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D'Agostino LW, Yong-Villalobos L, Herrera-Estrella L, Patil GB. Development of High-Quality Nuclei Isolation to Study Plant Root-Microbe Interaction for Single-Nuclei Transcriptomic Sequencing in Soybean. Plants (Basel) 2023; 12:2466. [PMID: 37447027 DOI: 10.3390/plants12132466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 06/22/2023] [Accepted: 06/27/2023] [Indexed: 07/15/2023]
Abstract
Single-nucleus RNA sequencing (sNucRNA-seq) is an emerging technology that has been rapidly adopted and demonstrated to be a powerful tool for detailed characterization of each cell- and sub cell-types in complex tissues of higher eukaryotes. sNucRNA-seq has also been used to dissect cell-type-specific transcriptional responses to environmental or developmental signals. In plants, this technology is being utilized to identify cell-type-specific trajectories for the study of several tissue types and important traits, including the single-cell dissection of the genetic determinants regulating plant-microbe interactions. The isolation of high-quality nuclei is one of the prerequisite steps to obtain high-quality sNucRNA-seq results. Although nuclei isolation from several plant tissues is well established, this process is highly troublesome when plant tissues are associated with beneficial or pathogenic microbes. For example, root tissues colonized with rhizobium bacteria (nodules), leaf tissue infected with bacterial or fungal pathogens, or roots infected with nematodes pose critical challenges to the isolation of high-quality nuclei and use for downstream application. Therefore, isolation of microbe-free, high-quality nuclei from plant tissues are necessary to avoid clogging or interference with the microfluidic channel (e.g., 10× Genomics) or particle-templated emulsion that are used in sNucRNA-seq platforms. Here, we developed a simple, effective, and efficient method to isolate high-quality nuclei from soybean roots and root nodules, followed by washing out bacterial contamination. This protocol has been designed to be easily implemented into any lab environment, and it can also be scaled up for use with multiple samples and applicable to a variety of samples with the presence of microbes. We validated this protocol by successfully generating a barcoded library using the 10× Genomics microfluidic platform from tissue subjected to this procedure. This workflow was developed to provide an accessible alternative to instrument-based approaches (e.g., fluorescent cell sorting) and will expand the ability of researchers to perform experiments such as sNucRNA-seq and sNucATAC-seq on inherently heterogeneous plant tissue samples.
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Affiliation(s)
- Leonidas W D'Agostino
- Institute of Genomics for Crop Abiotic Stress Tolerance, Department of Plant and Soil Science, Texas Tech University, Lubbock, TX 79409, USA
| | - Lenin Yong-Villalobos
- Institute of Genomics for Crop Abiotic Stress Tolerance, Department of Plant and Soil Science, Texas Tech University, Lubbock, TX 79409, USA
| | - Luis Herrera-Estrella
- Institute of Genomics for Crop Abiotic Stress Tolerance, Department of Plant and Soil Science, Texas Tech University, Lubbock, TX 79409, USA
- Unidad de Genomica Avanzada, Centro de Investigacion y de Estudios Avanzados, Instituto Politecnico Nacional, Irapuato 36821, Mexico
| | - Gunvant B Patil
- Institute of Genomics for Crop Abiotic Stress Tolerance, Department of Plant and Soil Science, Texas Tech University, Lubbock, TX 79409, USA
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2
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Ojha A, Zhang F, Patil GB. Genome editing and chromosome engineering in plants. Plant Genome 2023; 16:e20352. [PMID: 37334443 DOI: 10.1002/tpg2.20352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Accepted: 05/01/2023] [Indexed: 06/20/2023]
Affiliation(s)
- Arjun Ojha
- Institute of Genomics for Crop Abiotic Stress Tolerance, Department of Plant and Soil Sciences, Texas Tech University, Lubbock, Texas, USA
| | - Feng Zhang
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, Minnesota, USA
| | - Gunvant B Patil
- Institute of Genomics for Crop Abiotic Stress Tolerance, Department of Plant and Soil Sciences, Texas Tech University, Lubbock, Texas, USA
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3
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Rana N, Kumawat S, Kumar V, Bansal R, Mandlik R, Dhiman P, Patil GB, Deshmukh R, Sharma TR, Sonah H. Deciphering Haplotypic Variation and Gene Expression Dynamics Associated with Nutritional and Cooking Quality in Rice. Cells 2022; 11:cells11071144. [PMID: 35406707 PMCID: PMC8998046 DOI: 10.3390/cells11071144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 03/21/2022] [Accepted: 03/24/2022] [Indexed: 02/01/2023] Open
Abstract
Nutritional quality improvement of rice is the key to ensure global food security. Consequently, enormous efforts have been made to develop genomics and transcriptomics resources for rice. The available omics resources along with the molecular understanding of trait development can be utilized for efficient exploration of genetic resources for breeding programs. In the present study, 80 genes known to regulate the nutritional and cooking quality of rice were extensively studied to understand the haplotypic variability and gene expression dynamics. The haplotypic variability of selected genes were defined using whole-genome re-sequencing data of ~4700 diverse genotypes. The analytical workflow identified 133 deleterious single-nucleotide polymorphisms, which are predicted to affect the gene function. Furthermore, 788 haplotype groups were defined for 80 genes, and the distribution and evolution of these haplotype groups in rice were described. The nucleotide diversity for the selected genes was significantly reduced in cultivated rice as compared with that in wild rice. The utility of the approach was successfully demonstrated by revealing the haplotypic association of chalk5 gene with the varying degree of grain chalkiness. The gene expression atlas was developed for these genes by analyzing RNA-Seq transcriptome profiling data from 102 independent sequence libraries. Subsequently, weighted gene co-expression meta-analyses of 11,726 publicly available RNAseq libraries identified 19 genes as the hub of interactions. The comprehensive analyses of genetic polymorphisms, allelic distribution, and gene expression profiling of key quality traits will help in exploring the most desired haplotype for grain quality improvement. Similarly, the information provided here will be helpful to understand the molecular mechanism involved in the development of nutritional and cooking quality traits in rice.
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Affiliation(s)
- Nitika Rana
- Department of Agriculture Biotechnology, National Agri-Food Biotechnology Institute (NABI), Mohali 140306, India; (N.R.); (S.K.); (V.K.); (R.B.); (R.M.); (P.D.); (R.D.); (T.R.S.)
- Department of Biotechnology, Panjab University, Chandigarh 160014, India
| | - Surbhi Kumawat
- Department of Agriculture Biotechnology, National Agri-Food Biotechnology Institute (NABI), Mohali 140306, India; (N.R.); (S.K.); (V.K.); (R.B.); (R.M.); (P.D.); (R.D.); (T.R.S.)
- Department of Biotechnology, Panjab University, Chandigarh 160014, India
| | - Virender Kumar
- Department of Agriculture Biotechnology, National Agri-Food Biotechnology Institute (NABI), Mohali 140306, India; (N.R.); (S.K.); (V.K.); (R.B.); (R.M.); (P.D.); (R.D.); (T.R.S.)
| | - Ruchi Bansal
- Department of Agriculture Biotechnology, National Agri-Food Biotechnology Institute (NABI), Mohali 140306, India; (N.R.); (S.K.); (V.K.); (R.B.); (R.M.); (P.D.); (R.D.); (T.R.S.)
- Department of Biotechnology, Panjab University, Chandigarh 160014, India
| | - Rushil Mandlik
- Department of Agriculture Biotechnology, National Agri-Food Biotechnology Institute (NABI), Mohali 140306, India; (N.R.); (S.K.); (V.K.); (R.B.); (R.M.); (P.D.); (R.D.); (T.R.S.)
- Department of Biotechnology, Panjab University, Chandigarh 160014, India
| | - Pallavi Dhiman
- Department of Agriculture Biotechnology, National Agri-Food Biotechnology Institute (NABI), Mohali 140306, India; (N.R.); (S.K.); (V.K.); (R.B.); (R.M.); (P.D.); (R.D.); (T.R.S.)
| | - Gunvant B. Patil
- Department of Plant and Soil Sciences, Institute of Genomics for Crop Abiotic Stress Tolerance, Texas Tech University, Lubbock, TX 79409, USA;
| | - Rupesh Deshmukh
- Department of Agriculture Biotechnology, National Agri-Food Biotechnology Institute (NABI), Mohali 140306, India; (N.R.); (S.K.); (V.K.); (R.B.); (R.M.); (P.D.); (R.D.); (T.R.S.)
| | - Tilak Raj Sharma
- Department of Agriculture Biotechnology, National Agri-Food Biotechnology Institute (NABI), Mohali 140306, India; (N.R.); (S.K.); (V.K.); (R.B.); (R.M.); (P.D.); (R.D.); (T.R.S.)
- Department of Crop Science, Indian Council of Agriculture Research (ICAR), Krishi Bhavan, New Delhi 110001, India
| | - Humira Sonah
- Department of Agriculture Biotechnology, National Agri-Food Biotechnology Institute (NABI), Mohali 140306, India; (N.R.); (S.K.); (V.K.); (R.B.); (R.M.); (P.D.); (R.D.); (T.R.S.)
- Correspondence: ; Tel.: +91-6239715281
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Abstract
Protoplast is a versatile system for conducting cell-based assays, analyzing diverse signaling pathways, studying functions of cellular machineries, and functional genomics screening. Protoplast engineering has become an important tool for basic plant molecular biology research and developing genome-edited crops. This system allows the direct delivery of DNA, RNA, or proteins into plant cells and provides a high-throughput system to validate gene-editing reagents. It also facilitates the delivery of homology-directed repair templates (donor molecules) into plant cells, enabling precise DNA edits in the genome. There is a great deal of interest in the plant community to develop these precise edits, as they may expand the potential for developing value-added traits which may be difficult to achieve by other gene-editing applications and/or traditional breeding alone. This chapter provides improved working protocols for isolating and transforming protoplast from immature soybean seeds with 44% of transfection efficiency validated by the green fluorescent protein reporter. We also describe a method for gene editing in soybean protoplasts using single guide RNA molecules.
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Affiliation(s)
- Gunvant B Patil
- Institute of Genomics for Crop Abiotic Stress Tolerance, Department of Plant and Soil Science, Texas Tech University, Lubbock, TX, USA.
| | - Robert M Stupar
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, USA
| | - Feng Zhang
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, MN, USA
- Center for Precision Plant Genomics, University of Minnesota, Saint Paul, MN, USA
- Center for Genome Engineering, University of Minnesota, Saint Paul, MN, USA
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Usovsky M, Lakhssassi N, Patil GB, Vuong TD, Piya S, Hewezi T, Robbins RT, Stupar RM, Meksem K, Nguyen HT. Dissecting nematode resistance regions in soybean revealed pleiotropic effect of soybean cyst and reniform nematode resistance genes. Plant Genome 2021; 14:e20083. [PMID: 33724721 DOI: 10.1002/tpg2.20083] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 12/04/2020] [Indexed: 06/12/2023]
Abstract
Reniform nematode (RN, Rotylenchulus reniformis Linford & Oliveira) has emerged as one of the most important plant parasitic nematodes of soybean [Glycine max (L.) Merr.]. Planting resistant varieties is the most effective strategy for nematode management. The objective of this study was to identify quantitative trait loci (QTL) for RN resistance in an exotic soybean line, PI 438489B, using two linkage maps constructed from the Universal Soybean Linkage Panel (USLP 1.0) and next-generation whole-genome resequencing (WGRS) technology. Two QTL controlling RN resistance were identified-the soybean cyst nematode (SCN, Heterodera glycines) resistance gene GmSNAP18 at the rhg1 locus and its paralog GmSNAP11. Strong association between resistant phenotype and haplotypes of the GmSNAP11 and GmSNAP18 was observed. The results indicated that GmSNAP11 possibly could have epistatic effect on GmSNAP18, or vice versa, with the presence of a significant correlation in RN resistance of rhg1-a GmSNAP18 vs. rhg1-b GmSNAP18. Most importantly, our preliminary data suggested that GmSNAP18 and GmSNAP11 proteins physically interact in planta, suggesting that they belong to the same pathway for resistance. Unlike GmSNAP18, no indication of GmSNAP11 copy number variation was found. Moreover, gene-based single nucleotide polymorphism (SNP) markers were developed for rapid detection of RN or SCN resistance at these loci. Our analysis substantiates synergic interaction between GmSNAP11 and GmSNAP18 genes and confirms their roles in RN as well as SCN resistance. These results could contribute to a better understanding of evolution and subfunctionalization of genes conferring resistance to multiple nematode species and provide a framework for further investigations.
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Affiliation(s)
- Mariola Usovsky
- Division of Plant Sciences, University of Missouri, Columbia, MO, USA
| | - Naoufal Lakhssassi
- Department of Plant, Soil and Agricultural Systems, Southern Illinois University, Carbondale, IL, USA
| | - Gunvant B Patil
- Institute of Genomics for Crop Abiotic Stress Tolerance, Department of Plant and Soil Science, Texas Tech University, Lubbock, TX, USA
| | - Tri D Vuong
- Division of Plant Sciences, University of Missouri, Columbia, MO, USA
| | - Sarbottam Piya
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, USA
| | - Tarek Hewezi
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, USA
| | - Robert T Robbins
- Department of Plant Pathology, University of Arkansas, Fayetteville, AR, USA
| | - Robert M Stupar
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, USA
| | - Khalid Meksem
- Department of Plant, Soil and Agricultural Systems, Southern Illinois University, Carbondale, IL, USA
| | - Henry T Nguyen
- Division of Plant Sciences, University of Missouri, Columbia, MO, USA
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Deshmukh R, Rana N, Liu Y, Zeng S, Agarwal G, Sonah H, Varshney R, Joshi T, Patil GB, Nguyen HT. Soybean transporter database: A comprehensive database for identification and exploration of natural variants in soybean transporter genes. Physiol Plant 2021; 171:756-770. [PMID: 33231322 DOI: 10.1111/ppl.13287] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Revised: 10/05/2020] [Accepted: 11/17/2020] [Indexed: 06/11/2023]
Abstract
Transporters, a class of membrane proteins that facilitate exchange of solutes including diverse molecules and ions across the cellular membrane, are vital component for the survival of all organisms. Understanding plant transporters is important to get insight of the basic cellular processes, physiology, and molecular mechanisms including nutrient uptake, signaling, response to external stress, and many more. In this regard, extensive analysis of transporters predicted in soybean and other plant species was performed. In addition, an integrated database for soybean transporter protein, SoyTD, was developed that will facilitate the identification, classification, and extensive characterization of transporter proteins by integrating expression, gene ontology, conserved domain and motifs, gene structure organization, and chromosomal distribution features. A comprehensive analysis was performed to identify highly confident transporters by integrating various prediction tools. Initially, 7541 transmembrane (TM) proteins were predicted in the soybean genome; out of these, 3306 non-redundant transporter genes carrying two or more transmembrane domains were selected for further analysis. The identified transporter genes were classified according to a standard transporter classification (TC) system. Comparative analysis of transporter genes among 47 plant genomes provided insights into expansion and duplication of transporter genes in land plants. The whole genome resequencing (WGRS) and tissue-specific transcriptome datasets of soybean were integrated to investigate the natural variants and expression profile associated with transporter(s) of interest. Overall, SoyTD provides a comprehensive interface to study genetic and molecular function of soybean transporters. SoyTD is publicly available at http://artemis.cyverse.org/soykb_dev/SoyTD/.
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Affiliation(s)
- Rupesh Deshmukh
- Agriculture Biotechnology Department, National Agri-Food Biotechnology Institute (NABI), Mohali, India
| | - Nitika Rana
- Agriculture Biotechnology Department, National Agri-Food Biotechnology Institute (NABI), Mohali, India
- Department of Biotechnology, Panjab University, Chandigarh, India
| | - Yang Liu
- Christopher S. Bond Life Science Center, University of Missouri, Columbia, Missouri, USA
| | - Shuai Zeng
- Christopher S. Bond Life Science Center, University of Missouri, Columbia, Missouri, USA
- Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, Missouri, USA
| | - Gaurav Agarwal
- Department of Plant Pathology, University of Georgia, Tifton, Georgia, USA
| | - Humira Sonah
- Agriculture Biotechnology Department, National Agri-Food Biotechnology Institute (NABI), Mohali, India
| | - Rajeev Varshney
- Center of Excellence in Genomics and System Biology, International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, India
| | - Trupti Joshi
- Christopher S. Bond Life Science Center, University of Missouri, Columbia, Missouri, USA
- Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, Missouri, USA
| | - Gunvant B Patil
- Department of Plant and Soil Sciences, Institute of Genomics for Crop Abiotic Stress Tolerance, Texas Tech University, Lubbock, Texas, USA
| | - Henry T Nguyen
- Division of Plant Science, National Center for Soybean Biotechnology, University of Missouri, Columbia, Missouri, USA
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Usovsky M, Ye H, Vuong TD, Patil GB, Wan J, Zhou L, Nguyen HT. Fine-mapping and characterization of qSCN18, a novel QTL controlling soybean cyst nematode resistance in PI 567516C. Theor Appl Genet 2021; 134:621-631. [PMID: 33185711 DOI: 10.1007/s00122-020-03718-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 10/27/2020] [Indexed: 06/11/2023]
Abstract
KEY MESSAGE The qSCN18 QTL from PI 56756C was confirmed and fine-mapped to improve soybean resistance to the SCN population HG Type 2.5.7 using near-isogenic lines carrying recombination crossovers within the QTL region. The QTL underlying resistance was fine-mapped to a 166-Kbp region on chromosome 18, and the candidate genes were selected based on genomic analyses. Soybean cyst nematode (SCN, Heterodera glycines, Ichinohe) is the most devastating pathogen of soybean. Understanding the genetic basis of SCN resistance is crucial for managing this parasite in the field. Two major loci, rhg1 and Rhg4, were previously characterized as valuable resources for SCN resistance. However, their continuous use has caused shifts in the virulence of SCN populations, which can overcome the resistance conferred by these two major loci. Reduced effectiveness became a major concern in the soybean industry due to continuous use of rhg1 for decades. Thus, it is imperative to identify sources of SCN resistance for durable SCN management. A novel QTL qSCN18 was identified in PI567516C. To fine-map qSCN18 and identify resistance genes, a large backcross population was developed. Nineteen near-isogenic lines (NILs) carrying recombination crossovers within the QTL region were identified. The first phase of fine-mapping narrowed the QTL region to 549-Kbp, whereas the second phase confined the region to 166-Kbp containing 23 genes. Two flanking markers, MK-1 and MK-6, were developed and validated to detect the presence of the qSCN18 resistance allele. Haplotype analysis clustered the fine-mapped qSCN18 region from PI 567516C with the cqSCN-007 locus previously mapped in the wild soybean accession PI 468916. The NILs were developed to further characterize the causal gene(s) harbored in this QTL. This study also confirmed the previously identified qSCN18. The results will facilitate marker-assisted selection (MAS) introducing the qSCN18 locus from PI 567516C into high-yielding soybean cultivars with durable resistance to SCN.
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Affiliation(s)
- Mariola Usovsky
- Division of Plant Sciences, University of Missouri, Columbia, MO, USA
| | - Heng Ye
- Division of Plant Sciences, University of Missouri, Columbia, MO, USA
| | - Tri D Vuong
- Division of Plant Sciences, University of Missouri, Columbia, MO, USA
| | - Gunvant B Patil
- Institute for Genomics of Crop Abiotic Stress Tolerance, Department of Plant and Soil Science, Texas Tech University, Lubbock, TX, 79415, USA
| | - Jinrong Wan
- Division of Plant Sciences, University of Missouri, Columbia, MO, USA
| | - Lijuan Zhou
- Division of Plant Sciences, University of Missouri, Columbia, MO, USA
| | - Henry T Nguyen
- Division of Plant Sciences, University of Missouri, Columbia, MO, USA.
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Lakhssassi N, Zhou Z, Liu S, Piya S, Cullen MA, El Baze A, Knizia D, Patil GB, Badad O, Embaby MG, Meksem J, Lakhssassi A, AbuGhazaleh A, Hewezi T, Meksem K. Soybean TILLING-by-Sequencing+ reveals the role of novel GmSACPD members in unsaturated fatty acid biosynthesis while maintaining healthy nodules. J Exp Bot 2020; 71:6969-6987. [PMID: 32898219 DOI: 10.1093/jxb/eraa402] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 08/27/2020] [Indexed: 05/07/2023]
Abstract
Developing soybean lines with high levels of stearic acid is a primary goal of the soybean industry. Most high-stearic-acid soybeans carry different GmSACPD-C mutated alleles. However, due to the dual role of GmSACPD-C in seeds and nodule development, all derived deleterious GmSACPD-C mutant alleles are of extremely poor agronomic value because of defective nodulation. The soybean stearoyl-acyl carrier protein desaturase (GmSACPD) gene family is composed of five members. Comparative genomics analysis indicated that SACPD genes were duplicated and derived from a common ancestor that is still present in chlorophytic algae. Synteny analysis showed the presence of segment duplications between GmSACPD-A/GmSACPD-B, and GmSACPD-C/GmSACPD-D. GmSACPD-E was not contained in any duplicated segment and may be the result of tandem duplication. We developed a TILLING by Target Capture Sequencing (Tilling-by-Sequencing+) technology, a versatile extension of the conventional TILLING by sequencing, and successfully identified 12, 14, and 18 ethyl methanesulfonate mutants at the GmSACPD-A, GmSACPD-B, and GmSACPD-D genes, respectively. Functional analysis of all identified mutants revealed an unprecedented role of GmSACPD-A, GmSACPD-B, and GmSACPD-D in unsaturated fatty acid biosynthesis without affecting nodule development and structure. This discovery will positively impact the development of high-stearic-acid lines to enhance soybean nutritional value without potential developmental tradeoffs.
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Affiliation(s)
- Naoufal Lakhssassi
- Department of Plant, Soil and Agricultural Systems, Southern Illinois University, Carbondale, IL, USA
| | - Zhou Zhou
- Department of Plant, Soil and Agricultural Systems, Southern Illinois University, Carbondale, IL, USA
| | - Shiming Liu
- Department of Plant, Soil and Agricultural Systems, Southern Illinois University, Carbondale, IL, USA
| | - Sarbottam Piya
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, USA
| | - Mallory A Cullen
- Department of Plant, Soil and Agricultural Systems, Southern Illinois University, Carbondale, IL, USA
| | - Abdelhalim El Baze
- Department of Plant, Soil and Agricultural Systems, Southern Illinois University, Carbondale, IL, USA
| | - Dounya Knizia
- Department of Plant, Soil and Agricultural Systems, Southern Illinois University, Carbondale, IL, USA
| | - Gunvant B Patil
- Institute for Genomics of Crop Abiotic Stress Tolerance, Department of Plant and Soil Science, Texas Tech University, Lubbock, TX, USA
| | - Oussama Badad
- Department of Plant, Soil and Agricultural Systems, Southern Illinois University, Carbondale, IL, USA
| | - Mohamed G Embaby
- Department of Animal Science, Food, and Nutrition, Southern Illinois University, Carbondale, IL, USA
| | - Jonas Meksem
- Trinity College of Arts and Sciences, Duke University, Durham, NC, USA
| | - Aicha Lakhssassi
- Faculty of Sciences and Technologies, University of Lorraine, Nancy, France
| | - Amer AbuGhazaleh
- Department of Animal Science, Food, and Nutrition, Southern Illinois University, Carbondale, IL, USA
| | - Tarek Hewezi
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, USA
| | - Khalid Meksem
- Department of Plant, Soil and Agricultural Systems, Southern Illinois University, Carbondale, IL, USA
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9
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Graham N, Patil GB, Bubeck DM, Dobert RC, Glenn KC, Gutsche AT, Kumar S, Lindbo JA, Maas L, May GD, Vega-Sanchez ME, Stupar RM, Morrell PL. Plant Genome Editing and the Relevance of Off-Target Changes. Plant Physiol 2020; 183:1453-1471. [PMID: 32457089 PMCID: PMC7401131 DOI: 10.1104/pp.19.01194] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 05/07/2020] [Indexed: 05/12/2023]
Abstract
Site-directed nucleases (SDNs) used for targeted genome editing are powerful new tools to introduce precise genetic changes into plants. Like traditional approaches, such as conventional crossing and induced mutagenesis, genome editing aims to improve crop yield and nutrition. Next-generation sequencing studies demonstrate that across their genomes, populations of crop species typically carry millions of single nucleotide polymorphisms and many copy number and structural variants. Spontaneous mutations occur at rates of ∼10-8 to 10-9 per site per generation, while variation induced by chemical treatment or ionizing radiation results in higher mutation rates. In the context of SDNs, an off-target change or edit is an unintended, nonspecific mutation occurring at a site with sequence similarity to the targeted edit region. SDN-mediated off-target changes can contribute to a small number of additional genetic variants compared to those that occur naturally in breeding populations or are introduced by induced-mutagenesis methods. Recent studies show that using computational algorithms to design genome editing reagents can mitigate off-target edits in plants. Finally, crops are subject to strong selection to eliminate off-type plants through well-established multigenerational breeding, selection, and commercial variety development practices. Within this context, off-target edits in crops present no new safety concerns compared to other breeding practices. The current generation of genome editing technologies is already proving useful to develop new plant varieties with consumer and farmer benefits. Genome editing will likely undergo improved editing specificity along with new developments in SDN delivery and increasing genomic characterization, further improving reagent design and application.
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Affiliation(s)
- Nathaniel Graham
- Department of Genetics, Cell Biology and Development, University of Minnesota, St. Paul, Minnesota 55108
- Pairwise, Durham, North Carolina 27709
| | - Gunvant B Patil
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108
| | | | | | | | | | | | | | - Luis Maas
- Enza Zaden Research USA, San Juan Bautista, California 95045
| | | | | | - Robert M Stupar
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108
| | - Peter L Morrell
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108
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10
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Vats S, Kumawat S, Kumar V, Patil GB, Joshi T, Sonah H, Sharma TR, Deshmukh R. Genome Editing in Plants: Exploration of Technological Advancements and Challenges. Cells 2019; 8:E1386. [PMID: 31689989 PMCID: PMC6912757 DOI: 10.3390/cells8111386] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2019] [Revised: 10/04/2019] [Accepted: 10/12/2019] [Indexed: 12/19/2022] Open
Abstract
Genome-editing, a recent technological advancement in the field of life sciences, is one of the great examples of techniques used to explore the understanding of the biological phenomenon. Besides having different site-directed nucleases for genome editing over a decade ago, the CRISPR/Cas (clustered regularly interspaced short palindromic repeats/CRISPR-associated protein) based genome editing approach has become a choice of technique due to its simplicity, ease of access, cost, and flexibility. In the present review, several CRISPR/Cas based approaches have been discussed, considering recent advances and challenges to implicate those in the crop improvement programs. Successful examples where CRISPR/Cas approach has been used to improve the biotic and abiotic stress tolerance, and traits related to yield and plant architecture have been discussed. The review highlights the challenges to implement the genome editing in polyploid crop plants like wheat, canola, and sugarcane. Challenges for plants difficult to transform and germline-specific gene expression have been discussed. We have also discussed the notable progress with multi-target editing approaches based on polycistronic tRNA processing, Csy4 endoribonuclease, intron processing, and Drosha ribonuclease. Potential to edit multiple targets simultaneously makes it possible to take up more challenging tasks required to engineer desired crop plants. Similarly, advances like precision gene editing, promoter bashing, and methylome-editing will also be discussed. The present review also provides a catalog of available computational tools and servers facilitating designing of guide-RNA targets, construct designs, and data analysis. The information provided here will be useful for the efficient exploration of technological advances in genome editing field for the crop improvement programs.
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Affiliation(s)
- Sanskriti Vats
- National Agri-Food Biotechnology Institute (NABI), Mohali Punjab 140306, India.
| | - Surbhi Kumawat
- National Agri-Food Biotechnology Institute (NABI), Mohali Punjab 140306, India.
| | - Virender Kumar
- National Agri-Food Biotechnology Institute (NABI), Mohali Punjab 140306, India.
| | - Gunvant B Patil
- Department of Agronomy and Plant Genetics University of Minnesota, St. Paul, MN 55108-6026, USA.
| | - Trupti Joshi
- Department of Health Management and Informatics; Informatics Institute; Christopher S Bond Life Science Center, University of Missouri, Columbia, MO 65211-7310, USA.
| | - Humira Sonah
- National Agri-Food Biotechnology Institute (NABI), Mohali Punjab 140306, India.
| | - Tilak Raj Sharma
- National Agri-Food Biotechnology Institute (NABI), Mohali Punjab 140306, India.
| | - Rupesh Deshmukh
- National Agri-Food Biotechnology Institute (NABI), Mohali Punjab 140306, India.
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Patil GB, Lakhssassi N, Wan J, Song L, Zhou Z, Klepadlo M, Vuong TD, Stec AO, Kahil SS, Colantonio V, Valliyodan B, Rice JH, Piya S, Hewezi T, Stupar RM, Meksem K, Nguyen HT. Whole-genome re-sequencing reveals the impact of the interaction of copy number variants of the rhg1 and Rhg4 genes on broad-based resistance to soybean cyst nematode. Plant Biotechnol J 2019; 17:1595-1611. [PMID: 30688400 PMCID: PMC6662113 DOI: 10.1111/pbi.13086] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Revised: 01/09/2019] [Accepted: 01/10/2019] [Indexed: 05/19/2023]
Abstract
Soybean cyst nematode (SCN) is the most devastating plant-parasitic nematode. Most commercial soybean varieties with SCN resistance are derived from PI88788. Resistance derived from PI88788 is breaking down due to narrow genetic background and SCN population shift. PI88788 requires mainly the rhg1-b locus, while 'Peking' requires rhg1-a and Rhg4 for SCN resistance. In the present study, whole genome re-sequencing of 106 soybean lines was used to define the Rhg haplotypes and investigate their responses to the SCN HG-Types. The analysis showed a comprehensive profile of SNPs and copy number variations (CNV) at these loci. CNV of rhg1 (GmSNAP18) only contributed towards resistance in lines derived from PI88788 and 'Cloud'. At least 5.6 copies of the PI88788-type rhg1 were required to confer SCN resistance, regardless of the Rhg4 (GmSHMT08) haplotype. However, when the GmSNAP18 copies dropped below 5.6, a 'Peking'-type GmSHMT08 haplotype was required to ensure SCN resistance. This points to a novel mechanism of epistasis between GmSNAP18 and GmSHMT08 involving minimum requirements for copy number. The presence of more Rhg4 copies confers resistance to multiple SCN races. Moreover, transcript abundance of the GmSHMT08 in root tissue correlates with more copies of the Rhg4 locus, reinforcing SCN resistance. Finally, haplotype analysis of the GmSHMT08 and GmSNAP18 promoters inferred additional levels of the resistance mechanism. This is the first report revealing the genetic basis of broad-based resistance to SCN and providing new insight into epistasis, haplotype-compatibility, CNV, promoter variation and its impact on broad-based disease resistance in plants.
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Affiliation(s)
- Gunvant B. Patil
- Division of Plant SciencesUniversity of MissouriColumbiaMOUSA
- Department Agronomy and Plant GeneticsUniversity of MinnesotaSt. PaulMNUSA
| | - Naoufal Lakhssassi
- Department of Plant, Soil and Agricultural SystemsSouthern Illinois UniversityCarbondaleILUSA
| | - Jinrong Wan
- Division of Plant SciencesUniversity of MissouriColumbiaMOUSA
| | - Li Song
- Division of Plant SciencesUniversity of MissouriColumbiaMOUSA
| | - Zhou Zhou
- Department of Plant, Soil and Agricultural SystemsSouthern Illinois UniversityCarbondaleILUSA
| | | | - Tri D. Vuong
- Division of Plant SciencesUniversity of MissouriColumbiaMOUSA
| | - Adrian O. Stec
- Department Agronomy and Plant GeneticsUniversity of MinnesotaSt. PaulMNUSA
| | - Sondus S. Kahil
- Department of Plant, Soil and Agricultural SystemsSouthern Illinois UniversityCarbondaleILUSA
| | - Vincent Colantonio
- Department of Plant, Soil and Agricultural SystemsSouthern Illinois UniversityCarbondaleILUSA
| | - Babu Valliyodan
- Division of Plant SciencesUniversity of MissouriColumbiaMOUSA
| | - J. Hollis Rice
- Department of Plant SciencesUniversity of TennesseeKnoxvilleTNUSA
| | - Sarbottam Piya
- Department of Plant SciencesUniversity of TennesseeKnoxvilleTNUSA
| | - Tarek Hewezi
- Department of Plant SciencesUniversity of TennesseeKnoxvilleTNUSA
| | - Robert M. Stupar
- Department Agronomy and Plant GeneticsUniversity of MinnesotaSt. PaulMNUSA
| | - Khalid Meksem
- Department of Plant, Soil and Agricultural SystemsSouthern Illinois UniversityCarbondaleILUSA
| | - Henry T. Nguyen
- Division of Plant SciencesUniversity of MissouriColumbiaMOUSA
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Chen W, Yao Q, Patil GB, Agarwal G, Deshmukh RK, Lin L, Wang B, Wang Y, Prince SJ, Song L, Xu D, An YC, Valliyodan B, Varshney RK, Nguyen HT. Identification and Comparative Analysis of Differential Gene Expression in Soybean Leaf Tissue under Drought and Flooding Stress Revealed by RNA-Seq. Front Plant Sci 2016; 7:1044. [PMID: 27486466 PMCID: PMC4950259 DOI: 10.3389/fpls.2016.01044] [Citation(s) in RCA: 87] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Accepted: 07/04/2016] [Indexed: 05/18/2023]
Abstract
Drought and flooding are two major causes of severe yield loss in soybean worldwide. A lack of knowledge of the molecular mechanisms involved in drought and flood stress has been a limiting factor for the effective management of soybeans; therefore, it is imperative to assess the expression of genes involved in response to flood and drought stress. In this study, differentially expressed genes (DEGs) under drought and flooding conditions were investigated using Illumina RNA-Seq transcriptome profiling. A total of 2724 and 3498 DEGs were identified under drought and flooding treatments, respectively. These genes comprise 289 Transcription Factors (TFs) representing Basic Helix-loop Helix (bHLH), Ethylene Response Factors (ERFs), myeloblastosis (MYB), No apical meristem (NAC), and WRKY amino acid motif (WRKY) type major families known to be involved in the mechanism of stress tolerance. The expression of photosynthesis and chlorophyll synthesis related genes were significantly reduced under both types of stresses, which limit the metabolic processes and thus help prolong survival under extreme conditions. However, cell wall synthesis related genes were up-regulated under drought stress and down-regulated under flooding stress. Transcript profiles involved in the starch and sugar metabolism pathways were also affected under both stress conditions. The changes in expression of genes involved in regulating the flux of cell wall precursors and starch/sugar content can serve as an adaptive mechanism for soybean survival under stress conditions. This study has revealed the involvement of TFs, transporters, and photosynthetic genes, and has also given a glimpse of hormonal cross talk under the extreme water regimes, which will aid as an important resource for soybean crop improvement.
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Affiliation(s)
- Wei Chen
- Division of Plant Sciences, University of MissouriColumbia, MO, USA
| | - Qiuming Yao
- Department of Computer Science and Christopher S. Bond Life Sciences Center, University of MissouriColumbia, MO, USA
| | - Gunvant B. Patil
- Division of Plant Sciences, University of MissouriColumbia, MO, USA
| | - Gaurav Agarwal
- Division of Plant Sciences, University of MissouriColumbia, MO, USA
- Center of Excellence in Genomics, International Crops Research Institute for the Semi-Arid TropicsHyderabad, India
| | | | - Li Lin
- Division of Plant Sciences, University of MissouriColumbia, MO, USA
| | - Biao Wang
- Division of Plant Sciences, University of MissouriColumbia, MO, USA
- Legume Biotechnology Laboratory, School of Agriculture and Biology, Shanghai Jiao Tong UniversityShanghai, China
| | - Yongqin Wang
- Division of Plant Sciences, University of MissouriColumbia, MO, USA
| | - Silvas J. Prince
- Division of Plant Sciences, University of MissouriColumbia, MO, USA
| | - Li Song
- Division of Plant Sciences, University of MissouriColumbia, MO, USA
| | - Dong Xu
- Department of Computer Science and Christopher S. Bond Life Sciences Center, University of MissouriColumbia, MO, USA
| | - Yongqiang C. An
- Plant Genetics Research Unit, Donald Danforth Plant Science Center, US Department of Agriculture, Agricultural Research Service, Midwest AreaSt. Louis, MO, USA
| | - Babu Valliyodan
- Division of Plant Sciences, University of MissouriColumbia, MO, USA
| | - Rajeev K. Varshney
- Center of Excellence in Genomics, International Crops Research Institute for the Semi-Arid TropicsHyderabad, India
| | - Henry T. Nguyen
- Division of Plant Sciences, University of MissouriColumbia, MO, USA
- *Correspondence: Henry T. Nguyen
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Song L, Nguyen N, Deshmukh RK, Patil GB, Prince SJ, Valliyodan B, Mutava R, Pike SM, Gassmann W, Nguyen HT. Soybean TIP Gene Family Analysis and Characterization of GmTIP1;5 and GmTIP2;5 Water Transport Activity. Front Plant Sci 2016; 7:1564. [PMID: 27818669 PMCID: PMC5073556 DOI: 10.3389/fpls.2016.01564] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Accepted: 10/04/2016] [Indexed: 05/04/2023]
Abstract
Soybean, one of the most important crops worldwide, is severely affected by abiotic stress. Drought and flooding are the major abiotic stresses impacting soybean yield. In this regard, understanding water uptake by plants, its utilization and transport has great importance. In plants, water transport is mainly governed by channel forming aquaporin proteins (AQPs). Tonoplast intrinsic proteins (TIPs) belong to the plant-specific AQP subfamily and are known to have a role in abiotic stress tolerance. In this study, 23 soybean TIP genes were identified based on the latest soybean genome annotation. TIPs were characterized based on conserved structural features and phylogenetic distribution. Expression analysis of soybean TIP genes in various tissues and under abiotic stress conditions demonstrated tissue/stress-response specific differential expression. The natural variations for TIP genes were analyzed using whole genome re-sequencing data available for a set of 106 diverse soybean genotypes including wild types, landraces and elite lines. Results revealed 81 single-nucleotide polymorphisms (SNPs) and several large insertions/deletions in the coding region of TIPs. Among these, non-synonymous SNPs are most likely to have a greater impact on protein function and are candidates for molecular studies as well as for the development of functional markers to assist breeding. The solute transport function of two TIPs was further validated by expression in Xenopus laevis oocytes. GmTIP1;5 was shown to facilitate the rapid movement of water across the oocyte membrane, while GmTIP2;5 facilitated the movement of water and boric acid. The present study provides an initial insight into the possible roles of soybean TIP genes under abiotic stress conditions. Our results will facilitate elucidation of their precise functions during abiotic stress responses and plant development, and will provide potential breeding targets for modifying water movement in soybean.
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Affiliation(s)
- Li Song
- Division of Plant Science, National Center for Soybean Biotechnology, University of MissouriColumbia, MO, USA
| | - Na Nguyen
- Division of Plant Science, National Center for Soybean Biotechnology, University of MissouriColumbia, MO, USA
| | | | - Gunvant B. Patil
- Division of Plant Science, National Center for Soybean Biotechnology, University of MissouriColumbia, MO, USA
| | - Silvas J. Prince
- Division of Plant Science, National Center for Soybean Biotechnology, University of MissouriColumbia, MO, USA
| | - Babu Valliyodan
- Division of Plant Science, National Center for Soybean Biotechnology, University of MissouriColumbia, MO, USA
| | - Raymond Mutava
- Division of Plant Science, National Center for Soybean Biotechnology, University of MissouriColumbia, MO, USA
| | - Sharon M. Pike
- Division of Plant Sciences and Interdisciplinary Plant Group, Christopher S. Bond Life Sciences Center, University of MissouriColumbia, MO, USA
| | - Walter Gassmann
- Division of Plant Sciences and Interdisciplinary Plant Group, Christopher S. Bond Life Sciences Center, University of MissouriColumbia, MO, USA
| | - Henry T. Nguyen
- Division of Plant Science, National Center for Soybean Biotechnology, University of MissouriColumbia, MO, USA
- *Correspondence: Henry T. Nguyen,
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Chen W, He S, Liu D, Patil GB, Zhai H, Wang F, Stephenson TJ, Wang Y, Wang B, Valliyodan B, Nguyen HT, Liu Q. A Sweetpotato Geranylgeranyl Pyrophosphate Synthase Gene, IbGGPS, Increases Carotenoid Content and Enhances Osmotic Stress Tolerance in Arabidopsis thaliana. PLoS One 2015; 10:e0137623. [PMID: 26376432 PMCID: PMC4574098 DOI: 10.1371/journal.pone.0137623] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Accepted: 08/20/2015] [Indexed: 11/19/2022] Open
Abstract
Sweetpotato highly produces carotenoids in storage roots. In this study, a cDNA encoding geranylgeranyl phyrophosphate synthase (GGPS), named IbGGPS, was isolated from sweetpotato storage roots. Green fluorescent protein (GFP) was fused to the C-terminus of IbGGPS to obtain an IbGGPS-GFP fusion protein that was transiently expressed in both epidermal cells of onion and leaves of tobacco. Confocal microscopic analysis determined that the IbGGPS-GFP protein was localized to specific areas of the plasma membrane of onion and chloroplasts in tobacco leaves. The coding region of IbGGPS was cloned into a binary vector under the control of 35S promoter and then transformed into Arabidopsis thaliana to obtain transgenic plants. High performance liquid chromatography (HPLC) analysis showed a significant increase of total carotenoids in transgenic plants. The seeds of transgenic and wild-type plants were germinated on an agar medium supplemented with polyethylene glycol (PEG). Transgenic seedlings grew significantly longer roots than wild-type ones did. Further enzymatic analysis showed an increased activity of superoxide dismutase (SOD) in transgenic seedlings. In addition, the level of malondialdehyde (MDA) was reduced in transgenics. qRT-PCR analysis showed altered expressions of several genes involved in the carotenoid biosynthesis in transgenic plants. These data results indicate that IbGGPS is involved in the biosynthesis of carotenoids in sweetpotato storage roots and likely associated with tolerance to osmotic stress.
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Affiliation(s)
- Wei Chen
- Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis and Utilization, Ministry of Education, China Agricultural University, Beijing, China
| | - Shaozhen He
- Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis and Utilization, Ministry of Education, China Agricultural University, Beijing, China
| | - Degao Liu
- Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis and Utilization, Ministry of Education, China Agricultural University, Beijing, China
| | - Gunvant B. Patil
- Division of Plant Sciences and National Center for Soybean Biotechnology, University of Missouri, Columbia, Missouri, United States of America
| | - Hong Zhai
- Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis and Utilization, Ministry of Education, China Agricultural University, Beijing, China
| | - Feibing Wang
- Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis and Utilization, Ministry of Education, China Agricultural University, Beijing, China
| | - Troy J. Stephenson
- Division of Plant Sciences and National Center for Soybean Biotechnology, University of Missouri, Columbia, Missouri, United States of America
| | - Yannan Wang
- Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis and Utilization, Ministry of Education, China Agricultural University, Beijing, China
| | - Bing Wang
- Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis and Utilization, Ministry of Education, China Agricultural University, Beijing, China
| | - Babu Valliyodan
- Division of Plant Sciences and National Center for Soybean Biotechnology, University of Missouri, Columbia, Missouri, United States of America
| | - Henry T. Nguyen
- Division of Plant Sciences and National Center for Soybean Biotechnology, University of Missouri, Columbia, Missouri, United States of America
| | - Qingchang Liu
- Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis and Utilization, Ministry of Education, China Agricultural University, Beijing, China
- * E-mail:
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Chaudhary J, Patil GB, Sonah H, Deshmukh RK, Vuong TD, Valliyodan B, Nguyen HT. Expanding Omics Resources for Improvement of Soybean Seed Composition Traits. Front Plant Sci 2015; 6:1021. [PMID: 26635846 PMCID: PMC4657443 DOI: 10.3389/fpls.2015.01021] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Accepted: 11/05/2015] [Indexed: 05/19/2023]
Abstract
Food resources of the modern world are strained due to the increasing population. There is an urgent need for innovative methods and approaches to augment food production. Legume seeds are major resources of human food and animal feed with their unique nutrient compositions including oil, protein, carbohydrates, and other beneficial nutrients. Recent advances in next-generation sequencing (NGS) together with "omics" technologies have considerably strengthened soybean research. The availability of well annotated soybean genome sequence along with hundreds of identified quantitative trait loci (QTL) associated with different seed traits can be used for gene discovery and molecular marker development for breeding applications. Despite the remarkable progress in these technologies, the analysis and mining of existing seed genomics data are still challenging due to the complexity of genetic inheritance, metabolic partitioning, and developmental regulations. Integration of "omics tools" is an effective strategy to discover key regulators of various seed traits. In this review, recent advances in "omics" approaches and their use in soybean seed trait investigations are presented along with the available databases and technological platforms and their applicability in the improvement of soybean. This article also highlights the use of modern breeding approaches, such as genome-wide association studies (GWAS), genomic selection (GS), and marker-assisted recurrent selection (MARS) for developing superior cultivars. A catalog of available important resources for major seed composition traits, such as seed oil, protein, carbohydrates, and yield traits are provided to improve the knowledge base and future utilization of this information in the soybean crop improvement programs.
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Sagari SK, Vamsi KC, Shah D, Singh V, Patil GB, Saawarn S. Micro-marsupialization: a minimally invasive technique for mucocele in children and adolescents. J Indian Soc Pedod Prev Dent 2012; 30:188-91. [PMID: 23263419 DOI: 10.4103/0970-4388.105008] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
BACKGROUND Most common lesions seen in children are mucoceles. Different techniques have been described for their treatment; however, most of them are invasive. OBJECTIVE Aim of the study was to compare the practicability of micro-marsupialization with surgical excision in treatment of mucoceles. MATERIALS AND METHODS A pilot study was done on 15 patients to evaluate and compare variables like lesion evolution, surgical time period, healing, complications etc. when lesions were treated with micro-marsupialization and surgical excision. RESULTS Most of the mucoceles diagnosed in this pilot study were found in lower lip. Amongst cases that were treated with micro-marsupialization, recurrence was seen only in one case, whereas there were 3 cases of recurrence seen in surgical excision group. No statistically significant difference was found between the treatment methods used. CONCLUSION Micro-marsupialization can be a non-invasive option to treat mucoceles in pediatric dentistry owing to its simplicity, fewer complications involved and as well that it's well-tolerated by patients.
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Affiliation(s)
- S K Sagari
- Department of Oral Pathology and Microbiology, Jodhpur Dental College General Hospital, Jodhpur, Rajasthan, India.
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Sardana V, Balappanavar AY, Patil GB, Kulkarni N, Sagari SG, Gupta KD. Impact of a modified carbonated beverage on human dental plaque and salivary pH: an in vivo study. J Indian Soc Pedod Prev Dent 2012; 30:7-12. [PMID: 22565511 DOI: 10.4103/0970-4388.95563] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
BACKGROUND To assess the plaque and salivary pH changes at different time intervals in vivo after consumption of a carbonated beverage modified with sodium fluoride and calcium phosphate. MATERIALS AND METHODS Twenty-four subjects aged 18-25 years were recruited and randomly assigned to three groups (group A, original drink Sprite; group B, Sprite with sodium fluoride; group C, Sprite with calcium phosphate). Collection of pooled plaque and unstimulated saliva was done before and after the drinks were consumed by the subjects at 5-, 10-, 20- and 30-minute intervals. RESULTS The pH rise was higher with group C for plaque and group B for saliva. CONCLUSIONS Modification of the test carbonated beverage with calcium phosphate and fluoride may exert some protective potential, especially in high caries risk candidates.
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Affiliation(s)
- V Sardana
- Public Health Dentistry, Teerthanker Mahaveer Dental College and Research Center, Moradabad, Uttar Pradesh, India
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