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Rice Genetics and Molecular Design Breeding
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Rice Genetics and Molecular Design Breeding

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

Deadline for manuscript submissions: 28 February 2025 | Viewed by 6434

Special Issue Editors

Dr. Jiang Hu

E-Mail Website
Guest Editor
State Key Laboratory of Rice Biology, China National Rice Research Institute, No.28 Shuidaosuo Rd., Fuyang, Zhejiang 311400, China
Interests: QTL mapping and genetic analysis of rice-important agronomic traits; gene cloning and function analysis of rice seed and organ size; construction and utilization of rice germplasm resource bank; rice molecular design breeding by CRISPR-Cas9 and MAS
Special Issues, Collections and Topics in MDPI journals
Dr. Dawei Xue

E-Mail Website
Guest Editor
College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China
Interests: molecular physiology of crops; abiotic stress; crop molecular genetics
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Rice is an important staple crop in the world and also a model plant of monocotyledons. Identifying, mining and modifying the regulatory genes and their elite alleles of important agronomic traits, including plant type, yield, quality, resistance and nutrient efficiency，and exploring the corresponding molecular regulation mechanism, will be conducive to enriching the genetic regulation network and carrying out molecular design breeding. Especially in recent years, the gene editing technology has brought convenience to rice biological breeding and greatly reduced the cycle of rice variety improvement. This special issue of Plants will focus on the genetic analysis, physiological and biochemical, molecular assisted selection and biological breeding of important trait regulatory genes or alleles in rice.

Dr. Jiang Hu
Dr. Dawei Xue
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
  • important agronomic traits
  • genetic analysis
  • gene editing
  • molecular design breeding

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Published Papers (5 papers)

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Research

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17 pages, 4682 KiB  
Article
Improving Rice Quality by Regulating the Heading Dates of Rice Varieties without Yield Penalties
by Jianguo Liu, Qinqin Yi, Guojun Dong, Yuyu Chen, Longbiao Guo, Zhenyu Gao, Li Zhu, Deyong Ren, Qiang Zhang, Qing Li, Jingyong Li, Qiangming Liu, Guangheng Zhang, Qian Qian and Lan Shen
Plants 2024, 13(16), 2221; https://doi.org/10.3390/plants13162221 - 10 Aug 2024
Viewed by 1034
Abstract
The heading date, a critical trait influencing the rice yield and quality, has always been a hot topic in breeding research. Appropriately delaying the flowering time of excellent northern rice varieties is of great significance for improving yields and enhancing regional adaptability during [...] Read more.
The heading date, a critical trait influencing the rice yield and quality, has always been a hot topic in breeding research. Appropriately delaying the flowering time of excellent northern rice varieties is of great significance for improving yields and enhancing regional adaptability during the process for introducing varieties from north to south. In this study, genes influencing the heading date were identified through genome-wide association studies (GWAS). Using KenDao 12 (K12), an excellent cultivar from northern China, as the material, the specific flowering activator, OsMADS50, was edited using the genome-editing method to regulate the heading date to adapt to the southern planting environment. The results indicated that the osmads50 mutant line of K12 flowered about a week later, with a slight increase in the yield and good adaptability in the southern region in China. Additionally, the expressions of key flowering regulatory genes, such as Hd1, Ghd7, Ehd1, Hd3a, and RFT1, were reduced in the mutant plants, corroborating the delayed flowering phenotype. Yield trait analysis revealed that the primary factor for improved yield was an increase in the number of effective tillers, although there is potential for further enhancements in the seed-setting rate and grain plumpness. Furthermore, there were significant increases in the length-to-width ratio of the rice grains, fat content, and seed transparency, all contributing to an overall improvement in the rice quality. In summary, this study successfully obtained a rice variety with a delayed growth period through OsMADS50 gene editing, effectively implementing the strategy for adapting northern rice varieties to southern climates. This achievement significantly supports efforts to enhance the rice yield and quality as well as to optimize production management practices. Full article
(This article belongs to the Special Issue Rice Genetics and Molecular Design Breeding)
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11 pages, 1019 KiB  
Article
Dissection and Fine-Mapping of Two QTL Controlling Grain Size Linked in a 515.6-kb Region on Chromosome 10 of Rice
by Yi Shen, Derun Huang, Zhenhua Zhang, Yeyang Fan, Zhonghua Sheng, Jieyun Zhuang, Bo Shen and Yujun Zhu
Plants 2024, 13(15), 2054; https://doi.org/10.3390/plants13152054 - 25 Jul 2024
Viewed by 698
Abstract
Grain size is a primary determinant of grain weight, which is one of the three essential components of rice grain yield. Mining the genes that control grain size plays an important role in analyzing the regulation mechanism of grain size and improving grain [...] Read more.
Grain size is a primary determinant of grain weight, which is one of the three essential components of rice grain yield. Mining the genes that control grain size plays an important role in analyzing the regulation mechanism of grain size and improving grain appearance quality. In this study, two closely linked quantitative trait loci (QTL) controlling grain size, were dissected and fine-mapped in a 515.6-kb region on the long arm of chromosome 10 by using six near isogenic line populations. One of them, qGS10.2, which controlled 1000 grain weight (TGW) and grain width (GW), was delimited into a 68.1-kb region containing 14 annotated genes. The Teqing allele increased TGW and GW by 0.17 g and 0.011 mm with the R2 of 12.7% and 11.8%, respectively. The other one, qGL10.2, which controlled grain length (GL), was delimited into a 137.3-kb region containing 22 annotated genes. The IRBB52 allele increased GL by 0.018 mm with the R2 of 6.8%. Identification of these two QTL provides candidate regions for cloning of grain size genes. Full article
(This article belongs to the Special Issue Rice Genetics and Molecular Design Breeding)
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18 pages, 7192 KiB  
Article
Characterization of the Fatty Acyl-CoA Reductase (FAR) Gene Family and Its Response to Abiotic Stress in Rice (Oryza sativa L.)
by Danni Zhou, Mingyu Ding, Shuting Wen, Quanxiang Tian, Xiaoqin Zhang, Yunxia Fang and Dawei Xue
Plants 2024, 13(7), 1010; https://doi.org/10.3390/plants13071010 - 1 Apr 2024
Viewed by 1502
Abstract
Fatty acyl-CoA reductase (FAR) is an important NADPH-dependent enzyme that can produce primary alcohol from fatty acyl-CoA or fatty acyl-carrier proteins as substrates. It plays a pivotal role in plant growth, development, and stress resistance. Herein, we performed genome-wide identification and expression analysis [...] Read more.
Fatty acyl-CoA reductase (FAR) is an important NADPH-dependent enzyme that can produce primary alcohol from fatty acyl-CoA or fatty acyl-carrier proteins as substrates. It plays a pivotal role in plant growth, development, and stress resistance. Herein, we performed genome-wide identification and expression analysis of FAR members in rice using bioinformatics methods. A total of eight OsFAR genes were identified, and the OsFARs were comprehensively analyzed in terms of phylogenetic relationships, duplication events, protein motifs, etc. The cis-elements of the OsFARs were predicted to respond to growth and development, light, hormones, and abiotic stresses. Gene ontology annotation analysis revealed that OsFAR proteins participate in biological processes as fatty acyl-CoA reductase during lipid metabolism. Numerous microRNA target sites were present in OsFARs mRNAs. The expression analysis showed that OsFARs were expressed at different levels during different developmental periods and in various tissues. Furthermore, the expression levels of OsFARs were altered under abiotic stresses, suggesting that FARs may be involved in abiotic stress tolerance in rice. The findings presented here serve as a solid basis for further exploring the functions of OsFARs. Full article
(This article belongs to the Special Issue Rice Genetics and Molecular Design Breeding)
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18 pages, 3803 KiB  
Article
The ldp1 Mutation Affects the Expression of Auxin-Related Genes and Enhances SAM Size in Rice
by Zhanglun Sun, Tianrun Mei, Xuan Tan, Tingting Feng, Ruining Li, Sumei Duan, Heming Zhao, Yafeng Ye, Binmei Liu, Aifeng Zhou, Hao Ai and Xianzhong Huang
Plants 2024, 13(6), 759; https://doi.org/10.3390/plants13060759 - 7 Mar 2024
Viewed by 1437
Abstract
Panicle type is one of the important factors affecting rice (Oryza sativa L.) yield, and the identification of regulatory genes in panicle development can provide significant insights into the molecular network involved. This study identified a large and dense panicle 1 ( [...] Read more.
Panicle type is one of the important factors affecting rice (Oryza sativa L.) yield, and the identification of regulatory genes in panicle development can provide significant insights into the molecular network involved. This study identified a large and dense panicle 1 (ldp1) mutant produced from the Wuyunjing 7 (WYJ7) genotype, which displayed significant relative increases in panicle length, number of primary and secondary branches, number of grains per panicle, grain width, and grain yield per plant. Scanning electron microscopy results showed that the shoot apical meristem (SAM) of ldp1 was relatively larger at the bract stage (BM), with a significantly increased number of primary (PBM) and secondary branch (SBM) meristematic centers, indicating that the ldp1 mutation affects early stages in SAM development Comparative RNA-Seq analysis of meristem tissues from WYJ7 and ldp1 at the BM, PBM, and SBM developmental stages indicated that the number of differentially expressed genes (DEGs) were highest (1407) during the BM stage. Weighted gene coexpression network analysis (WGCNA) revealed that genes in one module (turquoise) are associated with the ldp1 phenotype and highly expressed during the BM stage, suggesting their roles in the identity transition and branch differentiation stages of rice inflorescences. Hub genes involved in auxin synthesis and transport pathways, such as OsAUX1, OsAUX4, and OsSAUR25, were identified. Moreover, GO and KEGG analysis of the DEGs in the turquoise module and the 1407 DEGs in the BM stage revealed that a majority of genes involved in tryptophan metabolism and auxin signaling pathway were differentially expressed between WYJ and ldp1. The genetic analysis indicated that the ldp1 phenotype is controlled by a recessive monogene (LDP1), which was mapped to a region between 16.9 and 18.1 Mb on chromosome seven. This study suggests that the ldp1 mutation may affect the expression of key genes in auxin synthesis and signal transduction, enhance the size of SAM, and thus affect panicle development. This study provides insights into the molecular regulatory network underlying rice panicle morphogenesis and lays an important foundation for further understanding the function and molecular mechanism of LDP1 during panicle development. Full article
(This article belongs to the Special Issue Rice Genetics and Molecular Design Breeding)
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Review

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22 pages, 2456 KiB  
Review
Mechanism of Rice Resistance to Bacterial Leaf Blight via Phytohormones
by Qianqian Zhong, Yuqing Xu and Yuchun Rao
Plants 2024, 13(18), 2541; https://doi.org/10.3390/plants13182541 - 10 Sep 2024
Viewed by 1264
Abstract
Rice is one of the most important food crops in the world, and its yield restricts global food security. However, various diseases and pests of rice pose a great threat to food security. Among them, bacterial leaf blight (BLB) caused by Xanthomonas oryzae [...] Read more.
Rice is one of the most important food crops in the world, and its yield restricts global food security. However, various diseases and pests of rice pose a great threat to food security. Among them, bacterial leaf blight (BLB) caused by Xanthomonas oryzae pv. oryzae (Xoo) is one of the most serious bacterial diseases affecting rice globally, creating an increasingly urgent need for research in breeding resistant varieties. Phytohormones are widely involved in disease resistance, such as auxin, abscisic acid (ABA), ethylene (ET), jasmonic acid (JA), and salicylic acid (SA). In recent years, breakthroughs have been made in the analysis of their regulatory mechanism in BLB resistance in rice. In this review, a series of achievements of phytohormones in rice BLB resistance in recent years were summarized, the genes involved and their signaling pathways were reviewed, and a breeding strategy combining the phytohormones regulation network with modern breeding techniques was proposed, with the intention of applying this strategy to molecular breeding work and playing a reference role for how to further improve rice resistance. Full article
(This article belongs to the Special Issue Rice Genetics and Molecular Design Breeding)
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