New Achievements in Gene Mining, Germplasm Innovation, Cultivation Technologies in Rice

Topic Information

Dear Colleagues,

Rice is one of the most important crops, feeding half of the population worldwide; however, under the sustained pressure of population growth, achieving a further increase in rice yield is of particular importance.

In recent years, rice has been recognized as a model crop for gene mining and molecular biology research. To date, at least 2000 genes controlling important agronomic traits and disease resistance have been isolated, and their molecular biological mechanisms have also been partially characterized. This poses a great foundation for generating new varieties with improved yield, quality and stress resilience via molecular technologies including gene editing, genome selection and transgene expression.

In addition, with the rapid development and application of rice cultivation technologies including precision quantitative cultivation; one-time fertilization with slow- and controlled-release fertilizer; unmanned cultivation; and cultivation techniques for the coordinated improvement of yield, quality and efficiency, the production of high-yield, good-quality and stress-resilient varieties is undergoing a new transformation, and accordingly, the corresponding physiological mechanisms are being elucidated.

The International Journal of Molecular Sciences has had increasing influence on the molecular genetics of key traits in agronomy, plants and crops, particularly in rice. In this Topic of IJMS in collaboration with Agronomy, Plants, Crops and CIMB, we aim to highlight new achievements in the following areas:

• The screening and development of new rice germplasms with special characteristics;
• The breeding of high-yield and stress-resilient rice cultivars through marker-assisted selection and genome editing;
• The mapping and cloning of genes controlling economically important traits in rice (GWAS, etc.);
• Molecular biology research on stress resistance or tolerance and yield-associated traits;
• New methods for stress phenotyping;
• New cultivation technologies and underlying physiological mechanisms towards achieving high yield, good quality and stress resistance or tolerance

Prof. Dr. Shimin Zuo
Prof. Dr. Yongmei Bao
Dr. Yajie Hu
Topic Editors

Keywords

Participating Journals

Journal Name	Impact Factor	CiteScore	Launched Year	First Decision (median)	APC
Agronomy agronomy	4.1	7.6	2011	17.7 Days	CHF 2600	Submit
Crops crops	2.1	2.9	2021	20.7 Days	CHF 1200	Submit
Current Issues in Molecular Biology cimb	4.1	5.0	1999	15.5 Days	CHF 2400	Submit
International Journal of Molecular Sciences ijms	5.6	10.0	2000	17.5 Days	CHF 2900	Submit
Plants plants	4.7	8.5	2012	14.8 Days	CHF 2700	Submit

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Published Papers (1 paper)

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Open AccessEditor’s ChoiceReview

Microbiome-Induced Effects on Root Architecture in Rice Crops: Mechanisms, Drivers, and Functional Consequences

by Misagh Parhizkar, Manuel Esteban Lucas-Borja and Demetrio Antonio Zema

Crops 2026, 6(2), 25; https://doi.org/10.3390/crops6020025 - 25 Feb 2026

Viewed by 1115

Abstract

Bacteria play an important role in addressing challenges in rice production by promoting plant growth and enhancing stress tolerance through multiple mechanisms. Different types of soil bacteria affect rice growth by improving nutrient absorption, managing stress, and enhancing root structure. The relationship between [...] Read more.

Bacteria play an important role in addressing challenges in rice production by promoting plant growth and enhancing stress tolerance through multiple mechanisms. Different types of soil bacteria affect rice growth by improving nutrient absorption, managing stress, and enhancing root structure. The relationship between rice plants and bacteria is intricate, as these bacteria can help reduce problems like salt stress, heavy metal toxicity, and infections. This review summarises studies published up to 2025 on how bacteria influence rice roots, including aspects like root length, density, biomass, and volume. Bibliometric analysis shows an increase of over 900% in research interest after 2020, with most studies conducted under controlled conditions and limited field validation. In addition to identifying key bacterial groups such as Bacillus, Pseudomonas, Burkholderia, and Azospirillum, this review identifies research gaps related to context dependency, strain specificity, and scalability. We have also emphasised the need for multi-strain inoculation strategies, field-scale experiments, and integration of microbial selection with rice breeding. The synthesis has highlighted that bacterial strains do not simply stimulate root growth but actively reprogram rice root architecture, modulating elongation, branching, density, and surface area as a response to environmental constraints. These effects are mediated by interconnected mechanisms that include phytohormone production, nutrient solubilisation, deaminase activity, stress-related gene regulation, and microbiome-driven feedback involving root exudation. Overall, viewing bacteria as regulators of root developmental dynamics rather than simple biofertilisers provides new insights for designing climate-adapted and sustainable rice production systems. Full article

(This article belongs to the Topic New Achievements in Gene Mining, Germplasm Innovation, Cultivation Technologies in Rice)

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