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Agronomy
Special Issues
Genetic and Molecular Research on Rice Grain Yield
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Genetic and Molecular Research on Rice Grain Yield

A special issue of Agronomy (ISSN 2073-4395).

Deadline for manuscript submissions: 30 June 2025 | Viewed by 9615

Special Issue Editors

Dr. Yu-Jun Zhu

E-Mail Website
Guest Editor
China National Rice Research Institute, Hangzhou, China
Interests: molecular breeding; yield-related trait; flowering time; map-based cloning; QTL; genome editing; genetic interaction
Special Issues, Collections and Topics in MDPI journals
Dr. Zhen-Hua Zhang

E-Mail Website
Guest Editor
China National Rice Research Institute, Hangzhou, China
Interests: gene identification; genome editing; molecular breeding; rice
Special Issues, Collections and Topics in MDPI journals
Dr. Chaolei Liu

E-Mail Website
Guest Editor
China National Rice Research Institute, Hangzhou, China
Interests: rice; synthetic apomixis; haploid breeding; QTL; genome editing
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The ever-growing world population is driving increases in global food demand. Shrinking farmland, climate change and disease incidence also threaten crop production. Rice (Oryza sativa L.) is one of the most important food crops in the world today, and serves as a staple food source for more than half of the world’s population. Raising rice grain yield potential is crucial for ensuring future food security. The intensive development and application of biotechnologies such as genome assembly, germplasm characterization, transformation and genome editing have greatly facilitated the genetic analysis and functional gene mining of rice germplasm resources. A number of genes/QTLs for yield-related traits have been identified. However, more efforts are needed to decipher the genetic basis of these key agronomic traits in order to improve rice grain yield potential. This Special Issue aims to provide a forum for presenting the most recent advances in genetic and molecular research on yield-related traits in rice. We seek original research articles and reviews covering all related topics, including genome-wide association studies (GWASs), quantitative trait loci (QTLs) mapping, map-based cloning, omics analysis, functional marker-assisted selection, etc., in the context of rice grain yield.

Potential topics include, but are not limited to: the identification of QTLs/genes for yield traits; genetic interaction involved in yield traits; genetic mechanism of trade-off among yield traits; genetic analysis of rice yield under biotic and abiotic stress; application of QTLs/genes for yield traits through marker-assisted selection in breeding practice; and the creation of new rice germplasm using genome editing. 

Dr. Yu-Jun Zhu
Dr. Zhen-Hua Zhang
Dr. Chaolei Liu
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 yield-related traits
  • GWAS
  • QTLs mapping
  • map-based cloning
  • multi-omics
  • marker-assisted selection
  • genome editing

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Published Papers (5 papers)

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Research

13 pages, 1477 KiB  
Article
Rice Yield and Grain Quality under Fluctuating Soil Moisture Stress
by Kotte Hewa Swarnamali Thilinika Deshabandu, Yasutaka Noda, Via Ann Candelaria Marcelo, Hiroshi Ehara, Yoshiaki Inukai and Mana Kano-Nakata
Agronomy 2024, 14(9), 1926; https://doi.org/10.3390/agronomy14091926 - 28 Aug 2024
Viewed by 1326
Abstract
In rainfed lowlands and water-saving cultivation systems, rice plants are often exposed to soil moisture fluctuation (SMF). Improving yield as well as grain quality is the main target for breeding under water-stressed environments. This study investigated the effects of different water treatment on [...] Read more.
In rainfed lowlands and water-saving cultivation systems, rice plants are often exposed to soil moisture fluctuation (SMF). Improving yield as well as grain quality is the main target for breeding under water-stressed environments. This study investigated the effects of different water treatment on yield, growth parameters, and grain quality under field conditions in Japan for 2 years. Two rice genotypes, Nipponbare (japonica) and G3-3 (derived from Nipponbare and KDML105, indica), were grown under continuous waterlogging (CWL) and SMF conditions. As the grain quality characteristics, grain appearance, dimension, and taste parameters were evaluated as well as yield and yield components. SMF reduced the yield, and G3-3 showed a higher yield than Nipponbare under SMF, which was attributed to the higher number of spikelets per panicle. G3-3 showed a better taste score (mark) with lower protein and amylose contents compared to Nipponbare. However, G3-3 had a higher percentage of broken grains, indicating a trade-off in grain quality traits. Non-structural carbohydrate dynamics may be involved as one of the grain quality characteristics. G3-3 demonstrated a superior yield under SMF conditions and have potential to show superior grain quality, indicating that the introgressed segments of G3-3 may be responsible for the grain quality traits associated with root plasticity. Full article
(This article belongs to the Special Issue Genetic and Molecular Research on Rice Grain Yield)
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16 pages, 27820 KiB  
Article
Gα Solicits OsNYC4 and GW2-WG1-OsbZIP47 Modules to Regulate Grain Size in Rice (Oryza sativa L.)
by Shiwei Ma, Yiqiong Sun, Xuan Chen, Jiayi Guo, Shuhong Wu, Guofeng Wu, Guanpeng Huang, Manegdebwaoga Arthur Fabrice Kabore, Samuel Tareke Woldegiorgis, Yufang Ai, Lina Zhang, Wei Liu and Huaqin He
Agronomy 2024, 14(7), 1514; https://doi.org/10.3390/agronomy14071514 - 12 Jul 2024
Viewed by 1146
Abstract
Grain size is one of the critical factors determining rice yield. Previous studies have found the grain-size-regulating function of Gα in rice. However, the regulatory mechanism underlying the development of rice grain mediated by Gα is still unclear. To reveal the functional mechanism [...] Read more.
Grain size is one of the critical factors determining rice yield. Previous studies have found the grain-size-regulating function of Gα in rice. However, the regulatory mechanism underlying the development of rice grain mediated by Gα is still unclear. To reveal the functional mechanism of Gα in grain size regulation, a mutant of Gα (Gα-Cas9) was firstly constructed through a CRISPR/Cas9 strategy and was then grown in a greenhouse and field. The results showed that the seed length, plant height, 1000-grain weight, and spike length were significantly decreased in Gα-Cas9 compared to wild-type (WT) Pi-4b. During the grain filling stage, the increase in the grain dry weight of Pi-4b occurred earlier than that of Gα-Cas9. The total starch content and amylose content of matured grains of Pi-4b were higher than those of Gα-Cas9. Secondly, transcriptome sequencing analysis of Gα-Cas9 and Pi-4b during grain filling was performed to elucidate the functional pathways regulated by Gα. In total, 2867 and 4534 differentially expressed genes (DEGs) were discovered at 5 DAF and 10 DAF, and the starch and sucrose metabolism pathway enriched by DEGs was involved in grain size regulation mediated by Gα. Gα regulated the expression of starch-synthesis-related genes during grain filling, and the Gα protein interacted with OsNYC4 to trigger the sugar signaling pathway to promote starch accumulation in grain. Additionally, the GW2-WG1-OsbZIP47 pathway was switched off by Gα to relieve the inhibition of rice grain development. In this study, the results should provide new insights into the G protein signal transduction pathway. Full article
(This article belongs to the Special Issue Genetic and Molecular Research on Rice Grain Yield)
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37 pages, 14582 KiB  
Article
Genome-Wide Analysis of Amino Acid Transporter Gene Family Revealed That the Allele Unique to the Aus Variety Is Associated with Amino Acid Permease 17 (OsAAP17) Amplifies Both the Tiller Count and Yield in Indica Rice (Oryza sativa L.)
by Itishree Nayak, Bijayalaxmi Sahoo, Chinmay Pradhan, Cayalvizhi Balasubramaniasai, Seenichamy Rathinam Prabhukarthikeyan, Jawahar Lal Katara, Jitendriya Meher, Sang-Min Chung, Abdel-Rhman Z. Gaafar, Mohamed S. Hodhod, Bhagwat Singh Kherawat, Chidambaranathan Parameswaran, Mahipal Singh Kesawat and Sanghamitra Samantaray
Agronomy 2023, 13(10), 2629; https://doi.org/10.3390/agronomy13102629 - 17 Oct 2023
Cited by 3 | Viewed by 2353
Abstract
Amino acid transporters (AATs) play a crucial role in facilitating the movement of amino acids across cellular membranes, which is vital for the growth and development of plants. Amino acid permease (AAP), which belongs to the AAT family, has been the subject of [...] Read more.
Amino acid transporters (AATs) play a crucial role in facilitating the movement of amino acids across cellular membranes, which is vital for the growth and development of plants. Amino acid permease (AAP), which belongs to the AAT family, has been the subject of extensive functional research in plants. Although its importance is recognized, a comprehensive grasp of this family’s dynamics in indica rice remains lacking. In this investigation, a total of 27 AAP genes were identified in the genome of indica rice. Further, the phylogenetic analysis unveiled that the 69 AAP genes from both the model species and other plant species could be classified into 16 distinct subfamilies. The analysis of chromosomal mapping revealed an uneven distribution of the 27 OsAAP genes across the 12 rice chromosomes. Notably, the OsAAP family displayed a total of 10 duplicated gene pairs, along with the identification of numerous conserved motifs. The examination of cis-elements within OsAAP genes unveiled that their promoters contain cis-elements related to phytohormones, plant growth and development, as well as stress responses. Additionally, transcriptome profiling demonstrated that a substantial portion of these genes exhibited responsiveness to various hormones, with their activation spanning multiple tissues and developmental stages in rice. The study identified miRNAs with a specific affinity for OsAAP genes. Out of the 27 OsAAP genes investigated, seventeen were discovered to be targeted by a total of forty-three miRNAs. Furthermore, the aus allele of OsAAP3 that we named OsAAP17 was validated for its effect on productive tillers and yield, and seventeen genetic variants of OsAAP17 were found to be associated with a culm number in indica rice. In addition, indica rice varieties were monomorphic, while aus genotypes displayed polymorphism for OsAAP17 gene-specific in/dels. Moreover, in Season II (rabi season), it was found that the aus allele of OsAAP17 increased the number of productive tillers and the single plant yield by 22.55% and 9.67%, respectively, in a recombinant inbred population created by crossing N22 and JR 201. Remarkably, this enhancement was more pronounced during the dry cultivation season, highlighting the influence of environmental factors in the regulation of tiller numbers mediated by OsAAP17. The discoveries presented here lay a strong foundation for further exploration into the roles of OsAAP family genes across a range of developmental processes. Therefore, the identified allelic variations in the utilization of OsAAP17 has the potential to enhance rice crop production via molecular breeding in the changing climate scenario. Full article
(This article belongs to the Special Issue Genetic and Molecular Research on Rice Grain Yield)
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12 pages, 1960 KiB  
Article
Detection of QTL for High-Temperature Tolerance in Rice Using a High-Density Bin Map
by Derun Huang, Zhenhua Zhang, Yeyang Fan, Shaoqing Tang, Jieyun Zhuang and Yujun Zhu
Agronomy 2023, 13(6), 1582; https://doi.org/10.3390/agronomy13061582 - 12 Jun 2023
Cited by 4 | Viewed by 1810
Abstract
Rice is sensitive to high-temperature stress during almost all stages of growth and development. High-temperature stress has become one of the main factors restricting high yield and superior quality of rice. In this study, recombinant inbred lines (RILs) derived from an indica rice [...] Read more.
Rice is sensitive to high-temperature stress during almost all stages of growth and development. High-temperature stress has become one of the main factors restricting high yield and superior quality of rice. In this study, recombinant inbred lines (RILs) derived from an indica rice cross between two restorer lines were planted in two years. One sowing date was applied in 2019, and four sowing dates were set in 2020 according to the period of local high temperatures in recent years. Two traits closely related to high-temperature tolerance, heading date (HD), and spikelet fertility (SF) were measured. In each trial, the HD showed a bimodal distribution, whereas SF had a continuous and left-skewed distribution. QTL analysis was performed using a high-density bin map. For HD, a total of six QTL were detected. All of them correspond in position to the cloned genes, among which qHD8 in the DTH8/Ghd8 region showed the largest genetic effect. For SF, a total of eight QTL were detected. Five of them, qSF1, qSF2, qSF3.1, qSF3.2, and qSF8, showed high-temperature tolerance and had an important potential in rice breeding. Full article
(This article belongs to the Special Issue Genetic and Molecular Research on Rice Grain Yield)
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10 pages, 3387 KiB  
Article
Development of Specific Molecular and Phenotypic Marker-Based Haploid Inducers in Rice
by Jian Wang, Huijing Yan, Xiaozhen Jiao, Jun Ren, Fengyue Hu, Huan Liang, Weihong Liang and Chaolei Liu
Agronomy 2023, 13(6), 1520; https://doi.org/10.3390/agronomy13061520 - 31 May 2023
Viewed by 1992
Abstract
Doubled haploid (DH) technology is an efficient strategy for producing completely homozygous lines for breeding programs. Mutations in the MATRILINEAL (MTL) phospholipase trigger intraspecific haploid induction in cereals. Although an in vivo haploid induction system based on OsMTL-edited plants has [...] Read more.
Doubled haploid (DH) technology is an efficient strategy for producing completely homozygous lines for breeding programs. Mutations in the MATRILINEAL (MTL) phospholipase trigger intraspecific haploid induction in cereals. Although an in vivo haploid induction system based on OsMTL-edited plants has been established in rice (Oryza sativa), DH technology is still limited by other factors, such as haploid identification, which is one of the essential steps required for DH technology. In the study, we addressed this technical challenge by integrating specific molecular and phenotypic markers into rice haploid inducers. We first generated large fragment insertion or deletion mutations within the OsMTL gene and designed a pair of primers flanking the mutational sites to be used as the specific and universal molecular markers between wild-type and Osmtl plants. Next, we screened for hairy leaf as a single dominant trait and integrated it into specific molecular marker-based haploid inducers using the cross and self-cross method. When crossing cytoplasmic male sterile lines with these haploid inducers, we utilized the specific InDel marker and hairy leaf phenotypic marker to identify putative haploids (or double haploids). These putative haploids were further confirmed through ploidy and phenotypic analysis, demonstrating the high efficiency of haploid identification using these markers. The haploid induction rate (HIR) of the developed specific molecular and phenotypic marker-based haploid inducers ranged from 3.7% to 12.5%. We have achieved successful integration of distinct molecular and phenotypic markers into rice haploid inducers. Our advanced marker-based system has significantly enhanced the accuracy of haploid identification, thereby expediting the adoption of DH technology in rice breeding. Full article
(This article belongs to the Special Issue Genetic and Molecular Research on Rice Grain Yield)
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