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Gowda RSR, Sharma S, Gill RS, Mangat GS, Bhatia D. Genome wide association studies and candidate gene mining for understanding the genetic basis of straw silica content in a set of Oryza nivara (Sharma et Shastry) accessions. FRONTIERS IN PLANT SCIENCE 2023; 14:1174266. [PMID: 37324704 PMCID: PMC10266271 DOI: 10.3389/fpls.2023.1174266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Accepted: 04/25/2023] [Indexed: 06/17/2023]
Abstract
Rice is a high-silica (SiO2·nH2O) accumulator. Silicon (Si) is designated as a beneficial element associated with multiple positive effects on crops. However, the presence of high silica content is detrimental to rice straw management, hampering its use as animal feed and as raw material in multiple industries. Rice straw management is a serious concern in north-western India, and it is eventually burned in situ by farmers, contributing to air pollution. A practical solution could lie in reducing the silica content in rice while also attaining sound plant growth. A set of 258 Oryza nivara accessions along with 25 cultivated varieties of Oryza sativa was used to assess the variation in straw silica content using the molybdenum blue colorimetry method. A large continuous variation was observed for straw silica content in O. nivara accessions, ranging from 5.08% to 16%, while it varied from 6.18% to 15.81% in the cultivated varieties. The O. nivara accessions containing 43%-54% lower straw silica content than the currently prominent cultivated varieties in the region were identified. A set of 22,528 high-quality single nucleotide polymorphisms (SNPs) among 258 O. nivara accessions was used for estimating population structure and genome-wide association studies (GWAS). A weak population structure with 59% admixtures was identified among O. nivara accessions. Further, multi-locus GWAS revealed the presence of 14 marker-trait associations (MTAs) for straw silica content, with six of them co-localizing with previously reported quantitative trait loci (QTL). Twelve out of 14 MTAs showed statistically significant allelic differences. Thorough candidate gene analyses revealed the presence of promising candidate genes, including those encoding the ATP-binding cassette (ABC) transporter, Casparian thickening, multi-drug and toxin extrusion (MATE) protein, F-box, and MYB-transcription factors. Besides, ortho-QTLs among rice and maize genomes were identified, which could open ways for further genetic analysis of this trait. The findings of the study could aid in further understanding and characterizing genes for Si transport and regulation in the plant body. The donors carrying the alleles for lower straw silica content can be used in further marker-assisted breeding programs to develop rice varieties with lower silica content and higher yield potential.
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Affiliation(s)
- Rakshith S. R. Gowda
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Sandeep Sharma
- Department of Soil Science, Punjab Agricultural University, Ludhiana, India
| | - Ranvir Singh Gill
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Gurjit Singh Mangat
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Dharminder Bhatia
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
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Pinson SRM, Heuschele DJ, Edwards JD, Jackson AK, Sharma S, Barnaby JY. Relationships Among Arsenic-Related Traits, Including Rice Grain Arsenic Concentration and Straighthead Resistance, as Revealed by Genome-Wide Association. Front Genet 2022; 12:787767. [PMID: 35371188 PMCID: PMC8974240 DOI: 10.3389/fgene.2021.787767] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 12/23/2021] [Indexed: 11/13/2022] Open
Abstract
There is global concern that rice grains and foods can contain harmful amounts of arsenic (As), motivating breeders to produce cultivars that restrict As accumulation in grains to protect human health. Arsenic is also toxic to plants, with straighthead disorder (StHD), causing panicle sterility, being observed in rice. The genetic variation in StHD resistance suggests that plants have evolved mechanisms that reduce As toxicity, possibly via regulation of As uptake, transport, or detoxification/sequestration. Because these mechanisms could also underlie the wide (3- to 100-fold) differences in grain As concentration (grain-As) observed among diverse rice genotypes, it was hypothesized that some genes reduce both grain-As content and StHD susceptibility and may be detectable as co-located StDH and As quantitative trait loci (QTL). We used a machine-learning Bayesian network approach plus high-resolution genome-wide association study (GWAS) to identify QTL for grain-As and StHD resistance within the USDA Rice Minicore Collection (RMC). Arsenic enters roots through phosphorus (P) and silica (Si) transporters, As detoxification involves sulfur (S), and cell signaling to activate stress tolerance mechanisms is impacted by Si, calcium (Ca), and copper (Cu). Therefore, concentrations of Si, P, S, Ca, and Cu were included in this study to elucidate physiological mechanisms underlying grain-As and StHD QTL. Multiple QTL (from 9 to 33) were identified for each of the investigated As-associated traits. Although the QTL for StHD, Si, and grain-As did not overlap as heavily as our hypothesis predicted (4/33 StHD and 4/15 As QTL co-located), they do provide useful guidance to future research. Furthermore, these are the first StHD and Si QTL to be identified using high-density mapping, resulting in their being mapped to shorter, more precise genomic regions than previously reported QTL. The candidate genes identified provide guidance for future research, such as gene editing or mutation studies to further investigate the role of antioxidants and ROS scavenging to StHD resistance, as indicated by candidate genes around the commonly reported qStHD8-2 QTL. Other genes indicated for future study for improving grain-As and StHD include several multidrug and toxic compound extrusion (MATE) genes, F-box genes, and NIPs not documented to date to transport As.
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Affiliation(s)
- Shannon R M Pinson
- Dale Bumpers National Rice Research Center, United States Department of Agriculture-Agricultural Research Service, Stuttgart, AR, United States
| | - D Jo Heuschele
- Plant Science Research Unit, United States Department of Agriculture-Agricultural Research Service, St. Paul, CO, United States
| | - Jeremy D Edwards
- Dale Bumpers National Rice Research Center, United States Department of Agriculture-Agricultural Research Service, Stuttgart, AR, United States
| | - Aaron K Jackson
- Dale Bumpers National Rice Research Center, United States Department of Agriculture-Agricultural Research Service, Stuttgart, AR, United States
| | - Santosh Sharma
- Dale Bumpers National Rice Research Center, United States Department of Agriculture-Agricultural Research Service, Stuttgart, AR, United States
| | - Jinyoung Y Barnaby
- Dale Bumpers National Rice Research Center, United States Department of Agriculture-Agricultural Research Service, Stuttgart, AR, United States
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Porrang S, Davaran S, Rahemi N, Allahyari S, Mostafavi E. How Advancing are Mesoporous Silica Nanoparticles? A Comprehensive Review of the Literature. Int J Nanomedicine 2022; 17:1803-1827. [PMID: 35498391 PMCID: PMC9043011 DOI: 10.2147/ijn.s353349] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Accepted: 03/31/2022] [Indexed: 12/12/2022] Open
Abstract
The application of mesoporous silica nanoparticles (MSNs) is ubiquitous in various sciences. MSNs possess unique features, including the diversity in manufacturing by different synthesis methods and from different sources, structure controllability, pore design capabilities, pore size tunability, nanoparticle size distribution adjustment, and the ability to create diverse functional groups on their surface. These characteristics have led to various types of MSNs as a unique system for drug delivery. In this review, first, the synthesis of MSNs by different methods via using different sources were studied. Then, the parameters affecting their physicochemical properties and functionalization have been discussed. Finally, the last decade’s novel strategies, including surface functionalization, drug delivery, and cancer treatment, based on the MSNs in drug delivery and cancer therapy have been addressed.
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Affiliation(s)
- Sahar Porrang
- Chemical Engineering Faculty, Sahand University of Technology, Tabriz, Iran
- Environmental Engineering Research Centre, Sahand University of Technology, Tabriz, Iran
| | - Soodabeh Davaran
- Department of Medical Nanotechnology, Faculty of Advanced Medical Science, Tabriz University of Medical Sciences, Tabriz, Iran
- Research Centre for Pharmaceutical Nanotechnology, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Nader Rahemi
- Chemical Engineering Faculty, Sahand University of Technology, Tabriz, Iran
- Environmental Engineering Research Centre, Sahand University of Technology, Tabriz, Iran
- Nader Rahemi, Sahand University of Technology, Tabriz, Iran, Tel +98-41-33459100, Email
| | - Somaiyeh Allahyari
- Chemical Engineering Faculty, Sahand University of Technology, Tabriz, Iran
- Environmental Engineering Research Centre, Sahand University of Technology, Tabriz, Iran
| | - Ebrahim Mostafavi
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Correspondence: Ebrahim Mostafavi, Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, 94305, USA, Email ;
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Sonarkhan MP, Singh L, Sungkaew S, Souvannakhoummane K, Thul ST. Silica and secondary metabolites as chemophenetic markers for characterization of bamboo species in relation to genetic and morphometric analysis. Mol Biol Rep 2021; 48:4487-4495. [PMID: 34117604 DOI: 10.1007/s11033-021-06469-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2021] [Accepted: 06/01/2021] [Indexed: 11/29/2022]
Abstract
Bamboo is a non-timber forest product and one of the most important grass plants of industrial and domestic use. It is widely distributed in tropical countries including India, China and Southeast Asian countries with wide genetic diversity. The diversity in the available genotypes becomes an important resource for the selection and improvement of the plants for ecological and commercial use. This study investigates eight commercially and ecologically important bamboo species of six genera (Bambusa, Dendrocalamus, Thyrsostachys, Vietnamosasa, Cephalostachyum and Indocalamus) from India, Thailand and Laos. These were evaluated for genetic differences by molecular makers, chemo-morphological variation and ability of silicon accumulation. The genetic cluster analyses of eight RAPD primers revealed genetic similarities in the ranges of 24-55%. The total silica content varied from 18.34 to 40.08 ppm in leaves of different bamboo species. Chemical analysis of the silicon content by ICP-OES and secondary metabolite profiling on TLC depicted the prominent distinction among the species. The PCA analysis of quantitative morphological data grouped the species in two major clusters and found to correlate with chemical pattern and genetic similarity to some extent. This is the first report that summarizes species-specific variability of leaf silica content, secondary metabolites, and quantitative morphological data towards delineation of genetic phylogeny of bamboo species.
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Affiliation(s)
- Maroti P Sonarkhan
- Environmental Biotechnology and Genomics Division, CSIR-National Environmental Engineering Research Institute, Nehru Marg, Nagpur, 440020, India
| | - Lal Singh
- Environmental Biotechnology and Genomics Division, CSIR-National Environmental Engineering Research Institute, Nehru Marg, Nagpur, 440020, India
| | - Sarawood Sungkaew
- Department of Forest Biology, Kasetsart University, Bangkok, Thailand
| | | | - Sanjog T Thul
- Environmental Biotechnology and Genomics Division, CSIR-National Environmental Engineering Research Institute, Nehru Marg, Nagpur, 440020, India.
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Identification of Superior Alleles for Seedling Stage Salt Tolerance in the USDA Rice Mini-Core Collection. PLANTS 2019; 8:plants8110472. [PMID: 31694217 PMCID: PMC6918172 DOI: 10.3390/plants8110472] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 10/30/2019] [Accepted: 10/31/2019] [Indexed: 12/24/2022]
Abstract
Salt stress is a major constraint to rice acreage and production worldwide. The purpose of this study was to evaluate the natural genetic variation available in the United States Department of Agriculture (USDA) rice mini-core collection (URMC) for early vigor traits under salt stress and identify quantitative trait loci (QTLs) for seedling-stage salt tolerance via a genome-wide association study (GWAS). Using a hydroponic system, the seedlings of 162 accessions were subjected to electrical conductivity (EC) 6.0 dS m−1 salt stress at the three-to-four leaf stage. After completion of the study, 59.4% of the accessions were identified as sensitive, 23.9% were identified as moderately tolerant, and 16.7% were identified as highly tolerant. Pokkali was the most tolerant variety, while Nerica-6 was the most sensitive. Adapting standard International Rice Research Institute (IRRI) protocols, eight variables associated with salt tolerance were determined. The GWAS of the URMC, using over three million single-nucleotide polymorphisms (SNPs), identified nine genomic regions associated with salt tolerance that were mapped to five different chromosomes. Of these, none were in the known Saltol QTL region, suggesting different probable genes and mechanisms responsible for salt tolerance in the URMC. The study uncovered genetic loci that explained a large portion of the variation in salt tolerance at the seedling stage. Fourteen highly salt-tolerant accessions, six novel loci, and 16 candidate genes in their vicinity were identified that may be useful in breeding for salt stress tolerance. Identified QTLs can be targeted for fine mapping, candidate gene verification, and marker-assisted breeding in future studies.
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Wang Z, Zeng S, Li Y, Wang W, Zhang Z, Zeng H, Wang W, Sun L. Luminescence Mechanism of Carbon-Incorporated Silica Nanoparticles Derived from Rice Husk Biomass. Ind Eng Chem Res 2017. [DOI: 10.1021/acs.iecr.7b00700] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Zhaofeng Wang
- Department of Chemical & Biomolecular Engineering and Polymer Program, Institute of Materials Science, University of Connecticut, Storrs, Connecticut 06269, United States
- State
Key Laboratory of Solid Lubrication, Lanzhou Institute of Chemical
Physics, Chinese Academy of Sciences, Lanzhou, Gansu 730000, China
| | - Songshan Zeng
- Department of Chemical & Biomolecular Engineering and Polymer Program, Institute of Materials Science, University of Connecticut, Storrs, Connecticut 06269, United States
| | - Yezhou Li
- Department of Chemical & Biomolecular Engineering and Polymer Program, Institute of Materials Science, University of Connecticut, Storrs, Connecticut 06269, United States
| | - Weilin Wang
- Department of Chemical & Biomolecular Engineering and Polymer Program, Institute of Materials Science, University of Connecticut, Storrs, Connecticut 06269, United States
- Ministry of Education Key Laboratory of Enhanced Heat Transfer & Energy Conservation, School of Chemistry and Chemical Engineering, South China University of Technology, Guangzhou, Guangdong 510640, China
| | - Zhengguo Zhang
- Ministry of Education Key Laboratory of Enhanced Heat Transfer & Energy Conservation, School of Chemistry and Chemical Engineering, South China University of Technology, Guangzhou, Guangdong 510640, China
| | - Huidan Zeng
- Key
Laboratory for Ultrafine Materials of Ministry of Education, School
of Materials Science and Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Weixing Wang
- Ministry of Education Key Laboratory of Enhanced Heat Transfer & Energy Conservation, School of Chemistry and Chemical Engineering, South China University of Technology, Guangzhou, Guangdong 510640, China
| | - Luyi Sun
- Department of Chemical & Biomolecular Engineering and Polymer Program, Institute of Materials Science, University of Connecticut, Storrs, Connecticut 06269, United States
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Yu Y, Liu J, Li F, Zhang X, Zhang C, Xiang J. Gene set based association analyses for the WSSV resistance of Pacific white shrimp Litopenaeus vannamei. Sci Rep 2017; 7:40549. [PMID: 28094323 PMCID: PMC5240139 DOI: 10.1038/srep40549] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Accepted: 12/07/2016] [Indexed: 11/09/2022] Open
Abstract
White Spot Syndrome Virus (WSSV) is regarded as a virus with the strongest pathogenicity to shrimp. For the threshold trait such as disease resistance, marker assisted selection (MAS) was considered to be a more effective approach. In the present study, association analyses of single nucleotide polymorphisms (SNPs) located in a set of immune related genes were conducted to identify markers associated with WSSV resistance. SNPs were detected by bioinformatics analysis on RNA sequencing data generated by Illimina sequencing platform and Roche 454 sequencing technology. A total of 681 SNPs located in the exons of immune related genes were selected as candidate SNPs. Among these SNPs, 77 loci were genotyped in WSSV susceptible group and resistant group. Association analysis was performed based on logistic regression method under an additive and dominance model in GenABEL package. As a result, five SNPs showed associations with WSSV resistance at a significant level of 0.05. Besides, SNP-SNP interaction analysis was conducted. The combination of SNP loci in TRAF6, Cu/Zn SOD and nLvALF2 exhibited a significant effect on the WSSV resistance of shrimp. Gene expression analysis revealed that these SNPs might influence the expression of these immune-related genes. This study provides a useful method for performing MAS in shrimp.
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Affiliation(s)
- Yang Yu
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
| | - Jingwen Liu
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fuhua Li
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Xiaojun Zhang
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
| | - Chengsong Zhang
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
| | - Jianhai Xiang
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
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Schläppi MR, Jackson AK, Eizenga GC, Wang A, Chu C, Shi Y, Shimoyama N, Boykin DL. Assessment of Five Chilling Tolerance Traits and GWAS Mapping in Rice Using the USDA Mini-Core Collection. FRONTIERS IN PLANT SCIENCE 2017; 8:957. [PMID: 28642772 PMCID: PMC5463297 DOI: 10.3389/fpls.2017.00957] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Accepted: 05/22/2017] [Indexed: 05/21/2023]
Abstract
Rice (Oryza sativa L.) is often exposed to cool temperatures during spring planting in temperate climates. A better understanding of genetic pathways regulating chilling tolerance will enable breeders to develop varieties with improved tolerance during germination and young seedling stages. To dissect chilling tolerance, five assays were developed; one assay for the germination stage, one assay for the germination and seedling stage, and three for the seedling stage. Based on these assays, five chilling tolerance indices were calculated and assessed using 202 O. sativa accessions from the Rice Mini-Core (RMC) collection. Significant differences between RMC accessions made the five indices suitable for genome-wide association study (GWAS) based quantitative trait loci (QTL) mapping. For young seedling stage indices, japonica and indica subspecies clustered into chilling tolerant and chilling sensitive accessions, respectively, while both subspecies had similar low temperature germinability distributions. Indica subspecies were shown to have chilling acclimation potential. GWAS mapping uncovered 48 QTL at 39 chromosome regions distributed across all 12 rice chromosomes. Interestingly, there was no overlap between the germination and seedling stage QTL. Also, 18 QTL and 32 QTL were in regions discovered in previously reported bi-parental and GWAS based QTL mapping studies, respectively. Two novel low temperature seedling survivability (LTSS)-QTL, qLTSS3-4 and qLTSS4-1, were not in a previously reported QTL region. QTL with strong effect alleles identified in this study will be useful for marker assisted breeding efforts to improve chilling tolerance in rice cultivars and enhance gene discovery for chilling tolerance.
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Affiliation(s)
- Michael R. Schläppi
- Department of Biological Sciences, Marquette University, MilwaukeeWI, United States
- *Correspondence: Michael R. Schläppi,
| | - Aaron K. Jackson
- Dale Bumpers National Rice Research Center, United States Department of Agriculture – Agricultural Research Service, StuttgartAR, United States
| | - Georgia C. Eizenga
- Dale Bumpers National Rice Research Center, United States Department of Agriculture – Agricultural Research Service, StuttgartAR, United States
| | - Aiju Wang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of SciencesBeijing, China
| | - Chengcai Chu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of SciencesBeijing, China
| | - Yao Shi
- Department of Biological Sciences, Marquette University, MilwaukeeWI, United States
| | - Naoki Shimoyama
- Department of Biological Sciences, Marquette University, MilwaukeeWI, United States
| | - Debbie L. Boykin
- United States Department of Agriculture – Agricultural Research Service, StonevilleMS, United States
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Mitchell C, Brennan RM, Graham J, Karley AJ. Plant Defense against Herbivorous Pests: Exploiting Resistance and Tolerance Traits for Sustainable Crop Protection. FRONTIERS IN PLANT SCIENCE 2016; 7:1132. [PMID: 27524994 PMCID: PMC4965446 DOI: 10.3389/fpls.2016.01132] [Citation(s) in RCA: 127] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Accepted: 07/15/2016] [Indexed: 05/03/2023]
Abstract
Interactions between plants and insect herbivores are important determinants of plant productivity in managed and natural vegetation. In response to attack, plants have evolved a range of defenses to reduce the threat of injury and loss of productivity. Crop losses from damage caused by arthropod pests can exceed 15% annually. Crop domestication and selection for improved yield and quality can alter the defensive capability of the crop, increasing reliance on artificial crop protection. Sustainable agriculture, however, depends on reduced chemical inputs. There is an urgent need, therefore, to identify plant defensive traits for crop improvement. Plant defense can be divided into resistance and tolerance strategies. Plant traits that confer herbivore resistance typically prevent or reduce herbivore damage through expression of traits that deter pests from settling, attaching to surfaces, feeding and reproducing, or that reduce palatability. Plant tolerance of herbivory involves expression of traits that limit the negative impact of herbivore damage on productivity and yield. Identifying the defensive traits expressed by plants to deter herbivores or limit herbivore damage, and understanding the underlying defense mechanisms, is crucial for crop scientists to exploit plant defensive traits in crop breeding. In this review, we assess the traits and mechanisms underpinning herbivore resistance and tolerance, and conclude that physical defense traits, plant vigor and herbivore-induced plant volatiles show considerable utility in pest control, along with mixed species crops. We highlight emerging approaches for accelerating the identification of plant defensive traits and facilitating their deployment to improve the future sustainability of crop protection.
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Affiliation(s)
| | - Rex M. Brennan
- Cell and Molecular Sciences, The James Hutton InstituteDundee, UK
| | - Julie Graham
- Cell and Molecular Sciences, The James Hutton InstituteDundee, UK
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Wang H, Xu X, Vieira FG, Xiao Y, Li Z, Wang J, Nielsen R, Chu C. The Power of Inbreeding: NGS-Based GWAS of Rice Reveals Convergent Evolution during Rice Domestication. MOLECULAR PLANT 2016; 9:975-85. [PMID: 27179918 DOI: 10.1016/j.molp.2016.04.018] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Revised: 04/16/2016] [Accepted: 04/27/2016] [Indexed: 05/22/2023]
Abstract
Low-coverage whole-genome sequencing is an effective strategy for genome-wide association studies in humans, due to the availability of large reference panels for genotype imputation. However, it is unclear whether this strategy can be utilized in other species without reference panels. Using simulations, we show that this approach is even more relevant in inbred species such as rice (Oryza sativa L.), which are effectively haploid, allowing easy haplotype construction and imputation-based genotype calling, even without the availability of large reference panels. We sequenced 203 rice varieties with well-characterized phenotypes from the United States Department of Agriculture Rice Mini-Core Collection at an average depth of 1.5× and used the data for mapping three traits. For the first two traits, amylose content and seed length, our approach leads to direct identification of the previously identified causal SNPs in the major-effect loci. For the third trait, pericarp color, an important trait underwent selection during domestication, we identified a new major-effect locus. Although known loci can explain color variation in the varieties of two main subspecies of Asian domesticated rice, japonica and indica, the new locus identified is unique to another domesticated rice subgroup, aus, and together with existing loci, can fully explain the major variation in pericarp color in aus. Our discovery of a unique genetic basis of white pericarp in aus provides an example of convergent evolution during rice domestication and suggests that aus may have a domestication history independent of japonica and indica.
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Affiliation(s)
- Hongru Wang
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100101, China
| | - Xun Xu
- BGI-Shenzhen, Shenzhen 518083, China
| | | | - Yunhua Xiao
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100101, China
| | - Zhikang Li
- Institute of Crop Sciences/National Key Facilities for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, 12 South Zhong-Guan-Cun Street, Beijing 100081, China
| | - Jun Wang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100101, China.
| | - Rasmus Nielsen
- Department of Integrative Biology, University of California, Berkeley, CA 94720 USA.
| | - Chengcai Chu
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.
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Functional Characterization of 9-/13-LOXs in Rice and Silencing Their Expressions to Improve Grain Qualities. BIOMED RESEARCH INTERNATIONAL 2016; 2016:4275904. [PMID: 27403427 PMCID: PMC4925972 DOI: 10.1155/2016/4275904] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/05/2015] [Accepted: 04/24/2016] [Indexed: 12/03/2022]
Abstract
Lipoxygenases (LOXs) are involved in oxidative rancidity and render rice unsuitable for human consumption. Here, RNA interference- (RNAi-) induced gene expression inhibition was used to analyze the functions of the bran/seed-specific LOXs in rice. r9-LOX1 and L-2 (9-LOX category) were the candidate genes expressing a bran/seed-specific LOX, while RCI-1 was (13-LOX category) a plastid-specific LOX. Real-time PCR showed that three LOXs were cultivar/tissue specific expression on a certain level. r9-LOX1 and L-2 were generally much higher in active bran/seed than in stabilized bran, mature seed, and regenerated plant. RCI-1 was barely expressed in seed. In transgenic lines, r9-LOX1, as well as L-2, expression was dramatically downregulated, compared to the nontransgenic controls. SPME/GC-MS analysis of r9-LOX1 RNAi transgenic lines showed 74.33% decrease in nonanal content (formed during oxidation of linoleic acid by lipoxygenase), but 388.24% increase in acetic acid and 184.84% hexanal (direct products of 13-LOX). These results indicate that r9-LOX1 positively regulates the amount of nonanal but negatively regulates acetic acid and hexanal. The negative regulation may be due to a mechanism of negative feedback between LOX family members. The information will help comprehensively understand the function of the bran/seed-specific LOXs, r9-LOX1, and improve the storage quality in the future.
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Lv Y, Guo Z, Li X, Ye H, Li X, Xiong L. New insights into the genetic basis of natural chilling and cold shock tolerance in rice by genome-wide association analysis. PLANT, CELL & ENVIRONMENT 2016; 39:556-70. [PMID: 26381647 DOI: 10.1111/pce.12635] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2015] [Revised: 09/11/2015] [Accepted: 09/12/2015] [Indexed: 05/19/2023]
Abstract
In order to understand cold adaptability and explore additional genetic resources for the cold tolerance improvement of rice, we investigated the genetic variation of 529 rice accessions under natural chilling and cold shock stress conditions at the seedling stage using genome-wide association studies; a total of 132 loci were identified. Among them, 12 loci were common for both chilling and cold shock tolerance, suggesting that rice has a distinct and overlapping genetic response and adaptation to the two stresses. Haplotype analysis of a known gene OsMYB2, which is involved in cold tolerance, revealed indica-japonica differentiation and latitude tendency for the haplotypes of this gene. By checking the subpopulation and geographical distribution of accessions with tolerance or sensitivity under these two stress conditions, we found that the chilling tolerance group, which mainly consisted of japonica accessions, has a wider latitudinal distribution than the chilling sensitivity group. We conclude that the genetic basis of natural chilling stress tolerance in rice is distinct from that of cold shock stress frequently used for low-temperature treatment in the laboratory and the cold adaptability of rice is associated with the subpopulation and latitudinal distribution.
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Affiliation(s)
- Yan Lv
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
- National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Zilong Guo
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
- National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Xiaokai Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
- National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Haiyan Ye
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
- National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Xianghua Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
- National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Lizhong Xiong
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
- National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
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Zhang P, Zhong K, Shahid MQ, Tong H. Association Analysis in Rice: From Application to Utilization. FRONTIERS IN PLANT SCIENCE 2016; 7:1202. [PMID: 27582745 PMCID: PMC4987372 DOI: 10.3389/fpls.2016.01202] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Accepted: 07/28/2016] [Indexed: 05/03/2023]
Abstract
Association analysis based on linkage disequilibrium (LD) is an efficient way to dissect complex traits and to identify gene functions in rice. Although association analysis is an effective way to construct fine maps for quantitative traits, there are a few issues which need to be addressed. In this review, we will first summarize type, structure, and LD level of populations used for association analysis of rice, and then discuss the genotyping methods and statistical approaches used for association analysis in rice. Moreover, we will review current shortcomings and benefits of association analysis as well as specific types of future research to overcome these shortcomings. Furthermore, we will analyze the reasons for the underutilization of the results within association analysis in rice breeding.
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Affiliation(s)
- Peng Zhang
- State Key Laboratory of Rice Biology, China National Rice Research InstituteHangzhou, China
- *Correspondence: Peng Zhang
| | - Kaizhen Zhong
- State Key Laboratory of Rice Biology, China National Rice Research InstituteHangzhou, China
| | - Muhammad Qasim Shahid
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural UniversityGuangzhou, China
| | - Hanhua Tong
- State Key Laboratory of Rice Biology, China National Rice Research InstituteHangzhou, China
- Hanhua Tong
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14
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Talukdar P, Douglas A, Price AH, Norton GJ. Biallelic and Genome Wide Association Mapping of Germanium Tolerant Loci in Rice (Oryza sativa L.). PLoS One 2015; 10:e0137577. [PMID: 26356220 PMCID: PMC4565582 DOI: 10.1371/journal.pone.0137577] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Accepted: 08/18/2015] [Indexed: 11/19/2022] Open
Abstract
Rice plants accumulate high concentrations of silicon. Silicon has been shown to be involved in plant growth, high yield, and mitigating biotic and abiotic stresses. However, it has been demonstrated that inorganic arsenic is taken up by rice through silicon transporters under anaerobic conditions, thus the ability to efficiently take up silicon may be considered either a positive or a negative trait in rice. Germanium is an analogue of silicon that produces brown lesions in shoots and leaves, and germanium toxicity has been used to identify mutants in silicon and arsenic transport. In this study, two different genetic mapping methods were performed to determine the loci involved in germanium sensitivity in rice. Genetic mapping in the biparental cross of Bala × Azucena (an F6 population) and a genome wide association (GWA) study with 350 accessions from the Rice Diversity Panel 1 were conducted using 15 μM of germanic acid. This identified a number of germanium sensitive loci: some co-localised with previously identified quantitative trait loci (QTL) for tissue silicon or arsenic concentration, none co-localised with Lsi1 or Lsi6, while one single nucleotide polymorphism (SNP) was detected within 200 kb of Lsi2 (these are genes known to transport silicon, whose identity was discovered using germanium toxicity). However, examining candidate genes that are within the genomic region of the loci detected above reveals genes homologous to both Lsi1 and Lsi2, as well as a number of other candidate genes, which are discussed.
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Affiliation(s)
- Partha Talukdar
- Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen, AB24 3UU, United Kingdom
| | - Alex Douglas
- Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen, AB24 3UU, United Kingdom
| | - Adam H. Price
- Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen, AB24 3UU, United Kingdom
| | - Gareth J. Norton
- Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen, AB24 3UU, United Kingdom
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15
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Bryant RJ, Jackson AK, Yeater KM, Yan WG, McClung AM, Fjellstrom RG. Genetic Variation and Association Mapping of Protein Concentration in Brown Rice Using a Diverse Rice Germplasm Collection. Cereal Chem 2013. [DOI: 10.1094/cchem-09-12-0122-r] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Rolfe J. Bryant
- U.S. Department of Agriculture–Agricultural Research Service (USDA-ARS), Dale Bumpers National Rice Research Center, 2890 Hwy 130 E., Stuttgart, AR 72160, U.S.A. Mention of a trademark or proprietary product in this article is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the USDA. USDA is an equal opportunity provider and employer
| | - Aaron K. Jackson
- U.S. Department of Agriculture–Agricultural Research Service (USDA-ARS), Dale Bumpers National Rice Research Center, 2890 Hwy 130 E., Stuttgart, AR 72160, U.S.A. Mention of a trademark or proprietary product in this article is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the USDA. USDA is an equal opportunity provider and employer
| | | | - Wengui G. Yan
- U.S. Department of Agriculture–Agricultural Research Service (USDA-ARS), Dale Bumpers National Rice Research Center, 2890 Hwy 130 E., Stuttgart, AR 72160, U.S.A. Mention of a trademark or proprietary product in this article is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the USDA. USDA is an equal opportunity provider and employer
| | - Anna M. McClung
- U.S. Department of Agriculture–Agricultural Research Service (USDA-ARS), Dale Bumpers National Rice Research Center, 2890 Hwy 130 E., Stuttgart, AR 72160, U.S.A. Mention of a trademark or proprietary product in this article is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the USDA. USDA is an equal opportunity provider and employer
| | - Robert G. Fjellstrom
- U.S. Department of Agriculture–Agricultural Research Service (USDA-ARS), Dale Bumpers National Rice Research Center, 2890 Hwy 130 E., Stuttgart, AR 72160, U.S.A. Mention of a trademark or proprietary product in this article is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the USDA. USDA is an equal opportunity provider and employer
- Corresponding author. Phone: (870) 672-9300, ext. 223. Fax: (870) 673-7581. E-mail:
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Ziska LH, Gealy DR, Tomecek MB, Jackson AK, Black HL. Recent and projected increases in atmospheric CO2 concentration can enhance gene flow between wild and genetically altered rice (Oryza sativa). PLoS One 2012; 7:e37522. [PMID: 22649533 PMCID: PMC3359302 DOI: 10.1371/journal.pone.0037522] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2012] [Accepted: 04/20/2012] [Indexed: 11/18/2022] Open
Abstract
Although recent and projected increases in atmospheric carbon dioxide can alter plant phenological development, these changes have not been quantified in terms of floral outcrossing rates or gene transfer. Could differential phenological development in response to rising CO2 between genetically modified crops and wild, weedy relatives increase the spread of novel genes, potentially altering evolutionary fitness? Here we show that increasing CO2 from an early 20th century concentration (300 µmol mol−1) to current (400 µmol mol−1) and projected, mid-21st century (600 µmol mol−1) values, enhanced the flow of genes from wild, weedy rice to the genetically altered, herbicide resistant, cultivated population, with outcrossing increasing from 0.22% to 0.71% from 300 to 600 µmol mol−1. The increase in outcrossing and gene transfer was associated with differential increases in plant height, as well as greater tiller and panicle production in the wild, relative to the cultivated population. In addition, increasing CO2 also resulted in a greater synchronicity in flowering times between the two populations. The observed changes reported here resulted in a subsequent increase in rice dedomestication and a greater number of weedy, herbicide-resistant hybrid progeny. Overall, these data suggest that differential phenological responses to rising atmospheric CO2 could result in enhanced flow of novel genes and greater success of feral plant species in agroecosystems.
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Affiliation(s)
- Lewis H Ziska
- Crop Systems and Global Change Laboratory, United States Department of Agriculture, Agricultural Research Service, Beltsville, Maryland, United States of America.
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