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Shahzad N, Nabi HG, Qiao L, Li W. The Molecular Mechanism of Cold-Stress Tolerance: Cold Responsive Genes and Their Mechanisms in Rice ( Oryza sativa L.). BIOLOGY 2024; 13:442. [PMID: 38927322 PMCID: PMC11200503 DOI: 10.3390/biology13060442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Revised: 06/11/2024] [Accepted: 06/12/2024] [Indexed: 06/28/2024]
Abstract
Rice (Oryza sativa L.) production is highly susceptible to temperature fluctuations, which can significantly reduce plant growth and development at different developmental stages, resulting in a dramatic loss of grain yield. Over the past century, substantial efforts have been undertaken to investigate the physiological, biochemical, and molecular mechanisms of cold stress tolerance in rice. This review aims to provide a comprehensive overview of the recent developments and trends in this field. We summarized the previous advancements and methodologies used for identifying cold-responsive genes and the molecular mechanisms of cold tolerance in rice. Integration of new technologies has significantly improved studies in this era, facilitating the identification of essential genes, QTLs, and molecular modules in rice. These findings have accelerated the molecular breeding of cold-resistant rice varieties. In addition, functional genomics, including the investigation of natural variations in alleles and artificially developed mutants, is emerging as an exciting new approach to investigating cold tolerance. Looking ahead, it is imperative for scientists to evaluate the collective impacts of these novel genes to develop rice cultivars resilient to global climate change.
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Affiliation(s)
- Nida Shahzad
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, College of Life Sciences, Northwest A&F University, Xianyang 712100, China; (N.S.); (L.Q.)
| | - Hafiz Ghulam Nabi
- State Key Laboratory of Agrobiotechnology/Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China;
| | - Lei Qiao
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, College of Life Sciences, Northwest A&F University, Xianyang 712100, China; (N.S.); (L.Q.)
| | - Wenqiang Li
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, College of Life Sciences, Northwest A&F University, Xianyang 712100, China; (N.S.); (L.Q.)
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Gautam RK, Singh PK, Sakthivel K, Venkatesan K, Rao SS, Srikumar M, Vijayan J, Rakesh B, Ray S, Akhtar J, Meena BR, Langyan S, Ali S, Krishnamurthy SL. Marker-assisted enhancement of bacterial blight ( Xanthomonas oryzae pv . oryzae) resistance in a salt-tolerant rice variety for sustaining rice production of tropical islands. FRONTIERS IN PLANT SCIENCE 2023; 14:1221537. [PMID: 37818314 PMCID: PMC10561094 DOI: 10.3389/fpls.2023.1221537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 08/21/2023] [Indexed: 10/12/2023]
Abstract
Introduction Bacterial blight (BB) caused by Xanthomonas oryzae pv. oryzae is a major disease of rice, specially in the tropical regions of the world. Developing rice varieties with host resistance against the disease is the most effective and economical solution for managing the disease. Methods Pyramiding resistance genes (Xa4, xa5, xa13,and Xa21) in popular rice varieties using marker-assisted backcross breeding (MABB) has been demonstrated as a cost-effective and sustainable approach for establishing durable BB resistance. Here, we report our successful efforts in introgressing four resistance genes (Xa4, xa5, xa13, and Xa21) from IRBB60 to CARI Dhan 5, a popular salt-tolerant variety developed from a somaclonal variant of Pokkali rice, through functional MABB. Results and discussion Both BB and coastal salinity are among the major challenges for rice production in tropical island and coastal ecosystems. Plants with four, three, and two gene pyramids were generated, which displayed high levels of resistance to the BB pathogen at the BC3F2 stage. Under controlled salinity microplot environments, the line 131-2-175-1223 identified with the presence of three gene pyramid (Xa21+xa13+xa5) displayed notable resistance across locations and years as well as exhibited a salinity tolerance comparable to the recurrent parent, CARI Dhan 5. Among two BB gene combinations (Xa21+xa13), two lines, 17-1-69-334 and 46-3-95-659, demonstrated resistance across locations and years, as well as salt tolerance and grain production comparable to CARI Dhan 5. Besides salinity tolerance, five lines, 17-1-69-179, 46-3-95-655, 131-2-190-1197, 131-2-175-1209, and 131-2-175-1239, exhibited complete resistance to BB disease. Following multilocation testing, potential lines have been identified that can serve as a prospective candidate for producing varieties for the tropical Andaman and Nicobar Islands and other coastal locations, which are prone to BB and coastal salinity stresses.
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Affiliation(s)
- Raj Kumar Gautam
- Indian Council of Agricultural Research (ICAR)-Central Island Agricultural Research Institute, Port Blair, India
- Indian Council of Agricultural Research (ICAR)-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Pankaj Kumar Singh
- Indian Council of Agricultural Research (ICAR)-Central Island Agricultural Research Institute, Port Blair, India
| | - Krishnan Sakthivel
- Indian Council of Agricultural Research (ICAR)-Central Island Agricultural Research Institute, Port Blair, India
- Indian Council of Agricultural Research (ICAR)-Indian Institute of Oilseeds Research, Hyderabad, India
| | - K. Venkatesan
- Indian Council of Agricultural Research (ICAR)-Central Island Agricultural Research Institute, Port Blair, India
- Indian Council of Agricultural Research (ICAR)-National Bureau of Plant Genetic Resources (NBPGR), Regional Research Station, Thrissur, Kerala, India
| | - Shyam S. Rao
- Indian Council of Agricultural Research (ICAR)-Central Island Agricultural Research Institute, Port Blair, India
| | - M. Srikumar
- Indian Council of Agricultural Research (ICAR)-Central Island Agricultural Research Institute, Port Blair, India
| | - Joshitha Vijayan
- Indian Council of Agricultural Research (ICAR)-Central Island Agricultural Research Institute, Port Blair, India
- Indian Council of Agricultural Research (ICAR)-National Institute for Plant Biotechnology, New Delhi, India
| | - B. Rakesh
- Indian Council of Agricultural Research (ICAR)-Central Island Agricultural Research Institute, Port Blair, India
| | - Soham Ray
- Indian Council of Agricultural Research (ICAR)-Indian Agricultural Research Institute, New Delhi, India
| | - Jameel Akhtar
- Indian Council of Agricultural Research (ICAR)-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Bharat Raj Meena
- Indian Council of Agricultural Research (ICAR)-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Sapna Langyan
- Indian Council of Agricultural Research (ICAR)-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Sharik Ali
- Indian Council of Agricultural Research (ICAR)-National Bureau of Plant Genetic Resources, New Delhi, India
| | - S. L. Krishnamurthy
- Indian Council of Agricultural Research (ICAR)-Central Soil Salinity Research Institute, Karnal, India
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Halim AABA, Rafii MY, Osman MB, Chukwu SC, Oladosu Y. Physicochemical Properties and Tissue Structure of High Kernel Elongation Rice ( Oryza sativa L.) Varieties as Affected by Heat Treatment. Foods 2023; 12:foods12112207. [PMID: 37297452 DOI: 10.3390/foods12112207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 02/03/2023] [Accepted: 05/24/2023] [Indexed: 06/12/2023] Open
Abstract
Heat treatment could affect the structure and properties of rice varieties. The present study was conducted in order to determine the effects of heat treatment on the physicochemical properties and tissue structure of Mahsuri Mutan, Basmati 370 and MR219 rice varieties. The three rice varieties were subjected to heat treatment (ageing) at 90 °C, using an oven, for 3 h. After the heat treatment, the samples were cooled at room temperature (25 °C) for 1 h. Physicochemical properties, such as alkali digestion value, water uptake ratio, solids in cooking water, high kernel elongation ratio and amylose contents, were determined. The procedure used in determining both apparent and absolute amylose involved measuring the iodine affinity of defatted whole starch. Ahigh-performance anion-exchange chromatograph was used to analyse branch chain length distribution of amylopectin quantitatively. The starch structure of the rice samples was observed under a scanning electron microscope. Data collected on physicochemical traits, heat treatment and control (ageing and non-ageing) were subjected to an analysis of variance using SAS software version 9.4. In this study, Mahsuri Mutan and Basmati 370 showed superior high kernel elongation as compared to their respective rice progenies. This study also found that heat treatment directly affected the increasingly high kernel elongation for both populations. The phenotypic correlation co-efficient indicated that there was a high positive correlation between high kernel elongation and water uptake ratio, implying that selection for water uptake ratio would increase the high kernel elongation characteristic. The heat treatment showed significant difference in all the physicochemical traits of the varieties studied. Heat treatment also affected the very long branch chains of starch, such as amylose. Observation under an electron microscope showed that the samples subjected to heat treatment had more cracks on the tissue structure compared to normal rice samples. The hexagon structure in Mahsuri Mutan produced a greater elongation effect on its kernel. The findings from this study could be useful to breeders in the selection and development of a new high kernel elongation rice variety.
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Affiliation(s)
- Anna Arina Bt Ab Halim
- Laboratory of Climate Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia (UPM), Serdang 43400, Selangor, Malaysia
| | - Mohd Y Rafii
- Laboratory of Climate Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia (UPM), Serdang 43400, Selangor, Malaysia
- Department of Crop Science, Faculty of Agriculture, Universiti Putra Malaysia (UPM), Serdang 43400, Selangor, Malaysia
| | - Mohamad B Osman
- Malaysia Agriculture Research and Development Institute (MARDI), Serdang 43400, Selangor, Malaysia
| | - Samuel C Chukwu
- Laboratory of Climate Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia (UPM), Serdang 43400, Selangor, Malaysia
- Department of Crop Production and Landscape Management, Faculty of Agriculture and Natural Resources Management, Ebonyi State University, Abakaliki PMB 053, Nigeria
| | - Yusuff Oladosu
- Laboratory of Climate Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia (UPM), Serdang 43400, Selangor, Malaysia
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Kassie FC, Nguepjop JR, Ngalle HB, Assaha DVM, Gessese MK, Abtew WG, Tossim HA, Sambou A, Seye M, Rami JF, Fonceka D, Bell JM. An Overview of Mapping Quantitative Trait Loci in Peanut ( Arachis hypogaea L.). Genes (Basel) 2023; 14:1176. [PMID: 37372356 DOI: 10.3390/genes14061176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 05/24/2023] [Accepted: 05/25/2023] [Indexed: 06/29/2023] Open
Abstract
Quantitative Trait Loci (QTL) mapping has been thoroughly used in peanut genetics and breeding in spite of the narrow genetic diversity and the segmental tetraploid nature of the cultivated species. QTL mapping is helpful for identifying the genomic regions that contribute to traits, for estimating the extent of variation and the genetic action (i.e., additive, dominant, or epistatic) underlying this variation, and for pinpointing genetic correlations between traits. The aim of this paper is to review the recently published studies on QTL mapping with a particular emphasis on mapping populations used as well as traits related to kernel quality. We found that several populations have been used for QTL mapping including interspecific populations developed from crosses between synthetic tetraploids and elite varieties. Those populations allowed the broadening of the genetic base of cultivated peanut and helped with the mapping of QTL and identifying beneficial wild alleles for economically important traits. Furthermore, only a few studies reported QTL related to kernel quality. The main quality traits for which QTL have been mapped include oil and protein content as well as fatty acid compositions. QTL for other agronomic traits have also been reported. Among the 1261 QTL reported in this review, and extracted from the most relevant studies on QTL mapping in peanut, 413 (~33%) were related to kernel quality showing the importance of quality in peanut genetics and breeding. Exploiting the QTL information could accelerate breeding to develop highly nutritious superior cultivars in the face of climate change.
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Affiliation(s)
- Fentanesh C Kassie
- Department of Plant Biology and Physiology, Faculty of Sciences, University of Yaounde I, Yaounde P.O. Box 337, Cameroon
- Department of Plant Science, College of Agriculture, Wolaita Sodo University, Sodo P.O. Box 138, Ethiopia
| | - Joël R Nguepjop
- UMR AGAP, CIRAD, F-34398 Montpellier, France
- AGAP Institute, Institut Agro, CIRAD, INRAE, University of Montpellier, F-34060 Montpellier, France
- Centre d'Etudes Régional Pour l'Amélioration de l'Adaptation à la Sécheresse (CERAAS/ISRA), Route de Khombole, Thiès BP 3320, Senegal
- Dispositif de Recherche et de Formation en Partenariat, Innovation et Amélioration Variétale en Afrique de l'Ouest (IAVAO), CERAAS, Route de Khombole, Thiès BP 3320, Senegal
| | - Hermine B Ngalle
- Department of Plant Biology and Physiology, Faculty of Sciences, University of Yaounde I, Yaounde P.O. Box 337, Cameroon
| | - Dekoum V M Assaha
- Department of Agriculture, Higher Technical Teachers Training College, University of Buea, Kumba P.O. Box 249, Cameroon
| | - Mesfin K Gessese
- Department of Plant Science, College of Agriculture, Wolaita Sodo University, Sodo P.O. Box 138, Ethiopia
| | - Wosene G Abtew
- Department of Horticulture and Plant Science, College of Agriculture and Veterinary Medicine, Jimma University, Jimma P.O. Box 378, Ethiopia
| | - Hodo-Abalo Tossim
- Centre d'Etudes Régional Pour l'Amélioration de l'Adaptation à la Sécheresse (CERAAS/ISRA), Route de Khombole, Thiès BP 3320, Senegal
- Dispositif de Recherche et de Formation en Partenariat, Innovation et Amélioration Variétale en Afrique de l'Ouest (IAVAO), CERAAS, Route de Khombole, Thiès BP 3320, Senegal
| | - Aissatou Sambou
- Centre d'Etudes Régional Pour l'Amélioration de l'Adaptation à la Sécheresse (CERAAS/ISRA), Route de Khombole, Thiès BP 3320, Senegal
- Dispositif de Recherche et de Formation en Partenariat, Innovation et Amélioration Variétale en Afrique de l'Ouest (IAVAO), CERAAS, Route de Khombole, Thiès BP 3320, Senegal
| | - Maguette Seye
- Centre d'Etudes Régional Pour l'Amélioration de l'Adaptation à la Sécheresse (CERAAS/ISRA), Route de Khombole, Thiès BP 3320, Senegal
- Dispositif de Recherche et de Formation en Partenariat, Innovation et Amélioration Variétale en Afrique de l'Ouest (IAVAO), CERAAS, Route de Khombole, Thiès BP 3320, Senegal
| | - Jean-François Rami
- UMR AGAP, CIRAD, F-34398 Montpellier, France
- AGAP Institute, Institut Agro, CIRAD, INRAE, University of Montpellier, F-34060 Montpellier, France
- Dispositif de Recherche et de Formation en Partenariat, Innovation et Amélioration Variétale en Afrique de l'Ouest (IAVAO), CERAAS, Route de Khombole, Thiès BP 3320, Senegal
| | - Daniel Fonceka
- UMR AGAP, CIRAD, F-34398 Montpellier, France
- AGAP Institute, Institut Agro, CIRAD, INRAE, University of Montpellier, F-34060 Montpellier, France
- Centre d'Etudes Régional Pour l'Amélioration de l'Adaptation à la Sécheresse (CERAAS/ISRA), Route de Khombole, Thiès BP 3320, Senegal
- Dispositif de Recherche et de Formation en Partenariat, Innovation et Amélioration Variétale en Afrique de l'Ouest (IAVAO), CERAAS, Route de Khombole, Thiès BP 3320, Senegal
| | - Joseph M Bell
- Department of Plant Biology and Physiology, Faculty of Sciences, University of Yaounde I, Yaounde P.O. Box 337, Cameroon
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Improvement of Salinity Tolerance in Water-Saving and Drought-Resistance Rice (WDR). Int J Mol Sci 2023; 24:ijms24065444. [PMID: 36982522 PMCID: PMC10049413 DOI: 10.3390/ijms24065444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 03/08/2023] [Accepted: 03/10/2023] [Indexed: 03/14/2023] Open
Abstract
Rice is one of the most economically important staple food crops in the world. Soil salinization and drought seriously restrict sustainable rice production. Drought aggravates the degree of soil salinization, and, at the same time, increased soil salinity also inhibits water absorption, resulting in physiological drought stress. Salt tolerance in rice is a complex quantitative trait controlled by multiple genes. This review presents and discusses the recent research developments on salt stress impact on rice growth, rice salt tolerance mechanisms, the identification and selection of salt-tolerant rice resources, and strategies to improve rice salt tolerance. In recent years, the increased cultivation of water-saving and drought-resistance rice (WDR) has shown great application potential in alleviating the water resource crisis and ensuring food and ecological security. Here, we present an innovative germplasm selection strategy of salt-tolerant WDR, using a population that is developed by recurrent selection based on dominant genic male sterility. We aim to provide a reference for efficient genetic improvement and germplasm innovation of complex traits (drought and salt tolerance) that can be translated into breeding all economically important cereal crops.
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Raj SRG, Nadarajah K. QTL and Candidate Genes: Techniques and Advancement in Abiotic Stress Resistance Breeding of Major Cereals. Int J Mol Sci 2022; 24:ijms24010006. [PMID: 36613450 PMCID: PMC9820233 DOI: 10.3390/ijms24010006] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 12/06/2022] [Accepted: 12/13/2022] [Indexed: 12/24/2022] Open
Abstract
At least 75% of the world's grain production comes from the three most important cereal crops: rice (Oryza sativa), wheat (Triticum aestivum), and maize (Zea mays). However, abiotic stressors such as heavy metal toxicity, salinity, low temperatures, and drought are all significant hazards to the growth and development of these grains. Quantitative trait locus (QTL) discovery and mapping have enhanced agricultural production and output by enabling plant breeders to better comprehend abiotic stress tolerance processes in cereals. Molecular markers and stable QTL are important for molecular breeding and candidate gene discovery, which may be utilized in transgenic or molecular introgression. Researchers can now study synteny between rice, maize, and wheat to gain a better understanding of the relationships between the QTL or genes that are important for a particular stress adaptation and phenotypic improvement in these cereals from analyzing reports on QTL and candidate genes. An overview of constitutive QTL, adaptive QTL, and significant stable multi-environment and multi-trait QTL is provided in this article as a solid framework for use and knowledge in genetic enhancement. Several QTL, such as DRO1 and Saltol, and other significant success cases are discussed in this review. We have highlighted techniques and advancements for abiotic stress tolerance breeding programs in cereals, the challenges encountered in introgressing beneficial QTL using traditional breeding techniques such as mutation breeding and marker-assisted selection (MAS), and the in roads made by new breeding methods such as genome-wide association studies (GWASs), the clustered regularly interspaced short palindromic repeat (CRISPR)/Cas9 system, and meta-QTL (MQTL) analysis. A combination of these conventional and modern breeding approaches can be used to apply the QTL and candidate gene information in genetic improvement of cereals against abiotic stresses.
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Li X, Wei Y, Ma Y, Cao G, Ma S, Zhang T, Zhan Z, Piao Z. Marker-Assisted Pyramiding of CRa and CRd Genes to Improve the Clubroot Resistance of Brassica rapa. Genes (Basel) 2022; 13:genes13122414. [PMID: 36553679 PMCID: PMC9777773 DOI: 10.3390/genes13122414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 12/07/2022] [Accepted: 12/12/2022] [Indexed: 12/23/2022] Open
Abstract
Clubroot, caused by Plasmodiophora brassicae, is an economically important soil-borne disease that threatens Brassicaceae crops worldwide. In recent years, the incidence area of Chinese cabbage (Brassica rapa ssp. pekinensis) clubroot disease has increased, which severely affects the yield and quality of Chinese cabbage. The resistance of varieties harboring the single clubroot-resistance (CR) gene is easily broken through by P. brassicae pathotypes. CRa and CRd, genetically identified in B. rapa, are CR genes known to be highly resistant to different P. brassicaea pathotypes. In our study, we perform the gene pyramiding of CRa and CRd in Chinese cabbages through marker-assisted selection (MAS), and develop homozygous pyramided lines. The newly generated pyramided lines exhibit greater resistance to six different pathotypes than that of two parental lines carrying a single CR gene. This study provides new CR-gene-pyramided lines for the development of clubroot-resistant Brassica varieties for future breeding programs.
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Liu Y, Zhao S, Gao X, Fu S, Chao Song, Dou Y, Shaozhong Song, Qi C, Lin J. Combined laser-induced breakdown spectroscopy and hyperspectral imaging with machine learning for the classification and identification of rice geographical origin. RSC Adv 2022; 12:34520-34530. [PMID: 36545607 PMCID: PMC9710531 DOI: 10.1039/d2ra06892c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 11/23/2022] [Indexed: 12/02/2022] Open
Abstract
With the events of fake and inferior rice and food products occurring frequently, how to establish a rapid and high accuracy monitoring method for rice food identification becomes an urgent problem. In this work, we investigate using combined laser-induced breakdown spectroscopy (LIBS) and hyperspectral imaging (HSI) with machine learning algorithms to identify the place of origin of rice production. Six geographical origin rice samples grown in different parts of China are selected and pretreated, and measured by the atomic emission spectra of LIBS and the reflection spectra of HSI, respectively. The principal component analysis (PCA) is utilized to realize data dimensionality and extract the data feat of LIBS, HSI and fusion data, and based on this, three models employing the partial least squares discriminant analysis (PLS-DA), the support vector machine (SVM) and the extreme learning machine (ELM) are used to identify the rice geographical origin. The results show that the accuracy of LIBS and HSI analysis with the SVM machine learning algorithm can reach 93.06% and 88.07%, respectively, and the accuracy of combined LIBS and HSI data fusion recognition can reach 99.85%. Besides, the classification accuracy of the three models measured after pretreatment is basically all above 95%, and up to 99.85%. This study proves the effectiveness of using the combined LIBS and HSI with the machine learning algorithm in rice geographical origin identification, which can achieve rapid and accurate rice quality and identity detection.
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Affiliation(s)
- Yuanyuan Liu
- School of Physics, Changchun University of Science and TechnologyJilin130022China
| | - Shangyong Zhao
- Department of Energy and Power Engineering, Tsinghua UniversityBeijing100084China
| | - Xun Gao
- School of Physics, Changchun University of Science and TechnologyJilin130022China
| | - Shaoyan Fu
- School of Physics, Changchun University of Science and TechnologyJilin130022China
| | - Chao Song
- School of Chemistry and Environmental Engineering, Changchun University of Science and TechnologyJilin130022China
| | - Yinping Dou
- School of Physics, Changchun University of Science and TechnologyJilin130022China
| | - Shaozhong Song
- School of Data Science and Artificial Intelligence, Jilin Engineering Normal UniversityJilin130052China
| | - Chunyan Qi
- Jilin Academy of Agricultural SciencesJilin130033China
| | - Jingquan Lin
- School of Physics, Changchun University of Science and TechnologyJilin130022China
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Mores A, Borrelli GM, Laidò G, Petruzzino G, Pecchioni N, Amoroso LGM, Desiderio F, Mazzucotelli E, Mastrangelo AM, Marone D. Genomic Approaches to Identify Molecular Bases of Crop Resistance to Diseases and to Develop Future Breeding Strategies. Int J Mol Sci 2021; 22:5423. [PMID: 34063853 PMCID: PMC8196592 DOI: 10.3390/ijms22115423] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 04/30/2021] [Accepted: 05/15/2021] [Indexed: 12/16/2022] Open
Abstract
Plant diseases are responsible for substantial crop losses each year and affect food security and agricultural sustainability. The improvement of crop resistance to pathogens through breeding represents an environmentally sound method for managing disease and minimizing these losses. The challenge is to breed varieties with a stable and broad-spectrum resistance. Different approaches, from markers to recent genomic and 'post-genomic era' technologies, will be reviewed in order to contribute to a better understanding of the complexity of host-pathogen interactions and genes, including those with small phenotypic effects and mechanisms that underlie resistance. An efficient combination of these approaches is herein proposed as the basis to develop a successful breeding strategy to obtain resistant crop varieties that yield higher in increasing disease scenarios.
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Affiliation(s)
- Antonia Mores
- Council for Agricultural Research and Economics, Research Centre for Cereal and Industrial Crops, S.S. 673, Km 25,200, 71122 Foggia, Italy; (A.M.); (G.M.B.); (G.L.); (G.P.); (N.P.); (A.M.M.)
| | - Grazia Maria Borrelli
- Council for Agricultural Research and Economics, Research Centre for Cereal and Industrial Crops, S.S. 673, Km 25,200, 71122 Foggia, Italy; (A.M.); (G.M.B.); (G.L.); (G.P.); (N.P.); (A.M.M.)
| | - Giovanni Laidò
- Council for Agricultural Research and Economics, Research Centre for Cereal and Industrial Crops, S.S. 673, Km 25,200, 71122 Foggia, Italy; (A.M.); (G.M.B.); (G.L.); (G.P.); (N.P.); (A.M.M.)
| | - Giuseppe Petruzzino
- Council for Agricultural Research and Economics, Research Centre for Cereal and Industrial Crops, S.S. 673, Km 25,200, 71122 Foggia, Italy; (A.M.); (G.M.B.); (G.L.); (G.P.); (N.P.); (A.M.M.)
| | - Nicola Pecchioni
- Council for Agricultural Research and Economics, Research Centre for Cereal and Industrial Crops, S.S. 673, Km 25,200, 71122 Foggia, Italy; (A.M.); (G.M.B.); (G.L.); (G.P.); (N.P.); (A.M.M.)
| | | | - Francesca Desiderio
- Council for Agricultural Research and Economics, Genomics and Bioinformatics Research Center, Via San Protaso 302, 29017 Fiorenzuola d’Arda, Italy; (F.D.); (E.M.)
| | - Elisabetta Mazzucotelli
- Council for Agricultural Research and Economics, Genomics and Bioinformatics Research Center, Via San Protaso 302, 29017 Fiorenzuola d’Arda, Italy; (F.D.); (E.M.)
| | - Anna Maria Mastrangelo
- Council for Agricultural Research and Economics, Research Centre for Cereal and Industrial Crops, S.S. 673, Km 25,200, 71122 Foggia, Italy; (A.M.); (G.M.B.); (G.L.); (G.P.); (N.P.); (A.M.M.)
| | - Daniela Marone
- Council for Agricultural Research and Economics, Research Centre for Cereal and Industrial Crops, S.S. 673, Km 25,200, 71122 Foggia, Italy; (A.M.); (G.M.B.); (G.L.); (G.P.); (N.P.); (A.M.M.)
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Kim MS, Yang JY, Yu JK, Lee Y, Park YJ, Kang KK, Cho YG. Breeding of High Cooking and Eating Quality in Rice by Marker-Assisted Backcrossing (MABc) Using KASP Markers. PLANTS 2021; 10:plants10040804. [PMID: 33921910 PMCID: PMC8073074 DOI: 10.3390/plants10040804] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Revised: 04/15/2021] [Accepted: 04/15/2021] [Indexed: 12/03/2022]
Abstract
The primary goals of rice breeding programs are grain quality and yield potential improvement. With the high demand for rice varieties of premium cooking and eating quality, we developed low-amylose content breeding lines crossed with Samgwang and Milkyqueen through the marker-assisted backcross (MABc) breeding program. Trait markers of the SSIIIa gene referring to low-amylose content were identified through an SNP mapping activity, and the markers were applied to select favorable lines for a foreground selection. To rapidly recover the genetic background of Samgwang (recurrent parent genome, RPG), 386 genome-wide markers were used to select BC1F1 and BC2F1 individuals. Seven BC2F1 lines with targeted traits were selected, and the genetic background recovery range varied within 97.4–99.1% of RPG. The amylose content of the selected BC2F2 grains ranged from 12.4–16.8%. We demonstrated the MABc using a trait and genome-wide markers, allowing us to efficiently select lines of a target trait and reduce the breeding cycle effectively. In addition, the BC2F2 lines confirmed by molecular markers in this study can be utilized as parental lines for subsequent breeding programs of high-quality rice for cooking and eating.
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Affiliation(s)
- Me-Sun Kim
- College of Agriculture and Life & Environment Sciences, Chungbuk National University, Cheongju 28644, Korea; (M.-S.K.); (J.-Y.Y.); (Y.L.)
| | - Ju-Young Yang
- College of Agriculture and Life & Environment Sciences, Chungbuk National University, Cheongju 28644, Korea; (M.-S.K.); (J.-Y.Y.); (Y.L.)
| | - Ju-Kyung Yu
- Syngenta Crop Protection LLC, Seeds Research, 9 Davis Dr. Research Triangle Park, Durham, NC 27709, USA;
| | - Yi Lee
- College of Agriculture and Life & Environment Sciences, Chungbuk National University, Cheongju 28644, Korea; (M.-S.K.); (J.-Y.Y.); (Y.L.)
| | - Yong-Jin Park
- College of Industrial Science, Kongju National University, Yesan 32439, Korea;
| | - Kwon-Kyoo Kang
- Division of Horticultural Biotechnology, Hankyong National University, Anseong 17579, Korea
- Correspondence: (K.-K.K.); (Y.-G.C.)
| | - Yong-Gu Cho
- College of Agriculture and Life & Environment Sciences, Chungbuk National University, Cheongju 28644, Korea; (M.-S.K.); (J.-Y.Y.); (Y.L.)
- Correspondence: (K.-K.K.); (Y.-G.C.)
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11
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Pan T, Zhang J, He L, Hafeez A, Ning C, Cai K. Silicon Enhances Plant Resistance of Rice against Submergence Stress. PLANTS (BASEL, SWITZERLAND) 2021; 10:767. [PMID: 33919738 PMCID: PMC8070673 DOI: 10.3390/plants10040767] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 04/09/2021] [Accepted: 04/11/2021] [Indexed: 12/17/2022]
Abstract
Flooding is an important natural disaster limiting rice production. Silicon (Si) has been shown to have an important role in alleviating varied environmental stress. However, very few studies have investigated the effects and mechanisms of Si in alleviating flood stress in rice. In the present study, wild type rice (cv. Oochikara, WT) and Si-defective mutant (lsi1) were chosen to examine the impacts of Si application on plant growth, photosynthesis, cell structure, and antioxidant enzyme activity of rice exposed to submergence stress at tillering stage. Our results showed that Si application improved root morphological traits, and increased Si uptake and plant biomass of WT under submergence stress, but non-significantly influenced lsi1 mutant. Under submergence stress, leaf photosynthesis of WT was significantly inhibited, and Si application had no significant effects on photosynthetic rate, transpiration rate, stomatal conductance, and intercellular carbon dioxide concentration for both of WT and lsi1 mutant, but the photochemical quenching of WT was increased and the integrity of cell structure was improved. In addition, Si application significantly reduced malondialdehyde concentration and increased the activity of peroxidase and catalase in WT leaves under submergence stress. These results suggested that Si could increase rice plant resistance against submergence stress by improving root morphological traits and chloroplast ultrastructure and enhancing antioxidant defense.
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Affiliation(s)
- Taowen Pan
- College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China; (T.P.); (J.Z.); (L.H.); (A.H.); (C.N.)
- Guangdong Provincial Key Laboratory of Eco-Circular Agriculture, South China Agricultural University, Guangzhou 510642, China
- Key Laboratory of Tropical Agro-Environment, Ministry of Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Jian Zhang
- College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China; (T.P.); (J.Z.); (L.H.); (A.H.); (C.N.)
| | - Lanmengqi He
- College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China; (T.P.); (J.Z.); (L.H.); (A.H.); (C.N.)
| | - Abdul Hafeez
- College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China; (T.P.); (J.Z.); (L.H.); (A.H.); (C.N.)
- Guangdong Provincial Key Laboratory of Eco-Circular Agriculture, South China Agricultural University, Guangzhou 510642, China
- Key Laboratory of Tropical Agro-Environment, Ministry of Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Chuanchuan Ning
- College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China; (T.P.); (J.Z.); (L.H.); (A.H.); (C.N.)
- Guangdong Provincial Key Laboratory of Eco-Circular Agriculture, South China Agricultural University, Guangzhou 510642, China
- Key Laboratory of Tropical Agro-Environment, Ministry of Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Kunzheng Cai
- College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China; (T.P.); (J.Z.); (L.H.); (A.H.); (C.N.)
- Guangdong Provincial Key Laboratory of Eco-Circular Agriculture, South China Agricultural University, Guangzhou 510642, China
- Key Laboratory of Tropical Agro-Environment, Ministry of Agriculture, South China Agricultural University, Guangzhou 510642, China
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12
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Mbanjo EGN, Rabbi IY, Ferguson ME, Kayondo SI, Eng NH, Tripathi L, Kulakow P, Egesi C. Technological Innovations for Improving Cassava Production in Sub-Saharan Africa. Front Genet 2021; 11:623736. [PMID: 33552138 PMCID: PMC7859516 DOI: 10.3389/fgene.2020.623736] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 12/23/2020] [Indexed: 11/17/2022] Open
Abstract
Cassava is crucial for food security of millions of people in sub-Saharan Africa. The crop has great potential to contribute to African development and is increasing its income-earning potential for small-scale farmers and related value chains on the continent. Therefore, it is critical to increase cassava production, as well as its quality attributes. Technological innovations offer great potential to drive this envisioned change. This paper highlights genomic tools and resources available in cassava. The paper also provides a glimpse of how these resources have been used to screen and understand the pattern of cassava genetic diversity on the continent. Here, we reviewed the approaches currently used for phenotyping cassava traits, highlighting the methodologies used to link genotypic and phenotypic information, dissect the genetics architecture of key cassava traits, and identify quantitative trait loci/markers significantly associated with those traits. Additionally, we examined how knowledge acquired is utilized to contribute to crop improvement. We explored major approaches applied in the field of molecular breeding for cassava, their promises, and limitations. We also examined the role of national agricultural research systems as key partners for sustainable cassava production.
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Affiliation(s)
| | | | | | | | - Ng Hwa Eng
- CGIAR Excellence in Breeding Platform, El Batan, Mexico
| | - Leena Tripathi
- International Institute of Tropical Agriculture, Nairobi, Kenya
| | - Peter Kulakow
- International Institute of Tropical Agriculture, Ibadan, Nigeria
| | - Chiedozie Egesi
- International Institute of Tropical Agriculture, Ibadan, Nigeria
- National Root Crops Research Institute, Umudike, Nigeria
- Department of Global Development, College of Agriculture and Life Sciences, Cornell University, Ithaca, NY, United States
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13
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Chen Q, Tang W, Zeng G, Sheng H, Shi W, Xiao Y. Reduction of cadmium accumulation in the grains of male sterile rice Chuang-5S carrying Pi48 or Pi49 through marker-assisted selection. 3 Biotech 2020; 10:539. [PMID: 33224708 PMCID: PMC7672139 DOI: 10.1007/s13205-020-02533-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 10/29/2020] [Indexed: 10/23/2022] Open
Abstract
To reduce cadmium (Cd) accumulation in the grains of rice Chuang-5S (C5S), a gene OsHMA3 and a QTL qlGCd3 related to low-Cd accumulation were separately introgressed into the recipient parent C5S (male sterile line) by molecular marker-assisted breeding. The recurrent parent C5S was then replaced by NIL (near-isogenic line)-C5S with the blast resistance gene Pi48 or Pi49 to construct the BC2F1 generation. Finally, two groups of improved materials of C5S, which pyramided the gene/QTL associated with low-Cd accumulation and blast resistance gene, were developed. The Cd accumulation, agronomic traits, genetic background and blast resistance of these improved C5S materials were evaluated. The results showed that the average Cd content of improved C5S material carrying OsHMA3 and qlGCd3 was, respectively, reduced by 52.8% and 50.8% compared with that of C5S, indicating that the gene related to low-Cd accumulation was, successfully, transferred to C5S with stable expression. The main agronomic traits of the improved materials were consistent with those of C5S. Besides, the improved C5S lines showed stronger blast resistance than C5S and more than 88% similarity to the genetic background of C5S. These two groups of improved materials may be further utilized for the breeding of advanced male sterile lines or superior hybrid rice.
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Affiliation(s)
- Qiuhong Chen
- Southern Regional Collaborative Innovation Center for Grain and Oil Crops, Hunan Agricultural University, Changsha 410128, China
| | - Wei Tang
- Southern Regional Collaborative Innovation Center for Grain and Oil Crops, Hunan Agricultural University, Changsha 410128, China
| | - Gai Zeng
- Southern Regional Collaborative Innovation Center for Grain and Oil Crops, Hunan Agricultural University, Changsha 410128, China
| | - Haowen Sheng
- Southern Regional Collaborative Innovation Center for Grain and Oil Crops, Hunan Agricultural University, Changsha 410128, China
| | - Weijie Shi
- Southern Regional Collaborative Innovation Center for Grain and Oil Crops, Hunan Agricultural University, Changsha 410128, China
| | - Yinghui Xiao
- Southern Regional Collaborative Innovation Center for Grain and Oil Crops, Hunan Agricultural University, Changsha 410128, China
- Beidahuang Kenfeng Seed Co., Ltd., Harbin, 150090 China
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14
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Chukwu SC, Rafii MY, Ramlee SI, Ismail SI, Oladosu Y, Muhammad I, Musa I, Ahmed M, Jatto MI, Yusuf BR. Recovery of Recurrent Parent Genome in a Marker-Assisted Backcrossing Against Rice Blast and Blight Infections Using Functional Markers and SSRs. PLANTS (BASEL, SWITZERLAND) 2020; 9:plants9111411. [PMID: 33105815 PMCID: PMC7690635 DOI: 10.3390/plants9111411] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 09/28/2020] [Accepted: 10/20/2020] [Indexed: 05/30/2023]
Abstract
The most vital aspect of marker-assisted backcross breeding is the recurrent parent genome recovery. This enables the selection of only parents with recovered recipient/recurrent parent genome in addition to the targeted genes. The recurrent parent genome recovery (RPGR) ensures that non-desirable genomic segments are removed while the gene of interest is sustained in the recombined progenies without further segregations. This work was aimed at quantifying the RPGR of backcross populations with introgression of bacterial leaf blight resistance genes. Putra-1, a Malaysian elite variety, high yielding with inherent resistance to blast but susceptible to bacterial leaf blight (BLB), was crossed with IRBB60 which is resistant to BLB disease. The IRBB60 has four Xoo resistance genes-Xa4, xa5, xa13 and Xa21. Tightly linked polymorphic functional and SSR markers were used for foreground selection at every stage of backcrossing to select progenies with introgressed target genes. Background selection was done to quantify the percentage of RPGR in the selected lines using 79 confirmed polymorphic microsatellites. Result obtained showed that the percentage of RPGR was 80.11% at BC1F1, 95.30% at BC2F1 and 95.9% at BC2F2. The introgression of Xa4, xa5, xa13 and Xa21 Xoo resistance genes were faster through the adopted marker-assisted backcross breeding compared to what could be obtained through conventional breeding. All the 16 selected lines displayed resistance to BLB with three lines showing high resistance to the disease. The blast resistance contained in the genetic background of Putra-1 was also sustained in all the selected lines. The newly developed lines were recommended as new rice varieties for commercial cultivation.
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Affiliation(s)
- Samuel Chibuike Chukwu
- Laboratory of Climate Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, UPM Serdang, Selangor 43400, Malaysia; (S.C.C.); (Y.O.); (I.M.); (I.M.); (M.A.); (M.I.J.); (B.R.Y.)
- Department of Crop Production and Landscape Management, Faculty of Agriculture and Natural Resources Management, Ebonyi State University, Abakaliki PMB 053, Nigeria
| | - Mohd Y. Rafii
- Laboratory of Climate Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, UPM Serdang, Selangor 43400, Malaysia; (S.C.C.); (Y.O.); (I.M.); (I.M.); (M.A.); (M.I.J.); (B.R.Y.)
- Department of Crop Science, Faculty of Agriculture, Universiti Putra Malaysia, UPM Serdang, Selangor 43400, Malaysia;
| | - Shairul Izan Ramlee
- Department of Crop Science, Faculty of Agriculture, Universiti Putra Malaysia, UPM Serdang, Selangor 43400, Malaysia;
| | - Siti Izera Ismail
- Department of Plant Protection, Faculty of Agriculture, Universiti Putra Malaysia, UPM Serdang, Selangor 43400, Malaysia;
| | - Yusuff Oladosu
- Laboratory of Climate Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, UPM Serdang, Selangor 43400, Malaysia; (S.C.C.); (Y.O.); (I.M.); (I.M.); (M.A.); (M.I.J.); (B.R.Y.)
| | - Isma’ila Muhammad
- Laboratory of Climate Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, UPM Serdang, Selangor 43400, Malaysia; (S.C.C.); (Y.O.); (I.M.); (I.M.); (M.A.); (M.I.J.); (B.R.Y.)
| | - Ibrahim Musa
- Laboratory of Climate Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, UPM Serdang, Selangor 43400, Malaysia; (S.C.C.); (Y.O.); (I.M.); (I.M.); (M.A.); (M.I.J.); (B.R.Y.)
| | - Muideen Ahmed
- Laboratory of Climate Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, UPM Serdang, Selangor 43400, Malaysia; (S.C.C.); (Y.O.); (I.M.); (I.M.); (M.A.); (M.I.J.); (B.R.Y.)
| | - Muhammed Itopa Jatto
- Laboratory of Climate Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, UPM Serdang, Selangor 43400, Malaysia; (S.C.C.); (Y.O.); (I.M.); (I.M.); (M.A.); (M.I.J.); (B.R.Y.)
| | - Bashir Rini Yusuf
- Laboratory of Climate Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, UPM Serdang, Selangor 43400, Malaysia; (S.C.C.); (Y.O.); (I.M.); (I.M.); (M.A.); (M.I.J.); (B.R.Y.)
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15
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Kulkarni SR, Balachandran SM, Ulaganathan K, Balakrishnan D, Praveen M, Prasad ASH, Fiyaz RA, Senguttuvel P, Sinha P, Kale RR, Rekha G, Kousik MBVN, Harika G, Anila M, Punniakoti E, Dilip T, Hajira SK, Pranathi K, Das MA, Shaik M, Chaitra K, Rao PK, Gangurde SS, Pandey MK, Sundaram RM. Molecular mapping of QTLs for yield related traits in recombinant inbred line (RIL) population derived from the popular rice hybrid KRH-2 and their validation through SNP genotyping. Sci Rep 2020; 10:13695. [PMID: 32792551 PMCID: PMC7427098 DOI: 10.1038/s41598-020-70637-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Accepted: 07/10/2020] [Indexed: 01/27/2023] Open
Abstract
The study was undertaken to identify the quantitative trait loci (QTLs) governing yield and its related traits using a recombinant inbred line (RIL) population derived from the popular rice hybrid, KRH-2 (IR58025A/KMR3R). A genetic map spanning 294.2 cM was constructed with 126 simple sequence repeats (SSR) loci uniformly distributed across the rice genome. QTL analysis using phenotyping and genotyping information identified a total of 22 QTLs. Of these, five major effect QTLs were identified for the following traits: total grain yield/plant (qYLD3-1), panicle weight (qPW3-1), plant height (qPH12-1), flag leaf width (qFLW4-1) and panicle length (qPL3-1), explaining 20.23–22.76% of the phenotypic variance with LOD scores range of 6.5–10.59. Few genomic regions controlling several traits (QTL hotspot) were identified on chromosome 3 for total grain yield/plant (qYLD3-1) and panicle length (qPL3-1). Significant epistatic interactions were also observed for total grain yield per plant (YLD) and panicle length (PL). While most of these QTLs were observed to be co-localized with the previously reported QTL regions, a novel, major QTL associated with panicle length (qPL3-1) was also identified. SNP genotyping of selected high and low yielding RILs and their QTL mapping with 1,082 SNPs validated most of the QTLs identified through SSR genotyping. This facilitated the identification of novel major effect QTLs with much better resolution and precision. In-silico analysis of novel QTLs revealed the biological functions of the putative candidate gene (s) associated with selected traits. Most of the high-yielding RILs possessing the major yield related QTLs were identified to be complete restorers, indicating their possible utilization in development of superior rice hybrids.
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Affiliation(s)
- Swapnil Ravindra Kulkarni
- Crop Improvement Section, ICAR-Indian Institute of Rice Research (ICAR-IIRR), Rajendranagar, Hyderabad, 500030, India
| | - S M Balachandran
- Crop Improvement Section, ICAR-Indian Institute of Rice Research (ICAR-IIRR), Rajendranagar, Hyderabad, 500030, India.
| | - K Ulaganathan
- Centre for Plant Molecular Biology (CPMB), Osmania University, Hyderabad, India
| | - Divya Balakrishnan
- Crop Improvement Section, ICAR-Indian Institute of Rice Research (ICAR-IIRR), Rajendranagar, Hyderabad, 500030, India
| | - M Praveen
- Crop Improvement Section, ICAR-Indian Institute of Rice Research (ICAR-IIRR), Rajendranagar, Hyderabad, 500030, India
| | - A S Hari Prasad
- Crop Improvement Section, ICAR-Indian Institute of Rice Research (ICAR-IIRR), Rajendranagar, Hyderabad, 500030, India
| | - R A Fiyaz
- Crop Improvement Section, ICAR-Indian Institute of Rice Research (ICAR-IIRR), Rajendranagar, Hyderabad, 500030, India
| | - P Senguttuvel
- Crop Improvement Section, ICAR-Indian Institute of Rice Research (ICAR-IIRR), Rajendranagar, Hyderabad, 500030, India
| | - Pragya Sinha
- Crop Improvement Section, ICAR-Indian Institute of Rice Research (ICAR-IIRR), Rajendranagar, Hyderabad, 500030, India
| | - Ravindra R Kale
- Crop Improvement Section, ICAR-Indian Institute of Rice Research (ICAR-IIRR), Rajendranagar, Hyderabad, 500030, India
| | - G Rekha
- Crop Improvement Section, ICAR-Indian Institute of Rice Research (ICAR-IIRR), Rajendranagar, Hyderabad, 500030, India
| | - M B V N Kousik
- Crop Improvement Section, ICAR-Indian Institute of Rice Research (ICAR-IIRR), Rajendranagar, Hyderabad, 500030, India
| | - G Harika
- Crop Improvement Section, ICAR-Indian Institute of Rice Research (ICAR-IIRR), Rajendranagar, Hyderabad, 500030, India
| | - M Anila
- Crop Improvement Section, ICAR-Indian Institute of Rice Research (ICAR-IIRR), Rajendranagar, Hyderabad, 500030, India
| | - E Punniakoti
- Crop Improvement Section, ICAR-Indian Institute of Rice Research (ICAR-IIRR), Rajendranagar, Hyderabad, 500030, India
| | - T Dilip
- Crop Improvement Section, ICAR-Indian Institute of Rice Research (ICAR-IIRR), Rajendranagar, Hyderabad, 500030, India
| | - S K Hajira
- Crop Improvement Section, ICAR-Indian Institute of Rice Research (ICAR-IIRR), Rajendranagar, Hyderabad, 500030, India
| | - K Pranathi
- Crop Improvement Section, ICAR-Indian Institute of Rice Research (ICAR-IIRR), Rajendranagar, Hyderabad, 500030, India
| | - M Ayyappa Das
- Crop Improvement Section, ICAR-Indian Institute of Rice Research (ICAR-IIRR), Rajendranagar, Hyderabad, 500030, India
| | - Mastanbee Shaik
- Crop Improvement Section, ICAR-Indian Institute of Rice Research (ICAR-IIRR), Rajendranagar, Hyderabad, 500030, India
| | - K Chaitra
- Crop Improvement Section, ICAR-Indian Institute of Rice Research (ICAR-IIRR), Rajendranagar, Hyderabad, 500030, India
| | - P Koteswara Rao
- Crop Improvement Section, ICAR-Indian Institute of Rice Research (ICAR-IIRR), Rajendranagar, Hyderabad, 500030, India
| | - Sunil S Gangurde
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Manish K Pandey
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - R M Sundaram
- Crop Improvement Section, ICAR-Indian Institute of Rice Research (ICAR-IIRR), Rajendranagar, Hyderabad, 500030, India.
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16
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Sarif HM, Rafii MY, Ramli A, Oladosu Y, Musa HM, Rahim HA, Zuki ZM, Chukwu SC. Genetic diversity and variability among pigmented rice germplasm using molecular marker and morphological traits. BIOTECHNOL BIOTEC EQ 2020. [DOI: 10.1080/13102818.2020.1804451] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Affiliation(s)
- Hamidah Mohd Sarif
- Department of Crop Science, Faculty of Agriculture, Universiti Putra Malaysia (UPM), Serdang, Selangor, Malaysia
| | - Mohd Y. Rafii
- Department of Crop Science, Faculty of Agriculture, Universiti Putra Malaysia (UPM), Serdang, Selangor, Malaysia
- Laboratory of Climate-Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia (UPM), Serdang, Selangor, Malaysia
| | - Asfaliza Ramli
- Rice Research Center, Malaysian Agriculture and Research Development Institute (MARDI), Serdang, Selangor, Malaysia
| | - Yusuff Oladosu
- Laboratory of Climate-Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia (UPM), Serdang, Selangor, Malaysia
| | - Hanafi M. Musa
- Laboratory of Climate-Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia (UPM), Serdang, Selangor, Malaysia
| | - Harun A. Rahim
- Agrotechnology and Bioscience Division, Malaysian Nuclear Agency Bangi, Selangor, Malaysia
| | - Zakiah Mohd Zuki
- Department of Crop Science, Faculty of Agriculture, Universiti Putra Malaysia (UPM), Serdang, Selangor, Malaysia
| | - Samuel Chibuike Chukwu
- Laboratory of Climate-Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia (UPM), Serdang, Selangor, Malaysia
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17
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Salgotra RK, Stewart CN. Functional Markers for Precision Plant Breeding. Int J Mol Sci 2020; 21:E4792. [PMID: 32640763 PMCID: PMC7370099 DOI: 10.3390/ijms21134792] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 06/19/2020] [Accepted: 07/02/2020] [Indexed: 01/24/2023] Open
Abstract
Advances in molecular biology including genomics, high-throughput sequencing, and genome editing enable increasingly faster and more precise cultivar development. Identifying genes and functional markers (FMs) that are highly associated with plant phenotypic variation is a grand challenge. Functional genomics approaches such as transcriptomics, targeting induced local lesions in genomes (TILLING), homologous recombinant (HR), association mapping, and allele mining are all strategies to identify FMs for breeding goals, such as agronomic traits and biotic and abiotic stress resistance. The advantage of FMs over other markers used in plant breeding is the close genomic association of an FM with a phenotype. Thereby, FMs may facilitate the direct selection of genes associated with phenotypic traits, which serves to increase selection efficiencies to develop varieties. Herein, we review the latest methods in FM development and how FMs are being used in precision breeding for agronomic and quality traits as well as in breeding for biotic and abiotic stress resistance using marker assisted selection (MAS) methods. In summary, this article describes the use of FMs in breeding for development of elite crop cultivars to enhance global food security goals.
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Affiliation(s)
- Romesh K. Salgotra
- School of Biotechnology, Sher-e-Kashmir University of Agricultural Sciences & Technology of Jammu, Chatha, Jammu 190008, India
| | - C. Neal Stewart
- Department of Plant Sciences, University of Tennessee, Knoxville, TN 37996, USA
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18
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Gouda G, Gupta MK, Donde R, Mohapatra T, Vadde R, Behera L. Marker-assisted selection for grain number and yield-related traits of rice ( Oryza sativa L.). PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2020; 26:885-898. [PMID: 32377039 PMCID: PMC7196572 DOI: 10.1007/s12298-020-00773-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 02/11/2020] [Accepted: 02/13/2020] [Indexed: 05/11/2023]
Abstract
Continuous rise in the human population has resulted in an upsurge in food demand, which in turn demand grain yield enhancement of cereal crops, including rice. Rice yield is estimated via the number of tillers, grain number per panicles, and the number of spikes present per panicle. Marker-assisted selection (MAS) serve as one of the best ways to introduce QTLs/gene associated with yield in the rice plant. MAS has also been employed effectively in dissecting several other complex agricultural traits, for instance, drought, cold tolerance, salinity, etc. in rice plants. Thus, in this review, authors attempted to collect information about various genes/QTLs associated with high yield, including grain number, in rice and how different scheme of MAS can be employed to introduce them in rice (Oryza sativa L.) plant, which in turn will enhance rice yield. Information obtained to date suggest that, numerous QTLs, e.g., Gn1a, Dep1, associated with grain number and yield-related traits, have been identified either via mapping or cloning approaches. These QTLs have been successfully introduced into rice plants using various schemes of MAS for grain yield enhancement in rice. However, sometimes, MAS does not perform well in breeding, which might be due to lack of resources, skilled labors, reliable markers, and high costs associated with MAS. Thus, by overcoming these problems, we can enhance the application of MAS in plant breeding, which, in turn, may help us in increasing yield, which subsequently may help in bridging the gap between demand and supply of food for the continuously growing population.
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Affiliation(s)
- Gayatri Gouda
- ICAR-National Rice Research Institute, Cuttack, Odisha 753 006 India
| | - Manoj Kumar Gupta
- Department of Biotechnology and Bioinformatics, Yogi Vemana University, Kadapa, Andhra Pradesh 516 005 India
| | - Ravindra Donde
- ICAR-National Rice Research Institute, Cuttack, Odisha 753 006 India
| | - Trilochan Mohapatra
- Secretary (DARE) and Director General (ICAR), Government of India, New Delhi, India
| | - Ramakrishna Vadde
- Department of Biotechnology and Bioinformatics, Yogi Vemana University, Kadapa, Andhra Pradesh 516 005 India
| | - Lambodar Behera
- ICAR-National Rice Research Institute, Cuttack, Odisha 753 006 India
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Submergence Tolerance in Rice: Review of Mechanism, Breeding and, Future Prospects. SUSTAINABILITY 2020. [DOI: 10.3390/su12041632] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Flooding or submergence is one of the major environmental stressors affecting many man-made and natural ecosystems worldwide. The increase in the frequency and duration of heavy rainfall due to climate change has negatively affected plant growth and development, which eventually causes the death of plants if it persists for days. Most crops, especially rice, being a semi-aquatic plant, are greatly affected by flooding, leading to yield losses each year. Genetic variability in the plant response to flooding includes the quiescence scheme, which allows underwater endurance of a prolonged period, escape strategy through stem elongation, and alterations in plant architecture and metabolism. Investigating the mechanism for flooding survival in wild species and modern rice has yielded significant insight into developmental, physiological, and molecular strategies for submergence and waterlogging survival. Significant progress in the breeding of submergence tolerant rice varieties has been made during the last decade following the successful identification and mapping of a quantitative trait locus for submergence tolerance, designated as SUBMERGENCE 1 (SUB1) from the FR13A landrace. Using marker-assisted backcrossing, the SUB1 QTL (quantitative trait locus) has been incorporated into many elite varieties within a short time and with high precision as compared with conventional breeding methods. Despite the advancement in submergence tolerance, for future studies, there is a need for practical approaches exploring genome-wide association studies (GWA) and QTL in combination with specific tolerance traits, such as drought, salinity, disease and insect resistance.
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Oladosu Y, Rafii MY, Samuel C, Fatai A, Magaji U, Kareem I, Kamarudin ZS, Muhammad I, Kolapo K. Drought Resistance in Rice from Conventional to Molecular Breeding: A Review. Int J Mol Sci 2019; 20:E3519. [PMID: 31323764 PMCID: PMC6678081 DOI: 10.3390/ijms20143519] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 05/06/2019] [Accepted: 05/06/2019] [Indexed: 11/30/2022] Open
Abstract
Drought is the leading threat to agricultural food production, especially in the cultivation of rice, a semi-aquatic plant. Drought tolerance is a complex quantitative trait with a complicated phenotype that affects different developmental stages in plants. The level of susceptibility or tolerance of rice to several drought conditions is coordinated by the action of different drought-responsive genes in relation with other stress components which stimulate signal transduction pathways. Interdisciplinary researchers have broken the complex mechanism of plant tolerance using various methods such as genetic engineering or marker-assisted selection to develop a new cultivar with improved drought resistance. The main objectives of this review were to highlight the current method of developing a durable drought-resistant rice variety through conventional breeding and the use of biotechnological tools and to comprehensively review the available information on drought-resistant genes, QTL analysis, gene transformation and marker-assisted selection. The response, indicators, causes, and adaptation processes to the drought stress were discussed in the review. Overall, this review provides a systemic glimpse of breeding methods from conventional to the latest innovation in molecular development of drought-tolerant rice variety. This information could serve as guidance for researchers and rice breeders.
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Affiliation(s)
- Yusuff Oladosu
- Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia (UPM), Serdang 43400, Selangor, Malaysia
| | - Mohd Y Rafii
- Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia (UPM), Serdang 43400, Selangor, Malaysia.
- Department of Crop Science, Faculty of Agriculture, Universiti Putra Malaysia (UPM), Serdang, 43400 UPM, Selangor, Malaysia.
| | - Chukwu Samuel
- Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia (UPM), Serdang 43400, Selangor, Malaysia
| | - Arolu Fatai
- Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia (UPM), Serdang 43400, Selangor, Malaysia
| | - Usman Magaji
- Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia (UPM), Serdang 43400, Selangor, Malaysia
| | - Isiaka Kareem
- Department of Agronomy, University of Ilorin, Ilorin, P.M.B. 1515, Nigeria
| | - Zarifth Shafika Kamarudin
- Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia (UPM), Serdang 43400, Selangor, Malaysia
| | - Isma'ila Muhammad
- Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia (UPM), Serdang 43400, Selangor, Malaysia
| | - Kazeem Kolapo
- Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia (UPM), Serdang 43400, Selangor, Malaysia
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