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Molecular Research in Rice, 2nd Edition

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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 March 2025 | Viewed by 10425

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Prof. Dr. Prasanta K. Subudhi

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School of Plant, Environmental, and Soil Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
Interests: abiotic stress; rice; maize
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Special Issue Information

Dear Colleagues,

This Special Issue follows the publication of the first edition on “Molecular Research in Rice”.

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 significant positive impact on global food security. However, rice farming in many parts of the world is threatened by a number of biotic and abiotic stresses due to climate change. To design novel rice genotypes, it is imperative to devise novel approaches to exploit world germplasm, understand the molecular basis of yield and yield component traits, tolerance to various biotic and abiotic stresses, and development of molecular tools to transfer desirable traits/genes. Due to spectacular advances in molecular biology, genetic engineering, and various omics fields, new molecular tools and technologies have been developed to realize these goals. As a model cereal crop due to its small genome size and genetic closeness to major cereal crops, advances in molecular research in rice will not only accelerate development of high yielding and stress tolerant rice varieties but also will help improve other cereal crops.

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, mapping and cloning of genes and QTLs, development of tools for marker-assisted selection, molecular basis of biotic and abiotic stress tolerance, nutrient use efficiency, grain quality, and yield enhancing traits.

Prof. Dr. Prasanta K. Subudhi
Guest Editor

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Keywords

molecular breeding and marker-assisted selection
QTL/Gene cloning
next generation sequencing
genetic engineering
candidate genes
germplasm enhancement
biotic and abiotic stresses
yield and quality traits

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Published Papers (8 papers)

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Research

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15 pages, 2267 KiB

Open AccessArticle

Heading Date 3a Stimulates Tiller Bud Outgrowth in Oryza sativa L. through Strigolactone Signaling Pathway

by Qiqi Zheng, Zejiao Zhou, Xinran Li, Yingshan Lan, Ruihua Huang, Shengchun Zhang and Hongqing Li

Int. J. Mol. Sci. 2024, 25(19), 10778; https://doi.org/10.3390/ijms251910778 - 7 Oct 2024

Viewed by 774

Abstract

Heading date 3a (Hd3a, a FLOWERING LOCUS T (FT) ortholog from rice) is well known for its important role in rice (Oryza sativa L.), controlling floral transition under short-day (SD) conditions. Although the effect of Hd3a on promoting branching has been found, the underlying mechanism remains largely unknown. In this report, we overexpressed an Hd3a and BirAG (encoding a biotin ligase) fusion gene in rice, and found that early flowering and tiller bud outgrowth was promoted in BHd3aOE transgenic plants. On the contrary, knockout of Hd3a delayed flowering and tiller bud outgrowth. By using the BioID method, we identified multiple Hd3a proximal proteins. Among them, D14, D53, TPR1, TPR2, and TPRs are central components of the strigolactone signaling pathway, which has an inhibitory effect on rice tillering. The interaction between Hd3a, on the one hand, and D14 and D53 was further confirmed by the bimolecular fluorescence complementation (BiFC), yeast two-hybrid (Y2H), and co-immunoprecipitation (Co-IP) methods. We also found that Hd3a prevented the degradation of D53 induced by rac-GR24 (a strigolactone analog) in rice protoplasts. RT-qPCR assay showed that the expression levels of genes involved in strigolactone biosynthesis and signal transduction were altered significantly between WT and Hd3a overexpression (Hd3aOE) or mutant (hd3a) plants. OsFC1, a downstream target of the strigolactone signaling transduction pathway in controlling rice tillering, was downregulated significantly in Hd3aOE plants, whereas it was upregulated in hd3a lines. Collectively, these results indicate that Hd3a promotes tiller bud outgrowth in rice by attenuating the negative effect of strigolactone signaling on tillering and highlight a novel molecular network regulating rice tiller outgrowth by Hd3a. Full article

(This article belongs to the Special Issue Molecular Research in Rice, 2nd Edition)

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18 pages, 9232 KiB

Open AccessArticle

Metabolome and Transcriptome Unveil the Correlated Metabolites and Transcripts with 2-acetyl-1-pyrroline in Fragrant Rice

by Yu Zeng, Baoxuan Nong, Xiuzhong Xia, Zongqiong Zhang, Yuhao Wang, Yong Xu, Rui Feng, Hui Guo, Yuntao Liang, Can Chen, Shuhui Liang, Xianbin Jiang, Xinghai Yang and Danting Li

Int. J. Mol. Sci. 2024, 25(15), 8207; https://doi.org/10.3390/ijms25158207 - 27 Jul 2024

Viewed by 758

Abstract

Fragrance is a valuable trait in rice varieties, with its aroma significantly influencing consumer preference. In this study, we conducted comprehensive metabolome and transcriptome analyses to elucidate the genetic and biochemical basis of fragrance in the Shangsixiangnuo (SSXN) variety, a fragrant indica rice cultivated in Guangxi, China. Through sensory evaluation and genetic analysis, we confirmed SSXN as strongly fragrant, with an 806 bp deletion in the BADH2 gene associated with fragrance production. In the metabolome analysis, a total of 238, 233, 105 and 60 metabolic compounds exhibited significant changes at the seedling (S), reproductive (R), filling (F), and maturation (M) stages, respectively. We identified four compounds that exhibited significant changes in SSXN across all four development stages. Our analyses revealed a significant upregulation of 2-acetyl-1-pyrroline (2AP), the well-studied aromatic compound, in SSXN compared to the non-fragrant variety. Additionally, correlation analysis identified several metabolites strongly associated with 2AP, including ethanone, 1-(1H-pyrrol-2-yl)-, 1H-pyrrole, and pyrrole. Furthermore, Weighted Gene Co-expression Network Analysis (WGCNA) analysis highlighted the magenta and yellow modules as particularly enriched in aroma-related metabolites, providing insights into the complex aromatic compounds underlying the fragrance of rice. In the transcriptome analysis, a total of 5582, 5506, 4965, and 4599 differential expressed genes (DEGs) were identified across the four developmental stages, with a notable enrichment of the common pathway amino sugar and nucleotide sugar metabolism in all stages. In our correlation analysis between metabolome and transcriptome data, the top three connected metabolites, phenol-, 3-amino-, and 2AP, along with ethanone, 1-(1H-pyrrol-2-yl)-, exhibited strong associations with transcripts, highlighting their potential roles in fragrance biosynthesis. Additionally, the downregulated expression of the P4H4 gene, encoding a procollagen-proline dioxygenase that specifically targets proline, in SSXN suggests its involvement in proline metabolism and potentially in aroma formation pathways. Overall, our study provides comprehensive insights into the genetic and biochemical mechanisms underlying fragrance production in rice, laying the foundation for further research aimed at enhancing fragrance quality in rice breeding programs. Full article

(This article belongs to the Special Issue Molecular Research in Rice, 2nd Edition)

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24 pages, 11854 KiB

Open AccessArticle

Compensatory Modulation of Seed Storage Protein Synthesis and Alteration of Starch Accumulation by Selective Editing of 13 kDa Prolamin Genes by CRISPR-Cas9 in Rice

by Hue Anh Pham, Kyoungwon Cho, Anh Duc Tran, Deepanwita Chandra, Jinpyo So, Hanh Thi Thuy Nguyen, Hyunkyu Sang, Jong-Yeol Lee and Oksoo Han

Int. J. Mol. Sci. 2024, 25(12), 6579; https://doi.org/10.3390/ijms25126579 - 14 Jun 2024

Viewed by 1025

Abstract

Rice prolamins are categorized into three groups by molecular size (10, 13, or 16 kDa), while the 13 kDa prolamins are assigned to four subgroups (Pro13a-I, Pro13a-II, Pro13b-I, and Pro13b-II) based on cysteine residue content. Since lowering prolamin content in rice is essential to minimize indigestion and allergy risks, we generated four knockout lines using CRISPR-Cas9, which selectively reduced the expression of a specific subgroup of the 13 kDa prolamins. These four mutant rice lines also showed the compensatory expression of glutelins and non-targeted prolamins and were accompanied by low grain weight, altered starch content, and atypically-shaped starch granules and protein bodies. Transcriptome analysis identified 746 differentially expressed genes associated with 13 kDa prolamins during development. Correlation analysis revealed negative associations between genes in Pro13a-I and those in Pro13a-II and Pro13b-I/II subgroups. Furthermore, alterations in the transcription levels of 9 ER stress and 17 transcription factor genes were also observed in mutant rice lines with suppressed expression of 13 kDa prolamin. Our results provide profound insight into the functional role of 13 kDa rice prolamins in the regulatory mechanisms underlying rice seed development, suggesting their promising potential application to improve nutritional and immunological value. Full article

(This article belongs to the Special Issue Molecular Research in Rice, 2nd Edition)

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15 pages, 10295 KiB

Open AccessArticle

Genome-Wide Association Analysis of Effective Tillers in Rice under Different Nitrogen Gradients

by Yuzhuo Liu, Wei Xin, Liqiang Chen, Yuqi Liu, Xue Wang, Cheng Ma, Laiyuan Zhai, Yingying Feng, Jiping Gao and Wenzhong Zhang

Int. J. Mol. Sci. 2024, 25(5), 2969; https://doi.org/10.3390/ijms25052969 - 4 Mar 2024

Cited by 1 | Viewed by 1291

Abstract

Nitrogen is a crucial element that impacts rice yields, and effective tillering is a significant agronomic characteristic that can influence rice yields. The way that reduced nitrogen affects effective tillering is a complex quantitative trait that is controlled by multiple genes, and its genetic basis requires further exploration. In this study, 469 germplasm varieties were used for a genome-wide association analysis aiming to detect quantitative trait loci (QTL) associated with effective tillering at low (60 kg/hm²) and high (180 kg/hm²) nitrogen levels. QTLs detected over multiple years or under different treatments were scrutinized in this study, and candidate genes were identified through haplotype analysis and spatio-temporal expression patterns. A total of seven genes (NAL1, OsCKX9, Os01g0690800, Os02g0550300, Os02g0550700, Os04g0615700, and Os04g06163000) were pinpointed in these QTL regions, and were considered the most likely candidate genes. These results provide favorable information for the use of auxiliary marker selection in controlling effective tillering in rice for improved yields. Full article

(This article belongs to the Special Issue Molecular Research in Rice, 2nd Edition)

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12 pages, 1454 KiB

Open AccessArticle

The QTL and Candidate Genes Regulating the Early Tillering Vigor Traits of Late-Season Rice in Double-Cropping Systems

by Wei Wu, Tian-Tian Zhang, Li-Li You, Zi-Yi Wang, Si-Qi Du, Hai-Yan Song, Zao-Hai Wang, Ying-Jin Huang and Jiang-Lin Liao

Int. J. Mol. Sci. 2024, 25(3), 1497; https://doi.org/10.3390/ijms25031497 - 25 Jan 2024

Viewed by 1320

Abstract

Rice effective panicle is a major trait for grain yield and is affected by both the genetic tiller numbers and the early tillering vigor (ETV) traits to survive environmental adversities. The mechanism behind tiller bud formation has been well described, while the genes and the molecular mechanism underlying rice-regulating ETV traits are unclear. In this study, the candidate genes in regulating ETV traits have been sought by quantitative trait locus (QTL) mapping and bulk-segregation analysis by resequencing method (BSA-seq) conjoint analysis using rice backcross inbred line (BIL) populations, which were cultivated as late-season rice of double-cropping rice systems. By QTL mapping, seven QTLs were detected on chromosomes 1, 3, 4, and 9, with the logarithm of the odds (LOD) values ranging from 3.52 to 7.57 and explained 3.23% to 12.98% of the observed phenotypic variance. By BSA-seq analysis, seven QTLs on chromosomes 1, 2, 4, 5, 7, and 9 were identified using single-nucleotide polymorphism (SNP) and insertions/deletions (InDel) index algorithm and Euclidean distance (ED) algorithm. The overlapping QTL resulting from QTL mapping and BSA-seq analysis was shown in a 1.39 Mb interval on chromosome 4. In the overlap interval, six genes, including the functional unknown genes Os04g0455650, Os04g0470901, Os04g0500600, and ethylene-insensitive 3 (Os04g0456900), sialyltransferase family domain containing protein (Os04g0506800), and ATOZI1 (Os04g0497300), showed the differential expression between ETV rice lines and late tillering vigor (LTV) rice lines and have a missense base mutation in the genomic DNA sequences of the parents. We speculate that the six genes are the candidate genes regulating the ETV trait in rice, which provides a research basis for revealing the molecular mechanism behind the ETV traits in rice. Full article

(This article belongs to the Special Issue Molecular Research in Rice, 2nd Edition)

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18 pages, 2673 KiB

Open AccessArticle

Genetic Enhancement for Biotic Stress Resistance in Basmati Rice through Marker-Assisted Backcross Breeding

by Gagandeep Singh, Niraj Singh, Ranjith Kumar Ellur, Alexander Balamurugan, G. Prakash, Rajeev Rathour, Kalyan Kumar Mondal, Prolay Kumar Bhowmick, S. Gopala Krishnan, Mariappan Nagarajan, Rakesh Seth, K. K. Vinod, Varsha Singh, Haritha Bollinedi and Ashok Kumar Singh

Int. J. Mol. Sci. 2023, 24(22), 16081; https://doi.org/10.3390/ijms242216081 - 8 Nov 2023

Cited by 1 | Viewed by 1699

Abstract

Pusa Basmati 1509 (PB1509) is one of the major foreign-exchange-earning varieties of Basmati rice; it is semi-dwarf and early maturing with exceptional cooking quality and strong aroma. However, it is highly susceptible to various biotic stresses including bacterial blight and blast. Therefore, bacterial blight resistance genes, namely, xa13 + Xa21 and Xa38, and fungal blast resistance genes Pi9 + Pib and Pita were incorporated into the genetic background of recurrent parent (RP) PB1509 using donor parents, namely, Pusa Basmati 1718 (PB1718), Pusa 1927 (P1927), Pusa 1929 (P1929) and Tetep, respectively. Foreground selection was carried out with respective gene-linked markers, stringent phenotypic selection for recurrent parent phenotype, early generation background selection with Simple sequence repeat (SSR) markers, and background analysis at advanced generations with Rice Pan Genome Array comprising 80K SNPs. This has led to the development of Near isogenic lines (NILs), namely, Pusa 3037, Pusa 3054, Pusa 3060 and Pusa 3066 carrying genes xa13 + Xa21, Xa38, Pi9 + Pib and Pita with genomic similarity of 98.25%, 98.92%, 97.38% and 97.69%, respectively, as compared to the RP. Based on GGE-biplot analysis, Pusa 3037-1-44-3-164-20-249-2 carrying xa13 + Xa21, Pusa 3054-2-47-7-166-24-261-3 carrying Xa38, Pusa 3060-3-55-17-157-4-124-1 carrying Pi9 + Pib, and Pusa 3066-4-56-20-159-8-174-1 carrying Pita were identified to be relatively stable and better-performing individuals in the tested environments. Intercrossing between the best BC₃F₁s has led to the generation of Pusa 3122 (xa13 + Xa21 + Xa38), Pusa 3124 (Xa38 + Pi9 + Pib) and Pusa 3123 (Pi9 + Pib + Pita) with agronomy, grain and cooking quality parameters at par with PB1509. Cultivation of such improved varieties will help farmers reduce the cost of cultivation with decreased pesticide use and improve productivity with ensured safety to consumers. Full article

(This article belongs to the Special Issue Molecular Research in Rice, 2nd Edition)

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13 pages, 8510 KiB

Open AccessArticle

Regulation of Grain Chalkiness and Starch Metabolism by FLO2 Interaction Factor 3, a bHLH Transcription Factor in Oryza sativa

by Xianyu Tang, Weiping Zhong, Kunmei Wang, Xin Gong, Yunong Xia, Jieying Nong, Langtao Xiao and Shitou Xia

Int. J. Mol. Sci. 2023, 24(16), 12778; https://doi.org/10.3390/ijms241612778 - 14 Aug 2023

Cited by 2 | Viewed by 1490

Abstract

Chalkiness is a key determinant that directly affects the appearance and cooking quality of rice grains. Previously, Floury endosperm 2 (FLO2) was reported to be involved in the formation of rice chalkiness; however, its regulation mechanism is still unclear. Here, FLO2 interaction factor 3 (OsFIF3), a bHLH transcription factor, was identified and analyzed in Oryza sativa. A significant increase in chalkiness was observed in OsFIF3-overexpressed grains, coupled with a round, hollow filling of starch granules and reduced grain weight. OsFIF3 is evolutionarily conserved in monocotyledons, but variable in dicotyledons. Subcellular localization revealed the predominant localization of OsFIF3 in the nucleus. The DAP-seq (DNA affinity purification sequencing) results showed that OsFIF3 could affect the transcriptional accumulation of β-amylase 1, α-amylase isozyme 2A-like, pectinesterase 11, β-glucosidase 28 like, pectinesterase, sucrose transport protein 1 (SUT1), and FLO2 through the binding of the CACGTG motif on their promoters. Moreover, FLO2 and SUT1 with abundant OsFIF3 binding signals showed significant expression reduction in OsFIF3 overexpression lines, further confirming OsFIF3’s role in starch metabolism regulation and energy material allocation. Taken together, these findings show that the overexpression of OsFIF3 inhibits the expression of FLO2 and SUT1, thereby increasing grain chalkiness and affecting grain weight. Full article

(This article belongs to the Special Issue Molecular Research in Rice, 2nd Edition)

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Review

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14 pages, 2819 KiB

Open AccessReview

Glutaredoxin in Rice Growth, Development, and Stress Resistance: Mechanisms and Research Advances

by Rongrong Zhai, Shenghai Ye, Jing Ye, Mingming Wu, Guofu Zhu, Faming Yu, Xingyu Wang, Yue Feng and Xiaoming Zhang

Int. J. Mol. Sci. 2023, 24(23), 16968; https://doi.org/10.3390/ijms242316968 - 30 Nov 2023

Cited by 1 | Viewed by 1465

Abstract

Rice (Oryza sativa L.) is a staple food for more than half of the global population. Various abiotic and biotic stresses lead to accumulation of reactive oxygen species in rice, which damage macromolecules and signaling pathways. Rice has evolved a variety of antioxidant systems, including glutaredoxin (GRX), that protect against various stressors. A total of 48 GRX gene loci have been identified on 11 of the 12 chromosomes of the rice genome; none were found on chromosome 9. GRX proteins were classified into four categories according to their active sites: CPYC, CGFS, CC, and GRL. In this paper, we summarized the recent research advances regarding the roles of GRX in rice development regulation and response to stresses, and discussed future research perspectives related to rice production. This review could provide information for rice researchers on the current status of the GRX and serve as guidance for breeding superior varieties. Full article

(This article belongs to the Special Issue Molecular Research in Rice, 2nd Edition)

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