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Molecular Research in Rice: Agronomically Important Traits 2.0
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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: closed (30 November 2021) | Viewed by 39702

Printed Edition Available!
A printed edition of this Special Issue is available here.

Special Issue Editors

Dr. Kiyosumi Hori

E-Mail 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, Collections and Topics in MDPI journals
Dr. Matthew Shenton

E-Mail 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, Collections and Topics 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

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Keywords

  • Rice
  • Plant molecular biology
  • Plant molecular genetics and genomics
  • Plant physiology
  • Plant pathology
  • Omics database
  • Genetic and environmental interaction
  • Agronomic trait

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Published Papers (12 papers)

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Editorial

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4 pages, 203 KiB  
Editorial
Current Advances and Future Prospects for Molecular Research for Agronomically Important Traits in Rice
by Kiyosumi Hori and Matthew Shenton
Int. J. Mol. Sci. 2022, 23(14), 7531; https://doi.org/10.3390/ijms23147531 - 7 Jul 2022
Viewed by 1317
Abstract
Rice (Oryza sativa L [...] Full article
(This article belongs to the Special Issue Molecular Research in Rice: Agronomically Important Traits 2.0)

Research

Jump to: Editorial, Review

12 pages, 31737 KiB  
Article
Whole-Tissue Three-Dimensional Imaging of Rice at Single-Cell Resolution
by Moeko Sato, Hiroko Akashi, Yuki Sakamoto, Sachihiro Matsunaga and Hiroyuki Tsuji
Int. J. Mol. Sci. 2022, 23(1), 40; https://doi.org/10.3390/ijms23010040 - 21 Dec 2021
Cited by 5 | Viewed by 4203
Abstract
The three-dimensional (3D) arrangement of cells in tissues provides an anatomical basis for analyzing physiological and biochemical aspects of plant and animal cellular development and function. In this study, we established a protocol for tissue clearing and 3D imaging in rice. Our protocol [...] Read more.
The three-dimensional (3D) arrangement of cells in tissues provides an anatomical basis for analyzing physiological and biochemical aspects of plant and animal cellular development and function. In this study, we established a protocol for tissue clearing and 3D imaging in rice. Our protocol is based on three improvements: clearing with iTOMEI (clearing solution suitable for plants), developing microscopic conditions in which the Z step is optimized for 3D reconstruction, and optimizing cell-wall staining. Our protocol successfully 3D imaged rice shoot apical meristems, florets, and root apical meristems at cellular resolution throughout whole tissues. Using fluorescent reporters of auxin signaling in rice root tips, we also revealed the 3D distribution of auxin signaling events that are activated in the columella, quiescent center, and multiple rows of cells in the stele of the root apical meristem. Examination of cells with higher levels of auxin signaling revealed that only the central row of cells was connected to the quiescent center. Our method provides opportunities to observe the 3D arrangement of cells in rice tissues. Full article
(This article belongs to the Special Issue Molecular Research in Rice: Agronomically Important Traits 2.0)
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14 pages, 1842 KiB  
Article
Submergence Gene Sub1A Transfer into Drought-Tolerant japonica Rice DT3 Using Marker-Assisted Selection
by Yong-Pei Wu, Shu-Mei Wang, Yu-Chi Chang, Chi Ho and Yu-Chia Hsu
Int. J. Mol. Sci. 2021, 22(24), 13365; https://doi.org/10.3390/ijms222413365 - 13 Dec 2021
Cited by 5 | Viewed by 2812
Abstract
Flash flooding is a major environmental stressor affecting rice production worldwide. DT3 is a drought-tolerant, recurrent parent with a good yield, edible quality, and agronomic traits akin to those of an elite Taiwanese variety, Taiken9 (TK9). Progenies carrying Sub1A can enhance submergence stress [...] Read more.
Flash flooding is a major environmental stressor affecting rice production worldwide. DT3 is a drought-tolerant, recurrent parent with a good yield, edible quality, and agronomic traits akin to those of an elite Taiwanese variety, Taiken9 (TK9). Progenies carrying Sub1A can enhance submergence stress tolerance and can be selected using the marker-assisted backcross (MAB) breeding method. For foreground selection, Sub1A and SubAB1 were utilized as markers on the BC2F1, BC3F1, and BC3F2 generations to select the submergence-tolerant gene, Sub1A. Background selection was performed in the Sub1A-BC3F2 genotypes, and the percentages of recurrent parent recovery within individuals ranged from 84.7–99.55%. BC3F3 genotypes (N = 100) were evaluated for agronomic traits, yield, and eating quality. Four of the eleven BC3F4 lines showed good yield, yield component, grain, and eating quality. Four BC3F4 lines, SU39, SU40, SU89, and SU92, exhibited desirable agronomic traits, including grain quality and palatability, consistent with those of DT3. These genotypes displayed a high survival rate between 92 and 96%, much better compared with DT3 with 64%, and demonstrated better drought tolerance compared to IR64 and IR96321-345-240. This study provides an efficient and precise MAB strategy for developing climate-resilient rice varieties with good grain quality for flood-prone regions. Full article
(This article belongs to the Special Issue Molecular Research in Rice: Agronomically Important Traits 2.0)
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19 pages, 5786 KiB  
Article
VPB1 Encoding BELL-like Homeodomain Protein Is Involved in Rice Panicle Architecture
by Mu Li, Debao Fu, Tingting Xu and Changyin Wu
Int. J. Mol. Sci. 2021, 22(15), 7909; https://doi.org/10.3390/ijms22157909 - 24 Jul 2021
Cited by 6 | Viewed by 2727
Abstract
Inflorescence architecture in rice (Oryza sativa) is mainly determined by spikelets and the branch arrangement. Primary branches initiate from inflorescence meristem in a spiral phyllotaxic manner, and further develop into the panicle branches. The branching patterns contribute largely to rice production. [...] Read more.
Inflorescence architecture in rice (Oryza sativa) is mainly determined by spikelets and the branch arrangement. Primary branches initiate from inflorescence meristem in a spiral phyllotaxic manner, and further develop into the panicle branches. The branching patterns contribute largely to rice production. In this study, we characterized a rice verticillate primary branch 1(vpb1) mutant, which exhibited a clustered primary branches phenotype. Gene isolation revealed that VPB1 was a allele of RI, that it encoded a BELL-like homeodomain (BLH) protein. VPB1 gene preferentially expressed in the inflorescence and branch meristems. The arrangement of primary branch meristems was disturbed in the vpb1 mutant. Transcriptome analysis further revealed that VPB1 affected the expression of some genes involved in inflorescence meristem identity and hormone signaling pathways. In addition, the differentially expressed gene (DEG) promoter analysis showed that OsBOPs involved in boundary organ initiation were potential target genes of VPB1 protein. Electrophoretic mobility shift assay (EMSA) and dual-luciferase reporter system further verified that VPB1 protein bound to the promoter of OsBOP1 gene. Overall, our findings demonstrate that VPB1 controls inflorescence architecture by regulating the expression of genes involved in meristem maintenance and hormone pathways and by interacting with OsBOP genes. Full article
(This article belongs to the Special Issue Molecular Research in Rice: Agronomically Important Traits 2.0)
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14 pages, 2508 KiB  
Article
Rice Transcription Factor OsWRKY55 Is Involved in the Drought Response and Regulation of Plant Growth
by Kai Huang, Tao Wu, Ziming Ma, Zhao Li, Haoyuan Chen, Mingxing Zhang, Mingdi Bian, Huijiao Bai, Wenzhu Jiang and Xinglin Du
Int. J. Mol. Sci. 2021, 22(9), 4337; https://doi.org/10.3390/ijms22094337 - 21 Apr 2021
Cited by 29 | Viewed by 3364
Abstract
WRKY transcription factors (TFs) have been reported to respond to biotic and abiotic stresses and regulate plant growth and development. However, the molecular mechanisms of WRKY TFs involved in drought stress and regulating plant height in rice remain largely unknown. In this study, [...] Read more.
WRKY transcription factors (TFs) have been reported to respond to biotic and abiotic stresses and regulate plant growth and development. However, the molecular mechanisms of WRKY TFs involved in drought stress and regulating plant height in rice remain largely unknown. In this study, we found that transgenic rice lines overexpressing OsWRKY55 (OsWRKY55-OE) exhibited reduced drought resistance. The OsWRKY55-OE lines showed faster water loss and greater accumulation of hydrogen peroxide (H2O2) and superoxide radical (O2−·) compared to wild-type (WT) plants under drought conditions. OsWRKY55 was expressed in various tissues and was induced by drought and abscisic acid (ABA) treatments. Through yeast two-hybrid assays, we found that OsWRKY55 interacted with four mitogen-activated protein kinases (MAPKs) that could be induced by drought, including OsMPK7, OsMPK9, OsMPK20-1, and OsMPK20-4. The activation effects of the four OsMPKs on OsWRKY55 transcriptional activity were demonstrated by a GAL4-dependent chimeric transactivation assay in rice protoplasts. Furthermore, OsWRKY55 was able to reduce plant height under normal conditions by decreasing the cell size. In addition, based on a dual luciferase reporter assay, OsWRKY55 was shown to bind to the promoter of OsAP2-39 through a yeast one-hybrid assay and positively regulate OsAP2-39 expression. These results suggest that OsWRKY55 plays a critical role in responses to drought stress and the regulation of plant height in rice, further providing valuable information for crop improvement. Full article
(This article belongs to the Special Issue Molecular Research in Rice: Agronomically Important Traits 2.0)
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16 pages, 4140 KiB  
Article
RETRACTED: Formation of Proto-Kranz in C3 Rice Induced by Spike-Stalk Injection Method
by Dexing Jiang, Feng Wang, Haizi Zhang, Wenwen Gao, Xi Tong, Chuangen Lv and Guoxiang Chen
Int. J. Mol. Sci. 2021, 22(9), 4305; https://doi.org/10.3390/ijms22094305 - 21 Apr 2021
Cited by 3 | Viewed by 2615 | Retraction
Abstract
Introduction of C4 photosynthetic traits into C3 crops is an important strategy for improving photosynthetic capacity and productivity. Here, we report the research results of a variant line of sorghum–rice (SR) plant with big panicle and high spikelet density by introducing sorghum genome [...] Read more.
Introduction of C4 photosynthetic traits into C3 crops is an important strategy for improving photosynthetic capacity and productivity. Here, we report the research results of a variant line of sorghum–rice (SR) plant with big panicle and high spikelet density by introducing sorghum genome DNA into rice by spike-stalk injection. The whole-genome resequencing showed that a few sorghum genes could be integrated into the rice genome. Gene expression was confirmed for two C4 photosynthetic enzymes containing pyruvate, orthophosphate dikinase and phosphoenolpyruvate carboxykinase. Exogenous sorghum DNA integration induced a series of key traits associated with the C4 pathway called “proto-Kranz” anatomy, including leaf thickness, bundle sheath number and size, and chloroplast size in bundle sheath cells. Significantly, transgenic plants exhibited enhanced photosynthetic capacity resulting from both photosynthetic CO2-concentrating effect and improved energy balance, which led to an increase in carbohydrate levels and productivity. Furthermore, such rice plant exhibited delayed leaf senescence. In summary, this study provides a proof for the feasibility of inducing the transition from C3 leaf anatomy to proto-Kranz by spike-stalk injection to achieve efficient photosynthesis and increase productivity. Full article
(This article belongs to the Special Issue Molecular Research in Rice: Agronomically Important Traits 2.0)
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19 pages, 5352 KiB  
Article
CRISPR/Cas9 Guided Mutagenesis of Grain Size 3 Confers Increased Rice (Oryza sativa L.) Grain Length by Regulating Cysteine Proteinase Inhibitor and Ubiquitin-Related Proteins
by Babar Usman, Neng Zhao, Gul Nawaz, Baoxiang Qin, Fang Liu, Yaoguang Liu and Rongbai Li
Int. J. Mol. Sci. 2021, 22(6), 3225; https://doi.org/10.3390/ijms22063225 - 22 Mar 2021
Cited by 24 | Viewed by 4677
Abstract
Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/CRISPR-associated protein (Cas9)-mediated genome editing has become an important way for molecular breeding in crop plants. To promote rice breeding, we edited the Grain Size 3 (GS3) gene for obtaining valuable and stable long-grain rice [...] Read more.
Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/CRISPR-associated protein (Cas9)-mediated genome editing has become an important way for molecular breeding in crop plants. To promote rice breeding, we edited the Grain Size 3 (GS3) gene for obtaining valuable and stable long-grain rice mutants. Furthermore, isobaric tags for the relative and absolute quantitation (iTRAQ)-based proteomic method were applied to determine the proteome-wide changes in the GS3 mutants compared with wild type (WT). Two target sites were designed to construct the vector, and the Agrobacterium-mediated method was used for rice transformation. Specific mutations were successfully introduced, and the grain length (GL) and 1000-grain weight (GWT) of the mutants were increased by 31.39% and 27.15%, respectively, compared with WT. The iTRAQ-based proteomic analysis revealed that a total of 31 proteins were differentially expressed in the GS3 mutants, including 20 up-regulated and 11 down-regulated proteins. Results showed that differentially expressed proteins (DEPs) were mainly related to cysteine synthase, cysteine proteinase inhibitor, vacuolar protein sorting-associated, ubiquitin, and DNA ligase. Furthermore, functional analysis revealed that DEPs were mostly enriched in cellular process, metabolic process, binding, transmembrane, structural, and catalytic activities. Pathway enrichment analysis revealed that DEPs were mainly involved in lipid metabolism and oxylipin biosynthesis. The protein-to-protein interaction (PPI) network found that proteins related to DNA damage-binding, ubiquitin-40S ribosomal, and cysteine proteinase inhibitor showed a higher degree of interaction. The homozygous mutant lines featured by stable inheritance and long-grain phenotype were obtained using the CRISPR/Cas9 system. This study provides a convenient and effective way of improving grain yield, which could significantly accelerate the breeding process of long-grain japonica parents and promote the development of high-yielding rice. Full article
(This article belongs to the Special Issue Molecular Research in Rice: Agronomically Important Traits 2.0)
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14 pages, 5665 KiB  
Article
OsBRKq1, Related Grain Size Mapping, and Identification of Grain Shape Based on QTL Mapping in Rice
by Jae-Ryoung Park, Dany Resolus and Kyung-Min Kim
Int. J. Mol. Sci. 2021, 22(5), 2289; https://doi.org/10.3390/ijms22052289 - 25 Feb 2021
Cited by 5 | Viewed by 2699
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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21 pages, 5196 KiB  
Article
New Insights into the Transcriptional Regulation of Genes Involved in the Nitrogen Use Efficiency under Potassium Chlorate in Rice (Oryza sativa L.)
by Nkulu Rolly Kabange, So-Yeon Park, Ji-Yun Lee, Dongjin Shin, So-Myeong Lee, Youngho Kwon, Jin-Kyung Cha, Jun-Hyeon Cho, Dang Van Duyen, Jong-Min Ko and Jong-Hee Lee
Int. J. Mol. Sci. 2021, 22(4), 2192; https://doi.org/10.3390/ijms22042192 - 22 Feb 2021
Cited by 10 | Viewed by 3485
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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16 pages, 4480 KiB  
Article
OsCRP1, a Ribonucleoprotein Gene, Regulates Chloroplast mRNA Stability That Confers Drought and Cold Tolerance
by Seung Woon Bang, Ho Suk Lee, Su-Hyun Park, Dong-Keun Lee, Jun Sung Seo, Youn Shic Kim, Soo-Chul Park and Ju-Kon Kim
Int. J. Mol. Sci. 2021, 22(4), 1673; https://doi.org/10.3390/ijms22041673 - 7 Feb 2021
Cited by 7 | Viewed by 3041
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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13 pages, 3325 KiB  
Article
Genetic Elucidation for Response of Flowering Time to Ambient Temperatures in Asian Rice Cultivars
by Kiyosumi Hori, Daisuke Saisho, Kazufumi Nagata, Yasunori Nonoue, Yukiko Uehara-Yamaguchi, Asaka Kanatani, Koka Shu, Takashi Hirayama, Jun-ichi Yonemaru, Shuichi Fukuoka and Keiichi Mochida
Int. J. Mol. Sci. 2021, 22(3), 1024; https://doi.org/10.3390/ijms22031024 - 20 Jan 2021
Cited by 7 | Viewed by 2615
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

Jump to: Editorial, Research

19 pages, 593 KiB  
Review
Molecular and Genetic Aspects of Grain Number Determination in Rice (Oryza sativa L.)
by Changxi Yin, Yanchun Zhu, Xuefei Li and Yongjun Lin
Int. J. Mol. Sci. 2021, 22(2), 728; https://doi.org/10.3390/ijms22020728 - 13 Jan 2021
Cited by 20 | Viewed by 4243
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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