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Molecular Breeding and Germplasm Improvement of Rice—2nd Edition
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Molecular Breeding and Germplasm Improvement of Rice—2nd Edition

A special issue of Plants (ISSN 2223-7747). This special issue belongs to the section "Plant Genetics, Genomics and Biotechnology".

Deadline for manuscript submissions: 31 March 2025 | Viewed by 4980

Special Issue Editors

Dr. Xiangjin Wei

E-Mail Website
Guest Editor
China National Center for Rice Improvement and State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 311400, China
Interests: genetic improvement of rice quality; developmental biology of rice
Special Issues, Collections and Topics in MDPI journals
Dr. Yingxin Zhang

E-Mail Website
Guest Editor
China National Center for Rice Improvement and State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 311400, China
Interests: rice; yield; quantitative trait locus
Special Issues, Collections and Topics in MDPI journals
Dr. Weixun Wu

E-Mail Website
Guest Editor
China National Center for Rice Improvement and State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 311400, China
Interests: rice; heading date; saline–alkali resistance; quantitative trait locus; map-based cloning; functional analysis
Special Issues, Collections and Topics in MDPI journals
Dr. Guiai Jiao

E-Mail
Guest Editor
China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310006, China
Interests: rice quality; rice genetics and breeding; physical and chemical properties of rice
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

In recent years, gene editing, whole-genome selection, synthetic biology frontier biotechnology and information technology such as artificial intelligence and big data have been integrated into conventional breeding techniques, breeding technology and intelligent design system, which continuously drives the modern breeding technology change iterations and has a significant influence on the crops of rice breeding. In addition, germplasm resources are the chip of crop breeding and every breakthrough in crop breeding is inseparable from the innovation of important germplasm.

In order to promote academic exchange on the latest trends and achievements of molecular breeding and germplasm improvement of rice, this Special Issue will focus on the promotion of the joint discussion of the latest research dynamics and directions, and find opportunities for collaboration in this field. All original research papers and reviews are welcome for submission to this Special Issue.

Contributions in this Special Issue may include, but are not limited to, the research and development of new technologies for rice molecular breeding and germplasm innovation. Particularly welcome is research on rice molecular breeding technologies such as gene editing, whole-genome selection, synthetic biology, intelligent design breeding and advances in the innovation of new rice germplasm with high yield, high quality, multiresistance, safety and high efficiency.

Dr. Xiangjin Wei
Dr. Yingxin Zhang
Dr. Weixun Wu
Dr. Guiai Jiao
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. Plants is an international peer-reviewed open access semimonthly 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 2700 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 molecular breeding
  • innovation of rice germplasm
  • gene editing
  • whole-genome selection
  • synthetic biology
  • intelligent design breeding

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Related Special Issue

Published Papers (5 papers)

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Research

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17 pages, 6263 KiB  
Article
Heterologous Expression of Sunflower HaHPT and HaTMT Genes Enhances Rice-Grain Vitamin E Content
by Shuang Song, Hang Li, Shaoyan Lin, Xiaoou Dong, Ruiping Tian, Zewan Wu, Qing Li, Mingyi Li, Keying Zhang, Xi Liu, Jianmin Wan and Linglong Liu
Plants 2024, 13(17), 2392; https://doi.org/10.3390/plants13172392 - 27 Aug 2024
Viewed by 700
Abstract
Insufficient dietary vitamin intake can lead to severe health conditions in humans. Improving the vitamin E (VE) content of food crops such as rice through breeding is an economical and effective means to alleviate this problem. In this study, Homogentisate phytyltransferase (HPT [...] Read more.
Insufficient dietary vitamin intake can lead to severe health conditions in humans. Improving the vitamin E (VE) content of food crops such as rice through breeding is an economical and effective means to alleviate this problem. In this study, Homogentisate phytyltransferase (HPT) and γ-tocopherol methyltransferase (γ-TMT), two genes derived from sunflower (Helianthus annuus L., a high VE species), were introduced into an elite rice (Oryza sativa L.) cultivar “Ningjing 7” for biofortification. We verified the successful expression of the two genes in multiple transformation events. High-performance liquid chromatography revealed that transgenic plants expressing either HaHPT alone or HaHPT and HaTMT accumulate more VE compared with the wild type. We also revealed that the level of α-tocopherol, the form of VE with the highest biological activity, had increased to 2.33 times in transgenic HaTMT plants compared with the wild type. Transcriptome analysis revealed that the expression levels of some chlorophyll synthesis pathway genes related to VE precursor synthesis significantly increased during grain filling in transgenic rice grains. No difference in agronomic traits was observed between the transgenic plants and their wild type except for a slightly reduced plant height associated with the transgenic plants. These data demonstrate that the heterologous expression of HaHPT gene is effective in increasing the total VE content, while HaTMT plays an important role in the relative abundance of α-tocopherol in rice grains. This study demonstrates a promising strategy for breeding rice with elevated VE content via metabolic engineering. Full article
(This article belongs to the Special Issue Molecular Breeding and Germplasm Improvement of Rice—2nd Edition)
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16 pages, 4997 KiB  
Article
Improvement of Flowering Stage in Japonica Rice Variety Jiahe212 by Using CRISPR/Cas9 System
by Dengmei He, Ran Zhou, Chenbo Huang, Yanhui Li, Zequn Peng, Dian Li, Wenjing Duan, Nuan Huang, Liyong Cao, Shihua Cheng, Xiaodeng Zhan, Lianping Sun and Shiqiang Wang
Plants 2024, 13(15), 2166; https://doi.org/10.3390/plants13152166 - 5 Aug 2024
Viewed by 864
Abstract
The flowering period of rice significantly impacts variety adaptability and yield formation. Properly shortening the reproductive period of rice varieties can expand their ecological range without significant yield reduction. Targeted genome editing, like CRISPR/Cas9, is an ideal tool to fine-tune rice growth stages [...] Read more.
The flowering period of rice significantly impacts variety adaptability and yield formation. Properly shortening the reproductive period of rice varieties can expand their ecological range without significant yield reduction. Targeted genome editing, like CRISPR/Cas9, is an ideal tool to fine-tune rice growth stages and boost yield synergistically. In this study, we developed a CRISPR/Cas9-mediated multiplex genome-editing vector containing five genes related to three traits, Hd2, Ghd7, and DTH8 (flowering-stage genes), along with the recessive rice blast resistance gene Pi21 and the aromatic gene BADH2. This vector was introduced into the high-quality japonica rice variety in Zhejiang province, Jiahe212 (JH212), resulting in 34 T0 plants with various effective mutations. Among the 17 mutant T1 lines, several displayed diverse flowering dates, but most exhibited undesirable agronomic traits. Notably, three homozygous mutant lines (JH-C15, JH-C18, and JH-C31) showed slightly earlier flowering dates without significant differences in yield-related traits compared to JH212. Through special Hyg and Cas marker selection of T2 plants, we identified seven, six, and two fragrant glutinous plants devoid of transgenic components. These single plants will serve as sib lines of JH212 and potential resources for breeding applications, including maintenance lines for indica–japonica interspecific three-line hybrid rice. In summary, our research lays the foundation for the creation of short-growth-period CMS (cytoplasmic male sterility, CMS) lines, and also provides materials and a theoretical basis for indica–japonica interspecific hybrid rice breeding with wider adaptability. Full article
(This article belongs to the Special Issue Molecular Breeding and Germplasm Improvement of Rice—2nd Edition)
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13 pages, 1334 KiB  
Article
Detection and Evaluation of Blast Resistance Genes in Backbone Indica Rice Varieties from South China
by Liqun Tang, Jian Song, Yongtao Cui, Honghuan Fan and Jianjun Wang
Plants 2024, 13(15), 2134; https://doi.org/10.3390/plants13152134 - 1 Aug 2024
Viewed by 671
Abstract
Rice blast caused by the pathogenic fungus Magnaporthe oryzae poses a significant threat to rice cultivation. The identification of robust resistance germplasm is crucial for breeding resistant varieties. In this study, we employed functional molecular markers for 10 rice blast resistance genes, namely [...] Read more.
Rice blast caused by the pathogenic fungus Magnaporthe oryzae poses a significant threat to rice cultivation. The identification of robust resistance germplasm is crucial for breeding resistant varieties. In this study, we employed functional molecular markers for 10 rice blast resistance genes, namely Pi1, Pi2, Pi5, Pi9, Pia, Pid2, Pid3, Pigm, Pikh, and Pita, to assess blast resistance across 91 indica rice backbone varieties in South China. The results showed a spectrum of resistance levels ranging from highly resistant (HR) to highly susceptible (HS), with corresponding frequencies of 0, 19, 40, 27, 5, and 0, respectively. Yearly correlations in blast resistance genes among the 91 key indica rice progenitors revealed Pid2 (60.44%), Pia (50.55%), Pita (45.05%), Pi2 (32.97%), Pikh (4.4%), Pigm (2.2%), Pi9 (2.2%), and Pi1 (1.1%). Significant variations were observed in the distribution frequencies of these 10 resistance genes among these progenitors across different provinces. Furthermore, as the number of aggregated resistance genes increased, parental resistance levels correspondingly improved, though the efficacy of different gene combinations varied significantly. This study provides the initial steps toward strategically distributing varieties of resistant indica rice genotypes across South China. Full article
(This article belongs to the Special Issue Molecular Breeding and Germplasm Improvement of Rice—2nd Edition)
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13 pages, 2652 KiB  
Article
A Novel Allele in the Promoter of Wx Decreases Gene Expression and Confers Lower Apparent Amylose Contents in Japonica Rice (Oryza sativa L.)
by Weijie Tang, Haiyuan Chen, Suobing Zhang, Jun Tang, Jing Lin, Xianwen Fang, Gaoming Chen and Yunhui Zhang
Plants 2024, 13(5), 745; https://doi.org/10.3390/plants13050745 - 6 Mar 2024
Cited by 1 | Viewed by 1058
Abstract
Wx is the key gene that controls amylose content (AC), and various alleles have been found in rice populations. Wxb is the major allele in japonica and produces moderate AC (15~18%). It was recently found that editing the promoter of Wx could [...] Read more.
Wx is the key gene that controls amylose content (AC), and various alleles have been found in rice populations. Wxb is the major allele in japonica and produces moderate AC (15~18%). It was recently found that editing the promoter of Wx could produce a series of alleles that have different Wx activities. Although some studies have edited the promoter, few studies have focused on the natural variations in Wx. Here, we used the Rice3K database to investigate variations in the Wx promoter and found that the allele Wx1764178 (A/G) has a higher LD (linkage disequilibrium) with the two key SNPs (1765751, T/G; 1768006, A/C), which could produce different Wx alleles and influence AC, as reported previously. Further study showed that the Wx1764178 allele (A/G) is functional and influences the expression of Wx positively. Editing the A allele using CRISPR‒Cas9 produced 36 and 3 bp deletions and caused a decrease in the expression of Wx. The apparent amylose content (AAC) in the edited lines was decreased by 7.09% and 11.50% compared with that of the wild type, which was the japonica variety Nipponbare with Wxb and the A allele at 1764178, while a complementary line with the G allele showed a lower AAC than the A allele with no effect on other agronomic traits. The AAC of the edited lines showed a higher increase than that of the wild type (Nipponbare, Wxb) in low-nitrogen conditions relative to high-nitrogen conditions. We also developed a dCAPS marker to identify the allele and found that the G allele has widely been used (82.95%) in japonica-bred varieties from Jiangsu Province, China. Overall, we found a functional allele (Wx1764178, A/G) in the Wx promoter that could affect AAC in japonica cultivars and be developed as markers for quality improvement in rice breeding programs. Full article
(This article belongs to the Special Issue Molecular Breeding and Germplasm Improvement of Rice—2nd Edition)
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Review

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21 pages, 1094 KiB  
Review
Research Progress on Mechanical Strength of Rice Stalks
by Huimin Yang, Jiahui Huang, Yuhan Ye, Yuqing Xu, Yao Xiao, Ziying Chen, Xinyu Li, Yingying Ma, Tao Lu and Yuchun Rao
Plants 2024, 13(13), 1726; https://doi.org/10.3390/plants13131726 - 22 Jun 2024
Cited by 1 | Viewed by 1033
Abstract
As one of the most important food crops in the world, rice yield is directly related to national food security. Lodging is one of the most important factors restricting rice production, and the cultivation of rice varieties with lodging resistance is of great [...] Read more.
As one of the most important food crops in the world, rice yield is directly related to national food security. Lodging is one of the most important factors restricting rice production, and the cultivation of rice varieties with lodging resistance is of great significance in rice breeding. The lodging resistance of rice is directly related to the mechanical strength of the stalks. In this paper, we reviewed the cell wall structure, its components, and its genetic regulatory mechanism, which improved the regulatory network of rice stalk mechanical strength. Meanwhile, we analyzed the new progress in genetic breeding and put forward some scientific problems that need to be solved in this field in order to provide theoretical support for the improvement and application of rice breeding. Full article
(This article belongs to the Special Issue Molecular Breeding and Germplasm Improvement of Rice—2nd Edition)
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Planned Papers

The below list represents only planned manuscripts. Some of these manuscripts have not been received by the Editorial Office yet. Papers submitted to MDPI journals are subject to peer-review.

Detection and Evaluation of Blast Resistance Genes in Backbone Indica Rice Parents from South China

Abstract: Rice blast caused by the pathogenic fungus Magnaporthe oryzae, poses a significant threat to rice cultivation. The identification of robust resistance germplasm is crucial for breeding resistant varieties. In this study, we employed functional molecular markers for 10 rice blast resistance genes, namely Pi1, Pi2, Pi5, Pi9, Pia, Pid2, Pid3, Pigm, Pikh, and Pita, to assess blast resistance across 91 indica rice backbone parents in South China. The results showed that a spectrum of resistance levels ranging from highly resistant (HR) to highly susceptible (HS), with corresponding frequencies of 0, 20, 40, 27, 16, and 0, respectively. Yearly correlations in blast resistance genes among the 91 indica rice backbone parents revealed: Pid2 (60.44%), Pia (50.55%), Pita (45.05%), Pi2 (32.97%), Pikh (4.4%), Pigm (2.2%), Pi9 (2.2%) and Pi1(1.1%). Significant variations were observed in the distribution frequencies of these 10 resistance genes among indica rice backbone parents across different provinces. Furthermore, as the number of aggregated resistance genes increased, parental resistance levels correspondingly improved, though the efficacy of different gene combinations varied significantly. This study provides the initial steps towards strategically distributing a variety of resistant indica rice genotypes across South China.

 

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