Current Plant Biology最新文献

{"title":"Two-year QTL dissecting of high harvest index and related traits in a novel rice variety Yuenongsimaio","authors":"Shiguang Wang ,&nbsp;Liting Zhang ,&nbsp;Wei Liu,&nbsp;Xiaofei Wang,&nbsp;Haoxiang Wu,&nbsp;Hao Chen,&nbsp;Tengkui Chen,&nbsp;Zhanhua Lu,&nbsp;Xiuying He","doi":"10.1016/j.cpb.2025.100475","DOIUrl":"10.1016/j.cpb.2025.100475","url":null,"abstract":"<div><div>High harvest index (HI), defined as the grain yield-to-biomass ratio (≥ 0.55), reflects a well-balanced source-sink relationship. It is a key trait in rice high-HI breeding programs, which has proven to be a successful strategy for developing super high-yield rice varieties. However, its genetic basis remains elusive. This study conducted QTL analysis for HI-related traits using a recombinant inbred line (RIL) population derived from a cross between a <em>geng</em>/<em>japonica</em> cultivar, Lijiangxintuanheigu (LTH), and a high HI <em>xian</em>/<em>indica</em> variety, Yuenongsimiao (YNSM). A high‑density genetic map with 6674 bin markers identified 97 QTLs across 12 HI-related traits, forming 13 QTL clusters that affect the source-sink related traits in rice. These bin markers were converted from 1,009,324 high-quality SNPs sourced from the sequenced RIL population. Notably, <em>qRSC1</em> (QTL cluster of <em>rice source capacity 1</em>), which included <em>qFLL1</em>, <em>qSTW1</em>, <em>qBM1.2</em>, and <em>qHI1</em>, was tightly linked to the semi-dwarf gene <em>sd1</em> and collectively shaped the high HI plant architecture of YNSM. In contrast, <em>qRSC3</em> (<em>qFLL3</em>/<em>qFLW3</em>/<em>qSTW3</em>/<em>qBM3.1</em>/<em>qHI3.1</em>) exhibited an opposite effect and positively regulated source-related traits. Among nine QTLs associated with yield per plant (YPP), only <em>qYPP2.2</em>, part of <em>qRSS2</em> (QTL cluster of <em>rice sink size 2</em>), was consistently detected over two consecutive years. <em>qRSS2</em> governed sink size by integrating multiple yield-related QTLs, including <em>qYPP2.2</em>. Overall, <em>qRSC1</em>, <em>qRSC3</em>, and <em>qRSS2</em> collectively optimized source-sink balance, enabling YNSM’s high HI and high yields. These findings provide insights into the genetic basis of high HI in YNSM and may facilitate breeding high-yielding rice with superior HI.</div></div>","PeriodicalId":38090,"journal":{"name":"Current Plant Biology","volume":"42 ","pages":"Article 100475"},"PeriodicalIF":5.4,"publicationDate":"2025-04-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143816036","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Meta-analysis of grapevine microbiota: Insights into the influence of cultivars, plant parts, geography, and vineyard practices on bacterial diversity","authors":"Daniel Legesse,&nbsp;Yassine Bouhouch,&nbsp;Cédric Jacquard,&nbsp;Lisa Sanchez,&nbsp;Essaid Ait-Barka,&nbsp;Qassim Esmaeel","doi":"10.1016/j.cpb.2025.100478","DOIUrl":"10.1016/j.cpb.2025.100478","url":null,"abstract":"<div><div>Investigating the grapevine microbiome is crucial for developing sustainable management practices in viticulture. This meta-analysis used amplicon metagenomics to analyze bacterial sequences from the Sequence Read Archive, covering 756 grapevine accessions. The dataset includes 378 paired end sequencing runs across twelve cultivars, four sample types, six origins, and two vineyard conditions. The analysis revealed significant variations in microbial communities across different grapevine cultivars and sample types, highlighting the influence of both the cultivar and ecological niche on microbial diversity. Differential abundance analyses further identified key microbial taxa driving variations across different grapevine plant parts. Furthermore, the study identified microbial taxa that consistently thrive across diverse conditions, suggesting their potential role in grapevine health and development. These findings support the possibility of utilizing specific microbial agents for biological control and sustainable vineyard management. This meta-analysis underscores the complexity of the grapevine microbiome and its pivotal role in vineyard ecosystems, providing valuable insights for future research and the advancement of sustainable viticulture practices.</div></div>","PeriodicalId":38090,"journal":{"name":"Current Plant Biology","volume":"42 ","pages":"Article 100478"},"PeriodicalIF":5.4,"publicationDate":"2025-04-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143799503","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}

{"title":"Physiological novelties for salinity tolerance created by transgressive effects and cryptic gene functions unlocked by alien introgression from Oryza rufipogon to Oryza sativa","authors":"Swarupa Nanda Mandal ,&nbsp;Ai Kitazumi ,&nbsp;Coenraad R. van Beek ,&nbsp;Isaiah C.M. Pabuayon ,&nbsp;Jacobo Sanchez ,&nbsp;Benildo G. de los Reyes","doi":"10.1016/j.cpb.2025.100477","DOIUrl":"10.1016/j.cpb.2025.100477","url":null,"abstract":"<div><div>The inherent complexity of adaptive mechanisms to salinity stress necessitates novel approaches to plant breeding. In rice, wide introgression is an approach that is yet to be fully exploited, especially from the not-so-distant species related to cultivars. We explored the genetic combining potential of the AA-genome wild species <em>Oryza rufipogon,</em> the closest progenitor of cultivated <em>Oryza sativa</em> ssp. japonica, to uncover physiological novelties for salinity tolerance created by transgressive effects. Comprehensive evaluation of a set of chromosome segment substitution lines (CSSL) for various physiometric traits revealed the occurrence of individuals transgressing the parental phenotypic range. This indicates that introgression of alien <em>O. rufipogon</em> genomic segments into <em>O. sativa</em> genomic background can alter the overall potential of the recipient by creating novel physiological attributes better than the donor or worse than the recipient. In-depth characterization of transgressive tolerant and transgressive sensitive CSSLs showed the occurrence of novel attributes in terms of energy balance and gas exchange that positively correlated with enhanced or reduced potential for salinity tolerance. Integrated morphological, physiological, biochemical, ionomic, genomic, and transcriptomic profiling revealed five genomic regions with QTL effects, and seven genes with putative eQTL effects that explain the occurrence of transgressive phenotypes. Genes with eQTL effects are associated with the regulation of cytokinin-mediated processes, MYB transcription factors, and transmembrane transport, that positively correlated with the maintenance of shoot biomass, regulation of stomatal conductance, and modulation of cellular homeostasis. The transgressive lines had non-parental expression patterns for eleven genes that originated from <em>O. rufipogon.</em> These genes gained new patterns of regulation (de-regulation effects) in the genomic background of <em>O. sativa</em> indicating the unleashing of cryptic functions through introgression.</div></div>","PeriodicalId":38090,"journal":{"name":"Current Plant Biology","volume":"42 ","pages":"Article 100477"},"PeriodicalIF":5.4,"publicationDate":"2025-04-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143816037","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genome-wide association study (GWAS) of rice (Oryza sativa L.) panicle compactness","authors":"Masoumeh Kordi ,&nbsp;Naser Farrokhi ,&nbsp;Asadollah Ahmadikhah ,&nbsp;Pär K. Ingvarsson ,&nbsp;Abbas Saidi ,&nbsp;Mehdi Jahanfar","doi":"10.1016/j.cpb.2025.100464","DOIUrl":"10.1016/j.cpb.2025.100464","url":null,"abstract":"<div><div>The Green Revolution altered the rice panicle by increasing grain numbers per panicle. Here, we perform a genome-wide association study to understand the molecular mechanisms determining the number of grains in a panicle in rice. Panicle image analyses were performed on 158 genetically diverse rice accessions, and GWAS was run using the FarmCPU model with 34,072 single nucleotide polymorphisms to relate genotypic variation to the corresponding phenotypes. Flanking regions of candidate SNPs were separately defined for each chromosome based on LD decay distance to identify putative-associated genes. An RNA-seq data analysis was performed between stem and panicle to emphasize the role of candidate genes in panicle compactness. The results were further confirmed by a PPI network analysis using the putative candidate genes. In total 95 significant SNPs were identified; as close SNPs were considered a QTL that resulted in 56 QTLs across the 12 rice chromosomes. We identified novel candidate genes for panicle compactness traits, such as <em>cytochrome P450</em>, <em>polygalacturonase</em>, <em>glycosyltransferase</em>, <em>MADS-box, WRKY</em>, <em>YABBY</em>, <em>WUSCHEL-related homeobox, protein kinase</em>, <em>lipase, zinc finger transcription factor</em> and <em>protein phosphatase</em>. Haplotype analysis identified haplogroups <em>qNSSBB53</em>, <em>qNSSBB102</em>, <em>qNSSBU3</em>, <em>qNSSBU21</em>, and <em>qLS3</em> for three traits of NSSBB, NSSBU and LS. An analysis of epistatic interactions among candidate SNPs identified 91 significant SNP-SNP interactions.</div></div>","PeriodicalId":38090,"journal":{"name":"Current Plant Biology","volume":"42 ","pages":"Article 100464"},"PeriodicalIF":5.4,"publicationDate":"2025-04-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143776659","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}

{"title":"Artificial intelligence for fostering sustainable agriculture","authors":"Konathala Kusumavathi ,&nbsp;Ramesh Konatala ,&nbsp;Priyanka Lal ,&nbsp;Smritikana Sarkar ,&nbsp;Hirak Banerjee ,&nbsp;Pintoo Bandopadhyay ,&nbsp;Debadatta Sethi ,&nbsp;Konga Upendar","doi":"10.1016/j.cpb.2025.100476","DOIUrl":"10.1016/j.cpb.2025.100476","url":null,"abstract":"<div><div>Agriculture intensification has a paradoxical effect, as it increases food production and productivity by increasing farmer’s return on investment while instantaneously posing a serious threat to long-term sustainability like depletion of resources, soil degradation, water scarcity and finally environmental pollution. All these challenges have flickered concerns about the quality of life. To bash all these concerns, the precise and judicious use of agricultural inputs is necessary. Bespoke solutions (Site-Specific) tailored to specific problems can optimize resource utilization while minimizing negative impacts. Integrating advanced technologies like automation by the use of sensors, drones and robotics guarantees solutions in the context of availability and efficiency of agricultural labour decline. This technology-driven approach can reform agriculture. So, the holistic approach of using technological advancements with sustainable practices is necessary for a long-term ecological balance with enhancement in productivity. The integration of driven solutions allows farmers to obtain real-time insights into soil health, water availability and nutrient status facilitating sustainable farming practices. The main goal of this manuscript is to review the applications of AI in agriculture for crop monitoring with sustainable use of resources such as soil, water, and nutrients, as well as to elevate food production with better quality maintenance. This article scrutinizes the findings of several researchers to get a brief outline of the subject of the recent execution of automation in agriculture and compares it with conventional methods followed by the farmer.</div></div>","PeriodicalId":38090,"journal":{"name":"Current Plant Biology","volume":"42 ","pages":"Article 100476"},"PeriodicalIF":5.4,"publicationDate":"2025-03-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143715009","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}

{"title":"Enhancing wheat yellow rust detection through modified deep learning approach","authors":"Shant Kumar ,&nbsp;Rohit Singh ,&nbsp;Sudheer Kumar ,&nbsp;Sandeep Gupta","doi":"10.1016/j.cpb.2025.100472","DOIUrl":"10.1016/j.cpb.2025.100472","url":null,"abstract":"<div><div>The study reports the effectiveness of machine learning and deep learning (ML/DL) algorithms in detecting yellow rust disease in wheat, keeping in view that early stage detection is crucial for minimizing the crop yield loss. Various traditional ML algorithms including Support Vector Machine (SVM), Decision Tree (DT), k-Nearest Neighbor KNN, Naïve Bayes (NB), Random Forest (RF) and Sequential Convolutional Neural Network (CNN) are utilized to access the plant disease detection efficiency. In contrast a modified version of CNN (MCNN), integrated with SVM principles, is proposed to enhance the performance of standard CNN. A newly established dataset named Yellow Rust 2022–2023 (YR-22/23) is used to estimate and compare the performance of considered ML/DL algorithms. Additionally, a benchmarked dataset named YellowRust-19 is considered for cross validation of ML/DL algorithms. The result indicates that the MCNN outperforms the standard algorithms (CNN) in terms of accuracy (1.2 %) metrics and is highly time efficient. Our proposed modified CNN method attained prediction accuracy of about 98 % for detection of yellow rust of wheat. Result highlights that merger of ML/DL approaches holds great promises to improve the overall efficiency of plant disease detection.</div></div>","PeriodicalId":38090,"journal":{"name":"Current Plant Biology","volume":"42 ","pages":"Article 100472"},"PeriodicalIF":5.4,"publicationDate":"2025-03-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143715008","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}

{"title":"Glycine max Sec61 complex genes function in the soybean defense response to the parasitic nematode Heterodera glycines","authors":"Hallie A. Troell ,&nbsp;Keshav Sharma ,&nbsp;Gary W. Lawrence ,&nbsp;Kathy S. Lawrence ,&nbsp;Nadim W. Alkharouf ,&nbsp;Vincent P. Klink","doi":"10.1016/j.cpb.2025.100474","DOIUrl":"10.1016/j.cpb.2025.100474","url":null,"abstract":"<div><div>The <em>Glycine max</em> (soybean) secretory pathway performs important roles during the defense response to <em>Heterodera glycines</em> parasitism. However, the involvement of some aspects of the secretory machinery remains unexamined. The Sec61 complex of the eukaryote secretory pathway is composed of Sec61-α, Sec61-β, and Sec61-γ which bind, forming a trimeric complex that imports proteins into the ER for their processing, transport, and secretion. Comparative analyses using <em>Saccharomyces cerevisiae</em> Sec61-α, Sec61-β, and Sec61-γ protein sequences show <em>G. max</em> has homologs of each, 4 Sec61-α, 6 Sec61-β, and 4 Sec61-γ paralogs. At least one paralog from each gene family is expressed in <em>H. glycines</em>-parasitized <em>G. max</em> root cells during its defense process. <em>GmSec61-</em>α, <em>GmSec61-</em>β, and <em>GmSec61-</em>γ overexpression in the <em>H. glycines</em>-susceptible <em>G. max</em>_{[Williams 82/PI 518671]} leads to an engineered defense response. In contrast, RNAi of <em>GmSec61-</em>α, <em>GmSec61-</em>β, and <em>GmSec61-</em>γ in the <em>H. glycines</em>-resistant <em>G. max</em>_{[Peking/PI 548402]} generates susceptibility. The combined opposite outcomes of <em>GmSec61</em> overexpression and RNAi provide evidence that they function in the defense process, consistent with the hypothesis that the <em>G. max</em> secretion system plays a role in its defense to <em>H. glycines</em> parasitism. The identification of Sec61-α, Sec61-β, and Sec61-γ homologs in 51 additional flowering plants spanning 20 Orders and 26 Families including the agriculturally-important <em>Beta vulgaris</em> ssp. vulgaris (sugar beet) demonstrates a potentially broad defense role not limited to these plant species. Computational studies identified genes encoding proteins having signal peptides in <em>B. vulgaris</em> parasitized by <em>H. schachtii</em> but undergoing a defense response further demonstrating the importance of Sec61 translocon in resistance.</div></div>","PeriodicalId":38090,"journal":{"name":"Current Plant Biology","volume":"42 ","pages":"Article 100474"},"PeriodicalIF":5.4,"publicationDate":"2025-03-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143704963","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}

{"title":"CaRcd1 positively regulates pepper (Capsicum annuum L.) regeneration by interacting with the transcription factor CaGATA26 to inhibiting CaTMKL1 expression","authors":"Han Qiao ,&nbsp;Mingxuan Li ,&nbsp;Yan Chen ,&nbsp;Xiangyun Cui ,&nbsp;Ruiquan Ye ,&nbsp;Sujun Liu ,&nbsp;Han Hui ,&nbsp;Liang Sun ,&nbsp;Qing Cheng ,&nbsp;Huolin Shen","doi":"10.1016/j.cpb.2025.100471","DOIUrl":"10.1016/j.cpb.2025.100471","url":null,"abstract":"<div><div>Pepper serves as a significant vegetable and spice crop, with fruits abundant in bioactive compounds and substantial potential applications in industries. As the crop widely regarded as recalcitrant to regeneration, the regeneration and transgenic system based on tissue culture for pepper remains underdeveloped. This study initially evaluated 60 varieties for regeneration potential and identified the differentiation of normal shoots (with meristem) during redifferentiation, as the most critical limiting factor in pepper regeneration. Selected R60 as the variety with superior regeneration capacity through pharmacological and RNA-seq analyses of the typical features of dedifferentiation and redifferentiation. Within the same genetic context, we observed that <em>CaRcd1</em> (<em>Required for cell differentiation 1</em>) was positively associated with the regenerative ability of pepper, while <em>CaTMKL1</em> (<em>Transmembrane Kinase-Like 1</em>) was negatively associated. Furthermore, transgenic experiments demonstrated that <em>CaRcd1</em>-OE significantly doubled the rate of normal shoot differentiation. At the protein level, transcription factor CaGATA26, as an interacting protein, is screened by IP-MS, and the interaction could inhibit the transcriptional promotion of TF CaGATA26 on the auxin binding protein encoding gene <em>CaTMKL1</em>, thereby reducing the expression of <em>CaTMKL1</em>, inhibiting the transfer of auxin in callus can improve the regenerative ability of pepper. Our study presents a novel pathway for regulating regeneration ability, centered on CaRcd1, and provides a novel reference framework for tissue culture in plants facing regeneration challenges.</div></div>","PeriodicalId":38090,"journal":{"name":"Current Plant Biology","volume":"42 ","pages":"Article 100471"},"PeriodicalIF":5.4,"publicationDate":"2025-03-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143682497","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}

{"title":"Physiological responses of Lemna minor to polystyrene and polymethyl methacrylate microplastics","authors":"Karla Košpić ,&nbsp;Sandra Vitko ,&nbsp;Luka Kobelščak ,&nbsp;Ana Matešković ,&nbsp;Petra Peharec Štefanić ,&nbsp;Nino Dimitrov ,&nbsp;Mirta Tkalec ,&nbsp;Biljana Balen","doi":"10.1016/j.cpb.2025.100473","DOIUrl":"10.1016/j.cpb.2025.100473","url":null,"abstract":"<div><div>Due to its economic viability, plastic has become an indispensable material whose mass production continues to increase, raising concerns about its impact on living organisms. Its long persistence in the environment and slow degradation to microplastics (MPs) pose a serious problem, as MPs can penetrate plants and animals and interfere with physiological processes. In this study, the <em>in vitro</em> cultured duckweed <em>Lemna minor</em> was exposed to 10, 50 and 100 mg L⁻¹ polystyrene (PS) and polymethyl methacrylate (PMMA) MPs for 7 days to investigate uptake and effects on growth, photosynthetic performance and oxidative stress parameters. We hypothesized that PS-MPs and PMMA-MPs would have different uptake patterns and effects on the physiology of <em>L. minor</em>, due to their different properties. A pronounced agglomeration of PMMA-MPs in the exposure medium correlated with a lower uptake of PMMA-MPs compared to PS-MPs. However, PMMA-MPs induced severe ultrastructural changes in the chloroplasts and a decrease in chlorophyll <em>a</em> and <em>b</em> content, resulting in reduced plant growth. In contrast, treatments with PS-MPs stimulated growth, especially frond area, probably as a result of increased content of photosynthetic pigments and improved photosynthetic efficiency. Both MP types induced mild oxidative stress, which triggered protective responses, but the activation of antioxidant defense was dependent on the polymer type, as PMMA-MPs slightly increased proline content and superoxide dismutase activity, while PS-MPs induced peroxidase activities. In conclusion, PS-MPs seem to be less harmful as they promote growth and photosynthetic efficiency, whereas PMMA-MPs have negative effects on <em>L. minor</em> physiology by causing structural damage to subcellular parts and inhibiting their function.</div></div>","PeriodicalId":38090,"journal":{"name":"Current Plant Biology","volume":"42 ","pages":"Article 100473"},"PeriodicalIF":5.4,"publicationDate":"2025-03-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143682496","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}

{"title":"Genome-wide sequence comparison and development of InDel and SNP markers to facilitate localized rice breeding","authors":"Juan Pariasca-Tanaka ,&nbsp;Yoshiaki Ueda ,&nbsp;Katsuhiko Kondo ,&nbsp;M. Asaduzzaman Prodhan ,&nbsp;Toavintsoa Rajonandraina ,&nbsp;Harisoa Nicole Ranaivo ,&nbsp;Mbolatantely Fahazavana Rakotondramanana ,&nbsp;Hiroki Saito ,&nbsp;Lam Thi Dinh ,&nbsp;Matthias Wissuwa","doi":"10.1016/j.cpb.2025.100469","DOIUrl":"10.1016/j.cpb.2025.100469","url":null,"abstract":"<div><div>Rice (<em>Oryza sativa</em> L.) is the staple crop for over half of the world's population and selection in different environmental and climatic conditions has led to the development of numerous local rice cultivars. In a changing environment, these local cultivars may need to be adapted to emerging stresses. Whole-genome sequences are available only for a small fraction of existing rice cultivars, limiting the opportunity for genomics-based marker-assisted selection (MAS) in most local cultivars. To efficiently develop locally-adapted rice cultivars resilient to adverse environmental conditions, our objective was to develop a pipeline for the analysis of re-sequencing data and the development of low-cost allele-specific markers that can be implemented in developing countries. This study focused on three rice cultivars (X265, F160, and Nerica4) commonly grown in Madagascar. We provide whole-genome sequencing data and identify sequence variations compared to publicly available sequences, followed by the development of simple PCR-based InDel and SNP markers. Their effectiveness in distinguishing different alleles at the <em>Ghd7</em> locus controlling heading date was demonstrated, enabling us to employ these markers for MAS in a breeding population developed between X265 and a donor “Liu He Xi He”. In addition, we developed PCR-based SNP markers for the same population on <em>qLFT-5</em>, a quantitative trait locus for low-fertility tolerance in which the donor allele increases total panicle weight under low-input conditions. This study presents a practical pipeline for the utilization of next generation sequencing-derived large-scale data to accelerate low-cost marker development for MAS in rice and other crop species.</div></div>","PeriodicalId":38090,"journal":{"name":"Current Plant Biology","volume":"42 ","pages":"Article 100469"},"PeriodicalIF":5.4,"publicationDate":"2025-03-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143654517","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}