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Special Issue "Molecular Research in Rice: Agronomically Important Traits 2.0"

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: 31 March 2021.

Special Issue Editors

Dr. Kiyosumi Hori
Website
Guest Editor
Institute of Crop Science, National Agriculture and Food Research Organization (NARO), Tsukuba, Japan
Interests: plant molecular genetics and breeding; environmental agriculture; rice; QTLs
Special Issues and Collections in MDPI journals
Dr. Matthew Shenton
Website
Guest Editor
Institute of Crop Science, National Agriculture and Food Research Organization (NARO), Tsukuba, Japan
Interests: plant genomics and genome evolution; genetic resources; rice; association analysis; omics analysis
Special Issues and Collections in MDPI journals

Special Issue Information

Dear Colleagues,

This Special Issue is the continuation of our Special Issue “Molecular Research in Rice: Agronomically Important Traits” (in which over 20 excellent papers have been published).

Rice (Oryza sativa L.) is the most important food crop in the world, being a staple food for more than half of the world’s population. Recent improvements in living standards have increased the worldwide demand for high-yielding and high-quality rice cultivars. To achieve improved agricultural performance in rice, while overcoming the challenges presented by climate change, it is essential to understand the molecular basis of agronomically important traits and their responses to various environmental conditions. Recently developed techniques in molecular biology, genomics related technologies can reveal the complex molecular mechanisms involved in the control of agronomic traits. As rice was the first crop genome to be sequenced, in 2004, molecular research tools are well-established in rice, and further molecular studies—both now and in the future—will enable the development of novel rice cultivars showing superior agronomic performance.

The purpose of this Special Issue is to explore the molecular basis of agronomically important traits in rice, which is a monocot model crop species. Submissions focusing on a wide range of agronomic traits related to grain yield, grain quality, stress tolerance, and disease resistance are welcome. We will also welcome articles about genetic and environmental interactions of agronomic traits. Studies using natural variation, mutants, and omics analysis such as transcriptomics, epigenetics, and metabolomics, will also be greatly appreciated.

Dr. Kiyosumi Hori
Dr. Matthew Shenton
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 papers will be 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
  • Plant molecular biology
  • Plant molecular genetics and genomics
  • Plant physiology
  • Plant pathology
  • Omics database
  • Genetic and environmental interaction
  • Agronomic trait

Published Papers (5 papers)

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Research

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Open AccessArticle
OsBRKq1, Related Grain Size Mapping, and Identification of Grain Shape Based on QTL Mapping in Rice
Int. J. Mol. Sci. 2021, 22(5), 2289; https://doi.org/10.3390/ijms22052289 (registering DOI) - 25 Feb 2021
Abstract
The world population is growing rapidly, and food shortage remains a critical issue. Quantitative trait locus (QTL) mapping is a statistical analytical method that uses both phenotypic and genotypic data. The purpose of QTL mapping is to determine the exact gene location for [...] Read more.
The world population is growing rapidly, and food shortage remains a critical issue. Quantitative trait locus (QTL) mapping is a statistical analytical method that uses both phenotypic and genotypic data. The purpose of QTL mapping is to determine the exact gene location for various complex traits. Increasing grain weight is a way to increase yield in rice. Genes related to grain size were mapped using the Samgang/Nagdong double haploid (SNDH) populations. Grain sizes were diversely distributed in SNDH 113 populations, and OsBRKq1 was detected on chromosome 1 in an analysis of QTL mapping that used 1000 grain weight, grain length, and grain width. OsBRKq1 exhibited high sequence similarity with the brassinosteroid leucine-rich repeat-receptor kinases of Arabidopsis thaliana and Zea mays. It was also predicted to have a similar function because of its high homology. OsBRKq1 interacts with various grain-size control genes. Among the SNDH populations, the analysis of the relative expression level during the panicle formation stage of OsBRKq1 in panicles of SNDH117, which has the largest grain size, and SNDH6, which has the smallest grain size, the relative expression level was significantly increased in SNDH117 panicles. SNDH populations have been advancing generations for 10 years; various genetic traits have been fixed and are currently being used as bridging parents. Therefore, the stable expression level of OsBRKq1 was confirmed via QTL mapping. In the future, OsBRKq1 can be effectively used to increase the yield of rice and solve food problems by increasing the size of seeds. Full article
(This article belongs to the Special Issue Molecular Research in Rice: Agronomically Important Traits 2.0)
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Open AccessArticle
New Insights into the Transcriptional Regulation of Genes Involved in the Nitrogen Use Efficiency under Potassium Chlorate in Rice (Oryza sativa L.)
Int. J. Mol. Sci. 2021, 22(4), 2192; https://doi.org/10.3390/ijms22042192 - 22 Feb 2021
Abstract
Potassium chlorate (KClO3) has been widely used to evaluate the divergence in nitrogen use efficiency (NUE) between indica and japonica rice subspecies. This study investigated the transcriptional regulation of major genes involved in the NUE in rice treated with KClO3 [...] Read more.
Potassium chlorate (KClO3) has been widely used to evaluate the divergence in nitrogen use efficiency (NUE) between indica and japonica rice subspecies. This study investigated the transcriptional regulation of major genes involved in the NUE in rice treated with KClO3, which acts as an inhibitor of the reducing activity of nitrate reductase (NR) in higher plants. A set of two KClO3 sensitive nitrate reductase (NR) and two nitrate transporter (NRT) introgression rice lines (BC2F7), carrying the indica alleles of NR or NRT, derived from a cross between Saeilmi (japonica, P1) and Milyang23 (indica, P2), were exposed to KClO3 at the seedling stage. The phenotypic responses were recorded 7 days after treatment, and samples for gene expression, physiological, and biochemical analyses were collected at 0 h (control) and 3 h after KClO3 application. The results revealed that Saeilmi (P1, japonica) and Milyang23 (P2, indica) showed distinctive phenotypic responses. In addition, the expression of OsNR2 was differentially regulated between the roots, stem, and leaf tissues, and between introgression lines. When expressed in the roots, OsNR2 was downregulated in all introgression lines. However, in the stem and leaves, OsNR2 was upregulated in the NR introgression lines, but downregulation in the NRT introgression lines. In the same way, the expression patterns of OsNIA1 and OsNIA2 in the roots, stem, and leaves indicated a differential transcriptional regulation by KClO3, with OsNIA2 prevailing over OsNIA1 in the roots. Under the same conditions, the activity of NR was inhibited in the roots and differentially regulated in the stem and leaf tissues. Furthermore, the transcriptional divergence of OsAMT1.3 and OsAMT2.3, OsGLU1 and OsGLU2, between NR and NRT, coupled with the NR activity pattern in the roots, would indicate the prevalence of nitrate (NO3¯) transport over ammonium (NH4+) transport. Moreover, the induction of catalase (CAT) and polyphenol oxidase (PPO) enzyme activities in Saeilmi (P1, KClO3 resistant), and the decrease in Milyang23 (P2, KClO3 sensitive), coupled with the malondialdehyde (MDA) content, indicated the extent of the oxidative stress, and the induction of the adaptive response mechanism, tending to maintain a balanced reduction–oxidation state in response to KClO3. The changes in the chloroplast pigments and proline content propose these compounds as emerging biomarkers for assessing the overall plant health status. These results suggest that the inhibitory potential of KClO3 on the reduction activity of the nitrate reductase (NR), as well as that of the genes encoding the nitrate and ammonium transporters, and glutamate synthase are tissue-specific, which may differentially affect the transport and assimilation of nitrate or ammonium in rice. Full article
(This article belongs to the Special Issue Molecular Research in Rice: Agronomically Important Traits 2.0)
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Open AccessArticle
OsCRP1, a Ribonucleoprotein Gene, Regulates Chloroplast mRNA Stability That Confers Drought and Cold Tolerance
Int. J. Mol. Sci. 2021, 22(4), 1673; https://doi.org/10.3390/ijms22041673 - 07 Feb 2021
Abstract
Chloroplast ribonucleoproteins (cpRNPs) are nuclear-encoded and highly abundant proteins that are proposed to function in chloroplast RNA metabolism. However, the molecular mechanisms underlying the regulation of chloroplast RNAs involved in stress tolerance are poorly understood. Here, we demonstrate that CHLOROPLAST RNA-BINDING PROTEIN 1 [...] Read more.
Chloroplast ribonucleoproteins (cpRNPs) are nuclear-encoded and highly abundant proteins that are proposed to function in chloroplast RNA metabolism. However, the molecular mechanisms underlying the regulation of chloroplast RNAs involved in stress tolerance are poorly understood. Here, we demonstrate that CHLOROPLAST RNA-BINDING PROTEIN 1 (OsCRP1), a rice (Oryza sativa) cpRNP gene, is essential for stabilization of RNAs from the NAD(P)H dehydrogenase (NDH) complex, which in turn enhances drought and cold stress tolerance. An RNA-immunoprecipitation assay revealed that OsCRP1 is associated with a set of chloroplast RNAs. Transcript profiling indicated that the mRNA levels of genes from the NDH complex significantly increased in the OsCRP1 overexpressing compared to non-transgenic plants, whereas the pattern in OsCRP1 RNAi plants were opposite. Importantly, the OsCRP1 overexpressing plants showed a higher cyclic electron transport (CET) activity, which is essential for elevated levels of ATP for photosynthesis. Additionally, overexpression of OsCRP1 resulted in significantly enhanced drought and cold stress tolerance with higher ATP levels compared to wild type. Thus, our findings suggest that overexpression of OsCRP1 stabilizes a set of mRNAs from genes of the NDH complex involved in increasing CET activity and production of ATP, which consequently confers enhanced drought and cold tolerance. Full article
(This article belongs to the Special Issue Molecular Research in Rice: Agronomically Important Traits 2.0)
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Open AccessArticle
Genetic Elucidation for Response of Flowering Time to Ambient Temperatures in Asian Rice Cultivars
Int. J. Mol. Sci. 2021, 22(3), 1024; https://doi.org/10.3390/ijms22031024 - 20 Jan 2021
Abstract
Climate resilience of crops is critical for global food security. Understanding the genetic basis of plant responses to ambient environmental changes is key to developing resilient crops. To detect genetic factors that set flowering time according to seasonal temperature conditions, we evaluated differences [...] Read more.
Climate resilience of crops is critical for global food security. Understanding the genetic basis of plant responses to ambient environmental changes is key to developing resilient crops. To detect genetic factors that set flowering time according to seasonal temperature conditions, we evaluated differences of flowering time over years by using chromosome segment substitution lines (CSSLs) derived from japonica rice cultivars “Koshihikari” × “Khao Nam Jen”, each with different robustness of flowering time to environmental fluctuations. The difference of flowering times in 9 years’ field tests was large in “Khao Nam Jen” (36.7 days) but small in “Koshihikari” (9.9 days). Part of this difference was explained by two QTLs. A CSSL with a “Khao Nam Jen” segment on chromosome 11 showed 28.0 days’ difference; this QTL would encode a novel flowering-time gene. Another CSSL with a segment from “Khao Nam Jen” in the region around Hd16 on chromosome 3 showed 23.4 days” difference. A near-isogenic line (NIL) for Hd16 showed 21.6 days’ difference, suggesting Hd16 as a candidate for this QTL. RNA-seq analysis showed differential expression of several flowering-time genes between early and late flowering seasons. Low-temperature treatment at panicle initiation stage significantly delayed flowering in the CSSL and NIL compared with “Koshihikari”. Our results unravel the molecular control of flowering time under ambient temperature fluctuations. Full article
(This article belongs to the Special Issue Molecular Research in Rice: Agronomically Important Traits 2.0)
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Review

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Open AccessReview
Molecular and Genetic Aspects of Grain Number Determination in Rice (Oryza sativa L.)
Int. J. Mol. Sci. 2021, 22(2), 728; https://doi.org/10.3390/ijms22020728 - 13 Jan 2021
Abstract
Rice grain yield is a complex trait determined by three components: panicle number, grain number per panicle (GNPP) and grain weight. GNPP is the major contributor to grain yield and is crucial for its improvement. GNPP is determined by a series of physiological [...] Read more.
Rice grain yield is a complex trait determined by three components: panicle number, grain number per panicle (GNPP) and grain weight. GNPP is the major contributor to grain yield and is crucial for its improvement. GNPP is determined by a series of physiological and biochemical steps, including inflorescence development, formation of rachis branches such as primary rachis branches and secondary rachis branches, and spikelet specialisation (lateral and terminal spikelets). The molecular genetic basis of GNPP determination is complex, and it is regulated by numerous interlinked genes. In this review, panicle development and the determination of GNPP is described briefly, and GNPP-related genes that influence its determination are categorised according to their regulatory mechanisms. We introduce genes related to rachis branch development and their regulation of GNPP, genes related to phase transition (from rachis branch meristem to spikelet meristem) and their regulation of GNPP, and genes related to spikelet specialisation and their regulation of GNPP. In addition, we describe other GNPP-related genes and their regulation of GNPP. Research on GNPP determination suggests that it is possible to cultivate rice varieties with higher grain yield by modifying GNPP-related genes. Full article
(This article belongs to the Special Issue Molecular Research in Rice: Agronomically Important Traits 2.0)
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