IF 4.6 4区农林科学

aBIOTECH Pub Date : 2025-02-18 DOI: 10.1007/s42994-025-00199-3

Jingjing Cao, Yue Ma, Jing Fu, Zhiqin Wang, Yonglong Zhao, Naiqin Zhong, Pan Zhao

{"title":"Bacillus atrophaeus DX-9 biocontrol against potato common scab involves significant changes in the soil microbiome and metabolome","authors":"Jingjing Cao, Yue Ma, Jing Fu, Zhiqin Wang, Yonglong Zhao, Naiqin Zhong, Pan Zhao","doi":"10.1007/s42994-025-00199-3","DOIUrl":"10.1007/s42994-025-00199-3","url":null,"abstract":"<div>Potato common scab (CS) is a worldwide disease, caused by Streptomyces spp., and its presence reduces the market value of potatoes. A nontoxic and potentially effective approach in many control strategies is the use of antagonistic microbes as biocontrol agents. In this study, Bacillus atrophaeus DX9 was isolated and assessed for its ability to protect against CS. Through integrated metagenomic and metabolomic analyses, changes in the soil microbial community structure and soil properties were analyzed to understand the effects of Bacillus atrophaeus DX9 on CS. These studies revealed that DX9 inoculation could significantly decrease CS disease rate, disease index, and the number of CS pathogens, along with an increase in soil N and P content. Our metagenomic assays identified 102 phyla and 1154 genera, and DX9 inoculation increased the relative abundances of the phyla Pseudomonadota, Chloroflexota and Gemmatimonadota. Additionally, an increase in the relative abundance of genera, such as Bradyrhizobium, Agrobacterium, and Nitrobacter, were significantly and positively correlated with soil N and P. Metabolomic analysis revealed that DX9 inoculation significantly increased the soil levels of phytolaccoside A, 7,8dihydropteroic acid, novobiocin, and azafrin. These compounds were enriched in microbe pathway metabolites, including xenobiotic biodegradation and metabolism, biosynthesis of other secondary metabolites, and metabolism of cofactors and vitamins. In summary, the use of Bacillus atrophaeus DX9 against potato CS offers an alternative biocontrol method that can improve both soil microbial community and properties. This study provides insight into the potential mechanisms by which microbial inoculants can control CS disease.</div>","PeriodicalId":53135,"journal":{"name":"aBIOTECH","volume":"6 1","pages":"33 - 49"},"PeriodicalIF":4.6,"publicationDate":"2025-02-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s42994-025-00199-3.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143564438","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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

Convenient, high-efficiency multiplex genome editing in autotetraploid alfalfa using endogenous U6 promoters and visual reporters 利用内源U6启动子和视觉报告子对同源四倍体苜蓿进行便捷、高效的多重基因组编辑

IF 4.6 4区农林科学

aBIOTECH Pub Date : 2025-02-10 DOI: 10.1007/s42994-025-00200-z

Xiuzhi Xia, Shihao Li, Na Wang, Panxu Cheng, Butuo Zhu, Pengcheng Zhang, Dahai Yang, Hao Lin, Lifang Niu

{"title":"Convenient, high-efficiency multiplex genome editing in autotetraploid alfalfa using endogenous U6 promoters and visual reporters","authors":"Xiuzhi Xia, Shihao Li, Na Wang, Panxu Cheng, Butuo Zhu, Pengcheng Zhang, Dahai Yang, Hao Lin, Lifang Niu","doi":"10.1007/s42994-025-00200-z","DOIUrl":"10.1007/s42994-025-00200-z","url":null,"abstract":"<div>CRISPR/Cas is a simple, robust, versatile tool for plant biology studies and precision plant breeding. However, establishing a high-efficiency gene editing system for multiplex editing of the autotetraploid crop alfalfa (Medicago sativa L.), the most important forage legume worldwide, remains a formidable challenge. Here, we systematically identified endogenous U6 promoters in alfalfa through transient expression via Agrobacterium-mediated infiltration of alfalfa leaves. We further demonstrated the efficacy of the three most active promoters for genome editing using an optimized alfalfa hairy root system. Subsequently, we established an improved CRISPR/Cas9 multiplex system containing three or four tandemly arrayed MsU6-promoter-driven polycistronic tRNA-sgRNA (PTG) expression cassettes, each consisting of three tRNA-sgRNA units, to simultaneously edit three or four alfalfa genes, coupled with the visual reporter RH1 or RUBY. This toolkit showed efficient multiplex editing in the hairy root system with visual selection. We successfully obtained regenerated, red-colored shoots resulting from the stable transformation of alfalfa. These results highlight the potential application of the visual reporter system for the stable transformation of alfalfa. Our improved CRISPR/Cas9 multiplex system enables convenient, high-efficiency multiplex genome editing in alfalfa, providing a versatile toolset to facilitate functional studies of multiple genes and gene families for basic research and the genetic improvement of alfalfa.</div>","PeriodicalId":53135,"journal":{"name":"aBIOTECH","volume":"6 1","pages":"81 - 90"},"PeriodicalIF":4.6,"publicationDate":"2025-02-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s42994-025-00200-z.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143564378","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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

Atypical RXLR effectors are involved in Phytophthora cactorum pathogenesis 非典型 RXLR 效应器参与了根瘤蚜的致病过程

IF 4.6 4区农林科学

aBIOTECH Pub Date : 2025-01-27 DOI: 10.1007/s42994-025-00198-4

Zeyang Zheng, Juanjuan Liu, Wenzhong You, Jun Sun, Kehan Wang, Xuemei Zhang, Xinyu Yan, Zhenpan Liu

{"title":"Atypical RXLR effectors are involved in Phytophthora cactorum pathogenesis","authors":"Zeyang Zheng, Juanjuan Liu, Wenzhong You, Jun Sun, Kehan Wang, Xuemei Zhang, Xinyu Yan, Zhenpan Liu","doi":"10.1007/s42994-025-00198-4","DOIUrl":"10.1007/s42994-025-00198-4","url":null,"abstract":"<div>RXLR effectors are pathogenic factors secreted from oomycetes to manipulate the immunity of the host. Typical RXLR effectors contain an RXLR-dEER motif at the N-terminus, whereas atypical RXLRs show variations on this motif. The oomycete Phytophthora cactorum is known to infect over 200 plant species, resulting in significant agricultural economic losses. Although genome-wide identification and functional analyses of typical RXLRs from P. cactorum have been performed, little is known of atypical PcaRXLRs. Here, we identified RXLRs, both typical and atypical, in P. cactorum and compared them with those of other oomycete pathogens. Fewer RXLRs were identified in P. cactorum compared with other Phytophthora species, possibly due to fewer duplication events of RXLRs. In contrast, the percentage of atypical RXLRs was higher in P. cactorum than in other species, suggesting significant roles in P. cactorum pathogenesis. Analysis of RXLR gene expression showed that most were transcribed, suggesting their functionality. Transient expression of two atypical RXLRs in Nicotiana benthamiana showed that they induced necrosis dependent on host SGT1 and HSP90. Furthermore, two additional atypical RXLRs suppressed the defense response in N. benthamiana and promoted P. cactorum infection. These results demonstrate the vital role of atypical RXLRs in P. cactorum and provide valuable information on their evolutionary patterns and interactions with host plants.</div>","PeriodicalId":53135,"journal":{"name":"aBIOTECH","volume":"6 1","pages":"50 - 62"},"PeriodicalIF":4.6,"publicationDate":"2025-01-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s42994-025-00198-4.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143564484","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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

Emerging strategies to improve heat stress tolerance in crops 提高作物抗热胁迫能力的新策略

IF 4.6 4区农林科学

aBIOTECH Pub Date : 2025-01-24 DOI: 10.1007/s42994-024-00195-z

Jiawei Xiong, Hao Wang, Zhaohui Zhong, Shigui Li, Peng Qin

{"title":"Emerging strategies to improve heat stress tolerance in crops","authors":"Jiawei Xiong, Hao Wang, Zhaohui Zhong, Shigui Li, Peng Qin","doi":"10.1007/s42994-024-00195-z","DOIUrl":"10.1007/s42994-024-00195-z","url":null,"abstract":"<div>The heat stress (HS) response in plants involves complex processes at the molecular, cellular, and whole-organism levels. Sensitivity to HS differs based on the species and developmental stage of the plant, making it challenging to define HS and its impacts. Efforts to enhance HS tolerance by traditional breeding are constrained by limited genetic resources, but understanding the mechanisms that regulate HS responses can enable efforts to improve heat tolerance by precision breeding and gene editing. Here, we review recent research on the effects of HS on major cereal crops at different developmental stages and identify key genes potentially involved in the HS response, offering insight for precision molecular breeding. Additionally, we discuss the use of favorable natural variants and gene editing to improve crop tolerance to HS, emphasizing the value of alleles involved in thermomemory, combined stress tolerance, and the stress response–growth balance. This review aims to summarize recent advancements in understanding HS responses in crops, highlighting potential avenues for generating heat-tolerant crops.</div>","PeriodicalId":53135,"journal":{"name":"aBIOTECH","volume":"6 1","pages":"97 - 115"},"PeriodicalIF":4.6,"publicationDate":"2025-01-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s42994-024-00195-z.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143564476","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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

Plant metabolomics: applications and challenges in the era of multi-omics big data 植物代谢组学：多组学大数据时代的应用与挑战

IF 4.6 4区农林科学

aBIOTECH Pub Date : 2025-01-23 DOI: 10.1007/s42994-024-00194-0

Yingchen Hao, Zhonghui Zhang, Enxi Luo, Jun Yang, Shouchuang Wang

{"title":"Plant metabolomics: applications and challenges in the era of multi-omics big data","authors":"Yingchen Hao, Zhonghui Zhang, Enxi Luo, Jun Yang, Shouchuang Wang","doi":"10.1007/s42994-024-00194-0","DOIUrl":"10.1007/s42994-024-00194-0","url":null,"abstract":"<div>Plant metabolites are crucial for the growth, development, environmental adaptation, and nutritional quality of plants. Plant metabolomics, a key branch of systems biology, involves the comprehensive analysis and interpretation of the composition, variation, and functions of these metabolites. Advances in technology have transformed plant metabolomics into a sophisticated process involving sample collection, metabolite extraction, high-throughput analysis, data processing, and multidimensional statistical analysis. In today’s era of big data, the field is witnessing an explosion in data acquisition, offering insight into the complexity and dynamics of plant metabolism. Moreover, multiple omics strategies can be integrated to reveal interactions and regulatory networks across different molecular levels, deepening our understanding of plant biological processes. In this review, we highlight recent advances and challenges in plant metabolomics, emphasizing the roles for this technique in improving crop varieties, enhancing nutritional value, and increasing stress resistance. We also explore the scientific foundations of plant metabolomics and its applications in medicine, and ecological conservation.</div>","PeriodicalId":53135,"journal":{"name":"aBIOTECH","volume":"6 1","pages":"116 - 132"},"PeriodicalIF":4.6,"publicationDate":"2025-01-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s42994-024-00194-0.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143564475","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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

A 6.49-Mb inversion associated with the purple embryo spot trait in potato 马铃薯紫色胚斑性状的6.49 mb反转

IF 4.6 4区农林科学

aBIOTECH Pub Date : 2025-01-18 DOI: 10.1007/s42994-025-00197-5

Pei Wang, Lin Cheng, Jun Pan, Lianlian Ma, Xiaojing Hu, Zhong Zhang, Dawei Li, Yanhui Zhu, Shiwei Chang, Pingping Yuan, Philip Kear, Ludivine Lassois, Guangtao Zhu, Sanwen Huang, Hui Du, Chunzhi Zhang

{"title":"A 6.49-Mb inversion associated with the purple embryo spot trait in potato","authors":"Pei Wang, Lin Cheng, Jun Pan, Lianlian Ma, Xiaojing Hu, Zhong Zhang, Dawei Li, Yanhui Zhu, Shiwei Chang, Pingping Yuan, Philip Kear, Ludivine Lassois, Guangtao Zhu, Sanwen Huang, Hui Du, Chunzhi Zhang","doi":"10.1007/s42994-025-00197-5","DOIUrl":"10.1007/s42994-025-00197-5","url":null,"abstract":"<div>The embryo spot trait leads to a deep purple or reddish coloration at the base of the cotyledons of the embryo, visible on both sides of flat potato (Solanum tuberosum) seeds. This trait has long been used by potato researchers and breeders as a morphological marker during dihaploid induction. The formation of embryo spots reflects the accumulation of anthocyanins, but the genetic basis of this trait remains unclear. In this study, we mapped the embryo spot trait to a 6.78-Mb region at the end of chromosome 10 using an F2 population derived from a cross between spotted and spotless plants. The recombination rate in the candidate region is severely suppressed, posing challenges for the map-based cloning of the underlying gene and suggesting large-scale rearrangements in this region. A de novo genome assembly of the spotted individual and a comparative genomic analysis to the reference genome of spotless potato revealed a 6.49-Mb inversion present in the spotted plant genome. The left breakpoint of this inversion occurred in the promoter region of an R2R3 MYB transcription factor gene that is highly expressed in the cotyledon base of spotted embryos but is not expressed in that of spotless embryos. This study elucidated the genetic basis for embryo spot formation in potato and provides a foundation for future cloning of the causative gene.</div>","PeriodicalId":53135,"journal":{"name":"aBIOTECH","volume":"6 1","pages":"22 - 32"},"PeriodicalIF":4.6,"publicationDate":"2025-01-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s42994-025-00197-5.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143564437","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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

LEAFY1 and 2 are required for floral organ development in soybean 大豆花器官发育需要LEAFY1和2

IF 4.6 4区农林科学

aBIOTECH Pub Date : 2024-12-22 DOI: 10.1007/s42994-024-00192-2

Lingshuang Wang, Huan Liu, Lei Chen, Tong Su, Shichen Li, Chao Fang, Sijia Lu, Baohui Liu, Hui Yang, Fanjiang Kong

{"title":"LEAFY1 and 2 are required for floral organ development in soybean","authors":"Lingshuang Wang, Huan Liu, Lei Chen, Tong Su, Shichen Li, Chao Fang, Sijia Lu, Baohui Liu, Hui Yang, Fanjiang Kong","doi":"10.1007/s42994-024-00192-2","DOIUrl":"10.1007/s42994-024-00192-2","url":null,"abstract":"<div>The transition from vegetative to reproductive growth is a vital step for the reproductive success of plants. In Arabidopsis thaliana, LEAFY (LFY) plays crucial roles in inflorescence primordium and floral organ development, but little is known about the roles of its homologs in crop plants such as soybean (Glycine max). Here, we investigated the expression patterns and functions of the two LFY genes (LFY1 and LFY2) in soybean. Both genes were predominantly expressed in unopened flowers and the shoot apical meristem, with LFY2 having the higher transcript abundance. In an in situ hybridization assay, LFY genes produced strong signals in the floral meristem. We next generated lfy1 and lfy2 knockout lines. The lfy2 mutants showed obvious changes in floral organ morphology, but the lfy1 mutants showed no obvious changes in floral organ morphology or pod development. The lfy1 lfy2 double mutants displayed more serious defects in floral organ development than lfy2, resulting in complete sterility. Gene expression analysis revealed differences in expression of the A-class APETALA (AP) genes AP1a and AP1b in the double mutant lines. These results suggest that LFY2 plays an important role in floral organ formation in soybean by regulating the expression of homeotic genes. Our findings increase the understanding of floral development, which could be useful for flower designs during hybrid soybean breeding.</div>","PeriodicalId":53135,"journal":{"name":"aBIOTECH","volume":"6 1","pages":"12 - 21"},"PeriodicalIF":4.6,"publicationDate":"2024-12-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s42994-024-00192-2.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143564472","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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

Correction: Inference and prioritization of tissue-specific regulons in Arabidopsis and Oryza 更正：拟南芥和稻谷中组织特异性调控的推断和优先排序

IF 4.6 4区农林科学

aBIOTECH Pub Date : 2024-12-19 DOI: 10.1007/s42994-024-00191-3

Honggang Dai, Yaxin Fan, Yichao Mei, Ling-Ling Chen, Junxiang Gao

引用次数: 0

MHZ3: a key regulator of ethylene signaling in rice MHZ3：水稻乙烯信号的关键调控因子

IF 4.6 4区农林科学

aBIOTECH Pub Date : 2024-12-06 DOI: 10.1007/s42994-024-00189-x

Arif Ali Khattak, Yingshan Huang, Muhammad Afzal, Xiaolin Wang