Integration of multi-omics technologies for crop improvement: Status and prospects DOI Creative Commons
Ru Zhang, Cuiping Zhang,

Cheng‐Yu Yu

и другие.

Frontiers in Bioinformatics, Год журнала: 2022, Номер 2

Опубликована: Окт. 19, 2022

With the rapid development of next-generation sequencing (NGS), multi-omics techniques have been emerging as effective approaches for crop improvement. Here, we focus mainly on addressing current status and future perspectives toward omics-related technologies bioinformatic resources with potential applications in breeding. Using a large amount omics-level data from functional genome, transcriptome, proteome, epigenome, metabolome, microbiome, clarifying interaction between gene phenotype formation will become possible. The integration datasets pan-omics platforms systems biology could predict complex traits crops elucidate regulatory networks genetic Different scales trait predictions decision-making models facilitate breeding more intelligent. Potential challenges that integrate studies function their network to efficiently select desirable agronomic are discussed by proposing some cutting-edge strategies Multi-omics-integrated together other artificial intelligence contribute broadening deepening our knowledge precision breeding, resulting speeding up process.

Язык: Английский

Cross-kingdom synthetic microbiota supports tomato suppression of Fusarium wilt disease DOI Creative Commons
Xin Zhou, Jinting Wang, Fang Liu

и другие.

Nature Communications, Год журнала: 2022, Номер 13(1)

Опубликована: Дек. 22, 2022

Abstract The role of rhizosphere microbiota in the resistance tomato plant against soil-borne Fusarium wilt disease (FWD) remains unclear. Here, we showed that FWD incidence was significantly negatively correlated with diversity both bacterial and fungal communities. Using microbiological culturomic approach, selected 205 unique strains to construct different synthetic communities (SynComs), which were inoculated into germ-free seedlings, their roles suppressing monitored using omics approach. Cross-kingdom (fungi bacteria) SynComs most effective than those Fungal or Bacterial alone. This effect underpinned by a combination molecular mechanisms related immunity microbial interactions contributed study provides new insight dynamics pathogen suppression host interactions. Also, formulation manipulation for functional complementation constitute beneficial strategy controlling disease.

Язык: Английский

Процитировано

120
Importance of Bacteroidetes in host–microbe interactions and ecosystem functioning DOI

Xinya Pan,

Jos M. Raaijmakers, Víctor J. Carrión

и другие.

Trends in Microbiology, Год журнала: 2023, Номер 31(9), С. 959 - 971

Опубликована: Май 10, 2023

Язык: Английский

Процитировано

92
Identifying plant genes shaping microbiota composition in the barley rhizosphere DOI Creative Commons
Carmen Escudero-Martinez, Max Coulter, Rodrigo Alegria Terrazas

и другие.

Nature Communications, Год журнала: 2022, Номер 13(1)

Опубликована: Июнь 16, 2022

A prerequisite to exploiting soil microbes for sustainable crop production is the identification of plant genes shaping microbiota composition in rhizosphere, interface between roots and soil. Here, we use metagenomics information as an external quantitative phenotype map host genetic determinants rhizosphere wild domesticated genotypes barley, fourth most cultivated cereal globally. We identify a small number loci with major effect on communities. One those, designated QRMC-3HS, emerges determinant composition. subject soil-grown sibling lines harbouring contrasting alleles at QRMC-3HS hosting microbiotas comparative root RNA-seq profiling. This allows us three primary candidate genes, including Nucleotide-Binding-Leucine-Rich-Repeat (NLR) gene region structural variation barley genome. Our results provide insights into footprint improvement plant's capacity microbes.

Язык: Английский

Процитировано

78
Rhizosphere bacterial interactions and impact on plant health DOI Creative Commons

Jane Chepsergon,

Lucy Moleleki

Current Opinion in Microbiology, Год журнала: 2023, Номер 73, С. 102297 - 102297

Опубликована: Март 30, 2023

The rhizosphere is a chemically complex environment that harbors strikingly diverse microbial community. past few decades have seen rapid growth in the body of literature on plant–microbe–microbe interactions and plant health. Thus, aim this paper to review current knowledge (specifically bacteria) how these influence microbiomes impact This article discusses (i) recruits beneficial bacteria ii) competition between mechanisms/weapons employed bacteria–bacteria shapes microbiome turn affects heath. discussion mainly focuses interference competition, characterized by production specialized metabolites (antibacterial compounds) exploitative where bacterial strain restricts competitor's access nutrients such as through secretion siderophores could allude cooperation. Understanding mechanisms plant–bacteria provide insights into manipulate for improved agricultural outcomes.

Язык: Английский

Процитировано

71
Recruitment of the rhizo-microbiome army: assembly determinants and engineering of the rhizosphere microbiome as a key to unlocking plant potential DOI Creative Commons
Inmyoung Park, Young‐Su Seo, Mohamed Mannaa

и другие.

Frontiers in Microbiology, Год журнала: 2023, Номер 14

Опубликована: Май 5, 2023

The viable community of microorganisms in the rhizosphere significantly impacts physiological development and vitality plants. assembly functional capacity microbiome are greatly influenced by various factors within rhizosphere. primary host plant genotype, developmental stage status, soil properties, resident microbiota. These drive composition, dynamics, activity microbiome. This review addresses intricate interplay between these how it facilitates recruitment specific microbes to support growth resilience under stress. also explores current methods for engineering manipulating microbiome, including plant-mediated manipulation, soil-related methods, microbe-mediated methods. Advanced techniques harness plant's ability recruit useful promising use rhizo-microbiome transplantation highlighted. goal this is provide valuable insights into knowledge, which will facilitate cutting-edge strategies enhanced stress tolerance. article indicates avenues future research field.

Язык: Английский

Процитировано

63
Microbes to support plant health: understanding bioinoculant success in complex conditions DOI Creative Commons
Sanne WM Poppeliers, Juan J. Sánchez-Gil, Ronnie de Jonge

и другие.

Current Opinion in Microbiology, Год журнала: 2023, Номер 73, С. 102286 - 102286

Опубликована: Март 4, 2023

A promising, sustainable way to enhance plant health and productivity is by leveraging beneficial microbes. Beneficial microbes are natural soil residents with proven benefits for performance health. When applied in agriculture improve crop yield performance, these commonly referred as bioinoculants. Yet, despite their promising properties, bioinoculant efficacy can vary dramatically the field, hampering applicability. Invasion of rhizosphere microbiome a critical determinant success. complex phenomenon that shaped interactions local, resident host plant. Here, we explore all dimensions cross-cutting ecological theory molecular biology microbial invasion rhizosphere. We refer famous Chinese philosopher strategist Sun Tzu, who believed solutions problems require deep understanding themselves, review major biotic factors determining effectiveness.

Язык: Английский

Процитировано

60
Microbiome homeostasis on rice leaves is regulated by a precursor molecule of lignin biosynthesis DOI Creative Commons
Pin Su, Houxiang Kang, Qianze Peng

и другие.

Nature Communications, Год журнала: 2024, Номер 15(1)

Опубликована: Янв. 2, 2024

In terrestrial ecosystems, plant leaves provide the largest biological habitat for highly diverse microbial communities, known as phyllosphere microbiota. However, underlying mechanisms of host-driven assembly these ubiquitous communities remain largely elusive. Here, we conduct a large-scale and in-depth assessment rice microbiome aimed at identifying specific host-microbe links. A genome-wide association study reveals strong between genotype members four bacterial orders, Pseudomonadales, Burkholderiales, Enterobacterales Xanthomonadales. Some associations are to distinct host genomic locus, pathway or even gene. The compound 4-hydroxycinnamic acid (4-HCA) is identified main driver enrichment bacteria belonging Pseudomonadales. 4-HCA can be synthesized by plant's OsPAL02 from phenylpropanoid biosynthesis pathway. knockout mutant results in reduced Pseudomonadales abundance, dysbiosis microbiota consequently higher susceptibility plants disease. Our provides direct link metabolite homeostasis opening possibilities new breeding strategies.

Язык: Английский

Процитировано

46
Dissection of rhizosphere microbiome and exploiting strategies for sustainable agriculture DOI Open Access
Weibing Xun, Yunpeng Liu,

Aiyuan Ma

и другие.

New Phytologist, Год журнала: 2024, Номер 242(6), С. 2401 - 2410

Опубликована: Март 17, 2024

Summary The rhizosphere microbiome plays critical roles in plant growth and provides promising solutions for sustainable agriculture. While the frequently fluctuates with soil environment, recent studies have demonstrated that a small proportion of is consistently assembled specific genotype regardless condition, which determined by host genetics. Based on these breakthroughs, involved exploiting plant‐beneficial function microbiome, we propose to divide into environment‐dominated genetic‐dominated components based their different assembly mechanisms. Subsequently, two strategies explore agricultural production are suggested, is, precise management agronomic practices, elucidation genetic basis breeding microbiome‐assisted crop varieties. We finally present major challenges need be overcome implement modulating microbiome.

Язык: Английский

Процитировано

34
Heritable microbiome variation is correlated with source environment in locally adapted maize varieties DOI

Xiaoming He,

Danning Wang, Yong Jiang

и другие.

Nature Plants, Год журнала: 2024, Номер 10(4), С. 598 - 617

Опубликована: Март 21, 2024

Язык: Английский

Процитировано

32
Fusaric acid mediates the assembly of disease-suppressive rhizosphere microbiota via induced shifts in plant root exudates DOI Creative Commons
Xue Jin,

Huiting Jia,

Lingyi Ran

и другие.

Nature Communications, Год журнала: 2024, Номер 15(1)

Опубликована: Июнь 15, 2024

Abstract The plant health status is determined by the interplay of plant-pathogen-microbiota in rhizosphere. Here, we investigate this tripartite system focusing on pathogen Fusarium oxysporum f. sp. lycopersici (FOL) and tomato plants as a model system. First, explore differences genotype resistance to FOL potentially associated with differential recruitment plant-protective rhizosphere taxa. Second, show production fusaric acid trigger systemic changes microbiota. Specifically, molecule have opposite effects disease-suppressive taxa resistant susceptible genotypes. Last, elucidate that induce root exudation direct specific Our study unravels mechanism mediating assembly disease suppression integrating physiological responses microbial-mediated mechanisms

Язык: Английский

Процитировано

27