer and strawberry growth to the tested climate conditions. Plants were supplied with or without DMPP, grown in controlled climate chambers under ambient CO₂ and temperature (aCT; 400 ppm + 25℃), and co-elevated CO₂ and temperature (eCT; 800 ppm + 27℃). The results showed that DMPP increased plant N accumulation by 9 % and 19 % under aCT and eCT conditions, respectively, compared to N treatment without DMPP. We also found a similar trend in total C content in the plants. Compared with aCT, DMPP demonstrated higher efficiency in improving N use efficiency (NUE, 51 % vs. 36 %) and reducing N loss (21 % vs. 29 %) under eCT, which could ensure higher N demand of plant, making fertilizer-N, rather than soil-N, a primary contributor to the N accumulation increment. Moreover, in terms of combating climate challenge, the combination with DMPP further strengthened the beneficial influence of eCT on the N accumulation and biomass in strawberry but reduced fertilizer-N loss. In summary, DMPP exhibits better performance under eCT, which may alleviate the potential adverse effects of co-elevated CO₂ and temperature on ecosystem by reducing fertilizer-N loss and soil-N mineralization more efficiently, providing a promising approach to optimizing sustainable agricultural management under future climate change.</div></div>","PeriodicalId":20273,"journal":{"name":"Plant Science","volume":"352 ","pages":"Article 112386"},"PeriodicalIF":4.2,"publicationDate":"2025-01-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142966430","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"WD40 proteins PaTTG1 interact with both bHLH and MYB to regulate trichome formation and anthocyanin biosynthesis in Platanus acerifolia","authors":"Qi Mengxuan,&nbsp;Tian Xinyue,&nbsp;Chen Yuqing,&nbsp;Lu Yongkang,&nbsp;Zhang Yanping","doi":"10.1016/j.plantsci.2025.112385","DOIUrl":"10.1016/j.plantsci.2025.112385","url":null,"abstract":"<div><div>Trichome development and anthocyanin accumulation are regulated by a complex regulatory network, the MBW complexe consists of MYB, bHLH, and WD40 transcription factors. In this study, two sequences, named <em>PaTTG1.1</em>, and <em>PaTTG1.2</em>, were cloned and functionally characterized from <em>Platanus acerifolia.</em> Quantitative real-time PCR results showed that <em>PaTTG1</em> genes were expressed in the trichomes and red leaves. Overexpression of <em>PaTTG1.1</em> and <em>PaTTG1.2</em> genes in <em>Arabidopsis ttg1</em> mutants restored the phenotypes of <em>ttg1</em> mutants that were glabrous and lacked purple anthocyanins in hypocotyls and seeds. In transgenic plants, the expression levels of the trichome regulation-related genes <em>AtCPC</em>, <em>AtTRY</em>, <em>AtETC1</em>, <em>AtMYB23,</em> and <em>AtGL2</em>, as well as early and late biosynthetic genes related to anthocyanin biosynthesis, were significantly upregulated. The results of the yeast two-hybrid showed that PaTTG1.1 and PaTTG1.2 proteins could physically interact with both bHLH and R2R3-MYB transcription factors from <em>Arabidopsis</em> and <em>P. Acerifolia</em>. Taken together, the results presented in this study suggest that the two <em>PaTTG1</em> genes share similar functions in the regulation of trichomes and anthocyanins. However, there may be some differences in their regulatory mechanisms.</div></div>","PeriodicalId":20273,"journal":{"name":"Plant Science","volume":"352 ","pages":"Article 112385"},"PeriodicalIF":4.2,"publicationDate":"2025-01-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142971939","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genome-wide association study of rice (Oryza sativa L.) inflorescence architecture","authors":"Masoumeh Kordi ,&nbsp;Naser Farrokhi ,&nbsp;Asadollah Ahmadikhah ,&nbsp;Pär K. Ingvarsson ,&nbsp;Abbas Saidi ,&nbsp;Mehdi Jahanfar","doi":"10.1016/j.plantsci.2024.112382","DOIUrl":"10.1016/j.plantsci.2024.112382","url":null,"abstract":"<div><div>Rice yield strongly depends on panicle size and architecture but the genetics underlying these traits and their coordination with environmental cues through various signaling pathways have remained elusive. A genome-wide association study (GWAS) was performed to pinpoint the underlying genetic determinants for rice panicle architecture by analyzing 20 panicle-related traits using a data set consisting of 44,100 SNPs. We defined QTL windows around significant SNPs by the rate of LD decay for each chromosome and used these windows to identify putative candidate genes associated with the trait. Using a publicly available RNA-seq data set we performed analyses to identify the differentially expressed genes between stem and panicle with putative functions in panicle architecture. In total, 52 significant SNPs were identified, corresponding to 41 unique QTLs across the 12 rice chromosomes, with the most signals appearing on chromosome 1 (nine associated SNPs), and seven significant SNPs for each of chromosomes 8 and 12. Some novel genes such as <em>Ankyrin</em>, <em>Duf</em>, <em>Kinesin</em> and <em>Brassinosteroid insensitive</em> were found to be associated with panicle size. A haplotype analysis showed that genetic variation in haplotypes qMIL2 and qNSBBH21 were related to two traits, MIL, the greatest distance between two nodes on the rachis, and NSBBH, the number of primary branches in the bottom half of a panicle, respectively. Analysis of epistatic interactions revealed a marker affecting clustered traits. Several QTLs were identified on different chromosomes for the first time which may explain the phenotypic diversity of rice panicle architecture we observe in our collection of accessions. The identified candidate genes and haplotypes could be used in marker-assisted selection to improve rice yield through gene pyramiding.</div></div>","PeriodicalId":20273,"journal":{"name":"Plant Science","volume":"352 ","pages":"Article 112382"},"PeriodicalIF":4.2,"publicationDate":"2025-01-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142971937","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}