Theoretical and Applied Genetics最新文献_第8页

Genome-wide association study reveals that the SUS domain protein SS7 positively regulates seed storability in rice (Oryza sativa L.). 全基因组关联研究表明，水稻SUS结构域蛋白SS7正调控种子贮藏性。

IF 4.2 1区农林科学

Theoretical and Applied Genetics Pub Date : 2025-08-07 DOI: 10.1007/s00122-025-04976-y

Xinyang Luo, Yuntao Yan, Xi He, Jinxing Gui, Yixin Wang, Chenyun Gong, Jinling Liu, Haiqin Zhang, Jiwai He

{"title":"Genome-wide association study reveals that the SUS domain protein SS7 positively regulates seed storability in rice (Oryza sativa L.).","authors":"Xinyang Luo, Yuntao Yan, Xi He, Jinxing Gui, Yixin Wang, Chenyun Gong, Jinling Liu, Haiqin Zhang, Jiwai He","doi":"10.1007/s00122-025-04976-y","DOIUrl":"https://doi.org/10.1007/s00122-025-04976-y","url":null,"abstract":"Key message: The rice seed storability gene Seed storability 7 (SS7) encodes a cytosol localized sucrose synthase (SUS) domain protein. SS7 positively regulates seed storability by enhancing the activity of peroxidase and nitrate reductase (NR) in seeds, resulting in the reduction of ROS and NO accumulation during seed storage. Long-term storage of crop seeds is essential for conserving germplasm resources, ensuring food security, and supporting sustainable agriculture. In this study, we characterized the function of Seed storability 7 (SS7), the causal gene for the QTL qSS7-1 responsible for rice seed storability identified by genome-wide association studies (GWAS). SS7 encodes a cytosol localized sucrose synthase (SUS) domain protein. Overexpression of SS7 significantly enhanced seed storability under both artificial and natural aging conditions. While knockout of SS7 has no significant effects in seed storability, but showed a phenotype of enhanced elongation of rice root. Transcriptome analysis revealed that differentially expressed genes (DEGs) involving in the hydrogen peroxide (H₂O₂) catabolic pathway were significantly enriched in SS7 overexpression lines; in contrast, the DEGs in both H₂O₂ catabolism and nitric oxide (NO) biosynthesis pathways were enriched in SS7 knockout lines. Furthermore, ROS accumulated significantly in SS7 knockout seeds, whereas SS7 overexpression in seeds resulted in a significant enhancement of peroxidase activity and a significant reduction in nitrate reductase (NR) activity, compared to SS7 knockout seeds. These results suggested that SS7 enhances seed storability by reducing the accumulation of peroxides, but inhibits root elongation by promoting NO accumulation, of which provides new insights into understanding the molecular mechanisms of rice seed storability.","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"138 9","pages":"202"},"PeriodicalIF":4.2,"publicationDate":"2025-08-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144795556","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Integrative genomic structural variation analysis unveils genetic architecture underlying important traits in Gossypium barbadense. 整合基因组结构变异分析揭示了巴氏棉重要性状的遗传结构。

IF 4.2 1区农林科学

Theoretical and Applied Genetics Pub Date : 2025-08-07 DOI: 10.1007/s00122-025-04987-9

Hongge Li, Zhenzhen Wang, Zhen Peng, Pengpeng Wang, Baojun Chen, Xiaoli Geng, Daowu Hu, Peng Zhang, Jun Ma, Shoupu He, Xiongming Du

{"title":"Integrative genomic structural variation analysis unveils genetic architecture underlying important traits in Gossypium barbadense.","authors":"Hongge Li, Zhenzhen Wang, Zhen Peng, Pengpeng Wang, Baojun Chen, Xiaoli Geng, Daowu Hu, Peng Zhang, Jun Ma, Shoupu He, Xiongming Du","doi":"10.1007/s00122-025-04987-9","DOIUrl":"https://doi.org/10.1007/s00122-025-04987-9","url":null,"abstract":"Key message: Through GWAS incorporating SVs, we identified 143 loci in Gossypium barbadense, including pleiotropic loci governing fiber quality (FQ1 and FQ2), maturity (GS1), and trichome development (LH1 and SH1). Gossypium barbadense is renowned for its exceptional fiber quality, yet its limited environmental adaptability has resulted in genetic research lagging far behind that of G. hirsutum. Here, we generated a comprehensive genomic variation map of 326 G. barbadense accessions, encompassing SNPs, InDels, and structural variations (SVs). Integrative genome-wide association studies (GWAS) of 25 traits identified 143 significant loci. The SV-based GWAS uncovered 61 loci linked to targeted traits, 53 of which were novel loci and undetectable using SNPs alone. Five pleiotropic hotspots were associated with fiber quality (FQ1, FQ2), maturity and plant architecture (GS1), and trichome development (LH1, SH1). We demonstrated additive effects of two fiber quality loci (FQ1 and FQ2) on D10 and D11, where pyramiding favorable haplotypes simultaneously improve fiber length (FL) and micronaire (FM). Transcriptome analysis further implicated Gbar_D10G011020 and Gbar_D11G011510 as candidate genes for FQ1 and FQ2, respectively. The genetic basis of trichome development was deciphered through the pleiotropic locus LH1 (A06), regulating leaf and stem trichomes in G. barbadense. Concurrently, the stem hair-specific locus SH1 on D08 harbored GbSTR, which synergizes with LH1 to increase stem trichome. Our study establishes a genomic framework for comprehensively identification of causal variations underlying key traits in G. barbadense, providing actionable loci and genes for more efficient genetic enhancement of both G. hirsutum and G. barbadense.","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"138 9","pages":"201"},"PeriodicalIF":4.2,"publicationDate":"2025-08-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144795557","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Integration of bulked segregant analysis and transcriptome sequencing reveals an interaction network associated with cluster buds trait in Brassica napus. 整合本体分离分析和转录组测序揭示了与甘蓝型油菜簇芽性状相关的相互作用网络。

IF 4.2 1区农林科学

Theoretical and Applied Genetics Pub Date : 2025-08-06 DOI: 10.1007/s00122-025-04989-7

Libin Zhang, Xin Cheng, Dengyan Chen, Lina Zhang, Weiguo Zhao, Hongbo Chao, Yongtai Yin, Hao Wang, Maoteng Li

{"title":"Integration of bulked segregant analysis and transcriptome sequencing reveals an interaction network associated with cluster buds trait in Brassica napus.","authors":"Libin Zhang, Xin Cheng, Dengyan Chen, Lina Zhang, Weiguo Zhao, Hongbo Chao, Yongtai Yin, Hao Wang, Maoteng Li","doi":"10.1007/s00122-025-04989-7","DOIUrl":"10.1007/s00122-025-04989-7","url":null,"abstract":"Key message: A core interaction network associated with cluster buds trait was discovered in Brassica napus, and indoleacetic acid-induced protein 8 (IAA8) might affect the shoot apical meristem (SAM) development through IAA8-ARF5 complex → DRN → CLV3 pathway. B. napus is one of the important oilseed crops in China. However, the low level of mechanized production restricts the industry due to the infinite inflorescence characteristics of B. napus. Therefore, the cultivation of new varieties suitable for mechanized harvesting is one of the main objectives of rapeseed breeding. In this study, a screened natural mutant of B. napus with no branching or short branches in the bolting stage and a relatively shorter flowering period showed distinct traits of cluster buds and uniform maturity, which made it suitable for high-density cultivation and mechanized harvesting. Microscopic examination between the wild-type (WT) and the cluster buds mutant (cbm) lines was performed across developmental stages. The results showed that the SAM regions of the mutants were widened and exhibited multiple growth points due to the loss of apical dominance. Transcriptome sequencing of SAM regions in the WT and cbm lines identified 2497 differentially expressed genes (DEGs). Bulk segregant analysis (BSA) pinpointed five significant genomic regions associated with the cluster buds trait and identified 799 candidate genes. Finally, an interaction network associated with the cluster buds trait was constructed, within which IAA8 was revealed as a candidate gene to regulate the SAM development in B. napus. Taken together, the present study elucidates the potential molecular regulation mechanism of cluster buds trait and laid a solid theoretical foundation for the cultivation of new varieties suitable for close planting and mechanized harvesting in B. napus.","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"138 8","pages":"200"},"PeriodicalIF":4.2,"publicationDate":"2025-08-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144790098","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Breaking genetic linkage barriers to improve brown planthopper resistance and grain yield in japonica rice. 突破遗传连锁障碍提高粳稻抗褐飞虱和产量。

IF 4.2 1区农林科学

Theoretical and Applied Genetics Pub Date : 2025-08-06 DOI: 10.1007/s00122-025-04978-w

Wenhui Wang, Jun He, Yunlong Wang, Na Li, Quanguang Sun, Menglong Zhang, Qi Li, Haosen Xu, Kun Shao, Shihao Zhang, Shijia Liu, Liangming Chen, Xi Liu, Yunlu Tian, Zhigang Zhao, Yuqiang Liu, Jianmin Wan

{"title":"Breaking genetic linkage barriers to improve brown planthopper resistance and grain yield in japonica rice.","authors":"Wenhui Wang, Jun He, Yunlong Wang, Na Li, Quanguang Sun, Menglong Zhang, Qi Li, Haosen Xu, Kun Shao, Shihao Zhang, Shijia Liu, Liangming Chen, Xi Liu, Yunlu Tian, Zhigang Zhao, Yuqiang Liu, Jianmin Wan","doi":"10.1007/s00122-025-04978-w","DOIUrl":"10.1007/s00122-025-04978-w","url":null,"abstract":"The brown planthopper (BPH) poses a persistent threat to global rice production as one of the most devastating insect pests. Development and utilization of BPH-resistant rice cultivars are believed to be the most sustainable and eco-friendly control strategy, which has been successfully implemented in indica rice subspecies but remains underdeveloped in japonica rice. Here, we introgressed the BPH resistance gene Bph27(t) into elite japonica cultivars. Although the introgressed lines demonstrated robust BPH resistance throughout all developmental stages, they unexpectedly exhibited a brown anther phenotype accompanied by significantly reduced spikelet fertility. Histological analyses revealed that the brown anther phenotype and spikelet sterility in Bph27(t)-carrying japonica plants were likely caused by delayed tapetum degradation, leading to anther indehiscence. Furthermore, a brown anther locus, Ba1, was identified and localized to a 1.3 Mb region closely linked to Bph27(t). Genome assembly of the donor parent, Balamawee, revealed an approximately 1.1 Mb inversion in the fine-mapped region. By breaking the genetic linkage between Bph27(t) and Ba1, BPH-resistant japonica rice with high seed-setting rates was subsequently developed. The identification of Ba1 provides a new genetic resource to further explore the molecular mechanisms underlying rice anther development. Moreover, the development of novel BPH-resistant japonica germplasm lays the foundation for breeding high-yield and BPH-resistant japonica rice varieties.","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"138 8","pages":"199"},"PeriodicalIF":4.2,"publicationDate":"2025-08-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144790097","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Map-based cloning of ZmSS5, construction and validation of its regulatory pathway for maize kernel weight. ZmSS5基因的克隆、玉米粒重调控途径的构建与验证

IF 4.2 1区农林科学

Theoretical and Applied Genetics Pub Date : 2025-08-05 DOI: 10.1007/s00122-025-04992-y

Yongsheng Tao, Mingting Zhou, Daxiao Zhang, Liqing Feng, Anyan Tao, Xuehai Zhang

{"title":"Map-based cloning of ZmSS5, construction and validation of its regulatory pathway for maize kernel weight.","authors":"Yongsheng Tao, Mingting Zhou, Daxiao Zhang, Liqing Feng, Anyan Tao, Xuehai Zhang","doi":"10.1007/s00122-025-04992-y","DOIUrl":"10.1007/s00122-025-04992-y","url":null,"abstract":"Key message: Map-based cloning of ZmSS5. ZmSS5 pathway was constructed and validated. The 'ZmSS5 hypothesis' was proposed. Kernel weight (KW) is an important determinant of maize yield. Despite the identification of numerous quantitative trait loci (QTL) for KW, research into the cloning and molecular regulation of these loci is limited, limiting progress in genetic improvement and molecular breeding for KW. In this study, linkage analysis by chromosomal segment introgression lines, marker development, high-throughput sequencing, amplification and sequence alignment of genome and cDNA, analysis of gene expression and variable splicing, detection of sucrose content and starch synthase activity, the AtSS5 T-DNA insertion mutant and the ZmSS5 EMS mutant were used, and Zm00001d051976 was finally confirmed as the functional gene of the QTL for KW (qKW4a) encoding starch synthase 5 (ZmSS5). Based on RNA-seq from two early stages of grain development, a weighted correlation network analysis was constructed to identify and verify the ZmSS5 pathway, which regulates starch metabolism and KW formation through C/N balance. We also proposed the 'ZmSS5 hypothesis', which suggests that proliferation of starch granules and an increase in ZmSS5 levels are accompanied by cell proliferation, which affects starch unit storage and KW formation by C/N balance. This will provide new ideas for the molecular regulation of KW formation in maize, as well as gene and marker resources for KW molecular breeding.","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"138 8","pages":"198"},"PeriodicalIF":4.2,"publicationDate":"2025-08-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144790099","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Large-scale identification and association analysis of wheat grain weight genes using rice orthologs. 利用水稻同源基因对小麦粒重基因进行大规模鉴定和关联分析。

IF 4.2 1区农林科学

Theoretical and Applied Genetics Pub Date : 2025-08-05 DOI: 10.1007/s00122-025-04988-8

Wensha Zhao, Shusong Zheng, Aoyan Zhang, Meng Yuan, Pengbo Song, Kefeng Song, Yueyue Li, Yuanhang Xing, Huiling Zhao, Jianqing Niu, Jianhui Wu, Hong-Qing Ling, Daojie Sun, Shengwei Ma

{"title":"Large-scale identification and association analysis of wheat grain weight genes using rice orthologs.","authors":"Wensha Zhao, Shusong Zheng, Aoyan Zhang, Meng Yuan, Pengbo Song, Kefeng Song, Yueyue Li, Yuanhang Xing, Huiling Zhao, Jianqing Niu, Jianhui Wu, Hong-Qing Ling, Daojie Sun, Shengwei Ma","doi":"10.1007/s00122-025-04988-8","DOIUrl":"10.1007/s00122-025-04988-8","url":null,"abstract":"Key message: The study identifies 314 wheat orthologs of rice grain weight-related genes, with multi-environment association analysis of 490 accessions uncovering 146 genes significantly linked to grain weight, offering potential targets for yield improvement. Grain weight is a key determinant of wheat yield. Dissection of more grain weight-related genes is crucial for improvement of wheat yield. Using homologous cloning method, a total of 104 rice grain weight-related genes was collected from published studies and their corresponding 314 orthologs were identified in wheat. Spatiotemporal expression analysis reveals that grain weight genes exhibit diverse expression profiles, with few showing grain-specific expression patterns. Approximately 36,000 variants in these grain weight-related genes were identified in a large natural wheat population. Candidate gene association analysis, using 490 common wheat accessions across five environments, reveals that 146 genes of them are significantly associated with grain weight. As a result of breeding practices, favorable alleles were significantly accumulated in modern wheat cultivars. These findings contribute to a better understanding of the genetic architecture of grain development and weight, offering potential targets for future wheat yield improvement.","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"138 8","pages":"197"},"PeriodicalIF":4.2,"publicationDate":"2025-08-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144785372","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Harnessing clonal diversity in grapevine: from genomic insights to modern breeding applications. 利用葡萄的克隆多样性：从基因组的见解到现代育种应用。

IF 4.2 1区农林科学

Theoretical and Applied Genetics Pub Date : 2025-08-04 DOI: 10.1007/s00122-025-04986-w

Paolo Callipo, Maximilian Schmidt, Timo Strack, Hannah Robinson, Akshaya Vasudevan, Kai P Voss-Fels

{"title":"Harnessing clonal diversity in grapevine: from genomic insights to modern breeding applications.","authors":"Paolo Callipo, Maximilian Schmidt, Timo Strack, Hannah Robinson, Akshaya Vasudevan, Kai P Voss-Fels","doi":"10.1007/s00122-025-04986-w","DOIUrl":"10.1007/s00122-025-04986-w","url":null,"abstract":"Grapevine has been clonally propagated for thousands of years. Though clonal propagation aims at maintaining varietal identity, somatic mutations and epigenetic modifications accumulated over hundreds to thousands of years lead to intra-varietal diversity. This intra-varietal variation is a very valuable resource in grapevine breeding, as it creates the opportunity to improve important traits related to yield, phenology, stress tolerance, and quality without altering the varietal identity which is extremely important for the industry. Recent advances in genomics, epigenetics, and phenotyping technologies are providing completely new opportunities to gain functional insights into the drivers underlying trait variation and to explore this for accelerated grapevine breeding. This review discusses the interaction between somatic mutations, epigenetic regulation, and emerging breeding technologies. We begin by exploring the phenotypic variation observed within clonal populations across various commercially important varieties, focusing on both agronomic and winemaking-related traits. Next, we examine the extent of genomic and epigenomic variation among clones, highlighting known mutations responsible for somatic variants. We also address how grapevine clonal populations serve as an advantageous model for understanding how genetic and epigenetic variants shape complex trait variation. Given recent advances, we discuss the potential of predictive breeding strategies to accelerate clonal evaluation and how genome editing technologies open new opportunities for targeted genetic improvements without passing through the tedium and unpredictability of clonal selection, driven by natural mutation. Ultimately, these new breeding technologies enable the integration of advanced methods into breeding programmes, optimizing grapevine performance while preserving the unique heritage of historic cultivars.","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"138 8","pages":"196"},"PeriodicalIF":4.2,"publicationDate":"2025-08-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12321930/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144785371","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Inspiration from apomictic species of Rutaceae: AGL11-FIE module induces autonomous development of maize embryo and endosperm without fertilization. 来自玉米科无融合种的启示：AGL11-FIE模块在不受精的情况下诱导玉米胚和胚乳自主发育。

IF 4.2 1区农林科学

Theoretical and Applied Genetics Pub Date : 2025-08-03 DOI: 10.1007/s00122-025-04985-x

Qianqian Shi, Xin Chen, Lei Ma, Anzhi Wei, Xitong Fei

{"title":"Inspiration from apomictic species of Rutaceae: AGL11-FIE module induces autonomous development of maize embryo and endosperm without fertilization.","authors":"Qianqian Shi, Xin Chen, Lei Ma, Anzhi Wei, Xitong Fei","doi":"10.1007/s00122-025-04985-x","DOIUrl":"10.1007/s00122-025-04985-x","url":null,"abstract":"Apomixis is a form of asexual reproduction that produces offspring with the same genetic material as the female parent. Introducing apomixis into major food crops would revolutionize agricultural breeding by allowing the self-propagation of superior hybrids. We found that the MADS-box transcription factor D-class member AGAMOUS-like 11 (AGL11) plays a key role in the apomictic species Zanthoxylum bungeanum during somatic embryogenesis. Specific overexpression of the AGL11 gene in the nucellus induces somatic cells (nucellus cells) to differentiate into asexual embryos (adventitious embryos) and appear to be polyembryonic. FERTILIZATION-INDEPENDENT ENDOSPERM (FIE) acts as a switch to repress the development of the endosperm until fertilization, and knockdown of the FIE gene activates early cellularization of the central polar nucleus and produces a diploid endosperm independent of fertilization. AGL11-OE/fie-mutant maize was constructed by overexpressing AGL11 and knocking out the FIE gene in food crop maize, which produces asexual seeds by inducing somatic embryogenesis and autonomous endosperm. The AGL11-FIE module bypasses sexual reproduction and meiosis and induces asexual embryos and endosperm without fertilization, realizing the transformation of sexual reproduction into asexual reproduction. The results provided a reference for the self-production of hybrid seeds represented by maize.","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"138 8","pages":"195"},"PeriodicalIF":4.2,"publicationDate":"2025-08-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144776228","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Alternative splicing-mediated regulation of a novel allele of Badh2 drives moderate accumulation of 2-AP in rice. Badh2新等位基因的选择性剪接调控驱动水稻2-AP的适度积累。

IF 4.2 1区农林科学

Theoretical and Applied Genetics Pub Date : 2025-08-01 DOI: 10.1007/s00122-025-04979-9

Xueyu Liang, Ying Chen, Kai Liu, Min Guo, Danhua Zhou, Cuihong Huang, Tao Guo, Hui Wang, Guili Yang

{"title":"Alternative splicing-mediated regulation of a novel allele of Badh2 drives moderate accumulation of 2-AP in rice.","authors":"Xueyu Liang, Ying Chen, Kai Liu, Min Guo, Danhua Zhou, Cuihong Huang, Tao Guo, Hui Wang, Guili Yang","doi":"10.1007/s00122-025-04979-9","DOIUrl":"10.1007/s00122-025-04979-9","url":null,"abstract":"Key message: A novel allele of Badh2, badh2-I11 undergoes alternative splicing and leads to reduced Badh2 expression and enhanced 2-AP accumulation in rice. Aroma is a crucial quality trait in rice and is primarily regulated by the Badh2 gene located on chromosome 8. In this study, we identified a novel allele of Badh2, badh2-I11, in the aromatic rice variety, Hei126 (H126). This allele harbors a 55-bp deletion in intron 11, inducing alternative splicing, that generates both wild-type transcripts and aberrant transcripts containing a premature stop codon. Consequently, Badh2 mRNA levels are reduced, leading to moderate accumulation of the aromatic compound 2-acetyl-1-pyrroline (2-AP). Genetic analysis of an F2 population derived from a cross between Huahang 48 (non-aromatic, Badh2/Badh2) and H126 (aromatic, badh2-I11/badh2-I11) revealed a genotypic segregation ratio 1:2:1 (Badh2/Badh2: Badh2/badh2-I11: badh2-I11/badh2-I11), consistent with Mendelian inheritance for a single codominant locus. The corresponding phenotypic ratio of non-aromatic to aromatic plants was 3:1. We developed a codominant InDel marker for efficient screening of badh2-I11 in breeding populations. This intermediate aromatic phenotype establishes H126 as a unique germplasm resource, accumulating 2-AP while retaining partial Badh2 function. Our findings elucidate a novel molecular mechanism of aroma production mediated by intronic alternative splicing and provide valuable genetic resources and molecular tools for aromatic rice breeding.","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"138 8","pages":"194"},"PeriodicalIF":4.2,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144765559","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

In silico prediction of variant effects: promises and limitations for precision plant breeding. 变异效应的计算机预测：精确植物育种的希望与局限。

IF 4.2 1区农林科学

Theoretical and Applied Genetics Pub Date : 2025-07-28 DOI: 10.1007/s00122-025-04973-1

Janek Sendrowski, Thomas Bataillon, Guillaume P Ramstein

{"title":"In silico prediction of variant effects: promises and limitations for precision plant breeding.","authors":"Janek Sendrowski, Thomas Bataillon, Guillaume P Ramstein","doi":"10.1007/s00122-025-04973-1","DOIUrl":"10.1007/s00122-025-04973-1","url":null,"abstract":"Key message: Sequence-based AI models show great potential for prediction of variant effects at high resolution, but their practical value in plant breeding remains to be confirmed through rigorous validation studies. Plant breeding has traditionally relied on phenotyping to select individuals with desirable traits-a process that is both costly and time-consuming. Increasingly, breeding strategies are shifting toward precision breeding, where causal variants are directly targeted based on their effects. To predict the effects of causal variants, in silico methods are emerging as efficient alternatives or complements to mutagenesis screens. Here, we review state-of-the-art machine learning methods for predicting variant effects in plants across both coding and noncoding regions, contrasting supervised approaches in functional genomics with unsupervised methods in comparative genomics. We discuss challenges in validating predictions, and compare these methods with traditional association and comparative genomics techniques. We argue that modern sequence models extend traditional methods by generalizing across genomic contexts, fitting a unified model across loci rather than a separate model for each locus. In doing so, they address inherent limitations of traditional quantitative and evolutionary comparative genetics techniques. However, the accuracy and generalizability of sequence models heavily depend on the training data, highlighting the need for validation experiments. We point to successful applications of sequence models, especially with protein sequences, and identify areas for further improvement, especially in modeling regulatory sequences. While not yet mature for in silico-driven precision breeding, sequence models show strong potential to become an integral part of the breeder's toolbox.","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"138 8","pages":"193"},"PeriodicalIF":4.2,"publicationDate":"2025-07-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12304032/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144733403","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0