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Molecular Research in Rice: Agronomically Important Traits
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Molecular Research in Rice: Agronomically Important Traits

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 (31 January 2020) | Viewed by 84813

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,

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. Recently developed techniques in molecular biology, including genomics and other omics, 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. 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

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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.

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Keywords

  • rice
  • plant molecular biology
  • plant molecular genetics and genomics
  • plant physiology
  • plant pathology
  • omics database
  • agronomic traits
  • genetic and environmental interaction

Published Papers (21 papers)

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Editorial

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4 pages, 171 KiB  
Editorial
Recent Advances in Molecular Research in Rice: Agronomically Important Traits
by Kiyosumi Hori and Matthew Shenton
Int. J. Mol. Sci. 2020, 21(17), 5945; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms21175945 - 19 Aug 2020
Cited by 4 | Viewed by 2277
Abstract
Rice (Oryza sativa L [...] Full article
(This article belongs to the Special Issue Molecular Research in Rice: Agronomically Important Traits)

Research

Jump to: Editorial

24 pages, 8212 KiB  
Article
Season Affects Yield and Metabolic Profiles of Rice (Oryza sativa) under High Night Temperature Stress in the Field
by Stephanie Schaarschmidt, Lovely Mae F. Lawas, Ulrike Glaubitz, Xia Li, Alexander Erban, Joachim Kopka, S. V. Krishna Jagadish, Dirk K. Hincha and Ellen Zuther
Int. J. Mol. Sci. 2020, 21(9), 3187; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms21093187 - 30 Apr 2020
Cited by 18 | Viewed by 4001
Abstract
Rice (Oryza sativa) is the main food source for more than 3.5 billion people in the world. Global climate change is having a strong negative effect on rice production. One of the climatic factors impacting rice yield is asymmetric warming, i.e., [...] Read more.
Rice (Oryza sativa) is the main food source for more than 3.5 billion people in the world. Global climate change is having a strong negative effect on rice production. One of the climatic factors impacting rice yield is asymmetric warming, i.e., the stronger increase in nighttime as compared to daytime temperatures. Little is known of the metabolic responses of rice to high night temperature (HNT) in the field. Eight rice cultivars with contrasting HNT sensitivity were grown in the field during the wet (WS) and dry season (DS) in the Philippines. Plant height, 1000-grain weight and harvest index were influenced by HNT in both seasons, while total grain yield was only consistently reduced in the WS. Metabolite composition was analysed by gas chromatography-mass spectrometry (GC-MS). HNT effects were more pronounced in panicles than in flag leaves. A decreased abundance of sugar phosphates and sucrose, and a higher abundance of monosaccharides in panicles indicated impaired glycolysis and higher respiration-driven carbon losses in response to HNT in the WS. Higher amounts of alanine and cyano-alanine in panicles grown in the DS compared to in those grown in the WS point to an improved N-assimilation and more effective detoxification of cyanide, contributing to the smaller impact of HNT on grain yield in the DS. Full article
(This article belongs to the Special Issue Molecular Research in Rice: Agronomically Important Traits)
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13 pages, 1631 KiB  
Article
Bulked Segregant Analysis Coupled with Whole-Genome Sequencing (BSA-Seq) Mapping Identifies a Novel pi21 Haplotype Conferring Basal Resistance to Rice Blast Disease
by Tingmin Liang, Wenchao Chi, Likun Huang, Mengyu Qu, Shubiao Zhang, Zi-Qiang Chen, Zai-Jie Chen, Dagang Tian, Yijie Gui, Xiaofeng Chen, Zonghua Wang, Weiqi Tang and Songbiao Chen
Int. J. Mol. Sci. 2020, 21(6), 2162; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms21062162 - 21 Mar 2020
Cited by 26 | Viewed by 4381
Abstract
Basal or partial resistance has been considered race-non-specific and broad-spectrum. Therefore, the identification of genes or quantitative trait loci (QTLs) conferring basal resistance and germplasm containing them is of significance in breeding crops with durable resistance. In this study, we performed a bulked [...] Read more.
Basal or partial resistance has been considered race-non-specific and broad-spectrum. Therefore, the identification of genes or quantitative trait loci (QTLs) conferring basal resistance and germplasm containing them is of significance in breeding crops with durable resistance. In this study, we performed a bulked segregant analysis coupled with whole-genome sequencing (BSA-seq) to identify QTLs controlling basal resistance to blast disease in an F2 population derived from two rice varieties, 02428 and LiXinGeng (LXG), which differ significantly in basal resistance to rice blast. Four candidate QTLs, qBBR-4, qBBR-7, qBBR-8, and qBBR-11, were mapped on chromosomes 4, 7, 8, and 11, respectively. Allelic and genotypic association analyses identified a novel haplotype of the durable blast resistance gene pi21 carrying double deletions of 30 bp and 33 bp in 02428 (pi21-2428) as a candidate gene of qBBR-4. We further assessed haplotypes of Pi21 in 325 rice accessions, and identified 11 haplotypes among the accessions, of which eight were novel types. While the resistant pi21 gene was found only in japonica before, three Chinese indica varieties, ShuHui881, Yong4, and ZhengDa4Hao, were detected carrying the resistant pi21-2428 allele. The pi21-2428 allele and pi21-2428-containing rice germplasm, thus, provide valuable resources for breeding rice varieties, especially indica rice varieties, with durable resistance to blast disease. Our results also lay the foundation for further identification and functional characterization of the other three QTLs to better understand the molecular mechanisms underlying rice basal resistance to blast disease. Full article
(This article belongs to the Special Issue Molecular Research in Rice: Agronomically Important Traits)
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20 pages, 3734 KiB  
Article
The Rice Basic Helix–Loop–Helix 79 (OsbHLH079) Determines Leaf Angle and Grain Shape
by Hyoseob Seo, Suk-Hwan Kim, Byoung-Doo Lee, Jung-Hyun Lim, Sang-Ji Lee, Gynheung An and Nam-Chon Paek
Int. J. Mol. Sci. 2020, 21(6), 2090; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms21062090 - 18 Mar 2020
Cited by 16 | Viewed by 4242
Abstract
Changes in plant architecture, such as leaf size, leaf shape, leaf angle, plant height, and floral organs, have been major factors in improving the yield of cereal crops. Moreover, changes in grain size and weight can also increase yield. Therefore, screens for additional [...] Read more.
Changes in plant architecture, such as leaf size, leaf shape, leaf angle, plant height, and floral organs, have been major factors in improving the yield of cereal crops. Moreover, changes in grain size and weight can also increase yield. Therefore, screens for additional factors affecting plant architecture and grain morphology may enable additional improvements in yield. Among the basic Helix-Loop-Helix (bHLH) transcription factors in rice (Oryza sativa), we found an enhancer-trap T-DNA insertion mutant of OsbHLH079 (termed osbhlh079-D). The osbhlh079-D mutant showed a wide leaf angle phenotype and produced long grains, similar to the phenotypes of mutants with increased brassinosteroid (BR) levels or enhanced BR signaling. Reverse transcription-quantitative PCR analysis showed that BR signaling-associated genes are largely upregulated in osbhlh079-D, but BR biosynthesis-associated genes are not upregulated, compared with its parental japonica cultivar ‘Dongjin’. Consistent with this, osbhlh079-D was hypersensitive to BR treatment. Scanning electron microscopy revealed that the expansion of cell size in the adaxial side of the lamina joint was responsible for the increase in leaf angle in osbhlh079-D. The expression of cell-elongation-associated genes encoding expansins and xyloglucan endotransglycosylases/hydrolases increased in the lamina joints of leaves in osbhlh079-D. The regulatory function of OsbHLH079 was further confirmed by analyzing 35S::OsbHLH079 overexpression and 35S::RNAi-OsbHLH079 gene silencing lines. The 35S::OsbHLH079 plants showed similar phenotypes to osbhlh079-D, and the 35S::RNAi-OsbHLH079 plants displayed opposite phenotypes to osbhlh079-D. Taking these observations together, we propose that OsbHLH079 functions as a positive regulator of BR signaling in rice. Full article
(This article belongs to the Special Issue Molecular Research in Rice: Agronomically Important Traits)
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17 pages, 2645 KiB  
Article
Systems Metabolic Alteration in a Semi-Dwarf Rice Mutant Induced by OsCYP96B4 Gene Mutation
by Limiao Jiang, Rengasamy Ramamoorthy, Srinivasan Ramachandran and Prakash P. Kumar
Int. J. Mol. Sci. 2020, 21(6), 1924; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms21061924 - 11 Mar 2020
Cited by 9 | Viewed by 3361
Abstract
Dwarfism and semi-dwarfism are among the most valuable agronomic traits in crop breeding, which were adopted by the “Green Revolution”. Previously, we reported a novel semi-dwarf rice mutant (oscyp96b4) derived from the insertion of a single copy of Dissociator (Ds) transposon [...] Read more.
Dwarfism and semi-dwarfism are among the most valuable agronomic traits in crop breeding, which were adopted by the “Green Revolution”. Previously, we reported a novel semi-dwarf rice mutant (oscyp96b4) derived from the insertion of a single copy of Dissociator (Ds) transposon into the gene OsCYP96B4. However, the systems metabolic effect of the mutation is not well understood, which is important for understanding the gene function and developing new semi-dwarf mutants. Here, the metabolic phenotypes in the semi-dwarf mutant (M) and ectopic expression (ECE) rice line were compared to the wild-type (WT) rice, by using nuclear magnetic resonance (NMR) metabolomics and quantitative real-time polymerase chain reaction (qRT-PCR). Compared with WT, ECE of the OsCYP96B4 gene resulted in significant increase of γ-aminobutyrate (GABA), glutamine, and alanine, but significant decrease of glutamate, aromatic and branched-chain amino acids, and some other amino acids. The ECE caused significant increase of monosaccharides (glucose, fructose), but significant decrease of disaccharide (sucrose); induced significant changes of metabolites involved in choline metabolism (phosphocholine, ethanolamine) and nucleotide metabolism (adenosine, adenosine monophosphate, uridine). These metabolic profile alterations were accompanied with changes in the gene expression levels of some related enzymes, involved in GABA shunt, glutamate and glutamine metabolism, choline metabolism, sucrose metabolism, glycolysis/gluconeogenesis pathway, tricarboxylic acid (TCA) cycle, nucleotide metabolism, and shikimate-mediated secondary metabolism. The semi-dwarf mutant showed corresponding but less pronounced changes, especially in the gene expression levels. It indicates that OsCYP96B4 gene mutation in rice causes significant alteration in amino acid metabolism, carbohydrate metabolism, nucleotide metabolism, and shikimate-mediated secondary metabolism. The present study will provide essential information for the OsCYP96B4 gene function analysis and may serve as valuable reference data for the development of new semi-dwarf mutants. Full article
(This article belongs to the Special Issue Molecular Research in Rice: Agronomically Important Traits)
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16 pages, 2109 KiB  
Article
Genetic and Global Epigenetic Modification, Which Determines the Phenotype of Transgenic Rice?
by Xiaoru Fan, Jingguang Chen, Yufeng Wu, CheeHow Teo, Guohua Xu and Xiaorong Fan
Int. J. Mol. Sci. 2020, 21(5), 1819; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms21051819 - 06 Mar 2020
Cited by 12 | Viewed by 3278
Abstract
Transgenic technologies have been applied to a wide range of biological research. However, information on the potential epigenetic effects of transgenic technology is still lacking. Here, we show that the transgenic process can simultaneously induce both genetic and epigenetic changes in rice. We [...] Read more.
Transgenic technologies have been applied to a wide range of biological research. However, information on the potential epigenetic effects of transgenic technology is still lacking. Here, we show that the transgenic process can simultaneously induce both genetic and epigenetic changes in rice. We analyzed genetic, epigenetic, and phenotypic changes in plants subjected to tissue culture regeneration, using transgenic lines expressing the same coding sequence from two different promoters in transgenic lines of two rice cultivars: Wuyunjing7 (WYJ7) and Nipponbare (NP). We determined the expression of OsNAR2.1 in two overexpression lines generated from the two cultivars, and in the RNA interference (RNAi) OsNAR2.1 line in NP. DNA methylation analyses were performed on wild-type cultivars (WYJ7 and NP), regenerated lines (CK, T0 plants), segregation-derived wild-type from pOsNAR2.1-OsNAR2.1 (SDWT), pOsNAR2.1-OsNAR2.1, pUbi-OsNAR2.1, and RNAi lines. Interestingly, we observed global methylation decreased in the T0 regenerated line of WYJ7 (CK-WJY7) and pOsNAR2.1-OsNAR2.1 lines but increased in pUbi-OsNAR2.1 and RNAi lines of NP. Furthermore, the methylation pattern in SDWT returned to the WYJ7 level after four generations. Phenotypic changes were detected in all the generated lines except for SDWT. Global methylation was found to decrease by 13% in pOsNAR2.1-OsNAR2.1 with an increase in plant height of 4.69% compared with WYJ7, and increased by 18% in pUbi-OsNAR2.1 with an increase of 17.36% in plant height compared with NP. This suggests an absence of a necessary link between global methylation and the phenotype of transgenic plants with OsNAR2.1 gene over-expression. However, epigenetic changes can influence phenotype during tissue culture, as seen in the massive methylation in CK-WYJ7, T0 regenerated lines, resulting in decreased plant height compared with the wild-type, in the absence of a transformed gene. We conclude that in the transgenic lines the phenotype is mainly determined by the nature and function of the transgene after four generations of transformation, while the global epigenetic modification is dependent on the genetic background. Our research suggests an innovative insight in explaining the reason behind the occurrence of transgenic plants with random and undesirable phenotypes. Full article
(This article belongs to the Special Issue Molecular Research in Rice: Agronomically Important Traits)
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18 pages, 3518 KiB  
Article
A RING-Type E3 Ubiquitin Ligase, OsGW2, Controls Chlorophyll Content and Dark-Induced Senescence in Rice
by Kyu-Chan Shim, Sun Ha Kim, Yun-A Jeon, Hyun-Sook Lee, Cheryl Adeva, Ju-Won Kang, Hyun-Jung Kim, Thomas H Tai and Sang-Nag Ahn
Int. J. Mol. Sci. 2020, 21(5), 1704; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms21051704 - 02 Mar 2020
Cited by 15 | Viewed by 4287
Abstract
Leaf senescence is the final stage of plant development. Many internal and external factors affect the senescence process in rice (Oryza sativa L.). In this study, we identified qCC2, a major quantitative trait locus (QTL) for chlorophyll content using a population [...] Read more.
Leaf senescence is the final stage of plant development. Many internal and external factors affect the senescence process in rice (Oryza sativa L.). In this study, we identified qCC2, a major quantitative trait locus (QTL) for chlorophyll content using a population derived from an interspecific cross between O. sativa (cv. Hwaseong) and Oryza grandiglumis. The O. grandiglumis allele at qCC2 increased chlorophyll content and delayed senescence. GW2 encoding E3 ubiquitin ligase in the qCC2 region was selected as a candidate for qCC2. To determine if GW2 is allelic to qCC2, a gw2-knockout mutant (gw2-ko) was examined using a dark-induced senescence assay. gw2-ko showed delayed leaf senescence in the dark with down-regulated expression of senescence-associated genes (SAGs) and chlorophyll degradation genes (CDGs). The association of the GW2 genotype with the delayed senescence phenotype was confirmed in an F2 population. RNA-seq analysis was conducted to investigate 30-day-old leaf transcriptome dynamics in Hwaseong and a backcross inbred line—CR2002—under dark treatment. This resulted in the identification of genes involved in phytohormone signaling and associated with senescence. These results suggested that transcriptional regulation was associated with delayed senescence in CR2002, and RING-type E3 ubiquitin ligase GW2 was a positive regulator of leaf senescence in rice. Full article
(This article belongs to the Special Issue Molecular Research in Rice: Agronomically Important Traits)
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16 pages, 2583 KiB  
Article
Rice OsAAA-ATPase1 is Induced during Blast Infection in a Salicylic Acid-Dependent Manner, and Promotes Blast Fungus Resistance
by Xinqiong Liu, Haruhiko Inoue, Xianying Tang, Yanping Tan, Xin Xu, Chuntai Wang and Chang-Jie Jiang
Int. J. Mol. Sci. 2020, 21(4), 1443; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms21041443 - 20 Feb 2020
Cited by 17 | Viewed by 3181
Abstract
Fatty acids (FAs) have been implicated in signaling roles in plant defense responses. We previously reported that mutation or RNAi-knockdown (OsSSI2-kd) of the rice OsSSI2 gene, encoding a stearoyl acyl carrier protein FA desaturase (SACPD), remarkably enhanced resistance to blast fungus [...] Read more.
Fatty acids (FAs) have been implicated in signaling roles in plant defense responses. We previously reported that mutation or RNAi-knockdown (OsSSI2-kd) of the rice OsSSI2 gene, encoding a stearoyl acyl carrier protein FA desaturase (SACPD), remarkably enhanced resistance to blast fungus Magnaporthe oryzae and the leaf-blight bacterium Xanthomonas oryzae pv. oryzae (Xoo). Transcriptomic analysis identified six AAA-ATPase family genes (hereafter OsAAA-ATPase1–6) upregulated in the OsSSI2-kd plants, in addition to other well-known defense-related genes. Here, we report the functional analysis of OsAAA-ATPase1 in rice’s defense response to M. oryzae. Recombinant OsAAA-ATPase1 synthesized in Escherichia coli showed ATPase activity. OsAAA-ATPase1 transcription was induced by exogenous treatment with a functional analogue of salicylic acid (SA), benzothiadiazole (BTH), but not by other plant hormones tested. The transcription of OsAAA-ATPase1 was also highly induced in response to M. oryzae infection in an SA-dependent manner, as gene induction was significantly attenuated in a transgenic rice line expressing a bacterial gene (nahG) encoding salicylate hydroxylase. Overexpression of OsAAA-ATPase1 significantly enhanced pathogenesis-related gene expression and the resistance to M. oryzae; conversely, RNAi-mediated suppression of this gene compromised this resistance. These results suggest that OsAAA-APTase1 plays an important role in SA-mediated defense responses against blast fungus M. oryzae. Full article
(This article belongs to the Special Issue Molecular Research in Rice: Agronomically Important Traits)
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22 pages, 11925 KiB  
Article
Effect of Low Temperature on Chlorophyll Biosynthesis and Chloroplast Biogenesis of Rice Seedlings during Greening
by Yuqing Zhao, Qiaohong Han, Chunbang Ding, Yan Huang, Jinqiu Liao, Tao Chen, Shiling Feng, Lijun Zhou, Zhongwei Zhang, Yanger Chen, Shu Yuan and Ming Yuan
Int. J. Mol. Sci. 2020, 21(4), 1390; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms21041390 - 19 Feb 2020
Cited by 82 | Viewed by 5813
Abstract
Rice (Oryza sativa L.) frequently suffers in late spring from severe damage due to cold spells, which causes the block of chlorophyll biosynthesis during early rice seedling greening. However, the inhibitory mechanism by which this occurs is still unclear. To explore the [...] Read more.
Rice (Oryza sativa L.) frequently suffers in late spring from severe damage due to cold spells, which causes the block of chlorophyll biosynthesis during early rice seedling greening. However, the inhibitory mechanism by which this occurs is still unclear. To explore the responsive mechanism of rice seedlings to low temperatures during greening, the effects of chilling stress on chlorophyll biosynthesis and plastid development were studied in rice seedlings. Chlorophyll biosynthesis was obviously inhibited and chlorophyll accumulation declined under low temperatures during greening. The decrease in chlorophyll synthesis was due to the inhibited synthesis of δ-aminolevulinic acid (ALA) and the suppression of conversion from protochlorophyllide (Pchlide) into chlorophylls (Chls). Meanwhile, the activities of glutamate-1-semialdehyde transaminase (GSA-AT), Mg-chelatase, and protochlorophyllide oxidoreductase (POR) were downregulated under low temperatures. Further investigations showed that chloroplasts at 18 °C had loose granum lamellae, while the thylakoid and lamellar structures of grana could hardly develop at 12 °C after 48 h of greening. Additionally, photosystem II (PSII) and photosystem I (PSI) proteins obviously declined in the stressed seedlings, to the point that the PSII and PSI proteins could hardly be detected after 48 h of greening at 12 °C. Furthermore, the accumulation of reactive oxygen species (ROS) and malondialdehyde (MDA) and cell death were all induced by low temperature. Chilling stress had no effect on the development of epidermis cells, but the stomata were smaller under chilling stress than those at 28 °C. Taken together, our study promotes more comprehensive understanding in that chilling could inhibit chlorophyll biosynthesis and cause oxidative damages during greening. Full article
(This article belongs to the Special Issue Molecular Research in Rice: Agronomically Important Traits)
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17 pages, 3188 KiB  
Article
Genetic Dissection of Seed Dormancy using Chromosome Segment Substitution Lines in Rice (Oryza sativa L.)
by Shaowen Yuan, Yuntong Wang, Chaopu Zhang, Hanzi He and Sibin Yu
Int. J. Mol. Sci. 2020, 21(4), 1344; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms21041344 - 17 Feb 2020
Cited by 11 | Viewed by 2876
Abstract
Timing of germination determines whether a new plant life cycle can be initiated; therefore, appropriate dormancy and rapid germination under diverse environmental conditions are the most important features for a seed. However, the genetic architecture of seed dormancy and germination behavior remains largely [...] Read more.
Timing of germination determines whether a new plant life cycle can be initiated; therefore, appropriate dormancy and rapid germination under diverse environmental conditions are the most important features for a seed. However, the genetic architecture of seed dormancy and germination behavior remains largely elusive. In the present study, a linkage analysis for seed dormancy and germination behavior was conducted using a set of 146 chromosome segment substitution lines (CSSLs), of which each carries a single or a few chromosomal segments of Nipponbare (NIP) in the background of Zhenshan 97 (ZS97). A total of 36 quantitative trait loci (QTLs) for six germination parameters were identified. Among them, qDOM3.1 was validated as a major QTL for seed dormancy in a segregation population derived from the qDOM3.1 near-isogenic line, and further delimited into a genomic region of 90 kb on chromosome 3. Based on genetic analysis and gene expression profiles, the candidate genes were restricted to eight genes, of which four were responsive to the addition of abscisic acid (ABA). Among them, LOC_Os03g01540 was involved in the ABA signaling pathway to regulate seed dormancy. The results will facilitate cloning the major QTLs and understanding the genetic architecture for seed dormancy and germination in rice and other crops. Full article
(This article belongs to the Special Issue Molecular Research in Rice: Agronomically Important Traits)
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15 pages, 1687 KiB  
Article
Genetic Dissection of Germinability under Low Temperature by Building a Resequencing Linkage Map in japonica Rice
by Shukun Jiang, Chao Yang, Quan Xu, Lizhi Wang, Xianli Yang, Xianwei Song, Jiayu Wang, Xijuan Zhang, Bo Li, Hongyu Li, Zhugang Li and Wenhua Li
Int. J. Mol. Sci. 2020, 21(4), 1284; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms21041284 - 14 Feb 2020
Cited by 25 | Viewed by 2805
Abstract
Among all cereals, rice is highly sensitive to cold stress, especially at the germination stage, which adversely impacts its germination ability, seed vigor, crop stand establishment, and, ultimately, grain yield. The dissection of novel quantitative trait loci (QTLs) or genes conferring a low-temperature [...] Read more.
Among all cereals, rice is highly sensitive to cold stress, especially at the germination stage, which adversely impacts its germination ability, seed vigor, crop stand establishment, and, ultimately, grain yield. The dissection of novel quantitative trait loci (QTLs) or genes conferring a low-temperature germination (LTG) ability can significantly accelerate cold-tolerant rice breeding to ensure the wide application of rice cultivation through the direct seeding method. In this study, we identified 11 QTLs for LTG using 144 recombinant inbred lines (RILs) derived from a cross between a cold-tolerant variety, Lijiangxintuanheigu (LTH), and a cold-sensitive variety, Shennong265 (SN265). By resequencing two parents and RIL lines, a high-density bin map, including 2,828 bin markers, was constructed using 123,859 single-nucleotide polymorphisms (SNPs) between two parents. The total genetic distance corresponding to all 12 chromosome linkage maps was 2,840.12 cm. Adjacent markers were marked by an average genetic distance of 1.01 cm, corresponding to a 128.80 kb physical distance. Eight and three QTL alleles had positive effects inherited from LTH and SN265, respectively. Moreover, a pleiotropic QTL was identified for a higher number of erected panicles and a higher grain number on Chr-9 near the previously cloned DEP1 gene. Among the LTG QTLs, qLTG3 and qLTG7b were also located at relatively small genetic intervals that define two known LTG genes, qLTG3-1 and OsSAP16. Sequencing comparisons between the two parents demonstrated that LTH possesses qLTG3-1 and OsSAP16 genes, and SN-265 owns the DEP1 gene. These comparison results strengthen the accuracy and mapping resolution power of the bin map and population. Later, fine mapping was done for qLTG6 at 45.80 kb through four key homozygous recombinant lines derived from a population with 1569 segregating plants. Finally, LOC_Os06g01320 was identified as the most possible candidate gene for qLTG6, which contains a missense mutation and a 32-bp deletion/insertion at the promoter between the two parents. LTH was observed to have lower expression levels in comparison with SN265 and was commonly detected at low temperatures. In conclusion, these results strengthen our understanding of the impacts of cold temperature stress on seed vigor and germination abilities and help improve the mechanisms of rice breeding programs to breed cold-tolerant varieties. Full article
(This article belongs to the Special Issue Molecular Research in Rice: Agronomically Important Traits)
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14 pages, 2556 KiB  
Article
Pyramiding Bacterial Blight Resistance Genes in Tainung82 for Broad-Spectrum Resistance Using Marker-Assisted Selection
by Yu-Chia Hsu, Chih-Hao Chiu, Ruishen Yap, Yu-Chien Tseng and Yong-Pei Wu
Int. J. Mol. Sci. 2020, 21(4), 1281; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms21041281 - 14 Feb 2020
Cited by 39 | Viewed by 4353
Abstract
Tainung82 (TNG82) is one of the most popular japonica varieties in Taiwan due to its relatively high yield and grain quality, however, TNG82 is susceptible to bacterial blight (BB) disease. The most economical and eco-friendly way to control BB disease in japonica is [...] Read more.
Tainung82 (TNG82) is one of the most popular japonica varieties in Taiwan due to its relatively high yield and grain quality, however, TNG82 is susceptible to bacterial blight (BB) disease. The most economical and eco-friendly way to control BB disease in japonica is through the utilization of varieties that are resistant to the disease. In order to improve TNG82’s resistance to BB disease, five bacterial blight resistance genes (Xa4, xa5, Xa7, xa13 and Xa21) were derived from a donor parent, IRBB66 and transferred into TNG82 via marker-assisted backcrossing breeding. Five BB-resistant gene-linked markers were integrated into the backcross breeding program in order to identify individuals possessing the five identified BB-resistant genes (Xa4, xa5, Xa7, xa13 and Xa21). The polymorphic markers between the donor and recurrent parent were used for background selection. Plants having maximum contribution from the recurrent parent genome were selected in each generation and crossed with the recipient parent. Selected BC3F1 plants were selfed in order to generate homozygous BC3F2 plants. Nine pyramided plants, possessing all five BB-resistant genes, were obtained. These individuals displayed a high level of resistance against the BB strain, XF89-b. Different BB gene pyramiding lines were also inoculated against the BB pathogen, resulting in more than three gene pyramided lines that exhibited high levels of resistance. The five identified BB gene pyramided lines exhibited yield levels and other desirable agronomic traits, including grain quality and palatability, consistent with TNG82. Bacterial blight-resistant lines possessing the five identified BB genes exhibited not only higher levels of resistance to the disease, but also greater yield levels and grain quality. Pyramiding multiple genes with potential characteristics into a single genotype through marker-assisted selection can improve the efficiency of generating new crop varieties exhibiting disease resistance, as well as other desirable traits. Full article
(This article belongs to the Special Issue Molecular Research in Rice: Agronomically Important Traits)
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17 pages, 6279 KiB  
Article
Dynamic Transcriptome Analysis of Anther Response to Heat Stress during Anthesis in Thermotolerant Rice (Oryza sativa L.)
by Gang Liu, Zhongping Zha, Haiya Cai, Dandan Qin, Haitao Jia, Changyan Liu, Dongfeng Qiu, Zaijun Zhang, Zhenghuang Wan, Yuanyuan Yang, Bingliang Wan, Aiqing You and Chunhai Jiao
Int. J. Mol. Sci. 2020, 21(3), 1155; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms21031155 - 10 Feb 2020
Cited by 32 | Viewed by 4672
Abstract
High temperature at anthesis is one of the most serious stress factors for rice (Oryza sativa L.) production, causing irreversible yield losses and reduces grain quality. Illustration of thermotolerance mechanism is of great importance to accelerate rice breeding aimed at thermotolerance improvement. [...] Read more.
High temperature at anthesis is one of the most serious stress factors for rice (Oryza sativa L.) production, causing irreversible yield losses and reduces grain quality. Illustration of thermotolerance mechanism is of great importance to accelerate rice breeding aimed at thermotolerance improvement. Here, we identified a new thermotolerant germplasm, SDWG005. Microscopical analysis found that stable anther structure of SDWG005 under stress may contribute to its thermotolerance. Dynamic transcriptomic analysis totally identified 3559 differentially expressed genes (DEGs) in SDWG005 anthers at anthesis under heat treatments, including 477, 869, 2335, and 2210 for 1, 2, 6, and 12 h, respectively; however, only 131 were regulated across all four-time-points. The DEGs were divided into nine clusters according to their expressions in these heat treatments. Further analysis indicated that some main gene categories involved in heat-response of SDWG005 anthers, such as transcription factors, nucleic acid and protein metabolisms related genes, etc. Comparison with previous studies indicates that a core gene-set may exist for thermotolerance mechanism. Expression and polymorphic analysis of agmatine-coumarin-acyltransferase gene OsACT in different accessions suggested that it may involve in SDWG005 thermotolerance. This study improves our understanding of thermotolerance mechanisms in rice anthers during anthesis, and also lays foundation for breeding thermotolerant varieties via molecular breeding. Full article
(This article belongs to the Special Issue Molecular Research in Rice: Agronomically Important Traits)
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16 pages, 2553 KiB  
Article
Targeted Mutagenesis of the Rice FW 2.2-Like Gene Family Using the CRISPR/Cas9 System Reveals OsFWL4 as a Regulator of Tiller Number and Plant Yield in Rice
by Qingsong Gao, Gang Li, Hui Sun, Ming Xu, Huanhuan Wang, Jianhui Ji, Di Wang, Caiyong Yuan and Xiangxiang Zhao
Int. J. Mol. Sci. 2020, 21(3), 809; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms21030809 - 26 Jan 2020
Cited by 27 | Viewed by 5248
Abstract
The FW2.2-like (FWL) genes encode cysteine-rich proteins with a placenta-specific 8 domain. They play roles in cell division and organ size control, response to rhizobium infection, and metal ion homeostasis in plants. Here, we target eight rice FWL genes using [...] Read more.
The FW2.2-like (FWL) genes encode cysteine-rich proteins with a placenta-specific 8 domain. They play roles in cell division and organ size control, response to rhizobium infection, and metal ion homeostasis in plants. Here, we target eight rice FWL genes using the CRISPR/Cas9 system delivered by Agrobacterium-mediated transformation. We successfully generate transgenic T0 lines for 15 of the 16 targets. The targeted mutations are detected in the T0 lines of all 15 targets and the average mutation rate is found to be 81.6%. Transfer DNA (T-DNA) truncation is a major reason for the failure of mutagenesis in T0 plants. T-DNA segregation analysis reveals that the T-DNA inserts in transgenic plants can be easily eliminated in the T1 generation. Of the 30 putative off-target sites examined, unintended mutations are detected in 13 sites. Phenotypic analysis reveals that tiller number and plant yield of OsFWL4 gene mutants are significantly greater than those of the wild type. Flag leaves of OsFWL4 gene mutants are wider than those of the wild type. The increase in leaf width of the mutants is caused by an increase in cell number. Additionally, grain length of OsFWL1 gene mutants is higher than that of the wild type. Our results suggest that transgene-free rice plants with targeted mutations can be produced in the T1 generation using the Agrobacterium-mediated CRISPR/Cas9 system and that the OsFWL4 gene is a negative regulator of tiller number and plant yield. Full article
(This article belongs to the Special Issue Molecular Research in Rice: Agronomically Important Traits)
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10 pages, 4537 KiB  
Article
Genome Sequence and QTL Analyses Using Backcross Recombinant Inbred Lines (BILs) and BILF1 Lines Uncover Multiple Heterosis-related Loci
by Yahui Yu, Mengmeng Zhu, Yue Cui, Yu Liu, Zhenyu Li, Nan Jiang, Zhengjin Xu, Quan Xu and Guomin Sui
Int. J. Mol. Sci. 2020, 21(3), 780; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms21030780 - 25 Jan 2020
Cited by 8 | Viewed by 2901
Abstract
Heterosis is an interesting topic for both breeders and biologists due to its practical importance and scientific significance. Cultivated rice (Oryza sativa L.) consists of two subspecies, indica and japonica, and hybrid rice is the predominant form of indica rice in [...] Read more.
Heterosis is an interesting topic for both breeders and biologists due to its practical importance and scientific significance. Cultivated rice (Oryza sativa L.) consists of two subspecies, indica and japonica, and hybrid rice is the predominant form of indica rice in China. However, the molecular mechanism underlying heterosis in japonica remains unclear. The present study determined the genome sequence and conducted quantitative trait locus (QTL) analysis using backcross recombinant inbred lines (BILs) and BILF1 lines to uncover the heterosis-related loci for rice yield increase under a japonica genetic background. The BIL population was derived from an admixture variety Habataki and japonica variety Sasanishiki cross to improve the genetic diversity but maintain the genetic background close to japonica. The results showed that heterosis in F1 mainly involved grain number per panicle. The BILF1s showed an increase in grain number per panicle but a decrease in plant height compared with the BILs. Genetic analysis then identified eight QTLs for heterosis in the BILF1s; four QTLs were detected exclusively in the BILF1 population only, presenting a mode of dominance or super-dominance in the heterozygotes. An additional four loci overlapped with QTLs detected in the BIL population, and we found that Grains Height Date 7 (Ghd7) was correlated in days to heading in both BILs and BILF1s. The admixture genetic background of Habataki was also determined by subspecies-specific single nucleotide polymorphisms (SNPs). This investigation highlights the importance of high-throughput sequencing to elucidate the molecular mechanism of heterosis and provides useful germplasms for the application of heterosis in japonica rice production. Full article
(This article belongs to the Special Issue Molecular Research in Rice: Agronomically Important Traits)
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13 pages, 2187 KiB  
Article
Genome-Wide Identification of QTLs for Grain Protein Content Based on Genotyping-by-Resequencing and Verification of qGPC1-1 in Rice
by Yi-Bo Wu, Guan Li, Yu-Jun Zhu, Yi-Chen Cheng, Jin-Yu Yang, Hui-Zhe Chen, Xian-Jun Song and Jie-Zheng Ying
Int. J. Mol. Sci. 2020, 21(2), 408; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms21020408 - 09 Jan 2020
Cited by 12 | Viewed by 3427
Abstract
To clarify the genetic mechanism underlying grain protein content (GPC) and to improve rice grain qualities, the mapping and cloning of quantitative trait loci (QTLs) controlling the natural variation of GPC are very important. Based on genotyping-by-resequencing, a total of 14 QTLs were [...] Read more.
To clarify the genetic mechanism underlying grain protein content (GPC) and to improve rice grain qualities, the mapping and cloning of quantitative trait loci (QTLs) controlling the natural variation of GPC are very important. Based on genotyping-by-resequencing, a total of 14 QTLs were detected with the Huanghuazhan/Jizi1560 (HHZ/JZ1560) recombinant inbred line (RIL) population in 2016 and 2017. Seven of the fourteen QTLs were repeatedly identified across two years. Using three residual heterozygote-derived populations, a stably inherited QTL named as qGPC1-1 was validated and delimited to a ~862 kb marker interval JD1006–JD1075 on the short arm of chromosome 1. Comparing the GPC values of the RIL population determined by near infrared reflectance spectroscopy (NIRS) and Kjeldahl nitrogen determination (KND) methods, high correlation coefficients (0.966 and 0.983) were observed in 2016 and 2017. Furthermore, 12 of the 14 QTLs were identically identified with the GPC measured by the two methods. These results indicated that instead of the traditional KND method, the rapid and easy-to-operate NIRS was suitable for analyzing a massive number of samples in mapping and cloning QTLs for GPC. Using the gel-based low-density map consisted of 208 simple sequence repeat (SSR) and insert/deletion (InDel) markers, the same number of QTLs (fourteen) were identified in the same HHZ/JZ1560 RIL population, and three QTLs were repeatedly detected across two years. More stably expressed QTLs were identified based on the genome resequencing, which might be attributed to the high-density map, increasing the detection power of minor QTLs. Our results are helpful in dissecting the genetic basis of GPC and improving rice grain qualities through molecular assisted selection. Full article
(This article belongs to the Special Issue Molecular Research in Rice: Agronomically Important Traits)
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25 pages, 11629 KiB  
Article
Transcriptomic and Co-Expression Network Profiling of Shoot Apical Meristem Reveal Contrasting Response to Nitrogen Rate between Indica and Japonica Rice Subspecies
by Xiaoxiang Zhang, Juan Zhou, Niansheng Huang, Lanjing Mo, Minjia Lv, Yingbo Gao, Chen Chen, Shuangyi Yin, Jing Ju, Guichun Dong, Yong Zhou, Zefeng Yang, Aihong Li, Yulong Wang, Jianye Huang and Youli Yao
Int. J. Mol. Sci. 2019, 20(23), 5922; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms20235922 - 25 Nov 2019
Cited by 15 | Viewed by 2934
Abstract
Reducing nitrogen (N) input is a key measure to achieve a sustainable rice production in China, especially in Jiangsu Province. Tiller is the basis for achieving panicle number that plays as a major factor in the yield determination. In actual production, excessive N [...] Read more.
Reducing nitrogen (N) input is a key measure to achieve a sustainable rice production in China, especially in Jiangsu Province. Tiller is the basis for achieving panicle number that plays as a major factor in the yield determination. In actual production, excessive N is often applied in order to produce enough tillers in the early stages. Understanding how N regulates tillering in rice plants is critical to generate an integrative management to reduce N use and reaching tiller number target. Aiming at this objective, we utilized RNA sequencing and weighted gene co-expression network analysis (WGCNA) to compare the transcriptomes surrounding the shoot apical meristem of indica (Yangdao6, YD6) and japonica (Nipponbare, NPB) rice subspecies. Our results showed that N rate influenced tiller number in a different pattern between the two varieties, with NPB being more sensitive to N enrichment, and YD6 being more tolerant to high N rate. Tiller number was positively related to N content in leaf, culm and root tissue, but negatively related to the soluble carbohydrate content, regardless of variety. Transcriptomic comparisons revealed that for YD6 when N rate enrichment from low (LN) to medium (MN), it caused 115 DEGs (LN vs. MN), from MN to high level (HN) triggered 162 DEGs (MN vs. HN), but direct comparison of low with high N rate showed a 511 DEGs (LN vs. HN). These numbers of DEG in NPB were 87 (LN vs. MN), 40 (MN vs. HN), and 148 (LN vs. HN). These differences indicate that continual N enrichment led to a bumpy change at the transcription level. For the reported sixty-five genes which affect tillering, thirty-six showed decent expression in SAM at tiller starting phase, among them only nineteen being significantly influenced by N level, and two genes showed significant interaction between N rate and variety. Gene ontology analysis revealed that the majority of the common DEGs are involved in general stress responses, stimulus responses, and hormonal signaling process. WGCNA network identified twenty-two co-expressing gene modules and ten candidate hubgenes for each module. Several genes associated with tillering and N rate fall on the related modules. These indicate that there are more genes participating in tillering regulation in response to N enrichment. Full article
(This article belongs to the Special Issue Molecular Research in Rice: Agronomically Important Traits)
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26 pages, 17847 KiB  
Article
GABA-Alleviated Oxidative Injury Induced by Salinity, Osmotic Stress and their Combination by Regulating Cellular and Molecular Signals in Rice
by Mohamed S. Sheteiwy, Hongbo Shao, Weicong Qi, Yousef Alhaj Hamoud, Hiba Shaghaleh, Nasr Ullah Khan, Ruiping Yang and Boping Tang
Int. J. Mol. Sci. 2019, 20(22), 5709; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms20225709 - 14 Nov 2019
Cited by 86 | Viewed by 4528
Abstract
This study was conducted in order to determine the effect of priming with γ-aminobutyric acid (GABA) at 0.5 mM on rice (Oryza sativa L.) seed germination under osmotic stress (OS) induced by polyethylene glycol (30 g/L PEG 6000); and salinity stress (S, [...] Read more.
This study was conducted in order to determine the effect of priming with γ-aminobutyric acid (GABA) at 0.5 mM on rice (Oryza sativa L.) seed germination under osmotic stress (OS) induced by polyethylene glycol (30 g/L PEG 6000); and salinity stress (S, 150 mM NaCl) and their combination (OS+S). Priming with GABA significantly alleviated the detrimental effects of OS, S and OS+S on seed germination and seedling growth. The photosynthetic system and water relation parameters were improved by GABA under stress. Priming treatment significantly increased the GABA content, sugars, protein, starch and glutathione reductase. GABA priming significantly reduced Na+ concentrations, proline, free radical and malonaldehyde and also significantly increased K+ concentration under the stress condition. Additionally, the activities of antioxidant enzymes, phenolic metabolism-related enzymes, detoxification-related enzymes and their transcription levels were improved by GABA priming under stress. In the GABA primed-plants, salinity stress alone resulted in an obvious increase in the expression level of Calcineurin B-like Protein-interacting protein Kinases (CIPKs) genes such as OsCIPK01, OsCIPK03, OsCIPK08 and OsCIPK15, and osmotic stress alone resulted in obvious increase in the expression of OsCIPK02, OsCIPK07 and OsCIPK09; and OS+S resulted in a significant up-regulation of OsCIPK12 and OsCIPK17. The results showed that salinity, osmotic stresses and their combination induced changes in cell ultra-morphology and cell cycle progression resulting in prolonged cell cycle development duration and inhibitory effects on rice seedlings growth. Hence, our findings suggested that the high tolerance to OS+S is closely associated with the capability of GABA priming to control the reactive oxygen species (ROS) level by inducing antioxidant enzymes, secondary metabolism and their transcription level. This knowledge provides new evidence for better understanding molecular mechanisms of GABA-regulating salinity and osmotic-combined stress tolerance during rice seed germination and development. Full article
(This article belongs to the Special Issue Molecular Research in Rice: Agronomically Important Traits)
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14 pages, 2466 KiB  
Article
Broad-Spectrum Disease Resistance Conferred by the Overexpression of Rice RLCK BSR1 Results from an Enhanced Immune Response to Multiple MAMPs
by Yasukazu Kanda, Hitoshi Nakagawa, Yoko Nishizawa, Takashi Kamakura and Masaki Mori
Int. J. Mol. Sci. 2019, 20(22), 5523; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms20225523 - 06 Nov 2019
Cited by 10 | Viewed by 3519
Abstract
Plants activate their immune system through intracellular signaling pathways after perceiving microbe-associated molecular patterns (MAMPs). Receptor-like cytoplasmic kinases mediate the intracellular signaling downstream of pattern-recognition receptors. BROAD-SPECTRUM RESISTANCE 1 (BSR1), a rice (Oryza sativa) receptor-like cytoplasmic kinase subfamily-VII protein, contributes to [...] Read more.
Plants activate their immune system through intracellular signaling pathways after perceiving microbe-associated molecular patterns (MAMPs). Receptor-like cytoplasmic kinases mediate the intracellular signaling downstream of pattern-recognition receptors. BROAD-SPECTRUM RESISTANCE 1 (BSR1), a rice (Oryza sativa) receptor-like cytoplasmic kinase subfamily-VII protein, contributes to chitin-triggered immune responses. It is valuable for agriculture because its overexpression confers strong disease resistance to fungal and bacterial pathogens. However, it remains unclear how overexpressed BSR1 reinforces plant immunity. Here we analyzed immune responses using rice suspension-cultured cells and sliced leaf blades overexpressing BSR1. BSR1 overexpression enhances MAMP-triggered production of hydrogen peroxide (H2O2) and transcriptional activation of the defense-related gene in cultured cells and leaf strips. Furthermore, the co-cultivation of leaves with conidia of the blast fungus revealed that BSR1 overexpression allowed host plants to produce detectable oxidative bursts against compatible pathogens. BSR1 was also involved in the immune responses triggered by peptidoglycan and lipopolysaccharide. Thus, we concluded that the hyperactivation of MAMP-triggered immune responses confers BSR1-mediated robust resistance to broad-spectrum pathogens. Full article
(This article belongs to the Special Issue Molecular Research in Rice: Agronomically Important Traits)
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26 pages, 3659 KiB  
Article
InDel Marker Based Estimation of Multi-Gene Allele Contribution and Genetic Variations for Grain Size and Weight in Rice (Oryza sativa L.)
by Sadia Gull, Zulqarnain Haider, Houwen Gu, Rana Ahsan Raza Khan, Jun Miao, Tan Wenchen, Saleem Uddin, Irshad Ahmad and Guohua Liang
Int. J. Mol. Sci. 2019, 20(19), 4824; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms20194824 - 28 Sep 2019
Cited by 11 | Viewed by 5724
Abstract
The market success of any rice cultivar is exceedingly dependent on its grain appearance, as well as its grain yield, which define its demand by consumers as well as growers. The present study was undertaken to explore the contribution of nine major genes, [...] Read more.
The market success of any rice cultivar is exceedingly dependent on its grain appearance, as well as its grain yield, which define its demand by consumers as well as growers. The present study was undertaken to explore the contribution of nine major genes, qPE9~1, GW2, SLG7, GW5, GS3, GS7, GW8, GS5, and GS2, in regulating four size and weight related traits, i.e., grain length (GL), grain width (GW), grain thickness (GT), and thousand grain weight (TGW) in 204 diverse rice germplasms using Insertion/Deletion (InDel) markers. The studied germplasm displayed wide-ranging variability in the four studied traits. Except for three genes, all six genes showed considerable association with these traits with varying strengths. Whole germplasm of 204 genotypes could be categorized into three major clusters with different grain sizes and weights that could be utilized in rice breeding programs where grain appearance and weight are under consideration. The study revealed that TGW was 24.9% influenced by GL, 37.4% influenced by GW, and 49.1% influenced by GT. Hence, assuming the trend of trait selection, i.e., GT > GW > GL, for improving TGW in the rice yield enhancement programs. The InDel markers successfully identified a total of 38 alleles, out of which 27 alleles were major and were found in more than 20 genotypes. GL was associated with four genes (GS3, GS7, GW8, and GS2). GT was also found to be regulated by four different genes (GS3, GS7, GW8, and GS2) out of the nine studied genes. GW was found to be under the control of three studied genes (GW5, GW8, and GS2), whereas TGW was found to be under the influence of four genes (SLG7, GW5, GW8, and GS5) in the germplasm under study. The Unweighted Pair Group Method with Arithmetic means (UPGMA) tree based on the studied InDel marker loci segregated the whole germplasm into three distinct clusters with dissimilar grain sizes and weights. A two-dimensional scatter plot constructed using Principal Coordinate Analysis (PCoA) based on InDel markers further separated the 204 rice germplasms into four sub-populations with prominent demarcations of extra-long, long, medium, and short grain type germplasms that can be utilized in breeding programs accordingly. The present study could help rice breeders to select a suitable InDel marker and in formulation of breeding strategies for improving grain appearance, as well as weight, to develop rice varieties to compete international market demands with higher yield returns. This study also confirms the efficient application of InDel markers in studying diverse types of rice germplasm, allelic frequencies, multiple-gene allele contributions, marker-trait associations, and genetic variations that can be explored further. Full article
(This article belongs to the Special Issue Molecular Research in Rice: Agronomically Important Traits)
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13 pages, 2888 KiB  
Article
OsCAF1, a CRM Domain Containing Protein, Influences Chloroplast Development
by Qiang Zhang, Lan Shen, Zhongwei Wang, Guanglian Hu, Deyong Ren, Jiang Hu, Li Zhu, Zhenyu Gao, Guangheng Zhang, Longbiao Guo, Dali Zeng and Qian Qian
Int. J. Mol. Sci. 2019, 20(18), 4386; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms20184386 - 06 Sep 2019
Cited by 15 | Viewed by 3831
Abstract
The chloroplast RNA splicing and ribosome maturation (CRM) domain proteins are involved in the splicing of chloroplast gene introns. Numerous CRM domain proteins have been reported to play key roles in chloroplast development in several plant species. However, the functions of CRM domain [...] Read more.
The chloroplast RNA splicing and ribosome maturation (CRM) domain proteins are involved in the splicing of chloroplast gene introns. Numerous CRM domain proteins have been reported to play key roles in chloroplast development in several plant species. However, the functions of CRM domain proteins in chloroplast development in rice remain poorly understood. In the study, we generated oscaf1 albino mutants, which eventually died at the seedling stage, through the editing of OsCAF1 with two CRM domains using CRISPR/Cas9 technology. The mesophyll cells in oscaf1 mutant had decreased chloroplast numbers and damaged chloroplast structures. OsCAF1 was located in the chloroplast, and transcripts revealed high levels in green tissues. In addition, the OsCAF1 promoted the splicing of group IIA and group IIB introns, unlike orthologous proteins of AtCAF1 and ZmCAF1, which only affected the splicing of subgroup IIB introns. We also observed that the C-terminal of OsCAF1 interacts with OsCRS2, and OsCAF1–OsCRS2 complex may participate in the splicing of group IIA and group IIB introns in rice chloroplasts. OsCAF1 regulates chloroplast development by influencing the splicing of group II introns. Full article
(This article belongs to the Special Issue Molecular Research in Rice: Agronomically Important Traits)
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