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Agronomy
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Innovative Research on Rice Breeding and Genetics
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Innovative Research on Rice Breeding and Genetics

A special issue of Agronomy (ISSN 2073-4395). This special issue belongs to the section "Crop Breeding and Genetics".

Deadline for manuscript submissions: 31 July 2025 | Viewed by 32137

Special Issue Editors

Dr. Zhijuan Ji

E-Mail Website
Guest Editor
China National Center of Rice Improvement, China National Rice Research Institute, Hangzhou 311400, China
Interests: hybrid rice; breeding methods; disease resistance
Dr. Yongqi He

E-Mail Website
Guest Editor
The Laboratory of Seed Science and Technology, South China Agricultural University, Guangzhou 510642, China
Interests: rice; seed vigor; stress response and regulation

Special Issue Information

Dear Colleagues,

Rice is an important food crop worldwide and is a major target of breeding efforts seeking to improve both agricultural production and nutritional quality to meet human demand for food. The development of germplasm resources and advances in breeding methods have led to steady increases in the yield and quality of rice. In particular, the development of hybrid rice has greatly contributed to ensuring food security globally. Hybrid rice breeding includes the three-, two-, and one-line methods. The one-line method of hybrid rice breeding fixes heterosis through apomixis with the ability to reproduce in the absence of fertilization.

This SI focuses on rice breeding methods, the creation of germplasm materials, genetics and genomics, biotic and abiotic stress, but is not limited to these topics. This Special Issue welcomes reviews, regular research papers, communications, and short notes.

Dr. Zhijuan Ji
Dr. Yongqi He
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Agronomy is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • rice
  • breeding methods
  • high yield
  • rice quality
  • resistance

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Published Papers (6 papers)

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Research

Jump to: Review

16 pages, 2206 KiB  
Article
Identification of Indica–Japonica Attributes and Analysis of Heterosis Using InDel Markers
by Lingling Huang, Jing Ye, Rongrong Zhai, Mingming Wu, Faming Yu, Xiaoming Zhang, Guofu Zhu, Jinling Han and Shenghai Ye
Agronomy 2024, 14(12), 2832; https://doi.org/10.3390/agronomy14122832 - 28 Nov 2024
Viewed by 1072
Abstract
With the development and improvement of indica–japonica hybrid rice breeding technologies, it has become possible to directly utilize the heterosis between indica and japonica subspecies to cultivate high-yielding rice varieties. Precisely analyzing the attributes and heterosis levels of indica–japonica varieties is crucial for [...] Read more.
With the development and improvement of indica–japonica hybrid rice breeding technologies, it has become possible to directly utilize the heterosis between indica and japonica subspecies to cultivate high-yielding rice varieties. Precisely analyzing the attributes and heterosis levels of indica–japonica varieties is crucial for successfully breeding indica–japonica hybrid rice and utilizing heterosis. This study employed 34 insertion–deletion (InDel) molecular markers to identify the indica–japonica attributes in 122 rice varieties and validated the results using cluster analyses and principal component analyses (PCAs). Additionally, the yield-related traits of the hybrids and parents were assessed, heterosis was analyzed, and the feasibility of predicting heterosis using parental genetic distance (GD) was explored. InDel molecular markers showed that all the hybrids were indica–japonica crosses with varying genetic components, confirmed by the cluster analyses and the PCAs. A heterosis analysis revealed that an increase in the effective panicle number per plant (EP) was the main factor in increasing the yield. Different GD intervals showed varying correlations with trait heterosis. These results indicate the effectiveness of InDel molecular markers in accurately distinguishing indica–japonica attributes and that hybrid combinations demonstrate significant heterosis. This study provides a reference for parent selection and utilizing heterosis in indica–japonica hybrid rice. Full article
(This article belongs to the Special Issue Innovative Research on Rice Breeding and Genetics)
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13 pages, 2918 KiB  
Article
Evolution of Rice Cultivar Performance Across China: A Multi-Dimensional Study on Yield and Agronomic Characteristics over Three Decades
by Song Hang, Qi Wang, Yuan Wang and Haitao Xiang
Agronomy 2024, 14(12), 2780; https://doi.org/10.3390/agronomy14122780 - 23 Nov 2024
Cited by 1 | Viewed by 24046
Abstract
Rice (Oryza sativa L.) is a staple food crop for over half of the world’s population, with China being the largest producer. However, the growth rate of rice yield per hectare has slowed in recent years, emphasizing the need for in-depth studies [...] Read more.
Rice (Oryza sativa L.) is a staple food crop for over half of the world’s population, with China being the largest producer. However, the growth rate of rice yield per hectare has slowed in recent years, emphasizing the need for in-depth studies on the evolution of rice cultivar performance. This study presents a comprehensive analysis of the yield and key agronomic traits of rice cultivars across China over three decades, utilizing data from 11,811 cultivar trials conducted between 1990 and 2023. We assessed the spatial distribution and temporal evolution of rice cultivar performance, exploring regional differences and the interplay between agronomic traits and environmental factors. Our results reveal significant variations in growth duration, plant height, grains per panicle, thousand-grain weight, effective panicle number, and seed setting rate across different regions. Temporal trends showed diverse patterns of improvement, with some regions experiencing rapid advancements (up to 1.42% annual yield increase in Jiangxi Province of Central China) and others nearing yield plateaus (0.16% in Jilin Province and 0.45% in Heilongjiang Province of Northeast China). Correlation analysis between agronomic traits and grain yield highlighted the complex relationships and potential for further genetic gains through targeted breeding. This study underscores the importance of region-specific breeding strategies to optimize rice production in the face of environmental challenges and yield ceilings. The insights gained provide a scientific basis for future rice cultivar development and regional agricultural policies aimed at enhancing sustainability and efficiency in China’s diverse rice-growing regions. Full article
(This article belongs to the Special Issue Innovative Research on Rice Breeding and Genetics)
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12 pages, 2730 KiB  
Article
Golden Hull: A Potential Biomarker for Assessing Seed Aging Tolerance in Rice
by Jing Ye, Chengjing Wang, Ling Chen, Rongrong Zhai, Mingming Wu, Yanting Lu, Faming Yu, Xiaoming Zhang, Guofu Zhu and Shenghai Ye
Agronomy 2024, 14(10), 2357; https://doi.org/10.3390/agronomy14102357 - 12 Oct 2024
Viewed by 1156
Abstract
Seed aging is a complex process that involves various physiological and biochemical changes leading to a decline in seed viability during storage. However, the specific biomarkers for assessing the degree of seed aging in rice remain elusive. In this study, we isolated a [...] Read more.
Seed aging is a complex process that involves various physiological and biochemical changes leading to a decline in seed viability during storage. However, the specific biomarkers for assessing the degree of seed aging in rice remain elusive. In this study, we isolated a golden hull mutant, gh15, from the indica rice Z15 by employing a radiation mutagenesis technique. Compared with the wild type (WT) Z15, the mutant gh15 displayed a golden hue in the hull, stem, and internodes, while no significant differences were observed in the key agronomic traits. A genetic analysis showed that the gh15 phenotype is regulated by a single recessive gene, which possibly encodes cinnamyl alcohol dehydrogenase OsCAD2. Significant differences of seed aging tolerance were observed between gh15 and WT after six months of natural storage and artificial aging treatment, with gh15 exhibiting a markedly lower aging tolerance compared to the WT. Haplotype assays indicated that the Hap2 of OsCAD2 was significantly associated with the dark coloration of the hull and lower seed aging tolerance. The molecular marker of OsCAD2 associated with seed color was explored in rice. These findings demonstrate that the golden hull serves as a potential biomarker for the rapid assessment of seed aging tolerance in rice. Full article
(This article belongs to the Special Issue Innovative Research on Rice Breeding and Genetics)
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19 pages, 4801 KiB  
Article
Genome-Wide Identification and Characterization of the PPPDE Gene Family in Rice
by Wangmin Lian, Xiaodeng Zhan, Daibo Chen, Weixun Wu, Qunen Liu, Yinxing Zhang, Shihua Cheng, Xiangyang Lou, Liyong Cao and Yongbo Hong
Agronomy 2024, 14(5), 1035; https://doi.org/10.3390/agronomy14051035 - 13 May 2024
Viewed by 1782
Abstract
Protein ubiquitination is common and crucial in cellular functions, however, little is known about how deubiquitinating enzymes (DUBs) reverse regulate the ubiquitination signaling process. PPPDE family proteins are a novel class of deubiquitinating peptidases with demonstrated deubiquitination/deSUMOylating activities. In this study, we identified [...] Read more.
Protein ubiquitination is common and crucial in cellular functions, however, little is known about how deubiquitinating enzymes (DUBs) reverse regulate the ubiquitination signaling process. PPPDE family proteins are a novel class of deubiquitinating peptidases with demonstrated deubiquitination/deSUMOylating activities. In this study, we identified 10 PPPDE genes from the rice (Oryza sativa L.) genome unevenly distributed on five chromosomes, where most of these members have not been reported to date. Based on the gene structure, the OsPPPDE family consists of three distinct subgroups within the phylogenetic tree. Cis-element analysis identified light/phytohormone-responsive, development, and abiotic stress-related elements in the promoters of OsPPPDE. Furthermore, we conducted and analyzed the transcript abundance of OsPPPDE under various tissues and stresses using the transcriptome data of 352 samples from the Rice Expression Database and GEO datasets. Moreover, OsPPPDE5 showed differential regulation of its transcript abundance during Cd and drought stress. Collinearity and syntenic analysis of 101 PPPDEs and PPPDE-like proteins in 10 plant genomes indicated that this family is evolutionarily conserved. Domestication analysis suggests that OsPPPDEs may contribute to indica–japonica divergence using the data from the 3K Rice Genome Project. Our study provides a foundation for further study on the function and molecular mechanism of the OsPPPDE gene family. Full article
(This article belongs to the Special Issue Innovative Research on Rice Breeding and Genetics)
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Review

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15 pages, 1825 KiB  
Review
Evaluation of Breeding Progress and Agronomic Traits for Japonica Rice in Anhui Province, China (2005–2024)
by Yu Zou, Muhammad Ahmad Hassan, Ending Xu, Yi Ren, Jie Wang, Xinchun Zhan, Dahu Ni and Peijiang Zhang
Agronomy 2024, 14(12), 2957; https://doi.org/10.3390/agronomy14122957 - 12 Dec 2024
Viewed by 869
Abstract
Rice is the staple diet for most of the world’s population and is considered a major staple crop in China. Anhui province of China is among the leading provinces for rice production, consumption, and commodities; it is well-known as the “land of fish [...] Read more.
Rice is the staple diet for most of the world’s population and is considered a major staple crop in China. Anhui province of China is among the leading provinces for rice production, consumption, and commodities; it is well-known as the “land of fish and rice”. Japonica rice cultivation in Anhui Province is mainly categorized into late-maturing medium, early-maturing medium, and early-maturing late japonica. This review explores the suitable ecological zone distribution and corresponding climate characteristics of the three types of japonica rice in Anhui Province. Data on japonica rice varieties approved in the province over the past twenty years were collected, illustrating the development process of japonica rice varieties in the province and their quality and resistance to rice blast disease. The review shows that the yield is positively and significantly correlated with agronomic traits, such as the number of effective panicles and the total number of grains per panicle, plant height, etc. In addition, it elucidates the major problems faced by Anhui’s japonica rice breeding and cultivation, such as frequent events of high temperatures, rice blast disease, and medium to low soil fertility levels. Considering the existing issues in breeding japonica rice varieties in Anhui Province, this review proposes a strategy for breeding high-yield and disease-resistant japonica rice varieties, particularly varieties adaptable to medium and low fertility soil conditions. In brief, this article provides a theoretical basis and practical recommendations for the sustainable development of japonica rice in the Anhui Province of China. Full article
(This article belongs to the Special Issue Innovative Research on Rice Breeding and Genetics)
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13 pages, 1023 KiB  
Review
Bakanae Disease Resistance in Rice: Current Status and Future Considerations
by Liwei Zhan, Ling Chen, Yuxuan Hou, Yuxiang Zeng and Zhijuan Ji
Agronomy 2024, 14(7), 1507; https://doi.org/10.3390/agronomy14071507 - 11 Jul 2024
Cited by 2 | Viewed by 2211
Abstract
Bakanae disease is mainly caused by Fusarium fujikuroi and is a significant fungal disease with a number of disastrous consequences. It causes great losses in rice production. However, few studies have focused on the details of bakanae disease resistance in rice. Here, we [...] Read more.
Bakanae disease is mainly caused by Fusarium fujikuroi and is a significant fungal disease with a number of disastrous consequences. It causes great losses in rice production. However, few studies have focused on the details of bakanae disease resistance in rice. Here, we summarize and discuss the progress of bakanae disease resistance in rice. Besides rice germplasm screening and resistance-related gene/quantitative trait locus (QTL) exploration, the route of pathogen invasion in rice plants was determined. We further discussed the regulation of phytohormone-related genes and changes in endogenous phytohormones in rice plants that are induced by the pathogen. To achieve better control of bakanae disease, the use of natural fungicides was assessed in this review. During rice—F. fujikuroi interactions, the infection processes and spatial distribution of F. fujikuroi in infected seedlings and adult plants exhibit different trends. Fungal growth normally occurs both in resistant and susceptible cultivars, with less abundance in the former. Generally, bakanae disease is seed-borne, and seed disinfection using effective fungicides should always be the first and main option to better control the disease. Besides the friendly and effective measure of using natural fungicides, breeding and utilization of resistant rice cultivars is also an effective control method. To some extent, rice cultivars with low grain quality, indica subspecies, and some dwarf or semi-dwarf rice germplasms are more resistant to bakanae disease. Although no highly resistant germplasms were obtained, 37 QTLs were located, with almost half of the QTLs being located on chromosome 1. Using omics methods, WRKYs and MAPKs were usually found to be regulated during rice—F. fujikuroi interactions. The regulation of certain phytohormone-related genes and changes in some endogenous phytohormones induced by the pathogen were clear, i.e., it downregulated gibberellin-related genes and repressed endogenous gibberellins in resistant genotypes, but the opposite results were noted in susceptible rice genotypes. Overall, exploring resistant germplasms or resistance-related genes/QTLs for the breeding of rice with bakanae disease resistance, expanding research on the complex mechanism of rice—F. fujikuroi interactions, and using cost-effective and eco-friendly innovative control methods against the disease are necessary for present and future bakanae disease management. Full article
(This article belongs to the Special Issue Innovative Research on Rice Breeding and Genetics)
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