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28 November 2022, Volume 29 Issue 6 Previous Issue    Next Issue
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Letter

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Transcriptome Analysis Provides Novel Insights into Salt Stress Response in Two Egyptian Rice Varieties with Different Tolerance Levels Shehab Mohamed, Iovene Marina, Ciancio Aurelio, Colagiero Mariantonietta, Finetti-Sialer Mariella 2022, 29(6): 499-502.  DOI: 10.1016/j.rsci.2022.09.001 Abstract ( )   HTML ( )   PDF (4759KB) ( )

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QTL Mapping for Plant Height Using Introgression Lines Derived from Zhonghui 8015 and Wild Rice (Oryza rufipogon) Yang Qinqin, Zhang Yingxin, Xue Pao, Wen Xiaoxia, Liu Ling, Xu Peng, Zhan Xiaodeng, Cao Liyong, Cheng Shihua, Wu Weixun 2022, 29(6): 503-506.  DOI: 10.1016/j.rsci.2022.06.001 Abstract ( )   HTML ( )   PDF (10767KB) ( )

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Genetic Dissection of Quantitative Trait Loci for Panicle Traits and Heat Tolerance by High-Density Bin Map in Rice Liu Hongyan, Ma Xiaosong, Li Enxi, Zeng Xianjun, Luo Lijun 2022, 29(6): 507-511.  DOI: 10.1016/j.rsci.2022.07.008 Abstract ( )   HTML ( )   PDF (2028KB) ( )

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Improvement of Rice Production under Drought Conditions in West Africa: Application of QTLs in Breeding for Drought Resistance Kossi Lorimpo Adjah, Maxwell Darko Asante, Aboubacar Toure, Mawuli Aziadekey, Francis Osei Amoako-Andoh, Michael Frei, Yacouba Diallo, Komi Agboka 2022, 29(6): 512-521.  DOI: 10.1016/j.rsci.2022.06.002 Abstract ( )   HTML ( )   PDF (9321KB) ( )   Rice plays a paramount role in food and nutrition security in many West African countries. Despite the doubling of production during the last decade, rice consumption has grown faster, creating a deficit between the demand and supply. Although the West African sub-region remains the main rice-producing centre on the continent, production is severely hampered by biotic and abiotic stresses. Drought is one of the factors that most severely reduce grain yields of rice. Systems of production need to be established in order to mitigate yield loss as a result of drought. This review discusses the effects of drought on rice production in West Africa and its mitigation with an emphasis on the improvement of tolerance to drought stress. Yield stability can be achieved by developing drought-tolerant varieties through several processes encompassing profiling of known QTLs and identification of new ones, marker-assisted selection, genomic selection, and extensive multi-locational yield trials. We suggest a comprehensive strategy for breeding drought-tolerant rice varieties in West Africa.

Research Paper

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Characterization of a Novel Weak Allele of RGA1/D1 and Its Potential Application in Rice Breeding Liu Yantong, Li Ting, Jiang Zhishu, Zeng Chuihai, He Rong, Qiu Jiao, Lin Xiaoli, Peng Limei, Song Yongping, Zhou Dahu, Cai Yicong, Zhu Changlan, Fu Junru, He Haohua, Xu Jie 2022, 29(6): 522-534.  DOI: 10.1016/j.rsci.2022.03.001 Abstract ( )   HTML ( )   PDF (5209KB) ( )   Semi-dwarfing improves the lodging resistance and yield of rice, and the vast majority of modern rice varieties harbor the sd1 allele to decrease plant height, resulting in reduced genetic diversity and negative agronomic traits. Thus, exploring alternative sources of dwarfism is imperative for rice breeding. Here, we identified a novel RGA1 allele, d1-w, from a local indica variety Xiaolixiang (XLX) using a map-based cloning approach. Compared with other rice varieties, RGA1 in XLX contained a unique single nucleotide polymorphism that resulted in an additional transcript and reduced functional RGA1 transcript level. The RGA1 from Nipponbare was introduced into XLX to estimate the value of d1-w in rice breeding. Compared with transgenic XLX plants (XLXD1), XLX exhibited reduced plant height, increased stem strength, lower reactive oxygen species accumulation, delayed senescence, stronger photosynthesis, higher grain yield and quality (including external, milling and nutritional qualities), and enhanced resistance to drought and Rhizoctonia solani. Therefore, we proposed that the d1-w allele has potential as an excellent dwarfism resource for rice breeding.

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CRISPR/Cas9-Targeted Knockout of Rice Susceptibility Genes OsDjA2 and OsERF104 Reveals Alternative Sources of Resistance to Pyricularia oryzae Fabiano T. P. K. Távora, Anne Cécile Meunier, Aurore Vernet, Murielle Portefaix, Joëlle Milazzo, Henri Adreit, Didier Tharreau, Octávio L. Franco, Angela Mehta 2022, 29(6): 535-544.  DOI: 10.1016/j.rsci.2022.04.001 Abstract ( )   HTML ( )   PDF (4273KB) ( )   Rice genes OsDjA2 and OsERF104, encoding a chaperone protein and an APETELA2/ ethylene-responsive factor, respectively, are strongly induced in a compatible interaction with blast fungus, and also have function in plant susceptibility validated through gene silencing. Here, we reported the CRISPR/Cas9 knockout of OsDjA2 and OsERF104 genes resulting in considerable improvement of blast resistance. A total of 15 OsDjA2 (62.5%) and 17 OsERF104 (70.8%) T0 transformed lines were identified from 24 regenerated plants for each target and used in downstream experiments. Phenotyping of homozygous T1 mutant lines revealed not only a significant decrease in the number of blast lesions but also a reduction in the percentage of diseased leaf area, compared with the infected control plants. Our results supported CRISPR/Cas9-mediated target mutation in rice susceptibility genes as a potential and alternative breeding strategy for building resistance to blast disease.

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Identification of Potential Zinc Deficiency Responsive Genes and Regulatory Pathways in Rice by Weighted Gene Co-expression Network Analysis Blaise Pascal Muvunyi, Lu Xiang, Zhan Junhui, He Sang, Ye Guoyou 2022, 29(6): 545-558.  DOI: 10.1016/j.rsci.2022.04.002 Abstract ( )   HTML ( )   PDF (3116KB) ( )   Zinc (Zn) malnutrition is a major public health issue. Genetic biofortification of Zn in rice grain can alleviate global Zn malnutrition. Therefore, elucidating the genetic mechanisms regulating Zn deprivation response in rice is essential to identify elite genes useful for breeding high grain Zn rice varieties. Here, a meta-analysis of previous RNA-Seq studies involving Zn deficient conditions was conducted using the weighted gene co-expression network analysis (WGCNA) and other in silico prediction tools to identify modules (denoting cluster of genes with related expression pattern) of co-expressed genes, modular genes which are conserved differentially expressed genes (DEGs) across independent RNA-Seq studies, and the molecular pathways of the conserved modular DEGs. WGCNA identified 16 modules of co-expressed genes. Twenty-eight and five modular DEGs were conserved in leaf and crown, and root tissues across two independent RNA-Seq studies. Functional enrichment analysis showed that 24 of the 28 conserved modular DEGs from leaf and crown tissues significantly up-regulated 2 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways and 15 Gene Ontology (GO) terms, including the substrate- specific transmembrane transporter and the small molecule metabolic process. Further, the well-studied transcription factors (OsWOX11 and OsbHLH120), protein kinase (OsCDPK20 and OsMPK17), and miRNAs (OSA-MIR397A and OSA-MIR397B) were predicted to target some of the identified conserved modular DEGs. Out of the 24 conserved and up-regulated modular DEGs, 19 were yet to be experimentally validated as Zn deficiency responsive genes. Findings from this study provide a comprehensive insight on the molecular mechanisms of Zn deficiency response and may facilitate gene and pathway prioritization for improving Zn use efficiency and Zn biofortification in rice.

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Screening of Brown Planthopper Resistant miRNAs in Rice and Their Roles in Regulation of Brown Planthopper Fecundity Lü Jun, Liu Jinhui, Chen Lin, Sun Jiawei, Su Qin, Li Shihui, Yang Jianhua, Zhang Wenqing 2022, 29(6): 559-568.  DOI: 10.1016/j.rsci.2022.05.003 Abstract ( )   HTML ( )   PDF (8606KB) ( )   MicroRNAs (miRNAs) can participate in plant-insect interactions, which regulate plant defense networks. In this study, we analyzed the miRNA expression profiles of six rice varieties before and after brown planthopper (BPH)-feeding. We identified 45 differentially expressed miRNAs between BPH- susceptible and BPH-resistant rice varieties and 144 miRNAs that responded to BPH-feeding. Thus, miRNAs may be involved in multiple pathways regulating rice defense response against BPH. In addition, we found that the genetic history of rice varieties determined the regulation mode of the miRNA and affected the amounts, types, changing trends and response periods of miRNAs in response to BPH- feeding. To conclude, we scanned seven potential cross-kingdom miRNAs, of which miR5795 may target the vitellogenin gene in BPH, causing a 16.07% reduction in BPH oviposition. The results provide new miRNA information of rice-BPH interactions and BPH-resistant rice variety breeding.

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Quantitative Trait Locus Mapping of High Photosynthetic Efficiency and Biomass in Oryza longistaminata Si Fengfeng, Fan Fengfeng, Wei Xiao, He Shihao, Li Xianlong, Peng Xiaojue, Li Shaoqing 2022, 29(6): 569-576.  DOI: 10.1016/j.rsci.2022.01.011 Abstract ( )   HTML ( )   PDF (3339KB) ( )   Photosynthetic efficiency, a key trait that determines yield potential in rice, is quantitatively regulated by multiple genes. Utilization of valuable genetic resources hidden in wild rice is an effective way to improve rice photosynthesis and yield potential. In this study, 152 backcross inbred lines derived from wild rice Oryza longistaminata were explored for QTL mapping of photosynthetic rate (Pn) and biomass (BM) in natural fields. Five novel QTLs for Pn and seven QTLs for BM or daily biomass (DBM) derived from O. longistaminata were identified. One of these QTLs, qPn8.1, could significantly improve Pn and was located in a 68-kb region containing only 11 candidate genes. Meanwhile, qBM1.1 and qDBM1.1 for BM and DBM on chromosome 1 were overlapped with qPn1.1 for Pn from 9311, and could affect both Pn and BM in natural fields. These QTLs identified in O. longistaminata may provide a novel alternative to explore new genes and resources for yield potentiality, highlighting the important role of wild rice in rice breeding programs.

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Differences of Physicochemical Properties Between Chalky and Translucent Parts of Rice Grains Wang Cuili, Guo Wen, Hu Peisong, Wei Xiangjin, Tang Shaoqing, Jiao Guiai 2022, 29(6): 577-588.  DOI: 10.1016/j.rsci.2022.03.002 Abstract ( )   HTML ( )   PDF (3970KB) ( )   Rice grain chalkiness is an important characteristic, but the difference between chalky and translucent parts in grains is still unclear. Here, we investigated the differences of flour made from the chalky or translucent part of rice grains in three indica and three japonica rice varieties. The chalky flour had significantly lower amylose and protein contents and looser starch granule morphology, and starches in the chalky flour had higher relative crystallinity, higher short chain content but lower long chain content than those in the translucent flour. The water states, determined with nuclear magnetic resonance, differed between the chalky and translucent flour after soaking, cooking and retrograding, and the chalky flour had more bound and free water but less constructural water than the translucent flour. Mostly, the chalky flour had lower viscosity and shorter gel consistency, but higher onset temperature and gelatinization enthalpy than the translucent flour. The results indicated that starch granule morphology would be more indicative than other attributions on pasting and gelatinization properties of chalky and translucent parts of rice grains.