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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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Ntakirutimana F, Tranchant-Dubreuil C, Cubry P, Chougule K, Zhang J, Wing RA, Adam H, Lorieux M, Jouannic S. Genome-wide association analysis identifies natural allelic variants associated with panicle architecture variation in African rice, Oryza glaberrima Steud. G3 (BETHESDA, MD.) 2023; 13:jkad174. [PMID: 37535690 PMCID: PMC10542218 DOI: 10.1093/g3journal/jkad174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 06/12/2023] [Accepted: 07/18/2023] [Indexed: 08/05/2023]
Abstract
African rice (Oryza glaberrima Steud), a short-day cereal crop closely related to Asian rice (Oryza sativa L.), has been cultivated in Sub-Saharan Africa for ∼ 3,000 years. Although less cultivated globally, it is a valuable genetic resource in creating high-yielding cultivars that are better adapted to diverse biotic and abiotic stresses. While inflorescence architecture, a key trait for rice grain yield improvement, has been extensively studied in Asian rice, the morphological and genetic determinants of this complex trait are less understood in African rice. In this study, using a previously developed association panel of 162 O. glaberrima accessions and new SNP variants characterized through mapping to a new version of the O. glaberrima reference genome, we conducted a genome-wide association study of four major morphological panicle traits. We have found a total of 41 stable genomic regions that are significantly associated with these traits, of which 13 co-localized with previously identified QTLs in O. sativa populations and 28 were unique for this association panel. Additionally, we found a genomic region of interest on chromosome 3 that was associated with the number of spikelets and primary and secondary branches. Within this region was localized the O. sativa ortholog of the PHYTOCHROME B gene (Oglab_006903/OgPHYB). Haplotype analysis revealed the occurrence of natural sequence variants at the OgPHYB locus associated with panicle architecture variation through modulation of the flowering time phenotype, whereas no equivalent alleles were found in O. sativa. The identification in this study of genomic regions specific to O. glaberrima indicates panicle-related intra-specific genetic variation in this species, increasing our understanding of the underlying molecular processes governing panicle architecture. Identified candidate genes and major haplotypes may facilitate the breeding of new African rice cultivars with preferred panicle traits.
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Affiliation(s)
| | | | - Philippe Cubry
- DIADE, University of Montpellier, IRD, CIRAD, 34394 Montpellier, France
| | - Kapeel Chougule
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Jianwei Zhang
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Rod A Wing
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA
- Center for Desert Agriculture, Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955, Saudi Arabia
| | - Hélène Adam
- DIADE, University of Montpellier, IRD, CIRAD, 34394 Montpellier, France
| | - Mathias Lorieux
- DIADE, University of Montpellier, IRD, CIRAD, 34394 Montpellier, France
| | - Stefan Jouannic
- DIADE, University of Montpellier, IRD, CIRAD, 34394 Montpellier, France
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Horgan FG. Slowing virulence adaptation in Asian rice planthoppers through migration-based deployment of resistance genes. CURRENT OPINION IN INSECT SCIENCE 2023; 55:101004. [PMID: 36640841 DOI: 10.1016/j.cois.2023.101004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 12/29/2022] [Accepted: 01/04/2023] [Indexed: 06/17/2023]
Abstract
Advances in molecular biology have accelerated rice breeding for resistance to Asian planthoppers. However, experience shows that planthoppers quickly adapt to resistance in tropical overwintering areas. With only limited sources available, the large-scale deployment of resistance genes can rapidly reduce the utility of these public goods. Planthoppers that migrate from tropical to temperate Asia carry virulence against many resistance genes, but adapt more slowly to resistant rice in temperate regions. Therefore, by restricting deployment of selected genes to temperate regions, virulence-adaptation rates and the volume of migrants returning to overwintering sites could be reduced. The current open exchange of breeding materials throughout Asia urgently requires an international, multidisciplinary, stakeholder coalition to promote a more sustainable deployment of planthopper-resistant rice.
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Affiliation(s)
- Finbarr G Horgan
- EcoLaVerna Integral Restoration Ecology, Bridestown, Kildinan, T56 P499 County Cork, Ireland; Escuela de Agronomía, Facultad de Ciencias Agrarias y Forestales, Universidad Católica del Maule, Casilla 7-D, Curicó 3349001, Chile; Centre for Pesticide Suicide Prevention, University/BHF Centre for Cardiovascular Science, University of Edinburgh, Edinburgh EH16 4TJ, UK.
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Liu X, Tian D, Li C, Tang B, Wang Z, Zhang R, Pan Y, Wang Y, Zou D, Zhang Z, Song S. GWAS Atlas: an updated knowledgebase integrating more curated associations in plants and animals. Nucleic Acids Res 2022; 51:D969-D976. [PMID: 36263826 PMCID: PMC9825481 DOI: 10.1093/nar/gkac924] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 10/02/2022] [Accepted: 10/19/2022] [Indexed: 01/30/2023] Open
Abstract
GWAS Atlas (https://ngdc.cncb.ac.cn/gwas/) is a manually curated resource of genome-wide genotype-to-phenotype associations for a wide range of species. Here, we present an updated implementation of GWAS Atlas by curating and incorporating more high-quality associations, with significant improvements and advances over the previous version. Specifically, the current release of GWAS Atlas incorporates a total of 278,109 curated genotype-to-phenotype associations for 1,444 different traits across 15 species (10 plants and 5 animals) from 830 publications and 3,432 studies. A collection of 6,084 lead SNPs of 439 traits and 486 experiment-validated causal variants of 157 traits are newly added. Moreover, 1,056 trait ontology terms are newly defined, resulting in 1,172 and 431 terms for Plant Phenotype and Trait Ontology and Animal Phenotype and Trait Ontology, respectively. Additionally, it is equipped with four online analysis tools and a submission platform, allowing users to perform data analysis and data submission. Collectively, as a core resource in the National Genomics Data Center, GWAS Atlas provides valuable genotype-to-phenotype associations for a diversity of species and thus plays an important role in agronomic trait study and molecular breeding.
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Affiliation(s)
| | | | | | - Bixia Tang
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
| | - Zhonghuang Wang
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China,CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Rongqin Zhang
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China,CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China,Sino-Danish College, University of Chinese Academy of Sciences, Beijing 100049, China,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yitong Pan
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China,CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformatics, Beijing 100101, China,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yi Wang
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China,CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Dong Zou
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
| | - Zhang Zhang
- Correspondence may also be addressed to Zhang Zhang. Tel: +86 10 84097261; Fax: +86 10 84097720;
| | - Shuhui Song
- To whom correspondence should be addressed. Tel: +86 10 84097620; Fax: +86 10 84097720;
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Hackauf B, Siekmann D, Fromme FJ. Improving Yield and Yield Stability in Winter Rye by Hybrid Breeding. PLANTS (BASEL, SWITZERLAND) 2022; 11:2666. [PMID: 36235531 PMCID: PMC9571156 DOI: 10.3390/plants11192666] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 09/27/2022] [Accepted: 10/04/2022] [Indexed: 06/16/2023]
Abstract
Rye is the only cross-pollinating small-grain cereal. The unique reproduction biology results in an exceptional complexity concerning genetic improvement of rye by breeding. Rye is a close relative of wheat and has a strong adaptation potential that refers to its mating system, making this overlooked cereal readily adjustable to a changing environment. Rye breeding addresses the emerging challenges of food security associated with climate change. The systematic identification, management, and use of its valuable natural diversity became a feasible option in outbreeding rye only following the establishment of hybrid breeding late in the 20th century. In this article, we review the most recent technological advances to improve yield and yield stability in winter rye. Based on recently released reference genome sequences, SMART breeding approaches are described to counterbalance undesired linkage drag effects of major restorer genes on grain yield. We present the development of gibberellin-sensitive semidwarf hybrids as a novel plant breeding innovation based on an approach that is different from current methods of increasing productivity in rye and wheat. Breeding of new rye cultivars with improved performance and resilience is indispensable for a renaissance of this healthy minor cereal as a homogeneous commodity with cultural relevance in Europe that allows for comparatively smooth but substantial complementation of wheat with rye-based diets, supporting the necessary restoration of the balance between human action and nature.
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Affiliation(s)
- Bernd Hackauf
- Julius Kühn Institute, Institute for Breeding Research on Agricultural Crops, Rudolf-Schick-Platz 3a, 18190 Sanitz, Germany
| | - Dörthe Siekmann
- Hybro Saatzucht GmbH & Co. KG, Langlinger Straße 3, 29565 Wriedel, Germany
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Tan YC, Kumar AU, Wong YP, Ling APK. Bioinformatics approaches and applications in plant biotechnology. J Genet Eng Biotechnol 2022; 20:106. [PMID: 35838847 PMCID: PMC9287518 DOI: 10.1186/s43141-022-00394-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 07/05/2022] [Indexed: 11/10/2022]
Abstract
BACKGROUND In recent years, major advance in molecular biology and genomic technologies have led to an exponential growth in biological information. As the deluge of genomic information, there is a parallel growth in the demands of tools in the storage and management of data, and the development of software for analysis, visualization, modelling, and prediction of large data set. MAIN BODY Particularly in plant biotechnology, the amount of information has multiplied exponentially with a large number of databases available from many individual plant species. Efficient bioinformatics tools and methodologies are also developed to allow rapid genome sequence and the study of plant genome in the 'omics' approach. This review focuses on the various bioinformatic applications in plant biotechnology, and their advantages in improving the outcome in agriculture. The challenges or limitations faced in plant biotechnology in the aspect of bioinformatics approach that explained the low progression in plant genomics than in animal genomics are also reviewed and assessed. CONCLUSION There is a critical need for effective bioinformatic tools, which are able to provide longer reads with unbiased coverage in order to overcome the complexity of the plant's genome. The advancement in bioinformatics is not only beneficial to the field of plant biotechnology and agriculture sectors, but will also contribute enormously to the future of humanity.
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Affiliation(s)
- Yung Cheng Tan
- Division of Applied Biomedical Sciences and Biotechnology, School of Health Sciences, International Medical University, 126 Jalan Jalil Perkasa 19, Bukit Jalil, 57000, Kuala Lumpur, Malaysia
| | - Asqwin Uthaya Kumar
- Division of Applied Biomedical Sciences and Biotechnology, School of Health Sciences, International Medical University, 126 Jalan Jalil Perkasa 19, Bukit Jalil, 57000, Kuala Lumpur, Malaysia.,School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Malaysia
| | - Ying Pei Wong
- Division of Applied Biomedical Sciences and Biotechnology, School of Health Sciences, International Medical University, 126 Jalan Jalil Perkasa 19, Bukit Jalil, 57000, Kuala Lumpur, Malaysia
| | - Anna Pick Kiong Ling
- Division of Applied Biomedical Sciences and Biotechnology, School of Health Sciences, International Medical University, 126 Jalan Jalil Perkasa 19, Bukit Jalil, 57000, Kuala Lumpur, Malaysia.
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Current Advances and Future Prospects for Molecular Research for Agronomically Important Traits in Rice. Int J Mol Sci 2022; 23:ijms23147531. [PMID: 35886876 PMCID: PMC9316905 DOI: 10.3390/ijms23147531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 07/02/2022] [Accepted: 07/05/2022] [Indexed: 02/04/2023] Open
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Muthuramalingam P, Jeyasri R, Rakkammal K, Satish L, Shamili S, Karthikeyan A, Valliammai A, Priya A, Selvaraj A, Gowri P, Wu QS, Karutha Pandian S, Shin H, Chen JT, Baskar V, Thiruvengadam M, Akilan M, Ramesh M. Multi-Omics and Integrative Approach towards Understanding Salinity Tolerance in Rice: A Review. BIOLOGY 2022; 11:biology11071022. [PMID: 36101403 PMCID: PMC9312129 DOI: 10.3390/biology11071022] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 07/04/2022] [Accepted: 07/04/2022] [Indexed: 11/16/2022]
Abstract
Rice (Oryza sativa L.) plants are simultaneously encountered by environmental stressors, most importantly salinity stress. Salinity is the major hurdle that can negatively impact growth and crop yield. Understanding the salt stress and its associated complex trait mechanisms for enhancing salt tolerance in rice plants would ensure future food security. The main aim of this review is to provide insights and impacts of molecular-physiological responses, biochemical alterations, and plant hormonal signal transduction pathways in rice under saline stress. Furthermore, the review highlights the emerging breakthrough in multi-omics and computational biology in identifying the saline stress-responsive candidate genes and transcription factors (TFs). In addition, the review also summarizes the biotechnological tools, genetic engineering, breeding, and agricultural practicing factors that can be implemented to realize the bottlenecks and opportunities to enhance salt tolerance and develop salinity tolerant rice varieties. Future studies pinpointed the augmentation of powerful tools to dissect the salinity stress-related novel players, reveal in-depth mechanisms and ways to incorporate the available literature, and recent advancements to throw more light on salinity responsive transduction pathways in plants. Particularly, this review unravels the whole picture of salinity stress tolerance in rice by expanding knowledge that focuses on molecular aspects.
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Affiliation(s)
- Pandiyan Muthuramalingam
- Department of Biotechnology, Science Campus, Alagappa University, Karaikudi 630 003, India; (P.M.); (R.J.); (K.R.); (A.V.); (A.P.); (A.S.); (S.K.P.)
- Department of Horticultural Science, Gyeongsang National University, Jinju 52725, Korea
- Department of GreenBio Science, Gyeongsang National University, Jinju 52725, Korea
| | - Rajendran Jeyasri
- Department of Biotechnology, Science Campus, Alagappa University, Karaikudi 630 003, India; (P.M.); (R.J.); (K.R.); (A.V.); (A.P.); (A.S.); (S.K.P.)
| | - Kasinathan Rakkammal
- Department of Biotechnology, Science Campus, Alagappa University, Karaikudi 630 003, India; (P.M.); (R.J.); (K.R.); (A.V.); (A.P.); (A.S.); (S.K.P.)
| | - Lakkakula Satish
- Avram and Stella Goldstein-Goren Department of Biotechnology Engineering, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel;
- The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel;
| | - Sasanala Shamili
- The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel;
| | - Adhimoolam Karthikeyan
- Subtropical Horticulture Research Institute, Jeju National University, Jeju 63243, Korea;
| | - Alaguvel Valliammai
- Department of Biotechnology, Science Campus, Alagappa University, Karaikudi 630 003, India; (P.M.); (R.J.); (K.R.); (A.V.); (A.P.); (A.S.); (S.K.P.)
| | - Arumugam Priya
- Department of Biotechnology, Science Campus, Alagappa University, Karaikudi 630 003, India; (P.M.); (R.J.); (K.R.); (A.V.); (A.P.); (A.S.); (S.K.P.)
| | - Anthonymuthu Selvaraj
- Department of Biotechnology, Science Campus, Alagappa University, Karaikudi 630 003, India; (P.M.); (R.J.); (K.R.); (A.V.); (A.P.); (A.S.); (S.K.P.)
| | - Pandiyan Gowri
- Department of Botany, Science Campus, Alagappa University, Karaikudi 630 003, India;
| | - Qiang-Sheng Wu
- College of Horticulture and Gardening, Yangtze University, Jingzhou 434025, China;
- Department of Chemistry, Faculty of Science, University of Hradec Kralove, 50003 Hradec Kralove, Czech Republic
| | - Shunmugiah Karutha Pandian
- Department of Biotechnology, Science Campus, Alagappa University, Karaikudi 630 003, India; (P.M.); (R.J.); (K.R.); (A.V.); (A.P.); (A.S.); (S.K.P.)
| | - Hyunsuk Shin
- Department of Horticultural Science, Gyeongsang National University, Jinju 52725, Korea
- Department of GreenBio Science, Gyeongsang National University, Jinju 52725, Korea
- Correspondence: (H.S.); (M.T.); (M.R.)
| | - Jen-Tsung Chen
- Department of Life Sciences, National University of Kaohsiung, Kaohsiung 811, Taiwan;
| | - Venkidasamy Baskar
- Department of Oral and Maxillofaciel Surgery, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Chennai 602 105, India;
| | - Muthu Thiruvengadam
- Department of Crop Science, College of Sanghuh Life Science, Konkuk University, Seoul 05029, Korea
- Correspondence: (H.S.); (M.T.); (M.R.)
| | - Manoharan Akilan
- Department of Plant Breeding and Genetics, Anbil Dharmalingam Agricultural College and Research Institute, Tamil Nadu Agricultural University, Trichy 620 027, India;
| | - Manikandan Ramesh
- Department of Biotechnology, Science Campus, Alagappa University, Karaikudi 630 003, India; (P.M.); (R.J.); (K.R.); (A.V.); (A.P.); (A.S.); (S.K.P.)
- Correspondence: (H.S.); (M.T.); (M.R.)
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Tian Y, Thrimawithana A, Ding T, Guo J, Gleave A, Chagné D, Ampomah‐Dwamena C, Ireland HS, Schaffer RJ, Luo Z, Wang M, An X, Wang D, Gao Y, Wang K, Zhang H, Zhang R, Zhou Z, Yan Z, Zhang L, Zhang C, Cong P, Deng CH, Yao J. Transposon insertions regulate genome-wide allele-specific expression and underpin flower colour variations in apple (Malus spp.). PLANT BIOTECHNOLOGY JOURNAL 2022; 20:1285-1297. [PMID: 35258172 PMCID: PMC9241373 DOI: 10.1111/pbi.13806] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 02/20/2022] [Accepted: 02/25/2022] [Indexed: 06/14/2023]
Abstract
Allele-specific expression (ASE) can lead to phenotypic diversity and evolution. However, the mechanisms regulating ASE are not well understood, particularly in woody perennial plants. In this study, we investigated ASE genes in the apple cultivar 'Royal Gala' (RG). A high quality chromosome-level genome was assembled using a homozygous tetra-haploid RG plant, derived from anther cultures. Using RNA-sequencing (RNA-seq) data from RG flower and fruit tissues, we identified 2091 ASE genes. Compared with the haploid genome of 'Golden Delicious' (GD), a parent of RG, we distinguished the genomic sequences between the two alleles of 817 ASE genes, and further identified allele-specific presence of a transposable element (TE) in the upstream region of 354 ASE genes. These included MYB110a that encodes a transcription factor regulating anthocyanin biosynthesis. Interestingly, another ASE gene, MYB10 also showed an allele-specific TE insertion and was identified using genome data of other apple cultivars. The presence of the TE insertion in both MYB genes was positively associated with ASE and anthocyanin accumulation in apple petals through analysis of 231 apple accessions, and thus underpins apple flower colour evolution. Our study demonstrated the importance of TEs in regulating ASE on a genome-wide scale and presents a novel method for rapid identification of ASE genes and their regulatory elements in plants.
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Affiliation(s)
- Yi Tian
- Research Institute of PomologyChinese Academy of Agricultural SciencesXinchengChina
- Present address:
Hebei Agricultural UniversityBaodingChina
| | - Amali Thrimawithana
- The New Zealand Institute for Plant and Food Research Limited (PFR)Mount Albert Research CentreAucklandNew Zealand
| | - Tiyu Ding
- Zhengzhou Fruit Research InstituteChinese Academy of Agricultural SciencesZhengzhouChina
| | - Jian Guo
- Zhengzhou Fruit Research InstituteChinese Academy of Agricultural SciencesZhengzhouChina
| | - Andrew Gleave
- The New Zealand Institute for Plant and Food Research Limited (PFR)Mount Albert Research CentreAucklandNew Zealand
| | - David Chagné
- PFRPalmerston North Research CentrePalmerston NorthNew Zealand
| | - Charles Ampomah‐Dwamena
- The New Zealand Institute for Plant and Food Research Limited (PFR)Mount Albert Research CentreAucklandNew Zealand
| | - Hilary S. Ireland
- The New Zealand Institute for Plant and Food Research Limited (PFR)Mount Albert Research CentreAucklandNew Zealand
| | - Robert J. Schaffer
- The New Zealand Institute for Plant and Food Research Limited (PFR)Mount Albert Research CentreAucklandNew Zealand
- School of Biological SciencesAuckland Mail CentreThe University of AucklandAucklandNew Zealand
| | - Zhiwei Luo
- The New Zealand Institute for Plant and Food Research Limited (PFR)Mount Albert Research CentreAucklandNew Zealand
| | - Meili Wang
- Zhengzhou Fruit Research InstituteChinese Academy of Agricultural SciencesZhengzhouChina
| | - Xiuhong An
- Research Institute of PomologyChinese Academy of Agricultural SciencesXinchengChina
- Present address:
Hebei Agricultural UniversityBaodingChina
| | - Dajiang Wang
- Research Institute of PomologyChinese Academy of Agricultural SciencesXinchengChina
| | - Yuan Gao
- Research Institute of PomologyChinese Academy of Agricultural SciencesXinchengChina
| | - Kun Wang
- Research Institute of PomologyChinese Academy of Agricultural SciencesXinchengChina
| | - Hengtao Zhang
- Zhengzhou Fruit Research InstituteChinese Academy of Agricultural SciencesZhengzhouChina
| | - Ruiping Zhang
- Zhengzhou Fruit Research InstituteChinese Academy of Agricultural SciencesZhengzhouChina
| | - Zhe Zhou
- Zhengzhou Fruit Research InstituteChinese Academy of Agricultural SciencesZhengzhouChina
| | - Zhenli Yan
- Zhengzhou Fruit Research InstituteChinese Academy of Agricultural SciencesZhengzhouChina
| | - Liyi Zhang
- Research Institute of PomologyChinese Academy of Agricultural SciencesXinchengChina
| | - Caixia Zhang
- Research Institute of PomologyChinese Academy of Agricultural SciencesXinchengChina
| | - Peihua Cong
- Research Institute of PomologyChinese Academy of Agricultural SciencesXinchengChina
| | - Cecilia H. Deng
- The New Zealand Institute for Plant and Food Research Limited (PFR)Mount Albert Research CentreAucklandNew Zealand
| | - Jia‐Long Yao
- The New Zealand Institute for Plant and Food Research Limited (PFR)Mount Albert Research CentreAucklandNew Zealand
- Zhengzhou Fruit Research InstituteChinese Academy of Agricultural SciencesZhengzhouChina
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The first long-read nuclear genome assembly of Oryza australiensis, a wild rice from northern Australia. Sci Rep 2022; 12:10823. [PMID: 35752642 PMCID: PMC9233661 DOI: 10.1038/s41598-022-14893-5] [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: 11/17/2021] [Accepted: 06/14/2022] [Indexed: 11/17/2022] Open
Abstract
Oryza australiensis is a wild rice native to monsoonal northern Australia. The International Oryza Map Alignment Project emphasises its significance as the sole representative of the EE genome clade. Assembly of the O. australiensis genome has previously been challenging due to its high Long Terminal Repeat (LTR) retrotransposon (RT) content. Oxford Nanopore long reads were combined with Illumina short reads to generate a high-quality ~ 858 Mbp genome assembly within 850 contigs with 46× long read coverage. Reference-guided scaffolding increased genome contiguity, placing 88.2% of contigs into 12 pseudomolecules. After alignment to the Oryza sativa cv. Nipponbare genome, we observed several structural variations. PacBio Iso-Seq data were generated for five distinct tissues to improve the functional annotation of 34,587 protein-coding genes and 42,329 transcripts. We also report SNV numbers for three additional O. australiensis genotypes based on Illumina re-sequencing. Although genetic similarity reflected geographical separation, the density of SNVs also correlated with our previous report on variations in salinity tolerance. This genome re-confirms the genetic remoteness of the O. australiensis lineage within the O. officinalis genome complex. Assembly of a high-quality genome for O. australiensis provides an important resource for the discovery of critical genes involved in development and stress tolerance.
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Understanding the Dynamics of Blast Resistance in Rice-Magnaporthe oryzae Interactions. J Fungi (Basel) 2022; 8:jof8060584. [PMID: 35736067 PMCID: PMC9224618 DOI: 10.3390/jof8060584] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 05/03/2022] [Accepted: 05/10/2022] [Indexed: 01/09/2023] Open
Abstract
Rice is a global food grain crop for more than one-third of the human population and a source for food and nutritional security. Rice production is subjected to various stresses; blast disease caused by Magnaporthe oryzae is one of the major biotic stresses that has the potential to destroy total crop under severe conditions. In the present review, we discuss the importance of rice and blast disease in the present and future global context, genomics and molecular biology of blast pathogen and rice, and the molecular interplay between rice–M. oryzae interaction governed by different gene interaction models. We also elaborated in detail on M. oryzae effector and Avr genes, and the role of noncoding RNAs in disease development. Further, rice blast resistance QTLs; resistance (R) genes; and alleles identified, cloned, and characterized are discussed. We also discuss the utilization of QTLs and R genes for blast resistance through conventional breeding and transgenic approaches. Finally, we review the demonstrated examples and potential applications of the latest genome-editing tools in understanding and managing blast disease in rice.
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Gupta R, Khan MIR, Gonzalez Hernandez JL, Wang W, Bindschedler LV. Editorial: Improvement of Rice Through "-omics" Approaches. FRONTIERS IN PLANT SCIENCE 2022; 13:926976. [PMID: 35685014 PMCID: PMC9171492 DOI: 10.3389/fpls.2022.926976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Accepted: 05/09/2022] [Indexed: 06/15/2023]
Affiliation(s)
- Ravi Gupta
- College of General Education, Kookmin University, Seoul, South Korea
| | | | - Jose Luis Gonzalez Hernandez
- Department of Agronomy, Horticulture, and Plant Science, South Dakota State University, Brookings, SD, United States
| | - Wei Wang
- College of Life Sciences, Henan Agricultural University, Zhengzhou, China
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Garibay-Hernández A, Kessler N, Józefowicz AM, Türksoy GM, Lohwasser U, Mock HP. Untargeted metabotyping to study phenylpropanoid diversity in crop plants. PHYSIOLOGIA PLANTARUM 2021; 173:680-697. [PMID: 33963574 DOI: 10.1111/ppl.13458] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 05/03/2021] [Accepted: 05/05/2021] [Indexed: 06/12/2023]
Abstract
Plant genebanks constitute a key resource for breeding to ensure crop yield under changing environmental conditions. Because of their roles in a range of stress responses, phenylpropanoids are promising targets. Phenylpropanoids comprise a wide array of metabolites; however, studies regarding their diversity and the underlying genes are still limited for cereals. The assessment of barley diversity via genotyping-by-sequencing is in rapid progress. Exploring these resources by integrating genetic association studies to in-depth metabolomic profiling provides a valuable opportunity to study barley phenylpropanoid metabolism; but poses a challenge by demanding large-scale approaches. Here, we report an LC-PDA-MS workflow for barley high-throughput metabotyping. Without prior construction of a species-specific library, this method produced phenylpropanoid-enriched metabotypes with which the abundance of putative metabolic features was assessed across hundreds of samples in a single-processed data matrix. The robustness of the analytical performance was tested using a standard mix and extracts from two selected cultivars: Scarlett and Barke. The large-scale analysis of barley extracts showed (1) that barley flag leaf profiles were dominated by glycosylation derivatives of isovitexin, isoorientin, and isoscoparin; (2) proved the workflow's capability to discriminate within genotypes; (3) highlighted the role of glycosylation in barley phenylpropanoid diversity. Using the barley S42IL mapping population, the workflow proved useful for metabolic quantitative trait loci purposes. The protocol can be readily applied not only to explore the barley phenylpropanoid diversity represented in genebanks but also to study species whose profiles differ from those of cereals: the crop Helianthus annuus (sunflower) and the model plant Arabidopsis thaliana.
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Affiliation(s)
| | | | | | - Gözde Merve Türksoy
- Leibniz Institute for Plant Genetics and Crop Plant Research, Gatersleben, Germany
| | - Ulrike Lohwasser
- Leibniz Institute for Plant Genetics and Crop Plant Research, Gatersleben, Germany
| | - Hans-Peter Mock
- Leibniz Institute for Plant Genetics and Crop Plant Research, Gatersleben, Germany
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Siekmann D, Jansen G, Zaar A, Kilian A, Fromme FJ, Hackauf B. A Genome-Wide Association Study Pinpoints Quantitative Trait Genes for Plant Height, Heading Date, Grain Quality, and Yield in Rye ( Secale cereale L.). FRONTIERS IN PLANT SCIENCE 2021; 12:718081. [PMID: 34777409 PMCID: PMC8586073 DOI: 10.3389/fpls.2021.718081] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 09/22/2021] [Indexed: 06/03/2023]
Abstract
Rye is the only cross-pollinating Triticeae crop species. Knowledge of rye genes controlling complex-inherited traits is scarce, which, currently, largely disables the genomics assisted introgression of untapped genetic variation from self-incompatible germplasm collections in elite inbred lines for hybrid breeding. We report on the first genome-wide association study (GWAS) in rye based on the phenotypic evaluation of 526 experimental hybrids for plant height, heading date, grain quality, and yield in 2 years and up to 19 environments. We established a cross-validated NIRS calibration model as a fast, effective, and robust analytical method to determine grain quality parameters. We observed phenotypic plasticity in plant height and tiller number as a resource use strategy of rye under drought and identified increased grain arabinoxylan content as a striking phenotype in osmotically stressed rye. We used DArTseq™ as a genotyping-by-sequencing technology to reduce the complexity of the rye genome. We established a novel high-density genetic linkage map that describes the position of almost 19k markers and that allowed us to estimate a low genome-wide LD based on the assessed genetic diversity in elite germplasm. We analyzed the relationship between plant height, heading date, agronomic, as well as grain quality traits, and genotype based on 20k novel single-nucleotide polymorphism markers. In addition, we integrated the DArTseq™ markers in the recently established 'Lo7' reference genome assembly. We identified cross-validated SNPs in 'Lo7' protein-coding genes associated with all traits studied. These include associations of the WUSCHEL-related homeobox transcription factor DWT1 and grain yield, the DELLA protein gene SLR1 and heading date, the Ethylene overproducer 1-like protein gene ETOL1 and thousand-grain weight, protein and starch content, as well as the Lectin receptor kinase SIT2 and plant height. A Leucine-rich repeat receptor protein kinase and a Xyloglucan alpha-1,6-xylosyltransferase count among the cross-validated genes associated with water-extractable arabinoxylan content. This study demonstrates the power of GWAS, hybrid breeding, and the reference genome sequence in rye genetics research to dissect and identify the function of genes shaping genetic diversity in agronomic and grain quality traits of rye. The described links between genetic causes and phenotypic variation will accelerate genomics-enabled rye improvement.
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Affiliation(s)
- Dörthe Siekmann
- Julius Kühn Institute, Federal Research Centre for Cultivated Plants, Institute for Breeding Research on Agricultural Crops, Sanitz, Germany
- HYBRO Saatzucht GmbH & Co. KG, Schenkenberg, Germany
| | - Gisela Jansen
- Julius Kühn Institute, Federal Research Centre for Cultivated Plants, Institute for Resistance Research and Stress Tolerance, Sanitz, Germany
| | - Anne Zaar
- Julius Kühn Institute, Federal Research Centre for Cultivated Plants, Institute for Resistance Research and Stress Tolerance, Sanitz, Germany
| | | | | | - Bernd Hackauf
- Julius Kühn Institute, Federal Research Centre for Cultivated Plants, Institute for Breeding Research on Agricultural Crops, Sanitz, Germany
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Iqbal Z, Iqbal MS, Khan MIR, Ansari MI. Toward Integrated Multi-Omics Intervention: Rice Trait Improvement and Stress Management. FRONTIERS IN PLANT SCIENCE 2021; 12:741419. [PMID: 34721467 PMCID: PMC8554098 DOI: 10.3389/fpls.2021.741419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 09/20/2021] [Indexed: 05/04/2023]
Abstract
Rice (Oryza sativa) is an imperative staple crop for nearly half of the world's population. Challenging environmental conditions encompassing abiotic and biotic stresses negatively impact the quality and yield of rice. To assure food supply for the unprecedented ever-growing world population, the improvement of rice as a crop is of utmost importance. In this era, "omics" techniques have been comprehensively utilized to decipher the regulatory mechanisms and cellular intricacies in rice. Advancements in omics technologies have provided a strong platform for the reliable exploration of genetic resources involved in rice trait development. Omics disciplines like genomics, transcriptomics, proteomics, and metabolomics have significantly contributed toward the achievement of desired improvements in rice under optimal and stressful environments. The present review recapitulates the basic and applied multi-omics technologies in providing new orchestration toward the improvement of rice desirable traits. The article also provides a catalog of current scenario of omics applications in comprehending this imperative crop in relation to yield enhancement and various environmental stresses. Further, the appropriate databases in the field of data science to analyze big data, and retrieve relevant information vis-à-vis rice trait improvement and stress management are described.
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Affiliation(s)
- Zahra Iqbal
- Molecular Crop Research Unit, Department of Biochemistry, Chulalongkorn University, Bangkok, Thailand
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Andrew-Peter-Leon MT, Selvaraj R, Kumar KK, Muthamilarasan M, Yasin JK, Pillai MA. Loss of Function of OsFBX267 and OsGA20ox2 in Rice Promotes Early Maturing and Semi-Dwarfism in γ-Irradiated IWP and Genome-Edited Pusa Basmati-1. FRONTIERS IN PLANT SCIENCE 2021; 12:714066. [PMID: 34630462 PMCID: PMC8494130 DOI: 10.3389/fpls.2021.714066] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 08/19/2021] [Indexed: 05/25/2023]
Abstract
Targeted mutagenesis is now becoming the most favored methodology to improve traits in popular rice cultivars selectively. Understanding the genetic basis of already available mutants could be the first step in designing such experiment. Improved White Ponni (IWP), a popularly grown South Indian rice variety, was subjected to γ irradiation to develop WP-22-2, an M6 line superior in semi-dwarfism, early flowering, and high yield, and it has grain qualities similar to those of IWP. The exogenous application of gibberellic acid (GA3) on WP-22-2 resulted in the elongation of shorter internodes to a level similar to IWP. The expression profiling of six genes regulating plant height showed their differential expression pattern at different time points post GA3 treatment. Furthermore, the sequencing of WP-22-2 and IWP genomes revealed several single nucleotide polymorphisms (SNPs) and large-scale deletions in WP-22-2. The conversion of functional codons to stop codons was observed in OsGA20ox2 and OsFBX267, which have been reported to have roles in regulating semi-dwarfism and early flowering, respectively. The loss of function of OsGA20ox2 and OsFBX267 in WP-22-2 resulted in reduced plant height as well as early flowering, and the same has been confirmed by editing OsGA20ox2 in the rice variety Pusa Basmati1 (PB1) using the CRISPR-Cas9 approach. The targeted editing of OsGA20ox2 in PB1 conferred shorter plant height to the edited lines compared with the wild type. Altogether, the study provides evidence on mutating OsGA20ox2 and OsFBX267 genes to develop early maturing and semi-dwarf varieties that can be released to farmers after functional characterization and field trials.
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Affiliation(s)
- M. T. Andrew-Peter-Leon
- Department of Plant Breeding and Genetics, Agricultural College and Research Institute, Tamil Nadu Agricultural University, Tuticorin, India
| | - Ramchander Selvaraj
- Department of Plant Breeding and Genetics, Agricultural College and Research Institute, Tamil Nadu Agricultural University, Tuticorin, India
| | - K. K. Kumar
- Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore, India
| | | | - Jeshima Khan Yasin
- Division of Genomic Resources, ICAR-Indian Council of Agricultural Research, National Bureau of Plant Genetic Resources, New Delhi, India
| | - M. Arumugam Pillai
- Department of Plant Breeding and Genetics, Agricultural College and Research Institute, Tamil Nadu Agricultural University, Tuticorin, India
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Arabia S, Sami AA, Akhter S, Sarker RH, Islam T. Comprehensive in silico Characterization of Universal Stress Proteins in Rice ( Oryza sativa L.) With Insight Into Their Stress-Specific Transcriptional Modulation. FRONTIERS IN PLANT SCIENCE 2021; 12:712607. [PMID: 34394169 PMCID: PMC8355530 DOI: 10.3389/fpls.2021.712607] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 07/07/2021] [Indexed: 06/10/2023]
Abstract
In a world where climate change is real and its consequences are unprecedented, understanding of the plant adaptive capacity and native stress-responsive machinery is crucial. In recent years, universal stress proteins (USPs) have received much attention in the field of plant science due to their stress-specific transcriptional regulation. This study focuses on the extensive characterization of the USP gene family members in the monocot crop rice (Oryza sativa L. var. japonica). Here, we report a total of 44 USP genes in the rice genome. In silico characterization of these genes showed that domain architecture played a major role in the functional diversification of the USP gene family which holds for all plant USPs. On top of that, a higher conservation of OsUSP members has been exhibited with a monocot genome (Zea mays L.) as compared to a dicot genome (Arabidopsis thaliana L.). Expression profiling of the identified genes led to the discovery of multiple OsUSP genes that showed pronounced transcript alteration under various abiotic stress conditions, indicating their potential role as multi-functional stress-specific modules. Furthermore, expression validation of OsUSP genes using qRT-PCR provided a strong evidence for the utility OsUSP genes in building multi-stress tolerant plants. Altogether, this study provides leads to suitable USP candidates that could be targeted for plant breeding and genetic engineering experiments to develop stress resilient crop species.
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Marker-Assisted Introgression and Stacking of Major QTLs Controlling Grain Number ( Gn1a) and Number of Primary Branching ( WFP) to NERICA Cultivars. PLANTS 2021; 10:plants10050844. [PMID: 33922112 PMCID: PMC8143528 DOI: 10.3390/plants10050844] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 04/19/2021] [Accepted: 04/19/2021] [Indexed: 11/16/2022]
Abstract
The era of the green revolution has significantly improved rice yield productivity. However, with the growing population and decreasing arable land, rice scientists must find new ways to improve rice productivity. Although hundreds of rice yield-related QTLs were already mapped and some of them were cloned, only a few were utilized for actual systematic introgression breeding programs. In this study, the major yield QTLs Grain Number 1a (Gn1a) and Wealthy Farmer’s Panicle (WFP) were introgressed and stacked in selected NERICA cultivars by marker-assisted backcross breeding (MABB). The DNA markers RM3360, RM3452, and RM5493 were used for foreground selection. At BC3F4 and BC3F5 generation, a combination of marker-assisted selection and phenotypic evaluation were carried out to select lines with target alleles and traits. Further, genotyping-by-sequencing (GBS) was conducted to validate the introgression and determine the recurrent parent genome recovery (RPGR) of the selected lines. The Gn1a and/or WFP introgression lines showed significantly higher numbers of spikelets per panicle and primary branching compared to the recurrent parents. In addition, lines with Gn1a and/or WFP alleles were comparatively similar to the recurrent parents (RP) in most yield-related traits. This study demonstrates the success of utilizing yield QTLs and marker-assisted selection to develop and improve rice cultivars.
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Tian L, Wang E, Lin X, Ji L, Chang J, Chen H, Wang J, Chen D, Tran LSP, Tian C. Wild rice harbors more root endophytic fungi than cultivated rice in the F1 offspring after crossbreeding. BMC Genomics 2021; 22:278. [PMID: 33865333 PMCID: PMC8052703 DOI: 10.1186/s12864-021-07587-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 04/07/2021] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Rice, which serves as a staple food for more than half of the world's population, is grown worldwide. The hybridization of wild and cultivated rice has enabled the incorporation of resistance to varying environmental conditions. Endophytic microbiota are known to be transferred with their host plants. Although some studies have reported on the endophytic microbiota of wild and cultivated rice, the inheritance from wild and cultivated rice accessions in next generations, in terms of endophytic microbiota, has not been examined. RESULTS In the present study, the endophytic microbial community structures of Asian and African wild and cultivated rice species were compared with those of their F1 offspring. High-throughput sequencing data of bacterial 16S rDNA and fungal internal transcribed spacer regions were used to classify the endophytic microbiota of collected samples of rice. Results indicated that when either African or Asian wild rice species were crossed with cultivated rice accessions, the first generation harbored a greater number of root endophytic fungi than the cultivated parent used to make the crosses. Network analysis of the bacterial and fungal operational taxonomic units revealed that Asian and African wild rice species clustered together and exhibited a greater number of significant correlations between fungal taxa than cultivated rice. The core bacterial genus Acidovorax and the core fungal order Pleosporales, and genera Myrothecium and Bullera connected African and Asian wild rice accessions together, and both the wild rice accessions with their F1 offspring. On the other hand, the core bacterial genus Bradyrhizobium and the core fungal genera Dendroclathra linked the African and Asian cultivated rice accessions together. CONCLUSIONS This study has theoretical significance for understanding the effect of breeding on the inheritance of endophytic microbiota of rice and identifying beneficial endophytic bacteria and fungi among wild and cultivated rice species, and their F1 offspring.
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Affiliation(s)
- Lei Tian
- Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, 130102, Jilin, China
| | - Enze Wang
- Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, 130102, Jilin, China
| | - Xiaolong Lin
- Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, 130102, Jilin, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Li Ji
- Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, 130102, Jilin, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jingjing Chang
- Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, 130102, Jilin, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hongping Chen
- Rice Research Institute, Jiangxi Academy of Agricultural Sciences, Nanchang, 330200, China
| | - Jilin Wang
- Rice Research Institute, Jiangxi Academy of Agricultural Sciences, Nanchang, 330200, China
| | - Dazhou Chen
- Rice Research Institute, Jiangxi Academy of Agricultural Sciences, Nanchang, 330200, China
| | - Lam-Son Phan Tran
- Institute of Research and Development, Duy Tan University, Da Nang, 550000, Vietnam.
- Institute of Genomics for Crop Abiotic Stress Tolerance, Department of Plant and Soil Science, Texas Tech University, Lubbock, TX, 79409, USA.
| | - Chunjie Tian
- Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, 130102, Jilin, China.
- Key Laboratory of Straw Biology and Utilization of the Ministry of Education, Jilin Agricultural University, Changchun, 130118, Jilin Province, China.
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Panzade KP, Kale SS, Kapale V, Chavan NR. Genome-Wide Analysis of Heat Shock Transcription Factors in Ziziphus jujuba Identifies Potential Candidates for Crop Improvement Under Abiotic Stress. Appl Biochem Biotechnol 2020; 193:1023-1041. [PMID: 33244672 DOI: 10.1007/s12010-020-03463-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 11/09/2020] [Indexed: 11/24/2022]
Abstract
Plant heat shock transcription factors (Hsfs) play a significant role in adoption under abiotic stress conditions by modulating the expression of several stress-responsive genes. Analysis of the Hsf gene family will serve to understand the molecular mechanism which is involved in response to abiotic stress. The Ziziphus species grows in warm and dry regions and is inherently tolerant to abiotic stress conditions; thus, Ziziphus is a highly enriched source of genes conferring abiotic stress tolerance. Therefore, the present study provides a comprehensive genome-wide analysis of the Hsf gene family in Z. jujuba. Identified 21 non-redundant Hsf genes were grouped into three major classes (classes A, B, and C) based on the phylogenetic analysis. Promoter and gene ontology analysis suggested that ZjHsfs perform diverse functions in response to abiotic stress conditions. Two paralogous pairs resulting from tandem gene duplication events were identified. Also, physio-chemical properties of chromosomal locations, gene structure, motifs, and protein domain organization of Hsfs were analyzed. Real-time PCR expression analyses revealed that most of the Z. jujuba Hsf genes are differentially expressed in response to heat stress. The analysis suggested ZjHsf-2, ZjHsf-3, ZjHsf-5, ZjHsf-7, ZjHsf-8, ZjHsf-10, ZjHsf-12, ZjHsf-17, and ZjHsf-18 were the outstanding candidate genes for imparting heat stress tolerance and for future functional analysis. The present analysis laid the foundation for understanding the molecular mechanism of the Hsf gene family regulating Z. jujuba development and tolerance to abiotic stress conditions.
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Affiliation(s)
- Kishor Prabhakar Panzade
- Division of Molecular Biology and Biotechnology, Indian Agriculture Research Institute, New Delhi, 110012, India
| | - Sonam S Kale
- Department of Plant Biotechnology, MGM College of Agricultural Biotechnology, Aurangabad, 431003, India
| | - Vijay Kapale
- Govind Ballabh Pant University of Agriculture and Technology, Pantnagar, 263153, India
| | - Narendra R Chavan
- Department of Plant Biotechnology, MGM College of Agricultural Biotechnology, Aurangabad, 431003, India.
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Zhang J, Lei Y, Wang B, Li S, Yu S, Wang Y, Li H, Liu Y, Ma Y, Dai H, Wang J, Zhang Z. The high-quality genome of diploid strawberry (Fragaria nilgerrensis) provides new insights into anthocyanin accumulation. PLANT BIOTECHNOLOGY JOURNAL 2020; 18:1908-1924. [PMID: 32003918 PMCID: PMC7415782 DOI: 10.1111/pbi.13351] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 01/15/2020] [Accepted: 01/20/2020] [Indexed: 05/11/2023]
Abstract
Fragaria nilgerrensis is a wild diploid strawberry species endemic to east and southeast region in Asia and provides a rich source of genetic variations for strawberry improvement. Here, we present a chromosome-scale assembly of F. nilgerrensis using single-molecule real-time (SMRT) Pacific Biosciences sequencing and chromosome conformation capture (Hi-C) genome scaffolding. The genome assembly size was 270.3 Mb, with a contig N50 of ∼8.5 Mb. A total of 28 780 genes and 117.2 Mb of transposable elements were annotated for this genome. Next, detailed comparative genomics with the high-quality F. vesca reference genome was conducted to obtain the difference among transposable elements, SNPs, Indels, and so on. The genome size of F. nilgerrensis was enhanced by around 50 Mb relatively to F. vesca, which is mainly due to expansion of transposable elements. In comparison with the F. vesca genome, we identified 4 561 825 SNPs, 846 301 Indels, 4243 inversions, 35 498 translocations and 10 099 relocations. We also found a marked expansion of genes involved in phenylpropanoid biosynthesis, starch and sucrose metabolism, cyanoamino acid metabolism, plant-pathogen interaction, brassinosteroid biosynthesis and plant hormone signal transduction in F. nilgerrensis, which may account for its specific phenotypes and considerable environmental adaptability. Interestingly, we found sequence variations in the upstream regulatory region of FnMYB10, a core transcriptional activator of anthocyanin biosynthesis, resulted in the low expression level of the FnMYB10 gene, which is likely responsible for white fruit phenotype of F. nilgerrensis. The high-quality F. nilgerrensis genome will be a valuable resource for biological research and comparative genomics research.
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Affiliation(s)
- Junxiang Zhang
- Liaoning Key Laboratory of Strawberry Breeding and CultivationCollege of HorticultureShenyang Agricultural UniversityShenyangChina
| | - Yingying Lei
- Liaoning Key Laboratory of Strawberry Breeding and CultivationCollege of HorticultureShenyang Agricultural UniversityShenyangChina
| | - Baotian Wang
- Liaoning Key Laboratory of Strawberry Breeding and CultivationCollege of HorticultureShenyang Agricultural UniversityShenyangChina
| | - Song Li
- Biomarker Technologies CorporationBeijingChina
| | - Shuang Yu
- Liaoning Key Laboratory of Strawberry Breeding and CultivationCollege of HorticultureShenyang Agricultural UniversityShenyangChina
| | - Yan Wang
- Liaoning Key Laboratory of Strawberry Breeding and CultivationCollege of HorticultureShenyang Agricultural UniversityShenyangChina
| | - He Li
- Liaoning Key Laboratory of Strawberry Breeding and CultivationCollege of HorticultureShenyang Agricultural UniversityShenyangChina
| | - Yuexue Liu
- Liaoning Key Laboratory of Strawberry Breeding and CultivationCollege of HorticultureShenyang Agricultural UniversityShenyangChina
| | - Yue Ma
- Liaoning Key Laboratory of Strawberry Breeding and CultivationCollege of HorticultureShenyang Agricultural UniversityShenyangChina
| | - Hongyan Dai
- Liaoning Key Laboratory of Strawberry Breeding and CultivationCollege of HorticultureShenyang Agricultural UniversityShenyangChina
| | | | - Zhihong Zhang
- Liaoning Key Laboratory of Strawberry Breeding and CultivationCollege of HorticultureShenyang Agricultural UniversityShenyangChina
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Hori K, Shenton M. Recent Advances in Molecular Research in Rice: Agronomically Important Traits. Int J Mol Sci 2020; 21:ijms21175945. [PMID: 32824902 PMCID: PMC7504012 DOI: 10.3390/ijms21175945] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 08/17/2020] [Indexed: 12/18/2022] Open
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Tian D, Wang P, Tang B, Teng X, Li C, Liu X, Zou D, Song S, Zhang Z. GWAS Atlas: a curated resource of genome-wide variant-trait associations in plants and animals. Nucleic Acids Res 2020; 48:D927-D932. [PMID: 31566222 PMCID: PMC6943065 DOI: 10.1093/nar/gkz828] [Citation(s) in RCA: 85] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 09/06/2019] [Accepted: 09/22/2019] [Indexed: 12/31/2022] Open
Abstract
GWAS Atlas (https://bigd.big.ac.cn/gwas/) is a manually curated resource of genome-wide variant-trait associations for a wide range of species. Unlike existing related resources, it features comprehensive integration of a high-quality collection of 75 467 variant-trait associations for 614 traits across 7 cultivated plants (cotton, Japanese apricot, maize, rapeseed, rice, sorghum and soybean) and two domesticated animals (goat and pig), which were manually curated from 254 publications. We integrated these associations into GWAS Atlas and presented them in terms of variants, genes, traits, studies and publications. More importantly, all associations and traits were annotated and organized based on a suite of ontologies (Plant Trait Ontology, Animal Trait Ontology for Livestock, etc.). Taken together, GWAS Atlas integrates high-quality curated GWAS associations for animals and plants and provides user-friendly web interfaces for data browsing and downloading, accordingly serving as a valuable resource for genetic research of important traits and breeding application.
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Affiliation(s)
- Dongmei Tian
- National Genomics Data Center, Beijing 100101, China.,BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Pei Wang
- National Genomics Data Center, Beijing 100101, China.,BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Bixia Tang
- National Genomics Data Center, Beijing 100101, China.,BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Xufei Teng
- National Genomics Data Center, Beijing 100101, China.,BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Cuiping Li
- National Genomics Data Center, Beijing 100101, China.,BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiaonan Liu
- National Genomics Data Center, Beijing 100101, China.,BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.,School of Future Technology, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Dong Zou
- National Genomics Data Center, Beijing 100101, China.,BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Shuhui Song
- National Genomics Data Center, Beijing 100101, China.,BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China.,CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhang Zhang
- National Genomics Data Center, Beijing 100101, China.,BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China.,School of Future Technology, University of Chinese Academy of Sciences, Beijing 100049, China.,CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
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24
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Akakpo R, Carpentier MC, Ie Hsing Y, Panaud O. The impact of transposable elements on the structure, evolution and function of the rice genome. THE NEW PHYTOLOGIST 2020; 226:44-49. [PMID: 31797393 DOI: 10.1111/nph.16356] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Accepted: 11/05/2019] [Indexed: 06/10/2023]
Abstract
Transposable elements (TEs) are ubiquitous in plants and are the primary genomic component of the majority of taxa. Knowledge of their impact on the structure, function and evolution of plant genomes is therefore a priority in the field of genomics. Rice, as one of the most prevalent crops for food security worldwide, has been subjected to intense research efforts over recent decades. Consequently, a considerable amount of genomic resources has been generated and made freely available to the scientific community. These can be exploited both to improve our understanding of some basic aspects of genome biology of this species and to develop new concepts for crop improvement. In this review, we describe the current knowledge on how TEs have shaped rice chromosomes and propose a new strategy based on a genome-wide association study (GWAS) to address the important question of their functional impact on this crop.
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Affiliation(s)
- Roland Akakpo
- Laboratoire Génome et Développement des Plantes, UMR 5096 CNRS/UPVD, Université de Perpignan, Via Domitia, 52 Avenue Paul Alduy, 66860, Perpignan Cedex, France
| | - Marie-Christine Carpentier
- Laboratoire Génome et Développement des Plantes, UMR 5096 CNRS/UPVD, Université de Perpignan, Via Domitia, 52 Avenue Paul Alduy, 66860, Perpignan Cedex, France
| | - Yue Ie Hsing
- Institute of Plant and Microbial Biology, Acadeia Sinica, 128, Section 2, Yien-chu-yuan Road, Nankang, 115, Taipei, Taiwan
| | - Olivier Panaud
- Laboratoire Génome et Développement des Plantes, UMR 5096 CNRS/UPVD, Université de Perpignan, Via Domitia, 52 Avenue Paul Alduy, 66860, Perpignan Cedex, France
- Institut Universitaire de France, 1 Rue Descartes, 75231, Paris Cedex 05, France
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25
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Kamboj R, Singh B, Mondal TK, Bisht DS. Current status of genomic resources on wild relatives of rice. BREEDING SCIENCE 2020; 70:135-144. [PMID: 32523396 PMCID: PMC7272243 DOI: 10.1270/jsbbs.19064] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2019] [Accepted: 09/26/2019] [Indexed: 06/02/2023]
Abstract
Rice is a food crop of global importance, cultivated in diverse agro-climatic zones of the world. However, in the process of domestication many beneficial alleles have been eroded from the gene pool of the rice cultivated globally and eventually has made it vulnerable to a plethora of stresses. In contrast, the wild relatives of rice, despite being agronomically inferior, have inherited a potential of surviving in a range of geographical habitats. These adaptations enrich them with novel traits that upon introgression to modern cultivated varieties offer tremendous potential of increasing yield and adaptability. But, due to the unavailability of their genetic as well as genomic resources, identification and characterisation of these novel beneficial alleles has been a challenging task. Nevertheless, with the unprecedented surge in the area of conservation genomics, researchers have now shifted their focus towards these natural repositories of beneficial traits. Presently, there are several generic and specialized databases harboring genome-wide information on wild species of rice, and are acting as a useful resource for identification of novel genes and alleles, designing of molecular markers, comparative analysis and evolutionary biology studies. In this review, we introduce the key features of these databases focusing on their utility in rice breeding programs.
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Affiliation(s)
- Richa Kamboj
- National Institute for Plant Biotechnology, LBS Building, Pusa Campus, New Delhi 110012, India
| | - Balwant Singh
- National Institute for Plant Biotechnology, LBS Building, Pusa Campus, New Delhi 110012, India
| | - Tapan Kumar Mondal
- National Institute for Plant Biotechnology, LBS Building, Pusa Campus, New Delhi 110012, India
| | - Deepak Singh Bisht
- National Institute for Plant Biotechnology, LBS Building, Pusa Campus, New Delhi 110012, India
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Rana N, Rahim MS, Kaur G, Bansal R, Kumawat S, Roy J, Deshmukh R, Sonah H, Sharma TR. Applications and challenges for efficient exploration of omics interventions for the enhancement of nutritional quality in rice (Oryza sativa L.). Crit Rev Food Sci Nutr 2019; 60:3304-3320. [DOI: 10.1080/10408398.2019.1685454] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Nitika Rana
- National Agri-Food Biotechnology Institute (NABI), Mohali, Punjab, India
| | | | - Gazaldeep Kaur
- National Agri-Food Biotechnology Institute (NABI), Mohali, Punjab, India
| | - Ruchi Bansal
- National Agri-Food Biotechnology Institute (NABI), Mohali, Punjab, India
| | - Surbhi Kumawat
- National Agri-Food Biotechnology Institute (NABI), Mohali, Punjab, India
| | - Joy Roy
- National Agri-Food Biotechnology Institute (NABI), Mohali, Punjab, India
| | - Rupesh Deshmukh
- National Agri-Food Biotechnology Institute (NABI), Mohali, Punjab, India
| | - Humira Sonah
- National Agri-Food Biotechnology Institute (NABI), Mohali, Punjab, India
| | - Tilak Raj Sharma
- National Agri-Food Biotechnology Institute (NABI), Mohali, Punjab, India
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27
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The potentiality of rice microsatellite markers in assessment of cross-species transferability and genetic diversity of rice and its wild relatives. 3 Biotech 2019; 9:217. [PMID: 31114741 DOI: 10.1007/s13205-019-1757-x] [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: 12/01/2018] [Accepted: 05/11/2019] [Indexed: 10/26/2022] Open
Abstract
The main aim of this study is to assess the potentiality of SSR markers for the identification of the cross-species transferability frequency in a large set of the diverse genome types of wild relative rice along with cultivated rice. Here, we used 18 different rice genotypes representing nine different genome types with 70 SSR markers to investigate the potentiality of cross-species transferability rate. The overall cross-species transferability of SSR markers across the 18 rice genotypes ranged from 38.9% (RM280 and RM447) to 100% (RM490, RM318, RM279, RM18877 and RM20033, RM19303) with an average of 76.58%. Also, cross-species transferability across chromosome ranged from 54.4% (chromosome 4) to 86.5% (chromosome 2) with an average of 74.35%. The polymorphism information content of the markers varied from 0.198 (RM263) to 0.868 (RM510) with a mean of 0.549 ± 0.153, showing high discriminatory power. The highest rate of cross-transferability was observed in O. rufipogon (97%), The highest rate of cross-species transferability was in O. rufipogon (97.00%), followed by O. glaberrima (94.20%), O. nivara (92.80%), Swarna (92.80%), O. longistaminata (91.40%), O. eichingeri (90%), O. barthii (88.50%), O. alta (82.80%), O. australiensis (77.10%), O. grandiglumis (74.20%), O. officinalis (74.20%), Zizania latifolia (70.00%), O. latifolia (68.50%), O. brachyantha (62.80%), Leersia perrieri (57.10%) and O. ridleyi (41.40%) with least in O. coarctata (28.50%). A total of 341 alleles from 70 loci were detected with the number of alleles per locus ranged from 2 to 12. Based on dendrogram analysis, the AA genome groups was separated as distinct group from the rest of the genome types. Similarly, principal coordinate analysis and structure analysis clearly separated the AA genome type from the rest of the genome types. Through the analysis of molecular variance, more variance (51%) was observed among the individual, whereas less (14%) was observed among the population. Thus, our findings may offer a valuable resource for studying the genetic diversity and relationship to facilitate the understanding of the complex mechanism of the origin and evolutionary processes of different Oryza species and wild relative rice.
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Yu J. A Time for Celebration: 40th Anniversary of GSC and 15th Anniversary of BIG, CAS. GENOMICS, PROTEOMICS & BIOINFORMATICS 2018; 16:387-388. [PMID: 30743051 PMCID: PMC6411949 DOI: 10.1016/j.gpb.2019.02.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 02/01/2019] [Indexed: 11/24/2022]
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