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Otarigho B, Butts AF, Aballay A. Neuronal NPR-15 modulates molecular and behavioral immune responses via the amphid sensory neuron-intestinal axis in C. elegans. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.07.27.550570. [PMID: 37546751 PMCID: PMC10402133 DOI: 10.1101/2023.07.27.550570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
The survival of hosts during infections relies on their ability to mount effective molecular and behavioral immune responses. Despite extensive research on these defense strategies in various species, including the model organism Caenorhabditis elegans, the neural mechanisms underlying their interaction remain poorly understood. Previous studies have highlighted the role of neural G protein-coupled receptors (GPCRs) in regulating both immunity and pathogen avoidance, which is particularly dependent on aerotaxis. To address this knowledge gap, we conducted a screen of mutants in neuropeptide receptor family genes. We found that loss-of-function mutations in npr-15 activated immunity while suppressing pathogen avoidance behavior. Through further analysis, NPR-15 was found to regulate immunity by modulating the activity of key transcription factors, namely GATA/ELT-2 and TFEB/HLH-30. Surprisingly, the lack of pathogen avoidance of npr-15 mutant animals was not influenced by oxygen levels. Moreover, our studies revealed that the amphid sensory neuron ASJ is involved in mediating the immune and behavioral responses orchestrated by NPR-15. Additionally, NPR-15 was found to regulate avoidance behavior via the TRPM gene, GON-2, which may sense the intestinal distension caused by bacterial colonization to elicit pathogen avoidance. Our study contributes to a broader understanding of host defense strategies and mechanisms underlining the interaction between molecular and behavioral immune responses.
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Affiliation(s)
- Benson Otarigho
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Anna Frances Butts
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Alejandro Aballay
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX
- Department of Microbiology and Molecular Genetics, McGovern Medical School at UTHealth Houston, TX
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2
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Shioya N, Ogiso-Tanaka E, Watanabe M, Anai T, Hoshino T. Development of a High-Quality/Yield Long-Read Sequencing-Adaptable DNA Extraction Method for Crop Seeds. PLANTS (BASEL, SWITZERLAND) 2023; 12:2971. [PMID: 37631182 PMCID: PMC10457885 DOI: 10.3390/plants12162971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 08/11/2023] [Accepted: 08/14/2023] [Indexed: 08/27/2023]
Abstract
Genome sequencing is important for discovering critical genes in crops and improving crop breeding efficiency. Generally, fresh, young leaves are used for DNA extraction from plants. However, seeds, the storage form, are more efficient because they do not require cultivation and can be ground at room temperature. Yet, only a few DNA extraction kits or methods suitable for seeds have been developed to date. In this study, we introduced an improved (IMP) Boom method that is relatively low-cost, simple to operate, and yields high-quality DNA that can withstand long-read sequencing. The method successfully extracted approximately 8 µg of DNA per gram of seed weight from soybean seeds at an average concentration of 48.3 ng/µL, approximately 40-fold higher than that extracted from seeds using a common extraction method kit. The A260/280 and A260/230 values of the DNA were 1.90 and 2.43, respectively, which exceeded the respective quality thresholds of 1.8 and 2.0. The DNA also had a DNA integrity number value (indicating the degree of DNA degradation) of 8.1, higher than that obtained using the kit and cetyltrimethylammonium bromide methods. Furthermore, the DNA showed a read length N50 of 20.96 kbp and a maximum read length of 127.8 kbp upon long-read sequencing using the Oxford Nanopore sequencer, with both values being higher than those obtained using the other methods. DNA extracted from seeds using the IMP Boom method showed an increase in the percentage of the nuclear genome with a decrease in the relative ratio of chloroplast DNA. These results suggested that the proposed IMP Boom method can extract high-quality and high-concentration DNA that can be used for long-read sequencing, which cannot be achieved from plant seeds using other conventional DNA extraction methods. The IMP Boom method could also be adapted to crop seeds other than soybeans, such as pea, okra, maize, and sunflower. This improved method is expected to improve the efficiency of various crop-breeding operations, including seed variety determination, testing of genetically modified seeds, and marker-assisted selection.
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Affiliation(s)
- Naohiro Shioya
- Laboratory of Crop Breeding, Graduate School of Agricultural Sciences, Yamagata University, 1-23 Wakaba-Machi, Tsuruoka 997-8555, Yamagata, Japan;
| | - Eri Ogiso-Tanaka
- Center for Molecular Biodiversity Research, National Museum of Nature and Science, 4-1-1 Amakubo, Tsukuba 305-0005, Ibaraki, Japan
| | - Masanori Watanabe
- Faculty of Agriculture, Yamagata University, 1-23 Wakaba-Machi, Tsuruoka 997-8555, Yamagata, Japan;
| | - Toyoaki Anai
- Laboratory of Agroecology, Faculty of Agriculture, Kyushu University, 744 Motooka, Nishi-Ku, Fukuoka 819-0395, Fukuoka, Japan;
| | - Tomoki Hoshino
- Laboratory of Crop Breeding, Graduate School of Agricultural Sciences, Yamagata University, 1-23 Wakaba-Machi, Tsuruoka 997-8555, Yamagata, Japan;
- Faculty of Agriculture, Yamagata University, 1-23 Wakaba-Machi, Tsuruoka 997-8555, Yamagata, Japan;
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3
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Ablazov A, Felemban A, Braguy J, Kuijer HNJ, Al-Babili S. A Fast and Cost-Effective Genotyping Method for CRISPR-Cas9-Generated Mutant Rice Lines. PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12112189. [PMID: 37299168 DOI: 10.3390/plants12112189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 05/16/2023] [Accepted: 05/18/2023] [Indexed: 06/12/2023]
Abstract
With increasing throughput in both the generation and phenotyping of mutant lines in plants, it is important to have an efficient and reliable genotyping method. Traditional workflows, still commonly used in many labs, have time-consuming and expensive steps, such as DNA purification, cloning and growing E. coli cultures. We propose an alternative workflow where these steps are bypassed, using Phire polymerase on fresh plant tissue, and ExoProStar treatment as preparation for sequencing. We generated CRISPR-Cas9 mutants for ZAS (ZAXINONE SYNTHASE) in rice with two guide RNAs. Using both a traditional workflow and our proposed workflow, we genotyped nine T1 plants. To interpret the sequencing output, which is often complex in CRISPR-generated mutants, we used free online automatic analysis systems and compared the results. Our proposed workflow produces results of the same quality as the old workflow, but in 1 day instead of 3 days and about 35 times cheaper. This workflow also consists of fewer steps and reduces the risk of cross contamination and mistakes. Furthermore, the automated sequence analysis packages are mostly accurate and could easily be used for bulk analysis. Based on these advantages, we encourage academic and commercial labs conducting genotyping to consider switching over to our proposed workflow.
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Affiliation(s)
- Abdugaffor Ablazov
- Center for Desert Agriculture (CDA), The BioActives Laboratory, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
- The Plant Science Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Abrar Felemban
- Center for Desert Agriculture (CDA), The BioActives Laboratory, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Justine Braguy
- Center for Desert Agriculture (CDA), The BioActives Laboratory, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Hendrik N J Kuijer
- Center for Desert Agriculture (CDA), The BioActives Laboratory, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Salim Al-Babili
- Center for Desert Agriculture (CDA), The BioActives Laboratory, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
- The Plant Science Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
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Nishii K, Möller M, Foster RG, Forrest LL, Kelso N, Barber S, Howard C, Hart ML. A high quality, high molecular weight DNA extraction method for PacBio HiFi genome sequencing of recalcitrant plants. PLANT METHODS 2023; 19:41. [PMID: 37120601 PMCID: PMC10148486 DOI: 10.1186/s13007-023-01009-x] [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: 11/02/2022] [Accepted: 03/20/2023] [Indexed: 05/03/2023]
Abstract
BACKGROUND PacBio HiFi sequencing provides highly accurate long-read sequencing datasets which are of great advantage for whole genome sequencing projects. One limitation of the method is the requirement for high quality, high molecular weight input DNA. This can be particularly challenging for plants that frequently contain common and species-specific secondary metabolites, which often interfere with downstream processes. Cape Primroses (genus Streptocarpus), are some of these recalcitrant plants and are selected here as material to develop a high quality, high molecular weight DNA extraction protocol for long read genome sequencing. RESULTS We developed a DNA extraction method for PacBio HiFi sequencing for Streptocarpus grandis and Streptocarpus kentaniensis. A CTAB lysis buffer was employed to avoid guanidine, and the traditional chloroform and phenol purification steps were replaced with pre-lysis sample washes. Best cells/nucleus lysis was achieved with 4 h at 58 °C. The obtained high quality and high molecular weight DNAs were tested in PacBio SMRTBell™ library preparations, which resulted in circular consensus sequencing (CCS) reads from 17 to 27 Gb per cell, and a read length N50 from 14 to 17 kbp. To evaluate the quality of the reads for whole genome sequencing, they were assembled with HiFiasm into draft genomes, with N50 = 49 Mb and 23 Mb, and L50 = 10 and 11. The longest contigs were 95 Mb and 57 Mb respectively, showing good contiguity as these are longer than the theoretical chromosome length (genome size/chromosome number) of 78 Mb and 55 Mb, for S. grandis and S. kentaniensis respectively. CONCLUSIONS DNA extraction is a critical step towards obtaining a complete genome assembly. Our DNA extraction method here provided the required high quality, high molecular weight DNA for successful standard-input PacBio HiFi library preparation. The contigs from those reads showed a high contiguity, providing a good starting draft assembly towards obtaining a complete genome. The results obtained here were highly promising, and demonstrated that the DNA extraction method developed here is compatible with PacBio HiFi sequencing and suitable for de novo whole genome sequencing projects of plants.
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Affiliation(s)
- Kanae Nishii
- Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh, EH3 5LR UK
- Kanagawa University, 2946 Tsuchiya, Hiratsuka, Kanagawa 259-1293 Japan
| | - Michael Möller
- Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh, EH3 5LR UK
| | - Robert G. Foster
- Edinburgh Genomics, The University of Edinburgh, Charlotte Auerbach Rd., Edinburgh, EH9 3FL UK
| | - Laura L. Forrest
- Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh, EH3 5LR UK
| | - Nathan Kelso
- Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh, EH3 5LR UK
| | - Sadie Barber
- Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh, EH3 5LR UK
| | - Caroline Howard
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Saffron Walden, CB10 1RQ UK
| | - Michelle L. Hart
- Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh, EH3 5LR UK
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Pearson SM, Griffiths AG, Maclean P, Larking AC, Hong SW, Jauregui R, Miller P, McKenzie CM, Lockhart PJ, Tate JA, Ford JL, Faville MJ. Outlier analyses and genome-wide association study identify glgC and ERD6-like 4 as candidate genes for foliar water-soluble carbohydrate accumulation in Trifolium repens. FRONTIERS IN PLANT SCIENCE 2023; 13:1095359. [PMID: 36699852 PMCID: PMC9868827 DOI: 10.3389/fpls.2022.1095359] [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: 11/11/2022] [Accepted: 12/09/2022] [Indexed: 06/17/2023]
Abstract
Increasing water-soluble carbohydrate (WSC) content in white clover is important for improving nutritional quality and reducing environmental impacts from pastoral agriculture. Elucidation of genes responsible for foliar WSC variation would enhance genetic improvement by enabling molecular breeding approaches. The aim of the present study was to identify single nucleotide polymorphisms (SNPs) associated with variation in foliar WSC in white clover. A set of 935 white clover individuals, randomly sampled from five breeding pools selectively bred for divergent (low or high) WSC content, were assessed with 14,743 genotyping-by-sequencing SNPs, using three outlier detection methods: PCAdapt, BayeScan and KGD-FST. These analyses identified 33 SNPs as discriminating between high and low WSC populations and putatively under selection. One SNP was located in the intron of ERD6-like 4, a gene coding for a sugar transporter located on the vacuole membrane. A genome-wide association study using a subset of 605 white clover individuals and 5,757 SNPs, identified a further 12 SNPs, one of which was associated with a starch biosynthesis gene, glucose-1-phosphate adenylyltransferase, glgC. Our results provide insight into genomic regions underlying WSC accumulation in white clover, identify candidate genomic regions for further functional validation studies, and reveal valuable information for marker-assisted or genomic selection in white clover.
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Affiliation(s)
- Sofie M. Pearson
- School of Natural Sciences, Massey University, Palmerston North, New Zealand
- Resilient Agriculture, AgResearch Grasslands, Palmerston North, New Zealand
| | | | - Paul Maclean
- Resilient Agriculture, AgResearch Grasslands, Palmerston North, New Zealand
| | - Anna C. Larking
- Resilient Agriculture, AgResearch Grasslands, Palmerston North, New Zealand
| | - S. Won Hong
- Resilient Agriculture, AgResearch Grasslands, Palmerston North, New Zealand
| | - Ruy Jauregui
- Resilient Agriculture, AgResearch Grasslands, Palmerston North, New Zealand
| | - Poppy Miller
- Resilient Agriculture, AgResearch Grasslands, Palmerston North, New Zealand
| | | | - Peter J. Lockhart
- School of Natural Sciences, Massey University, Palmerston North, New Zealand
| | - Jennifer A. Tate
- School of Natural Sciences, Massey University, Palmerston North, New Zealand
| | - John L. Ford
- Grasslands, PGG Wrightson Seeds Limited, Palmerston North, New Zealand
| | - Marty J. Faville
- Resilient Agriculture, AgResearch Grasslands, Palmerston North, New Zealand
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6
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Hutin S, Blanc-Mathieu R, Rieu P, Parcy F, Lai X, Zubieta C. Identification of Plant Transcription Factor DNA-Binding Sites Using seq-DAP-seq. Methods Mol Biol 2023; 2698:119-145. [PMID: 37682473 DOI: 10.1007/978-1-0716-3354-0_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/09/2023]
Abstract
The identification of genome-wide transcription factor binding sites (TFBS) is a critical step in deciphering gene and transcriptional regulatory networks. However, determining the genome-wide binding of specific TFs or TF complexes remains a technical challenge. DNA affinity purification sequencing (DAP-seq) and modifications such as sequential DAP-seq (seq-DAP-seq) are robust in vitro methods for mapping individual TF or TF complex binding sites in a genome-wide manner. DAP-seq protocols use a genomic DNA (gDNA) library from any target organism with or without amplification, allowing the determination of TF binding on naked or endogenously modified DNA, respectively. As a first step, the gDNA is fragmented to ~200 bp, end-repaired, and sequencing adaptors are added. This gDNA library can be used directly or an amplification step may be performed to remove DNA modifications such as cytosine methylation. DNA libraries are then incubated with an affinity-tagged TF or TF- complex immobilized on magnetic beads. The TF or TF complex of interest is generally produced using recombinant protein expression and purified prior to DNA affinity purification. After incubation of the DNA library with the immobilized TF of interest, multiple wash steps are performed to reduce non-specific DNA binding and the TF-DNA complexes eluted. The eluted DNA is PCR-amplified and sequenced using next-generation sequencing. The resulting sequence reads are mapped to the corresponding reference genome, identifying direct potential bound regions and binding sites of the TF or TF complex of interest. Predictive TFBS models are generated from the bound regions using downstream bioinformatics analysis pipelines. Here, we present a detailed protocol outlining the steps required for seq-DAP-seq of a heterooligomeric TF complex (Fig. 1) and briefly describe the downstream bioinformatics pipeline used to develop a robust TFBS model from sequencing data generated from a DAP-seq experiment.
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Affiliation(s)
- Stephanie Hutin
- Laboratoire de Physiologie Cellulaire et Végétale, CNRS, CEA, Université Grenoble Alpes, INRAE, IRIG, CEA Grenoble, Grenoble, France
| | - Romain Blanc-Mathieu
- Laboratoire de Physiologie Cellulaire et Végétale, CNRS, CEA, Université Grenoble Alpes, INRAE, IRIG, CEA Grenoble, Grenoble, France
| | - Philippe Rieu
- Laboratoire de Physiologie Cellulaire et Végétale, CNRS, CEA, Université Grenoble Alpes, INRAE, IRIG, CEA Grenoble, Grenoble, France
| | - François Parcy
- Laboratoire de Physiologie Cellulaire et Végétale, CNRS, CEA, Université Grenoble Alpes, INRAE, IRIG, CEA Grenoble, Grenoble, France
| | - Xuelei Lai
- Laboratoire de Physiologie Cellulaire et Végétale, CNRS, CEA, Université Grenoble Alpes, INRAE, IRIG, CEA Grenoble, Grenoble, France
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Chloe Zubieta
- Laboratoire de Physiologie Cellulaire et Végétale, CNRS, CEA, Université Grenoble Alpes, INRAE, IRIG, CEA Grenoble, Grenoble, France.
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Taniguti CH, Taniguti LM, Amadeu RR, Lau J, Gesteira GDS, Oliveira TDP, Ferreira GC, Pereira GDS, Byrne D, Mollinari M, Riera-Lizarazu O, Garcia AAF. Developing best practices for genotyping-by-sequencing analysis in the construction of linkage maps. Gigascience 2022; 12:giad092. [PMID: 37889010 PMCID: PMC10603770 DOI: 10.1093/gigascience/giad092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 06/27/2023] [Accepted: 10/06/2023] [Indexed: 10/28/2023] Open
Abstract
BACKGROUND Genotyping-by-sequencing (GBS) provides affordable methods for genotyping hundreds of individuals using millions of markers. However, this challenges bioinformatic procedures that must overcome possible artifacts such as the bias generated by polymerase chain reaction duplicates and sequencing errors. Genotyping errors lead to data that deviate from what is expected from regular meiosis. This, in turn, leads to difficulties in grouping and ordering markers, resulting in inflated and incorrect linkage maps. Therefore, genotyping errors can be easily detected by linkage map quality evaluations. RESULTS We developed and used the Reads2Map workflow to build linkage maps with simulated and empirical GBS data of diploid outcrossing populations. The workflows run GATK, Stacks, TASSEL, and Freebayes for single-nucleotide polymorphism calling and updog, polyRAD, and SuperMASSA for genotype calling, as well as OneMap and GUSMap to build linkage maps. Using simulated data, we observed which genotype call software fails in identifying common errors in GBS sequencing data and proposed specific filters to better handle them. We tested whether it is possible to overcome errors in a linkage map using genotype probabilities from each software or global error rates to estimate genetic distances with an updated version of OneMap. We also evaluated the impact of segregation distortion, contaminant samples, and haplotype-based multiallelic markers in the final linkage maps. Through our evaluations, we observed that some of the approaches produce different results depending on the dataset (dataset dependent) and others produce consistent advantageous results among them (dataset independent). CONCLUSIONS We set as default in the Reads2Map workflows the approaches that showed to be dataset independent for GBS datasets according to our results. This reduces the number of required tests to identify optimal pipelines and parameters for other empirical datasets. Using Reads2Map, users can select the pipeline and parameters that best fit their data context. The Reads2MapApp shiny app provides a graphical representation of the results to facilitate their interpretation.
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Affiliation(s)
- Cristiane Hayumi Taniguti
- Department of Genetics, University of São Paulo, São Paulo 13418-900, Brazil
- Department of Horticultural Sciences, Texas A&M University, College Station, TX 77843-0001, USA
| | - Lucas Mitsuo Taniguti
- Department of Genetics, University of São Paulo, São Paulo 13418-900, Brazil
- Mendelics Genomic Analysis, São Paulo 02511-000, Brazil
| | | | - Jeekin Lau
- Department of Horticultural Sciences, Texas A&M University, College Station, TX 77843-0001, USA
| | - Gabriel de Siqueira Gesteira
- Department of Genetics, University of São Paulo, São Paulo 13418-900, Brazil
- Bioinformatics Research Center, Department of Horticultural Sciences, North Carolina State University, Raleigh, NC 27695-7566, USA
| | | | | | | | - David Byrne
- Department of Horticultural Sciences, Texas A&M University, College Station, TX 77843-0001, USA
| | - Marcelo Mollinari
- Bioinformatics Research Center, Department of Horticultural Sciences, North Carolina State University, Raleigh, NC 27695-7566, USA
| | - Oscar Riera-Lizarazu
- Department of Horticultural Sciences, Texas A&M University, College Station, TX 77843-0001, USA
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Utthiya S, Wonnapinij P, Napaumpaiporn P, Kittiwongwattana C, Sakulkoo J, Suttangkakul A, Vuttipongchaikij S. Gel purification of gDNA for next-generation sequencing applications. Biotechniques 2022; 73:99-103. [PMID: 35950336 DOI: 10.2144/btn-2022-0013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
We demonstrate that gDNA can be conveniently and efficiently isolated and purified using standard agarose gel electrophoresis, band excision and gel purification. This method yields a substantial amount at microgram levels of gDNA per gel cleanup with high purity. An RNase A treatment step can be omitted. The quality of gDNA is suitable for next-generation sequencing, resulting in >10 Mb reads and high-quality read data (Phred score >28 up to 100 of 150 base reads). Furthermore, the gDNA can be kept intact in a gel slice for several days. This method has been tested for dictyostelids, bacteria and plants.
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Affiliation(s)
- Supanut Utthiya
- Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand
| | - Passorn Wonnapinij
- Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand.,Center of Advanced studies for Tropical Natural Resources, Kasetsart University, Bangkok, 10900, Thailand.,Omics Center for Agriculture, Bioresources, Food & Health, Kasetsart University (OmiKU), Bangkok, 10900, Thailand
| | - Pondpan Napaumpaiporn
- Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand
| | - Chokchai Kittiwongwattana
- Department of Biology, Faculty of Science, King Mongkut's Institute of Technology Ladkrabang, Bangkok, 10520, Thailand
| | - Jenjira Sakulkoo
- Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand
| | - Anongpat Suttangkakul
- Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand.,Center of Advanced studies for Tropical Natural Resources, Kasetsart University, Bangkok, 10900, Thailand.,Omics Center for Agriculture, Bioresources, Food & Health, Kasetsart University (OmiKU), Bangkok, 10900, Thailand
| | - Supachai Vuttipongchaikij
- Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand.,Center of Advanced studies for Tropical Natural Resources, Kasetsart University, Bangkok, 10900, Thailand.,Omics Center for Agriculture, Bioresources, Food & Health, Kasetsart University (OmiKU), Bangkok, 10900, Thailand
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Offornedo Q, Menkir A, Babalola D, Gedil M. Developing and deploying an efficient genotyping workflow for accelerating maize improvement in developing countries. Gates Open Res 2022. [DOI: 10.12688/gatesopenres.13338.3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Background: Molecular breeding is an essential tool for accelerating genetic gain in crop improvement towards meeting the need to feed an ever-growing world population. Establishing low-cost, flexible genotyping platforms in small, public and regional laboratories can stimulate the application of molecular breeding in developing countries. These laboratories can serve plant breeding projects requiring low- to medium-density markers for marker-assisted selection (MAS) and quality control (QC) activities. Methods: We performed two QC and MAS experiments consisting of 637 maize lines, using an optimised genotyping workflow involving an in-house competitive allele-specific PCR (KASP) genotyping system with an optimised sample collection, preparation, and DNA extraction and quantitation process. A smaller volume of leaf-disc size plant samples was collected directly in 96-well plates for DNA extraction, using a slightly modified CTAB-based DArT DNA extraction protocol. DNA quality and quantity analyses were performed using a microplate reader, and the KASP genotyping and data analysis was performed in our laboratory. Results: Applying the optimized genotyping workflow expedited the QC and MAS experiments from over five weeks (when outsourcing) to two weeks and eliminated the shipping cost. Using a set of 28 KASP single nucleotide polymorphisms (SNPs) validated for maize, the QC experiment revealed the genetic identity of four maize varieties taken from five seed sources. Another set of 10 KASP SNPs was sufficient in verifying the parentage of 390 F1 lines. The KASP-based MAS was successfully applied to a maize pro-vitamin A (PVA) breeding program and for introgressing the aflatoxin resistance gene into elite tropical maize lines. Conclusion: This improved workflow has helped accelerate maize improvement activities of IITA's Maize Improvement Program and facilitated DNA fingerprinting for tracking improved crop varieties. National Agricultural Research Systems (NARS) in developing countries can adopt this workflow to fast-track molecular marker-based genotyping for crop improvement.
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Offornedo Q, Menkir A, Babalola D, Gedil M. Developing and deploying an efficient genotyping workflow for accelerating maize improvement in developing countries. Gates Open Res 2022. [DOI: 10.12688/gatesopenres.13338.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Background: Molecular breeding is an essential tool for accelerating genetic gain in crop improvement, towards meeting the need to feed an ever-growing world population. Establishing low-cost, flexible genotyping platforms in small, public and regional laboratories can stimulate the application of molecular breeding in developing countries. These laboratories can serve plant breeding projects requiring low- to medium-density markers for marker-assisted selection (MAS) and quality control (QC) activities. Methods: We performed two QC and MAS experiments consisting of 637 maize lines, using an optimised genotyping workflow involving an in-house competitive allele-specific PCR (KASP) genotyping system with an optimised sample collection, preparation, and DNA extraction and quantitation process. A smaller volume of leaf-disc size plant samples was collected directly in 96-well plates for DNA extraction, using a slightly modified CTAB-based DArT DNA extraction protocol. DNA quality and quantity analyses were performed using a microplate reader, and the KASP genotyping and data analysis was performed in our laboratory. Results: Applying the optimized genotyping workflow expedited the QC and MAS experiments from over five weeks (when outsourcing) to two weeks and eliminated the shipping cost. Using a set of 28 KASP single nucleotide polymorphisms (SNPs) validated for maize, the QC experiment revealed the genetic identity of four maize varieties taken from five seed sources. Another set of 10 KASP SNPs was sufficient in verifying the parentage of 390 F1 lines. The KASP-based MAS was successfully applied to a maize pro-vitamin A (PVA) breeding program and for introgressing the aflatoxin resistance gene into elite tropical maize lines. Conclusion: This improved workflow has helped accelerate maize improvement activities of IITA's Maize Improvement Program and facilitated DNA fingerprinting for tracking improved crop varieties. National Agricultural Research Systems (NARS) in developing countries can adopt this workflow to fast-track molecular marker-based genotyping for crop improvement.
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11
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Ghanizadeh H, Buddenhagen CE, Harrington KC, Griffiths AG, Ngow Z. Pinoxaden resistance in Lolium perenne L. is due to both target-site and non-target-site mechanisms. PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2022; 184:105103. [PMID: 35715042 DOI: 10.1016/j.pestbp.2022.105103] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 03/30/2022] [Accepted: 04/15/2022] [Indexed: 06/15/2023]
Abstract
Application of herbicides inhibiting acetyl CoA carboxylase (ACCase) has been one of the main strategies for selectively controlling grass weed species such as perennial ryegrass (Lolium perenne L.) in wheat and barley crops in New Zealand. In this study, we have confirmed and characterized resistance to pinoxaden, an ACCase-inhibiting herbicide, in a population of L. perenne. Dose-response experiments were conducted to assess the level of pinoxaden resistance, and based on the LD50 values, the studied population was 41.4-times more resistant to pinoxaden than a susceptible population. Application of malathion, an inhibitor of the cytochrome P450s, preceding pinoxaden treatment reduced the level of resistance to 9.7-fold. However, pre-treatment with the glutathione S-transferase (GST) inhibitor 4-chloro7- nitrobenzoxadiazole prior to pinoxaden treatment did not affect pinoxaden resistance. Partial sequencing of the ACCase gene revealed that the resistant population had an isoleucine to valine replacement at position 2041. These results suggest that both cytochrome P450-based and target-site mechanisms are jointly associated with this instance of pinoxaden resistance in L. perenne. The pinoxaden-resistant L. perenne individuals were also resistant to quizalofop-p-ethyl (108.6-fold), but they were susceptible to clethodim, which can, therefore, be used to manage this pinoxaden-resistant L. perenne. This is the first report of a L. perenne population in which a rare target-site mutation works in concert with enhanced cytochrome P-450 activity to confer pinoxaden resistance. Evolution of resistance to ACCase-inhibiting herbicides in this L. perenne population indicates that integrated weed management practices are required to prevent widespread resistance developing in New Zealand cereal crop systems.
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Affiliation(s)
- Hossein Ghanizadeh
- School of Agriculture and Environment, Massey University, Palmerston North, New Zealand.
| | | | - Kerry C Harrington
- School of Agriculture and Environment, Massey University, Palmerston North, New Zealand
| | - Andrew G Griffiths
- AgResearch Grasslands Research Centre, Palmerston North 4442, New Zealand
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12
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Phan KAT, Paeng SK, Chae HB, Park JH, Lee ES, Wi SD, Bae SB, Kim MG, Yun D, Kim W, Lee SY. Universal Stress Protein (
USP
) regulates the circadian rhythm of central oscillator genes in
Arabidopsis. FEBS Lett 2022; 596:1871-1880. [DOI: 10.1002/1873-3468.14410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 05/18/2022] [Indexed: 11/08/2022]
Affiliation(s)
- Kieu Anh Thi Phan
- Division of Applied Life Science (BK21+) and PMBBRC, 2College of Pharmacy Gyeongsang National University Jinju, 52828 Korea
| | - Seol Ki Paeng
- Division of Applied Life Science (BK21+) and PMBBRC, 2College of Pharmacy Gyeongsang National University Jinju, 52828 Korea
| | - Ho Byoung Chae
- Division of Applied Life Science (BK21+) and PMBBRC, 2College of Pharmacy Gyeongsang National University Jinju, 52828 Korea
| | - Joung Hun Park
- Division of Applied Life Science (BK21+) and PMBBRC, 2College of Pharmacy Gyeongsang National University Jinju, 52828 Korea
| | - Eun Seon Lee
- Division of Applied Life Science (BK21+) and PMBBRC, 2College of Pharmacy Gyeongsang National University Jinju, 52828 Korea
| | - Seong Dong Wi
- Division of Applied Life Science (BK21+) and PMBBRC, 2College of Pharmacy Gyeongsang National University Jinju, 52828 Korea
| | - Su Bin Bae
- Division of Applied Life Science (BK21+) and PMBBRC, 2College of Pharmacy Gyeongsang National University Jinju, 52828 Korea
| | | | - Dae‐Jin Yun
- Department of Biomedical Science & Engineering Konkuk University Seoul, 05029 Korea
| | - Woe‐Yeon Kim
- Division of Applied Life Science (BK21+) and PMBBRC, 2College of Pharmacy Gyeongsang National University Jinju, 52828 Korea
| | - Sang Yeol Lee
- Division of Applied Life Science (BK21+) and PMBBRC, 2College of Pharmacy Gyeongsang National University Jinju, 52828 Korea
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13
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Offornedo Q, Menkir A, Babalola D, Gedil M. Developing and deploying an efficient genotyping workflow for accelerating maize improvement in developing countries. Gates Open Res 2022. [DOI: 10.12688/gatesopenres.13338.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Background: Molecular breeding is an essential tool for accelerating genetic gain in crop improvement, towards meeting the need to feed an ever-growing world population. Establishing low-cost, flexible genotyping platforms in small, public and regional laboratories can stimulate the application of molecular breeding in developing countries. These laboratories can serve plant breeding projects requiring low- to medium-density markers for marker-assisted selection (MAS) and quality control (QC) activities. Methods: We performed two QC and MAS experiments consisting of 637 maize lines, using an optimised genotyping workflow involving an in-house competitive allele-specific PCR (KASP) genotyping system with an optimised sample collection, preparation, and DNA extraction and quantitation process. A smaller volume of leaf-disc size plant samples was collected directly in 96-well plates for DNA extraction, using a slightly modified CTAB-based DArT DNA extraction protocol. DNA quality and quantity analyses were performed using a microplate reader, and the KASP genotyping and data analysis was performed in our laboratory. Results: Applying the optimized genotyping workflow expedited the QC and MAS experiments from over five weeks (when outsourcing) to two weeks and eliminated the shipping cost. Using a set of 28 KASP single nucleotide polymorphisms (SNPs) validated for maize, the QC experiment revealed the genetic identity of four maize varieties taken from five seed sources. Another set of 10 KASP SNPs was sufficient in verifying the parentage of 390 F1 lines. The KASP-based MAS was successfully applied to a maize pro-vitamin A (PVA) breeding program and for introgressing the aflatoxin resistance gene into elite tropical maize lines. Conclusion: This improved workflow has helped accelerate maize improvement activities of IITA's Maize Improvement Program and facilitated DNA fingerprinting for tracking improved crop varieties. National Agricultural Research Systems (NARS) in developing countries can adopt this workflow to fast-track molecular marker-based genotyping for crop improvement.
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14
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Ghanizadeh H, Griffiths AG, Buddenhagen CE, Anderson CB, Harrington KC. A PCR plus restriction enzyme-based technique for detecting target-enzyme mutations at position Pro-106 in glyphosate-resistant Lolium perenne. PLoS One 2021; 16:e0246028. [PMID: 33529261 PMCID: PMC7853469 DOI: 10.1371/journal.pone.0246028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 01/12/2021] [Indexed: 11/26/2022] Open
Abstract
The first step in managing herbicide-resistant weeds is to confirm their resistance status. It is, therefore, crucial to have a rapid, reliable and cost-effective technique to assess samples for herbicide resistance. We designed and evaluated three derived cleaved amplified polymorphic sequence (dCAPS) markers for detecting glyphosate resistance in Lolium perenne. conferred by non-synonymous mutations at codon-106 in the enolpyruvylshikimate-3-phosphate synthase (EPSPS) gene. The dCAPS markers involve amplification of the target region, digestion of the amplified products with restriction enzymes and gel-based visualisation of the digested products. The results showed that all three dCAPS markers could successfully detect mutations at codon-106 in the target enzyme. The dCAPS markers can also inform us of the zygosity state of the resistance allele and was confirmed by sequencing the target region of the EPSPS gene. The markers described here are effective quick tests for the monitoring and evaluation of the target-enzyme mechanism of glyphosate resistance in Lolium perenne.
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Affiliation(s)
- Hossein Ghanizadeh
- School of Agriculture and Environment, Massey University, Palmerston North, New Zealand
| | | | | | - Craig B. Anderson
- AgResearch Grasslands Research Centre, Palmerston North, New Zealand
| | - Kerry C. Harrington
- School of Agriculture and Environment, Massey University, Palmerston North, New Zealand
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15
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Kalendar R, Boronnikova S, Seppänen M. Isolation and Purification of DNA from Complicated Biological Samples. Methods Mol Biol 2021; 2222:57-67. [PMID: 33301087 DOI: 10.1007/978-1-0716-0997-2_3] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The isolation of nucleic acids from a biological sample is an important step for many molecular biology applications and medical diagnostic assays. This chapter describes an efficient protocol using established acidic CTAB (with a pH value of 5.0 to 6.8) based extraction method for isolation and/or purification of high molecular weight genomic DNA from a range of fresh and difficult sources from plant, animal, fungi, and soil material. This protocol is suitable for many sequencing and genotyping applications, including large-scale sample screening.
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Affiliation(s)
- Ruslan Kalendar
- Department of Agricultural Sciences, Viikki Plant Science Centre and Helsinki Sustainability Centre, University of Helsinki, Helsinki, Finland. .,National Laboratory Astana, Nazarbayev University, Nur-Sultan, Kazakhstan.
| | - Svetlana Boronnikova
- Department of Botany and Genetics of Plants, Faculty of Biology, Perm State University, Perm, Russia
| | - Mervi Seppänen
- Department of Agricultural Sciences, Viikki Plant Science Centre and Helsinki Sustainability Centre, University of Helsinki, Helsinki, Finland
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16
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Jamsari J, Arif Setiawan M, Nova B, Syukriani L, Nur Aisyah S, Asben A. Development of Rapid and Less Hazardous Plant DNA Extraction Protocol using Potassium Phosphate Buffer. Pak J Biol Sci 2021; 24:1309-1315. [PMID: 34989207 DOI: 10.3923/pjbs.2021.1309.1315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
<b>Background and Objective:</b> Protocols commonly used in plant DNA extraction were known to be highly time-consuming and harmful due to the application of some hazardous reagents. Therefore, it was not applicable for such laboratories with limited resources as well as for high-throughput analysis. This study was aimed to develop a rapid yet less hazardous DNA extraction protocol for a plant using potassium phosphate buffer. <b>Materials and Methods:</b> Genomic DNA of chili pepper (<i>Capsicum annuum</i>) was extracted using potassium phosphate buffer and its efficacy was compared to three widely known protocols (CTAB-based, mini preparation and commercial kit). The extracted DNA from those four methods was evaluated based on its quality, quantity, practicality and cost per reaction. <b>Results:</b> Genomic DNA resulted from potassium phosphate buffer-based protocol exhibited comparable quality with adequate concentration for further downstream analysis. Results of PCR and sequencing were also emphasized the amplifiable DNA quality from this developed protocol. Compared to those commonly used protocols, potassium phosphate buffer consisted of 5 main working steps only, thus providing a simple yet rapid plant DNA extraction protocol. Since this protocol used ethanol only, it also offered a less hazardous and low-cost protocol that applicable for those resource-limited laboratories. <b>Conclusion:</b> This developed protocol provided a promising alternative of plant DNA extraction that might be applicable for both large scale analysis and any laboratory type. Further investigation was needed to evaluate its efficacy in extracting genomic DNA from various plants with different morphological characteristic.
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17
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Vilanova S, Alonso D, Gramazio P, Plazas M, García-Fortea E, Ferrante P, Schmidt M, Díez MJ, Usadel B, Giuliano G, Prohens J. SILEX: a fast and inexpensive high-quality DNA extraction method suitable for multiple sequencing platforms and recalcitrant plant species. PLANT METHODS 2020; 16:110. [PMID: 32793297 PMCID: PMC7419208 DOI: 10.1186/s13007-020-00652-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 08/03/2020] [Indexed: 05/11/2023]
Abstract
BACKGROUND The use of sequencing and genotyping platforms has undergone dramatic improvements, enabling the generation of a wealth of genomic information. Despite this progress, the availability of high-quality genomic DNA (gDNA) in sufficient concentrations is often a main limitation, especially for third-generation sequencing platforms. A variety of DNA extraction methods and commercial kits are available. However, many of these are costly and frequently give either low yield or low-quality DNA, inappropriate for next generation sequencing (NGS) platforms. Here, we describe a fast and inexpensive DNA extraction method (SILEX) applicable to a wide range of plant species and tissues. RESULTS SILEX is a high-throughput DNA extraction protocol, based on the standard CTAB method with a DNA silica matrix recovery, which allows obtaining NGS-quality high molecular weight genomic plant DNA free of inhibitory compounds. SILEX was compared with a standard CTAB extraction protocol and a common commercial extraction kit in a variety of species, including recalcitrant ones, from different families. In comparison with the other methods, SILEX yielded DNA in higher concentrations and of higher quality. Manual extraction of 48 samples can be done in 96 min by one person at a cost of 0.12 €/sample of reagents and consumables. Hundreds of tomato gDNA samples obtained with either SILEX or the commercial kit were successfully genotyped with Single Primer Enrichment Technology (SPET) with the Illumina HiSeq 2500 platform. Furthermore, DNA extracted from Solanum elaeagnifolium using this protocol was assessed by Pulsed-field gel electrophoresis (PFGE), obtaining a suitable size ranges for most sequencing platforms that required high-molecular-weight DNA such as Nanopore or PacBio. CONCLUSIONS A high-throughput, fast and inexpensive DNA extraction protocol was developed and validated for a wide variety of plants and tissues. SILEX offers an easy, scalable, efficient and inexpensive way to extract DNA for various next-generation sequencing applications including SPET and Nanopore among others.
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Affiliation(s)
- Santiago Vilanova
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Camino de Vera 14, 46022 Valencia, Spain
| | - David Alonso
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Camino de Vera 14, 46022 Valencia, Spain
| | - Pietro Gramazio
- Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, 305-8572 Tsukuba, Japan
| | - Mariola Plazas
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Camino de Vera 14, 46022 Valencia, Spain
| | - Edgar García-Fortea
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Camino de Vera 14, 46022 Valencia, Spain
| | - Paola Ferrante
- ENEA, Italian National Agency for New Technologies, Energy and Sustainable Economic Development, Rome, Italy
| | | | - María José Díez
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Camino de Vera 14, 46022 Valencia, Spain
| | - Björn Usadel
- BG-4 Bioinformatics, Forschungszentrum Jülich, 52428 Jülich, Germany
- CEPLAS, Institute for Biological Data Science, Heinrich Heine University Düsseldorf, 40225 Düsselforf, Germany
| | - Giovanni Giuliano
- ENEA, Italian National Agency for New Technologies, Energy and Sustainable Economic Development, Rome, Italy
| | - Jaime Prohens
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Camino de Vera 14, 46022 Valencia, Spain
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18
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Jensen SE, Charles JR, Muleta K, Bradbury PJ, Casstevens T, Deshpande SP, Gore MA, Gupta R, Ilut DC, Johnson L, Lozano R, Miller Z, Ramu P, Rathore A, Romay MC, Upadhyaya HD, Varshney RK, Morris GP, Pressoir G, Buckler ES, Ramstein GP. A sorghum practical haplotype graph facilitates genome-wide imputation and cost-effective genomic prediction. THE PLANT GENOME 2020; 13:e20009. [PMID: 33016627 DOI: 10.1002/tpg2.20009] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Accepted: 01/04/2020] [Indexed: 05/22/2023]
Abstract
Successful management and utilization of increasingly large genomic datasets is essential for breeding programs to accelerate cultivar development. To help with this, we developed a Sorghum bicolor Practical Haplotype Graph (PHG) pangenome database that stores haplotypes and variant information. We developed two PHGs in sorghum that were used to identify genome-wide variants for 24 founders of the Chibas sorghum breeding program from 0.01x sequence coverage. The PHG called single nucleotide polymorphisms (SNPs) with 5.9% error at 0.01x coverage-only 3% higher than PHG error when calling SNPs from 8x coverage sequence. Additionally, 207 progenies from the Chibas genomic selection (GS) training population were sequenced and processed through the PHG. Missing genotypes were imputed from PHG parental haplotypes and used for genomic prediction. Mean prediction accuracies with PHG SNP calls range from .57-.73 and are similar to prediction accuracies obtained with genotyping-by-sequencing or targeted amplicon sequencing (rhAmpSeq) markers. This study demonstrates the use of a sorghum PHG to impute SNPs from low-coverage sequence data and shows that the PHG can unify genotype calls across multiple sequencing platforms. By reducing input sequence requirements, the PHG can decrease the cost of genotyping, make GS more feasible, and facilitate larger breeding populations. Our results demonstrate that the PHG is a useful research and breeding tool that maintains variant information from a diverse group of taxa, stores sequence data in a condensed but readily accessible format, unifies genotypes across genotyping platforms, and provides a cost-effective option for genomic selection.
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Affiliation(s)
- Sarah E Jensen
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
| | - Jean Rigaud Charles
- Chibas and Department of Agriculture and Environmental Sciences, Quisqueya University, Port-au-Prince, Haiti
| | - Kebede Muleta
- Department of Agronomy, Kansas State University, Manhattan, KS, 66506, USA
| | - Peter J Bradbury
- Institute for Genomic Diversity, Cornell University, Ithaca, NY, 14853, USA
- United States Department of Agriculture-Agricultural Research Service, Robert W. Holley Center for Agriculture and Health, Ithaca, NY, 14853, USA
| | - Terry Casstevens
- Institute for Genomic Diversity, Cornell University, Ithaca, NY, 14853, USA
| | - Santosh P Deshpande
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Telangana, 502324, India
| | - Michael A Gore
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
| | - Rajeev Gupta
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Telangana, 502324, India
| | - Daniel C Ilut
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
| | - Lynn Johnson
- Institute for Genomic Diversity, Cornell University, Ithaca, NY, 14853, USA
| | - Roberto Lozano
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
| | - Zachary Miller
- Institute for Genomic Diversity, Cornell University, Ithaca, NY, 14853, USA
| | - Punna Ramu
- Institute for Genomic Diversity, Cornell University, Ithaca, NY, 14853, USA
| | - Abhishek Rathore
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Telangana, 502324, India
| | - M Cinta Romay
- Institute for Genomic Diversity, Cornell University, Ithaca, NY, 14853, USA
| | - Hari D Upadhyaya
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Telangana, 502324, India
| | - Rajeev K Varshney
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Telangana, 502324, India
| | - Geoffrey P Morris
- Department of Agronomy, Kansas State University, Manhattan, KS, 66506, USA
| | - Gael Pressoir
- Chibas and Department of Agriculture and Environmental Sciences, Quisqueya University, Port-au-Prince, Haiti
| | - Edward S Buckler
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
- Institute for Genomic Diversity, Cornell University, Ithaca, NY, 14853, USA
- United States Department of Agriculture-Agricultural Research Service, Robert W. Holley Center for Agriculture and Health, Ithaca, NY, 14853, USA
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19
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Griffiths AG, Moraga R, Tausen M, Gupta V, Bilton TP, Campbell MA, Ashby R, Nagy I, Khan A, Larking A, Anderson C, Franzmayr B, Hancock K, Scott A, Ellison NW, Cox MP, Asp T, Mailund T, Schierup MH, Andersen SU. Breaking Free: The Genomics of Allopolyploidy-Facilitated Niche Expansion in White Clover. THE PLANT CELL 2019; 31:1466-1487. [PMID: 31023841 PMCID: PMC6635854 DOI: 10.1105/tpc.18.00606] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Revised: 03/15/2019] [Accepted: 04/22/2019] [Indexed: 05/18/2023]
Abstract
The merging of distinct genomes, allopolyploidization, is a widespread phenomenon in plants. It generates adaptive potential through increased genetic diversity, but examples demonstrating its exploitation remain scarce. White clover (Trifolium repens) is a ubiquitous temperate allotetraploid forage crop derived from two European diploid progenitors confined to extreme coastal or alpine habitats. We sequenced and assembled the genomes and transcriptomes of this species complex to gain insight into the genesis of white clover and the consequences of allopolyploidization. Based on these data, we estimate that white clover originated ∼15,000 to 28,000 years ago during the last glaciation when alpine and coastal progenitors were likely colocated in glacial refugia. We found evidence of progenitor diversity carryover through multiple hybridization events and show that the progenitor subgenomes have retained integrity and gene expression activity as they traveled within white clover from their original confined habitats to a global presence. At the transcriptional level, we observed remarkably stable subgenome expression ratios across tissues. Among the few genes that show tissue-specific switching between homeologous gene copies, we found flavonoid biosynthesis genes strongly overrepresented, suggesting an adaptive role of some allopolyploidy-associated transcriptional changes. Our results highlight white clover as an example of allopolyploidy-facilitated niche expansion, where two progenitor genomes, adapted and confined to disparate and highly specialized habitats, expanded to a ubiquitous global presence after glaciation-associated allopolyploidization.
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Affiliation(s)
- Andrew G Griffiths
- AgResearch, Grasslands Research Centre, Palmerston North 4442, New Zealand
| | - Roger Moraga
- AgResearch, Grasslands Research Centre, Palmerston North 4442, New Zealand
| | - Marni Tausen
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus C, Denmark
- Bioinformatics Research Centre, Aarhus University, 8000 Aarhus C, Denmark
| | - Vikas Gupta
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus C, Denmark
| | - Timothy P Bilton
- AgResearch, Invermay Agricultural Centre, Mosgiel 9053, New Zealand
| | - Matthew A Campbell
- Bioinformatics and Statistics Group, Institute of Fundamental Sciences, Massey University, Palmerston North 4410, New Zealand
| | - Rachael Ashby
- AgResearch, Invermay Agricultural Centre, Mosgiel 9053, New Zealand
| | - Istvan Nagy
- Department of Molecular Biology and Genetics, Aarhus University, 200 Slagelse, Denmark
| | - Anar Khan
- AgResearch, Invermay Agricultural Centre, Mosgiel 9053, New Zealand
| | - Anna Larking
- AgResearch, Grasslands Research Centre, Palmerston North 4442, New Zealand
| | - Craig Anderson
- AgResearch, Grasslands Research Centre, Palmerston North 4442, New Zealand
| | - Benjamin Franzmayr
- AgResearch, Grasslands Research Centre, Palmerston North 4442, New Zealand
| | - Kerry Hancock
- AgResearch, Grasslands Research Centre, Palmerston North 4442, New Zealand
| | - Alicia Scott
- AgResearch, Grasslands Research Centre, Palmerston North 4442, New Zealand
| | - Nick W Ellison
- AgResearch, Grasslands Research Centre, Palmerston North 4442, New Zealand
| | - Murray P Cox
- Bioinformatics and Statistics Group, Institute of Fundamental Sciences, Massey University, Palmerston North 4410, New Zealand
| | - Torben Asp
- Department of Molecular Biology and Genetics, Aarhus University, 200 Slagelse, Denmark
| | - Thomas Mailund
- Bioinformatics Research Centre, Aarhus University, 8000 Aarhus C, Denmark
| | - Mikkel H Schierup
- AgResearch, Invermay Agricultural Centre, Mosgiel 9053, New Zealand
- Department of Bioscience, Aarhus University, 8000 Aarhus C, Denmark
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20
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Optimized Nuclear Pellet Method for Extracting Next-Generation Sequencing Quality Genomic DNA from Fresh Leaf Tissue. Methods Protoc 2019; 2:mps2020054. [PMID: 31242613 PMCID: PMC6632156 DOI: 10.3390/mps2020054] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 06/20/2019] [Accepted: 06/21/2019] [Indexed: 01/10/2023] Open
Abstract
Next-generation sequencing (NGS) is a revolutionary advancement allowing large-scale discovery of functional molecular markers that has many applications, including plant breeding. High-quality genomic DNA (gDNA) is a prerequisite for successful NGS library preparation and sequencing; however, few reliable protocols to obtain such plant gDNA exist. A previously reported nuclear pellet (NP) method enables extraction of high-yielding gDNA from fresh leaf tissue of maize (Zea mays L.), but the quality does not meet the stringent requirements of NGS. In this study, we optimized the NP method for whole-genome sequencing of rice (Oryza sativa L.) through the integration of simple purification steps. The optimized NP method relied on initial nucleus enrichment, cell lysis, extraction, and subsequent gDNA purification buffers. The purification steps used proteinase K, RNase A, phenol/chloroform/isoamyl alcohol (25:24:1), and chloroform/isoamyl alcohol (24:1) treatments for protein digestion and RNA, protein, and phenol removal, respectively. Our data suggest that this optimized NP method allowed extraction of consistently high-yielding and high-quality undegraded gDNA without contamination by protein and RNA. Moreover, the extracted gDNA fulfilled the quality metrics of NGS library preparation for the Illumina HiSeq X Ten platform by the TruSeq DNA PCR-Free Library Prep Kit (Illumina). We provide a reliable step-by-step guide to the extraction of high-quality gDNA from fresh leaf tissues of rice for molecular biologists with limited resources.
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