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Molecular Genetics, Breeding, and Multi-Omics Approaches in Rice Research
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Molecular Genetics, Breeding, and Multi-Omics Approaches in Rice Research

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Plant Sciences".

Deadline for manuscript submissions: 20 September 2025 | Viewed by 2008

Special Issue Editor

Dr. Zakaria Prodhan

E-Mail Website
Guest Editor
AgriLife Research Center, Texas A&M University, Beaumont, TX, USA
Interests: plant genetics; plant breeding; plant molecular biology; plant molecular breeding; aromatic rice

Special Issue Information

Dear Colleagues,

Rice is the most valuable and widely consumed staple crop in the world. Rice research has become an integral part of modern scientific innovation. Complete genomic and genome-based sequencing datasets, along with numerous databases, form the backbone of current molecular research into rice. Modernistic molecular genetics and breeding methods are accelerating conventional genetic studies and breeding approaches and revolutionizing rice research. This Special Issue will cover a range of topics related to the molecular genetics, breeding, and multi-omics-based approaches that enable modern-day rice production. We welcome submissions of original research papers and reviews.

In this Special Issue, we will consider contributions to rice research that focus on the combination of molecular genetics and conventional breeding in rice improvement, molecular biological studies of rice resistance to abiotic stress, and the use of genomics, proteomics, and new multi-omics technologies in rice development.

Dr. Zakaria Hossain Prodhan
Guest Editor

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. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. 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 genetics and breeding
  • molecular breeding of rice
  • rice genomics and proteomics
  • genes related to abiotic stress tolerance in rice
  • molecular biology and multi-omics in rice research

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Published Papers (2 papers)

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Research

15 pages, 3225 KiB  
Article
Increased Photosynthetic Capacity and Energy Status Contribute to Higher Grain Yield in Early Rice
by Haoran Su, Wenting Wang, Tingting Lu, Wenfei Hu, Junjiang Lin, Weimeng Fu, Yan Liang, Yvxiang Zeng, Guanfu Fu, Jie Xiong and Tingting Chen
Int. J. Mol. Sci. 2025, 26(4), 1508; https://doi.org/10.3390/ijms26041508 - 11 Feb 2025
Viewed by 597
Abstract
As the economy develops and urbanization progresses, the amount of arable land continues to decline. In this context, the cultivation of double-season rice is particularly important for enhancing yield per unit area. However, research on the physiological mechanisms that contribute to high yields [...] Read more.
As the economy develops and urbanization progresses, the amount of arable land continues to decline. In this context, the cultivation of double-season rice is particularly important for enhancing yield per unit area. However, research on the physiological mechanisms that contribute to high yields in double-season early rice varieties with short growing seasons is still limited. To address this gap, we conducted a field study using two early rice varieties, Zhongzu18 and Yongxian15, to examine their production characteristics, photosynthesis, fluorescence, and energy metabolism. The results indicate that Zhongzu18 has a significantly higher seed-setting rate, grain weight, and total grain yield compared to Yongxian15. Additionally, Zhongzu18 exhibits a higher head rice rate and a lower degree of chalkiness, along with a reduced chalky grain rate. Furthermore, the total dry matter weight and the ratio of panicle weight to total weight for Zhongzu18 were significantly greater than those for Yongxian15. After anthesis, Zhongzu18 also demonstrated a higher leaf net photosynthetic rate and actual fluorescence quantum efficiency compared to Yongxian15. Moreover, the levels of ATP and ATPase, as well as the activities of antioxidant enzymes and the expression of sucrose transport-related genes, were significantly increased in Zhongzu18 plants relative to Yongxian15. We conclude that the enhanced photosynthetic efficiency and energy production in Zhongzu18 lead to more effective assimilation and carbohydrate transport to the grains, resulting in higher grain yields and improved rice quality. Full article
(This article belongs to the Special Issue Molecular Genetics, Breeding, and Multi-Omics Approaches in Rice Research)
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15 pages, 3286 KiB  
Article
Cell Wall Invertases from Maternal Tissues Modulate Sucrose Flux in Apoplastic Pathways During Rice Anther and Seed Development
by Sang-Kyu Lee, Su-Hyeon Shim, Joon-Seob Eom, Jung-Il Cho, Jae-Ung Kwak, Seong-Cheol Eom and Jong-Seong Jeon
Int. J. Mol. Sci. 2024, 25(21), 11557; https://doi.org/10.3390/ijms252111557 - 28 Oct 2024
Viewed by 1012
Abstract
Efficient sucrose transport and metabolism are vital for seed and pollen development in plants. Cell wall invertases (CINs) hydrolyze sucrose into glucose and fructose, maintaining a sucrose gradient in the apoplast of sink tissues. In rice, two CIN isoforms, OsCIN1 and OsCIN2, were [...] Read more.
Efficient sucrose transport and metabolism are vital for seed and pollen development in plants. Cell wall invertases (CINs) hydrolyze sucrose into glucose and fructose, maintaining a sucrose gradient in the apoplast of sink tissues. In rice, two CIN isoforms, OsCIN1 and OsCIN2, were identified as being specifically expressed in the anthers but not in pollen. Functional analyses through genetic crosses and mutant characterization showed that oscin1/2 double mutants exhibit a sporophytic male-sterile phenotype and produce shrunken seeds. This suggests that CIN activity is essential for proper pollen development and seed formation in rice. Observation of the progeny genotypes and phenotypes from various genetic crosses revealed that the phenotype of oscin1/2 seeds is determined by the genotype of the maternal tissue, indicating the critical role of CIN function in the apoplast between maternal and filial tissues for sucrose transport and metabolism. The CIN activity in the anthers and seeds of wild-type rice was found to be significantly higher—over 500-fold in the anthers and 5-fold in the seeds—than in the leaves, highlighting the importance of CIN in facilitating the efficient unloading of sucrose. These findings suggest that the fine-tuning of CIN activity in the apoplast, achieved through tissue-specific expression and CIN isoform regulation, plays a key role in determining the carbohydrate distribution across different tissues. Understanding this regulatory mechanism could provide opportunities to manipulate carbohydrate allocation to sink organs, potentially enhancing crop yields. Full article
(This article belongs to the Special Issue Molecular Genetics, Breeding, and Multi-Omics Approaches in Rice Research)
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