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Research on Genetics and Breeding of Rice
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Research on Genetics and Breeding of Rice

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Plant Genetics and Genomics".

Deadline for manuscript submissions: 20 June 2026 | Viewed by 689

Special Issue Editor

Prof. Dr. Xiaojin Luo

E-Mail Website
Guest Editor
School of Life Sciences, Fudan University, Shanghai 200433, China
Interests: molecular genetics; genomics; bioinformatics; rice; yield and quality; breeding portrait

Special Issue Information

Dear Colleagues,

Rice (Oryza sativa L.) is a crop of global importance because it provides sustenance to more than half of the world population. Since the global population is expected to reach 9 billion by 2050, increased rice production will have a significantly positive impact on global food security. However, current rice breeding cannot keep up with the requirements of the situation. In order to achieve a further breakthrough in yield, abiotic/biotic stress resistance, quality, efficient planting management, environmental adaptation, etc., it is necessary to devise novel approaches and genetic resources to exploit rice germplasm, find and utilize the key “Genetic-Bricks” related to advantage traits construction, and to understand the molecular basis of rice improvement. On this basis, we need to develop and use new breeding technologies to promote the leapfrog development of the modern seed industry.

Contributions of both original research articles and reviews are welcome for this Special Issue on the following topics: novel approaches of germplasm utilization, application of next generation sequencing for rice improvement, mining of key genetic loci and biochemical functional elements, development of ecological varieties and crop resource, genetic and molecular basis of rice production improvement traits, new breeding technologies such as molecular design breeding, gene editing, haploid breeding, transgenic technology, and bioengineering.

Prof. Dr. Xiaojin Luo
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 250 words) can be sent to the Editorial Office for assessment.

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. Genes 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
  • molecular genetics
  • rice germplasm
  • QTL identification and gene cloning
  • genetic function and genetic network
  • breeding technologies

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Published Papers (2 papers)

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Research

12 pages, 1874 KB  
Article
Novel Wx Gene Functional Markers for High-Resistant Starch Rice Breeding
by Jie Ouyang, Zichao Zhu, Yusheng Guan, Qianlong Huang, Tao Huang, Shun Zang and Chuxiang Pan
Genes 2026, 17(1), 89; https://doi.org/10.3390/genes17010089 - 14 Jan 2026
Viewed by 140
Abstract
Background/Objectives: Chemical methods for quantifying resistant starch (RS) in rice are labor-intensive, costly, and lack high repeatability, creating a bottleneck in breeding. This study aimed to develop specific, codominant molecular markers for the Wx gene to enable rapid and accurate genotype screening [...] Read more.
Background/Objectives: Chemical methods for quantifying resistant starch (RS) in rice are labor-intensive, costly, and lack high repeatability, creating a bottleneck in breeding. This study aimed to develop specific, codominant molecular markers for the Wx gene to enable rapid and accurate genotype screening for RS content, thereby accelerating the development of high-RS rice varieties. Methods: Based on sequence alignment of the Wx gene in rice varieties with divergent RS content, a key single-nucleotide polymorphism was targeted. Two sets of tetra-primer amplification refractory mutation system polymerase chain reaction (ARMS-PCR) markers, T-Wx9-RS1 and T-Wx9-RS2, were designed. These markers were used to genotype diverse rice varieties and F4 segregating populations, with results validated against standard chemical assays. Results: Sequence analysis identified a critical T → C base mutation at position 202 of the ninth exon in high-RS varieties. The developed ARMS-PCR markers successfully and consistently distinguished all three possible genotypes (homozygous mutant, homozygous wild-type, and heterozygous). The genotyping results showed complete concordance with the phenotypes determined by chemical methods. Conclusions: The developed molecular markers, T-Wx9-RS1 and T-Wx9-RS2, provide a rapid, reliable, and cost-effective tool for marker-assisted selection of high resistant starch content in rice. Their implementation can significantly enhance screening efficiency and expedite the breeding pipeline for novel, nutritionally improved rice cultivars. Full article
(This article belongs to the Special Issue Research on Genetics and Breeding of Rice)
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14 pages, 6199 KB  
Article
Multiplex Gene Editing and Effect Analysis of Yield, Fragrance, and Blast Resistance Genes in Rice
by Shuhui Guan, Yingchun Han, Jingwen Zhang, Yanxiu Du, Zhen Chen, Chunbo Miao and Junzhou Li
Genes 2026, 17(1), 77; https://doi.org/10.3390/genes17010077 - 9 Jan 2026
Viewed by 196
Abstract
Background: The coordinated improvement of yield, quality and resistance is a primary goal in rice breeding. Gene editing technology is a novel method for precise multiplex gene improvement. Methods: In this study, we constructed a multiplex CRISPR/Cas9 vector targeting yield-related genes (GS3 [...] Read more.
Background: The coordinated improvement of yield, quality and resistance is a primary goal in rice breeding. Gene editing technology is a novel method for precise multiplex gene improvement. Methods: In this study, we constructed a multiplex CRISPR/Cas9 vector targeting yield-related genes (GS3, OsPIL15, Gn1a), fragrance gene (OsBADH2) and rice blast resistance gene (Pi21) to pyramid traits for enhanced yield, quality, and disease resistance in rice. A tRNA-assisted CRISPR/Cas9 multiplex gene editing vector, M601-OsPIL15/GS3/Gn1a/OsBADH2/Pi21-gRNA, was constructed. Genetic transformation was performed using the Agrobacterium-mediated method with the japonica rice variety Xin Dao 53 as the recipient. Mutation editing efficiency was detected in T0 transgenic plants. Grain length, grain number per panicle, thousand-grain weight, 2-acetyl-1-pyrroline (2-AP) content, and rice blast resistance of homozygous lines were measured in the T3 generations. Results: Effectively edited plants were obtained in the T0 generation. The simultaneous editing efficiency for all five genes reached 9.38%. The individual gene editing efficiencies for Pi21, GS3, OsBADH2, Gn1a, and OsPIL15 were 78%, 63%, 56%, 54%, and 13%, respectively. Five five-gene homozygous edited lines with two genotypes were selected in the T2 generation. In the T3 generation, compared with the wild-type (WT), the edited homozygous lines showed increased grain number per panicle (14.60–25.61%), increased grain length (7.39–11.16%), increased grain length–width ratio (8.37–13.02%), increased thousand-grain weight (3.79–9.15%), a 42–64 folds increase in the fragrant substance 2-AP content, and significantly enhanced rice blast resistance. Meanwhile, there were no significant changes in other agronomic traits. Conclusions: CRISPR/Cas9-mediated multiplex gene editing technology enabled the simultaneous editing of genes related to rice yield, quality, and disease resistance. This provides an effective approach for obtaining new japonica rice germplasm with blast resistance, long grains, and fragrance. Full article
(This article belongs to the Special Issue Research on Genetics and Breeding of Rice)
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