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Ashraf H, Ghouri F, Baloch FS, Nadeem MA, Fu X, Shahid MQ. Hybrid Rice Production: A Worldwide Review of Floral Traits and Breeding Technology, with Special Emphasis on China. PLANTS (BASEL, SWITZERLAND) 2024; 13:578. [PMID: 38475425 DOI: 10.3390/plants13050578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Revised: 01/26/2024] [Accepted: 02/08/2024] [Indexed: 03/14/2024]
Abstract
Rice is an important diet source for the majority of the world's population, and meeting the growing need for rice requires significant improvements at the production level. Hybrid rice production has been a significant breakthrough in this regard, and the floral traits play a major role in the development of hybrid rice. In grass species, rice has structural units called florets and spikelets and contains different floret organs such as lemma, palea, style length, anther, and stigma exsertion. These floral organs are crucial in enhancing rice production and uplifting rice cultivation at a broader level. Recent advances in breeding techniques also provide knowledge about different floral organs and how they can be improved by using biotechnological techniques for better production of rice. The rice flower holds immense significance and is the primary focal point for researchers working on rice molecular biology. Furthermore, the unique genetics of rice play a significant role in maintaining its floral structure. However, to improve rice varieties further, we need to identify the genomic regions through mapping of QTLs (quantitative trait loci) or by using GWAS (genome-wide association studies) and their validation should be performed by developing user-friendly molecular markers, such as Kompetitive allele-specific PCR (KASP). This review outlines the role of different floral traits and the benefits of using modern biotechnological approaches to improve hybrid rice production. It focuses on how floral traits are interrelated and their possible contribution to hybrid rice production to satisfy future rice demand. We discuss the significance of different floral traits, techniques, and breeding approaches in hybrid rice production. We provide a historical perspective of hybrid rice production and its current status and outline the challenges and opportunities in this field.
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Affiliation(s)
- Humera Ashraf
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Fozia Ghouri
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Faheem Shehzad Baloch
- Department of Biotechnology, Faculty of Science, Mersin University, Mersin 33100, Türkiye
| | - Muhammad Azhar Nadeem
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas 58140, Türkiye
| | - Xuelin Fu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Muhammad Qasim Shahid
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou 510642, China
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Rahim MS, Sharma V, Pragati Yadav, Parveen A, Kumar A, Roy J, Kumar V. Rethinking underutilized cereal crops: pan-omics integration and green system biology. PLANTA 2023; 258:91. [PMID: 37777666 DOI: 10.1007/s00425-023-04242-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 09/12/2023] [Indexed: 10/02/2023]
Abstract
MAIN CONCLUSION Due to harsh lifestyle changes, in the present era, nutritional security is needed along with food security so it is necessary to include underutilized cereal crops (UCCs) in our daily diet to counteract the rising danger of human metabolic illness. We can attain both the goal of zero hunger and nutritional security by developing improved UCCs using advanced pan-omics (genomics, transcriptomics, proteomics, metabolomics, nutrigenomics, phenomics and ionomics) practices. Plant sciences research progressed profoundly since the last few decades with the introduction of advanced technologies and approaches, addressing issues of food demand of the growing population, nutritional security challenges and climate change. However, throughout the expansion and popularization of commonly consumed major cereal crops such as wheat and rice, other cereal crops such as millet, rye, sorghum, and others were impeded, despite their potential medicinal and nutraceutical qualities. Undoubtedly neglected underutilized cereal crops (UCCs) also have the capability to withstand diverse climate change. To relieve the burden of major crops, it is necessary to introduce the new crops in our diet in the way of UCCs. Introgression of agronomically and nutritionally important traits by pan-omics approaches in UCCs could be a defining moment for the population's well-being on the globe. This review discusses the importance of underutilized cereal crops, as well as the application of contemporary omics techniques and advanced bioinformatics tools that could open up new avenues for future study and be valuable assets in the development and usage of UCCs in the perspective of green system biology. The increased and improved use of UCCs is dependent on number of factors that necessitate a concerted research effort in agricultural sciences. The emergence of functional genomics with molecular genetics might gear toward the reawakening of interest in underutilized cereals crops. The need of this era is to focus on potential UCCs in advanced agriculture and breeding programmes. Hence, targeting the UCCs, might provide a bright future for better health and scientific rationale for its use.
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Affiliation(s)
- Mohammed Saba Rahim
- Department of Botany, School of Basic Sciences, Central University of Punjab, Punjab, 151401, India
- National Agri-Food Biotechnology Institute (NABI), Sector-81, SAS Nagar, Mohali, Punjab, 140 306, India
| | - Vinita Sharma
- National Agri-Food Biotechnology Institute (NABI), Sector-81, SAS Nagar, Mohali, Punjab, 140 306, India
| | - Pragati Yadav
- National Agri-Food Biotechnology Institute (NABI), Sector-81, SAS Nagar, Mohali, Punjab, 140 306, India
| | - Afsana Parveen
- National Agri-Food Biotechnology Institute (NABI), Sector-81, SAS Nagar, Mohali, Punjab, 140 306, India
| | - Adarsh Kumar
- Department of Botany, School of Basic Sciences, Central University of Punjab, Punjab, 151401, India
| | - Joy Roy
- National Agri-Food Biotechnology Institute (NABI), Sector-81, SAS Nagar, Mohali, Punjab, 140 306, India.
| | - Vinay Kumar
- Department of Botany, School of Basic Sciences, Central University of Punjab, Punjab, 151401, India.
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Yan H, Guo H, Li T, Zhang H, Xu W, Xie J, Zhu X, Yu Y, Chen J, Zhao S, Xu J, Hu M, Jiang Y, Zhang H, Ma M, He Z. High-precision early warning system for rice cadmium accumulation risk assessment. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 859:160135. [PMID: 36375547 DOI: 10.1016/j.scitotenv.2022.160135] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 10/01/2022] [Accepted: 11/07/2022] [Indexed: 06/16/2023]
Abstract
Rapid global industrialization has resulted in widespread cadmium contamination in agricultural soils and products. A considerable proportion of rice consumers are exposed to Cd levels above the provisional safe intake limit, raising widespread environmental concerns on risk management. Therefore, a generalized approach is urgently needed to enable correct evaluation and early warning of cadmium contaminants in rice products. Combining big data and computer science together, this study developed a system named "SMART Cd Early Warning", which integrated 4 modules including genotype-to-phenotype (G2P) modelling, high-throughput sequencing, G2P prediction and rice Cd contamination risk assessment, for rice cadmium accumulation early warning. This system can rapidly assess the risk of rice cadmium accumulation by genotyping leaves at seeding stage. The parameters including statistical methods, population size, training population-testing population ratio, SNP density were assessed to ensure G2P model exhibited superior performance in terms of prediction precision (up to 0.76 ± 0.003) and computing efficiency (within 2 h). In field trials of cadmium-contaminated farmlands in Wenling and Fuyang city, Zhejiang Province, "SMART Cd Early Warning" exhibited superior capability for identification risk rice varieties, suggesting a potential of "SMART Cd Early-Warning system" in OsGCd risk assessment and early warning in the age of smart.
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Affiliation(s)
- Huili Yan
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Hanyao Guo
- Hebei Normal University, Shijiazhuang 050024, China
| | - Ting Li
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hezifan Zhang
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wenxiu Xu
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Jianyin Xie
- Key Lab of Crop Heterosis and Utilization of Ministry of Education, Beijing Key Lab of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Xiaoyang Zhu
- Key Lab of Crop Heterosis and Utilization of Ministry of Education, Beijing Key Lab of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Yijun Yu
- Zhejiang Station for Management of Arable Land Quality and Fertilizer, Hangzhou 310020, China
| | - Jian Chen
- Plant Protection, Fertilizer and Rural Energy Agency of Wenling, Wenling 317500, China
| | - Shouqing Zhao
- Plant Protection, Fertilizer and Rural Energy Agency of Wenling, Wenling 317500, China
| | - Jun Xu
- Fuyang Agricultural Technology Extension Center, Fuyang 311400, China
| | - Minjun Hu
- Fuyang Agricultural Technology Extension Center, Fuyang 311400, China
| | - Yugen Jiang
- Fuyang Agricultural Technology Extension Center, Fuyang 311400, China
| | - Hongliang Zhang
- Key Lab of Crop Heterosis and Utilization of Ministry of Education, Beijing Key Lab of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China; Sanya Institute of China Agricultural University, Sanya 572024, China
| | - Mi Ma
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Zhenyan He
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.
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Gao B, Lu W, Jin M, Chen Y. Non-targeted metabolomics of moldy wheat by ultra-performance liquid chromatography - quadrupole time-of-flight mass spectrometry. Front Microbiol 2023; 14:1136516. [PMID: 37089557 PMCID: PMC10119584 DOI: 10.3389/fmicb.2023.1136516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 02/28/2023] [Indexed: 04/25/2023] Open
Abstract
Introduction As one of the staple foods for the world's major populations, the safety of wheat is critical in ensuring people's wellbeing. However, mildew is one of the prevalent safety issues that threatens the quality of wheat during growth, production, and storage. Due to the complex nature of the microbial metabolites, the rapid identification of moldy wheat is challenging. Methods In this research, identification of moldy wheat samples was studied using ultra-performance liquid chromatography - quadrupole time-of-flight mass spectrometry (UPLC-QTOF-MS) coupled with chemometrics. The non-targeted PCA model for identifying moldy wheat from normal wheat was established by using previously established compounds database of authentic wheat samples. The partial least squares-discriminant analysis (PLS-DA) was performed. Results and discussion By optimizing the model parameters, correct discrimination of the moldy wheat as low as 5% (w/w) adulteration level could be achieved. Differential biomarkers unique to moldy wheat were also extracted to identify between the moldy and authentic wheat samples. The results demonstrated that the chemical information of wheat combined with the existing PCA model could efficiently discriminate between the constructed moldy wheat samples. The study offered an effective method toward screening wheat safety.
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Rahim MS, Kumar V, Roy J. Genetic dissection of quantitative traits loci identifies new genes for gelatinization parameters of starch and amylose-lipid complex (Resistant starch 5) in bread wheat. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2022; 325:111452. [PMID: 36087884 DOI: 10.1016/j.plantsci.2022.111452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 08/08/2022] [Accepted: 09/01/2022] [Indexed: 06/15/2023]
Abstract
Starch is a major component of cereal grains such as wheat. Physicochemical and functional properties of starch affect end-use food quality and nutrients. To improve cultivars that preserve superior starch quality, the genetic foundation of the wheat starch and amylose-lipid complex (ALc, Resistant starch type 5) gelatinization are needed. This genome-wide association (GWA) mapping used 192 wheat genotypes (previously reported) to generate SNPs using an enhanced version of sequencing termed ddRAD on the Illumina Hi-seq X platform and 3696 high-quality influential SNPs were filtered out. The heterozygosity and Fst ranges in five subpopulations were 0.31-0.40 and 0.18-0.30 respectively. Nucleotide diversity and PIC ranged from 0.21 (6A) to 0.32 (2A) and 0.29 (6A) to 0.39 (4D) respectively. The Shannon waiver index was 1.7 and the whole-genome LD decay was 22 Mb at r2 = 0.38. Following FDR, 23 and 8 SNPs showed association with starch properties in the year 2017 and 2018, respectively while 93 and 20 SNPs were associated with ALc gelatinization in the year 2017 and 2018 respectively. The identified potential new genes (GSK3-alpha, RING-type domain-containing protein, Tetratricopeptide repeat, Hexosyltransferase, GLP, SNF1, and WRKY transcription factor) within LD range (∼16 Kb to ∼15 Mb), BLUP value, and cis and trans-position of SNPs network provide valuable information for the future wheat breeding strategy for the improvement of the starch quality trait.
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Affiliation(s)
- Mohammed Saba Rahim
- National Agri-Food Biotechnology Institute (NABI), Sector-81, SAS Nagar, Mohali-140 306, Punjab, India; Department of Botany, School of Basic Sciences, Central University of Punjab, Bathinda.
| | - Vinay Kumar
- Department of Botany, School of Basic Sciences, Central University of Punjab, Bathinda.
| | - Joy Roy
- National Agri-Food Biotechnology Institute (NABI), Sector-81, SAS Nagar, Mohali-140 306, Punjab, India.
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Rana N, Kumawat S, Kumar V, Bansal R, Mandlik R, Dhiman P, Patil GB, Deshmukh R, Sharma TR, Sonah H. Deciphering Haplotypic Variation and Gene Expression Dynamics Associated with Nutritional and Cooking Quality in Rice. Cells 2022; 11:cells11071144. [PMID: 35406707 PMCID: PMC8998046 DOI: 10.3390/cells11071144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 03/21/2022] [Accepted: 03/24/2022] [Indexed: 02/01/2023] Open
Abstract
Nutritional quality improvement of rice is the key to ensure global food security. Consequently, enormous efforts have been made to develop genomics and transcriptomics resources for rice. The available omics resources along with the molecular understanding of trait development can be utilized for efficient exploration of genetic resources for breeding programs. In the present study, 80 genes known to regulate the nutritional and cooking quality of rice were extensively studied to understand the haplotypic variability and gene expression dynamics. The haplotypic variability of selected genes were defined using whole-genome re-sequencing data of ~4700 diverse genotypes. The analytical workflow identified 133 deleterious single-nucleotide polymorphisms, which are predicted to affect the gene function. Furthermore, 788 haplotype groups were defined for 80 genes, and the distribution and evolution of these haplotype groups in rice were described. The nucleotide diversity for the selected genes was significantly reduced in cultivated rice as compared with that in wild rice. The utility of the approach was successfully demonstrated by revealing the haplotypic association of chalk5 gene with the varying degree of grain chalkiness. The gene expression atlas was developed for these genes by analyzing RNA-Seq transcriptome profiling data from 102 independent sequence libraries. Subsequently, weighted gene co-expression meta-analyses of 11,726 publicly available RNAseq libraries identified 19 genes as the hub of interactions. The comprehensive analyses of genetic polymorphisms, allelic distribution, and gene expression profiling of key quality traits will help in exploring the most desired haplotype for grain quality improvement. Similarly, the information provided here will be helpful to understand the molecular mechanism involved in the development of nutritional and cooking quality traits in rice.
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Affiliation(s)
- Nitika Rana
- Department of Agriculture Biotechnology, National Agri-Food Biotechnology Institute (NABI), Mohali 140306, India; (N.R.); (S.K.); (V.K.); (R.B.); (R.M.); (P.D.); (R.D.); (T.R.S.)
- Department of Biotechnology, Panjab University, Chandigarh 160014, India
| | - Surbhi Kumawat
- Department of Agriculture Biotechnology, National Agri-Food Biotechnology Institute (NABI), Mohali 140306, India; (N.R.); (S.K.); (V.K.); (R.B.); (R.M.); (P.D.); (R.D.); (T.R.S.)
- Department of Biotechnology, Panjab University, Chandigarh 160014, India
| | - Virender Kumar
- Department of Agriculture Biotechnology, National Agri-Food Biotechnology Institute (NABI), Mohali 140306, India; (N.R.); (S.K.); (V.K.); (R.B.); (R.M.); (P.D.); (R.D.); (T.R.S.)
| | - Ruchi Bansal
- Department of Agriculture Biotechnology, National Agri-Food Biotechnology Institute (NABI), Mohali 140306, India; (N.R.); (S.K.); (V.K.); (R.B.); (R.M.); (P.D.); (R.D.); (T.R.S.)
- Department of Biotechnology, Panjab University, Chandigarh 160014, India
| | - Rushil Mandlik
- Department of Agriculture Biotechnology, National Agri-Food Biotechnology Institute (NABI), Mohali 140306, India; (N.R.); (S.K.); (V.K.); (R.B.); (R.M.); (P.D.); (R.D.); (T.R.S.)
- Department of Biotechnology, Panjab University, Chandigarh 160014, India
| | - Pallavi Dhiman
- Department of Agriculture Biotechnology, National Agri-Food Biotechnology Institute (NABI), Mohali 140306, India; (N.R.); (S.K.); (V.K.); (R.B.); (R.M.); (P.D.); (R.D.); (T.R.S.)
| | - Gunvant B. Patil
- Department of Plant and Soil Sciences, Institute of Genomics for Crop Abiotic Stress Tolerance, Texas Tech University, Lubbock, TX 79409, USA;
| | - Rupesh Deshmukh
- Department of Agriculture Biotechnology, National Agri-Food Biotechnology Institute (NABI), Mohali 140306, India; (N.R.); (S.K.); (V.K.); (R.B.); (R.M.); (P.D.); (R.D.); (T.R.S.)
| | - Tilak Raj Sharma
- Department of Agriculture Biotechnology, National Agri-Food Biotechnology Institute (NABI), Mohali 140306, India; (N.R.); (S.K.); (V.K.); (R.B.); (R.M.); (P.D.); (R.D.); (T.R.S.)
- Department of Crop Science, Indian Council of Agriculture Research (ICAR), Krishi Bhavan, New Delhi 110001, India
| | - Humira Sonah
- Department of Agriculture Biotechnology, National Agri-Food Biotechnology Institute (NABI), Mohali 140306, India; (N.R.); (S.K.); (V.K.); (R.B.); (R.M.); (P.D.); (R.D.); (T.R.S.)
- Correspondence: ; Tel.: +91-6239715281
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Transcriptomics View over the Germination Landscape in Biofortified Rice. Genes (Basel) 2021; 12:genes12122013. [PMID: 34946962 PMCID: PMC8700799 DOI: 10.3390/genes12122013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 12/14/2021] [Accepted: 12/15/2021] [Indexed: 12/29/2022] Open
Abstract
Hidden hunger, or micronutrient deficiency, is a worldwide problem. Several approaches are employed to alleviate its effects (e.g., promoting diet diversity, use of dietary supplements, chemical fortification of processed food), and among these, biofortification is considered as one of the most cost-effective and highly sustainable. Rice is one of the best targets for biofortification since it is a staple food for almost half of the world’s population as a high-energy source but with low nutritional value. Multiple biofortified rice lines have been produced during the past decades, while few studies also reported modifications in germination behavior (in terms of enhanced or decreased germination percentage or speed). It is important to underline that rapid, uniform germination, and seedling establishment are essential prerequisites for crop productivity. Combining the two traits, biofortified, highly-nutritious seeds with improved germination behavior can be envisaged as a highly-desired target for rice breeding. To this purpose, information gathered from transcriptomics studies can reveal useful insights to unveil the molecular players governing both traits. The present review aims to provide an overview of transcriptomics studies applied at the crossroad between biofortification and seed germination, pointing out potential candidates for trait pyramiding.
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Chen Z, Li P, Du Y, Jiang Y, Cai M, Cao C. Dry cultivation and cultivar affect starch synthesis and traits to define rice grain quality in various panicle parts. Carbohydr Polym 2021; 269:118336. [PMID: 34294346 DOI: 10.1016/j.carbpol.2021.118336] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Revised: 05/30/2021] [Accepted: 06/09/2021] [Indexed: 12/22/2022]
Abstract
A pot experiment was conducted to explore the effects of high-quality (Huanghuazhan, HH), drought-resistant (IR, IRAT109) and drought-susceptible cultivars (ZS, Zhenshan97) under flooding irrigation and dry cultivation (D) on the starch accumulation and synthesis, physicochemical traits of starch granules and rice grain quality at the upper (U) and lower panicle. Under D treatment, IR and ZS had lower rice quality, especially the appearance and cooking quality. DHH-U had the highest appearance, nutritional and cooking quality among all cultivars under D treatment, which could be ascribed to the synthesis of more short-branch chain amylopectin and correspondingly higher starch granule tightness. DHH-U also maintained ordered carbohydrate structure, crystalline regions, and many hydrophilic and hydrophobic functional groups in starch granules before pasting. It could prevent the polymerization of small molecules to avoid the formation of macromolecules after pasting. Overall, these findings may facilitate the improvement of grain quality in rice dry cultivation.
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Affiliation(s)
- Zongkui Chen
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Ping Li
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Yunfeng Du
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Yang Jiang
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Mingli Cai
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Cougui Cao
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China.
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Sathe AP, Kumar A, Mandlik R, Raturi G, Yadav H, Kumar N, Shivaraj SM, Jaswal R, Kapoor R, Gupta SK, Sharma TR, Sonah H. Role of silicon in elevating resistance against sheath blight and blast diseases in rice (Oryza sativa L.). PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2021; 166:128-139. [PMID: 34102436 DOI: 10.1016/j.plaphy.2021.05.045] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 05/25/2021] [Indexed: 06/12/2023]
Abstract
Rice blast caused by Magnaporthe oryzae and sheath blight caused by Rhizoctonia solani, are the two major diseases of rice that cause enormous losses in rice production worldwide. Identification and utilization of broad-spectrum resistance resources have been considered sustainable and effective strategies. However, the majority of the resistance genes and QTLs identified have often been found to be race-specific, and their resistance is frequently broken down due to continuous exposure to the pathogen. Therefore, integrated approaches to improve plant resistance against such devastating pathogen have great importance. Silicon (Si), a beneficial element for plant growth, has shown to provide a prophylactic effect against many pathogens. The application of Si helps the plants to combat the disease-causing pathogens, either through its deposition in different parts of the plant or through modulation/induction of specific defense genes by yet an unknown mechanism. Some reports have shown that Si imparts resistance to rice blast and sheath blight. The present review summarizes the mechanism of Si transport and deposition and its effect on rice growth and development. A special emphasis has been given to explore the existing evidence showing Si mediated blast and sheath blight resistance and the mechanism involved in resistance. This review will help to understand the prophylactic effects of Si against sheath blight and blast disease at the mechanical, physiological, and genetic levels. The information provided here will help develop a strategy to explore Si derived benefits for sustainable rice production.
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Affiliation(s)
| | - Amit Kumar
- National Agri-Food Biotechnology Institute (NABI), Mohali, India
| | - Rushil Mandlik
- National Agri-Food Biotechnology Institute (NABI), Mohali, India; Department of Biotechnology, Panjab University, Chandigarh, India
| | - Gaurav Raturi
- National Agri-Food Biotechnology Institute (NABI), Mohali, India; Department of Biotechnology, Panjab University, Chandigarh, India
| | - Himanshu Yadav
- National Agri-Food Biotechnology Institute (NABI), Mohali, India
| | - Nirbhay Kumar
- National Agri-Food Biotechnology Institute (NABI), Mohali, India
| | - S M Shivaraj
- National Agri-Food Biotechnology Institute (NABI), Mohali, India
| | - Rajdeep Jaswal
- National Agri-Food Biotechnology Institute (NABI), Mohali, India
| | - Ritu Kapoor
- National Agri-Food Biotechnology Institute (NABI), Mohali, India
| | | | - Tilak Raj Sharma
- Department of Crop Science, Indian Council of Agriculture Research (ICAR), New Delhi, India
| | - Humira Sonah
- National Agri-Food Biotechnology Institute (NABI), Mohali, India.
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Deshmukh R, Rana N, Liu Y, Zeng S, Agarwal G, Sonah H, Varshney R, Joshi T, Patil GB, Nguyen HT. Soybean transporter database: A comprehensive database for identification and exploration of natural variants in soybean transporter genes. PHYSIOLOGIA PLANTARUM 2021; 171:756-770. [PMID: 33231322 DOI: 10.1111/ppl.13287] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Revised: 10/05/2020] [Accepted: 11/17/2020] [Indexed: 06/11/2023]
Abstract
Transporters, a class of membrane proteins that facilitate exchange of solutes including diverse molecules and ions across the cellular membrane, are vital component for the survival of all organisms. Understanding plant transporters is important to get insight of the basic cellular processes, physiology, and molecular mechanisms including nutrient uptake, signaling, response to external stress, and many more. In this regard, extensive analysis of transporters predicted in soybean and other plant species was performed. In addition, an integrated database for soybean transporter protein, SoyTD, was developed that will facilitate the identification, classification, and extensive characterization of transporter proteins by integrating expression, gene ontology, conserved domain and motifs, gene structure organization, and chromosomal distribution features. A comprehensive analysis was performed to identify highly confident transporters by integrating various prediction tools. Initially, 7541 transmembrane (TM) proteins were predicted in the soybean genome; out of these, 3306 non-redundant transporter genes carrying two or more transmembrane domains were selected for further analysis. The identified transporter genes were classified according to a standard transporter classification (TC) system. Comparative analysis of transporter genes among 47 plant genomes provided insights into expansion and duplication of transporter genes in land plants. The whole genome resequencing (WGRS) and tissue-specific transcriptome datasets of soybean were integrated to investigate the natural variants and expression profile associated with transporter(s) of interest. Overall, SoyTD provides a comprehensive interface to study genetic and molecular function of soybean transporters. SoyTD is publicly available at http://artemis.cyverse.org/soykb_dev/SoyTD/.
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Affiliation(s)
- Rupesh Deshmukh
- Agriculture Biotechnology Department, National Agri-Food Biotechnology Institute (NABI), Mohali, India
| | - Nitika Rana
- Agriculture Biotechnology Department, National Agri-Food Biotechnology Institute (NABI), Mohali, India
- Department of Biotechnology, Panjab University, Chandigarh, India
| | - Yang Liu
- Christopher S. Bond Life Science Center, University of Missouri, Columbia, Missouri, USA
| | - Shuai Zeng
- Christopher S. Bond Life Science Center, University of Missouri, Columbia, Missouri, USA
- Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, Missouri, USA
| | - Gaurav Agarwal
- Department of Plant Pathology, University of Georgia, Tifton, Georgia, USA
| | - Humira Sonah
- Agriculture Biotechnology Department, National Agri-Food Biotechnology Institute (NABI), Mohali, India
| | - Rajeev Varshney
- Center of Excellence in Genomics and System Biology, International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, India
| | - Trupti Joshi
- Christopher S. Bond Life Science Center, University of Missouri, Columbia, Missouri, USA
- Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, Missouri, USA
| | - Gunvant B Patil
- Department of Plant and Soil Sciences, Institute of Genomics for Crop Abiotic Stress Tolerance, Texas Tech University, Lubbock, Texas, USA
| | - Henry T Nguyen
- Division of Plant Science, National Center for Soybean Biotechnology, University of Missouri, Columbia, Missouri, USA
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11
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Vats S, Bansal R, Rana N, Kumawat S, Bhatt V, Jadhav P, Kale V, Sathe A, Sonah H, Jugdaohsingh R, Sharma TR, Deshmukh R. Unexplored nutritive potential of tomato to combat global malnutrition. Crit Rev Food Sci Nutr 2020; 62:1003-1034. [PMID: 33086895 DOI: 10.1080/10408398.2020.1832954] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Tomato, a widely consumed vegetable crop, offers a real potential to combat human nutritional deficiencies. Tomatoes are rich in micronutrients and other bioactive compounds (including vitamins, carotenoids, and minerals) that are known to be essential or beneficial for human health. This review highlights the current state of the art in the molecular understanding of the nutritional aspects, conventional and molecular breeding efforts, and biofortification studies undertaken to improve the nutritional content and quality of tomato. Transcriptomics and metabolomics studies, which offer a deeper understanding of the molecular regulation of the tomato's nutrients, are discussed. The potential uses of the wastes from the tomato processing industry (i.e., the peels and seed extracts) that are particularly rich in oils and proteins are also discussed. Recent advancements with CRISPR/Cas mediated gene-editing technology provide enormous opportunities to enhance the nutritional content of agricultural produces, including tomatoes. In this regard, genome editing efforts with respect to biofortification in the tomato plant are also discussed. The recent technological advancements and knowledge gaps described herein aim to help explore the unexplored nutritional potential of the tomato.
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Affiliation(s)
- Sanskriti Vats
- National Agri-Food Biotechnology Institute (NABI), Mohali, Punjab, India
| | - Ruchi Bansal
- National Agri-Food Biotechnology Institute (NABI), Mohali, Punjab, India.,Department of Biotechnology, Panjab University, Chandigarh, India
| | - Nitika Rana
- National Agri-Food Biotechnology Institute (NABI), Mohali, Punjab, India.,Department of Biotechnology, Panjab University, Chandigarh, India
| | - Surbhi Kumawat
- National Agri-Food Biotechnology Institute (NABI), Mohali, Punjab, India.,Department of Biotechnology, Panjab University, Chandigarh, India
| | - Vacha Bhatt
- Department of Botany, Savitribai Phule Pune University, Pune, MS, India
| | - Pravin Jadhav
- Dr. Panjabrao Deshmukh Krishi Vidyapeeth, Akola, MS, India
| | - Vijay Kale
- Dr. Panjabrao Deshmukh Krishi Vidyapeeth, Akola, MS, India
| | - Atul Sathe
- National Agri-Food Biotechnology Institute (NABI), Mohali, Punjab, India
| | - Humira Sonah
- National Agri-Food Biotechnology Institute (NABI), Mohali, Punjab, India
| | - Ravin Jugdaohsingh
- Biomineral Research Group, Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Tilak Raj Sharma
- Division of Crop Science, Indian Council of Agricultural Research, New Delhi, India
| | - Rupesh Deshmukh
- National Agri-Food Biotechnology Institute (NABI), Mohali, Punjab, India
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