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Hu Y, Ren J, Peng Z, Umana AA, Le H, Danilova T, Fu J, Wang H, Robertson A, Hulbert SH, White FF, Liu S. Analysis of Extreme Phenotype Bulk Copy Number Variation (XP-CNV) Identified the Association of rp1 with Resistance to Goss's Wilt of Maize. FRONTIERS IN PLANT SCIENCE 2018; 9:110. [PMID: 29479358 PMCID: PMC5812337 DOI: 10.3389/fpls.2018.00110] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 01/19/2018] [Indexed: 05/19/2023]
Abstract
Goss's wilt (GW) of maize is caused by the Gram-positive bacterium Clavibacter michiganensis subsp. nebraskensis (Cmn) and has spread in recent years throughout the Great Plains, posing a threat to production. The genetic basis of plant resistance is unknown. Here, a simple method for quantifying disease symptoms was developed and used to select cohorts of highly resistant and highly susceptible lines known as extreme phenotypes (XP). Copy number variation (CNV) analyses using whole genome sequences of bulked XP revealed 141 genes containing CNV between the two XP groups. The CNV genes include the previously identified common rust resistant locus rp1. Multiple Rp1 accessions with distinct rp1 haplotypes in an otherwise susceptible accession exhibited hypersensitive responses upon inoculation. GW provides an excellent system for the genetic dissection of diseases caused by closely related subspecies of C. michiganesis. Further work will facilitate breeding strategies to control GW and provide needed insight into the resistance mechanism of important related diseases such as bacterial canker of tomato and bacterial ring rot of potato.
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Affiliation(s)
- Ying Hu
- Department of Plant Pathology, Kansas State University, Manhattan, KS, United States
| | - Jie Ren
- Department of Plant Pathology, Kansas State University, Manhattan, KS, United States
| | - Zhao Peng
- Department of Plant Pathology, University of Florida, Gainesville, FL, United States
| | - Arnoldo A. Umana
- Department of Plant Pathology, Kansas State University, Manhattan, KS, United States
| | - Ha Le
- Department of Plant Pathology, Kansas State University, Manhattan, KS, United States
| | - Tatiana Danilova
- Department of Plant Pathology, Kansas State University, Manhattan, KS, United States
| | - Junjie Fu
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Haiyan Wang
- Department of Statistics, Kansas State University, Manhattan, KS, United States
| | - Alison Robertson
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, United States
| | - Scot H. Hulbert
- Department of Plant Pathology, Washington State University, Pullman, WA, United States
| | - Frank F. White
- Department of Plant Pathology, University of Florida, Gainesville, FL, United States
| | - Sanzhen Liu
- Department of Plant Pathology, Kansas State University, Manhattan, KS, United States
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Darracq A, Vitte C, Nicolas S, Duarte J, Pichon JP, Mary-Huard T, Chevalier C, Bérard A, Le Paslier MC, Rogowsky P, Charcosset A, Joets J. Sequence analysis of European maize inbred line F2 provides new insights into molecular and chromosomal characteristics of presence/absence variants. BMC Genomics 2018; 19:119. [PMID: 29402214 PMCID: PMC5800051 DOI: 10.1186/s12864-018-4490-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 01/22/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Maize is well known for its exceptional structural diversity, including copy number variants (CNVs) and presence/absence variants (PAVs), and there is growing evidence for the role of structural variation in maize adaptation. While PAVs have been described in this important crop species, they have been only scarcely characterized at the sequence level and the extent of presence/absence variation and relative chromosomal landscape of inbred-specific regions remain to be elucidated. RESULTS De novo genome sequencing of the French F2 maize inbred line revealed 10,044 novel genomic regions larger than 1 kb, making up 88 Mb of DNA, that are present in F2 but not in B73 (PAV). This set of maize PAV sequences allowed us to annotate PAV content and to analyze sequence breakpoints. Using PAV genotyping on a collection of 25 temperate lines, we also analyzed Linkage Disequilibrium in PAVs and flanking regions, and PAV frequencies within maize genetic groups. CONCLUSIONS We highlight the possible role of MMEJ-type double strand break repair in maize PAV formation and discover 395 new genes with transcriptional support. Pattern of linkage disequilibrium within PAVs strikingly differs from this of flanking regions and is in accordance with the intuition that PAVs may recombine less than other genomic regions. We show that most PAVs are ancient, while some are found only in European Flint material, thus pinpointing structural features that may be at the origin of adaptive traits involved in the success of this material. Characterization of such PAVs will provide useful material for further association genetic studies in European and temperate maize.
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Affiliation(s)
- Aude Darracq
- Genetique Quantitative et Evolution – Le Moulon, INRA, Université Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Clémentine Vitte
- Genetique Quantitative et Evolution – Le Moulon, INRA, Université Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Stéphane Nicolas
- Genetique Quantitative et Evolution – Le Moulon, INRA, Université Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Gif-sur-Yvette, France
| | | | | | - Tristan Mary-Huard
- Genetique Quantitative et Evolution – Le Moulon, INRA, Université Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Gif-sur-Yvette, France
- MIA, INRA, AgroParisTech, Université Paris-Saclay, Paris, France
| | - Céline Chevalier
- Genetique Quantitative et Evolution – Le Moulon, INRA, Université Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Aurélie Bérard
- EPGV US 1279, INRA, CEA, IG-CNG, Université Paris-Saclay, Evry, France
| | | | - Peter Rogowsky
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRA, Lyon, France
| | - Alain Charcosset
- Genetique Quantitative et Evolution – Le Moulon, INRA, Université Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Johann Joets
- Genetique Quantitative et Evolution – Le Moulon, INRA, Université Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Gif-sur-Yvette, France
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Dolatabadian A, Patel DA, Edwards D, Batley J. Copy number variation and disease resistance in plants. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2017; 130:2479-2490. [PMID: 29043379 DOI: 10.1007/s00122-017-2993-2] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Accepted: 09/27/2017] [Indexed: 05/06/2023]
Abstract
Plant genome diversity varies from single nucleotide polymorphisms to large-scale deletions, insertions, duplications, or re-arrangements. These re-arrangements of sequences resulting from duplication, gains or losses of DNA segments are termed copy number variations (CNVs). During the last decade, numerous studies have emphasized the importance of CNVs as a factor affecting human phenotype; in particular, CNVs have been associated with risks for several severe diseases. In plants, the exploration of the extent and role of CNVs in resistance against pathogens and pests is just beginning. Since CNVs are likely to be associated with disease resistance in plants, an understanding of the distribution of CNVs could assist in the identification of novel plant disease-resistance genes. In this paper, we review existing information about CNVs; their importance, role and function, as well as their association with disease resistance in plants.
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Affiliation(s)
- Aria Dolatabadian
- School of Biological Sciences and Institute of Agriculture, University of Western Australia, Crawley, WA, 6009, Australia
| | - Dhwani Apurva Patel
- School of Biological Sciences and Institute of Agriculture, University of Western Australia, Crawley, WA, 6009, Australia
| | - David Edwards
- School of Biological Sciences and Institute of Agriculture, University of Western Australia, Crawley, WA, 6009, Australia
| | - Jacqueline Batley
- School of Biological Sciences and Institute of Agriculture, University of Western Australia, Crawley, WA, 6009, Australia.
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Neik TX, Barbetti MJ, Batley J. Current Status and Challenges in Identifying Disease Resistance Genes in Brassica napus. FRONTIERS IN PLANT SCIENCE 2017; 8:1788. [PMID: 29163558 PMCID: PMC5681527 DOI: 10.3389/fpls.2017.01788] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 10/02/2017] [Indexed: 05/18/2023]
Abstract
Brassica napus is an economically important crop across different continents including temperate and subtropical regions in Europe, Canada, South Asia, China and Australia. Its widespread cultivation also brings setbacks as it plays host to fungal, oomycete and chytrid pathogens that can lead to serious yield loss. For sustainable crop production, identification of resistance (R) genes in B. napus has become of critical importance. In this review, we discuss four key pathogens affecting Brassica crops: Clubroot (Plasmodiophora brassicae), Blackleg (Leptosphaeria maculans and L. biglobosa), Sclerotinia Stem Rot (Sclerotinia sclerotiorum), and Downy Mildew (Hyaloperonospora parasitica). We first review current studies covering prevalence of these pathogens on Brassica crops and highlight the R genes and QTL that have been identified from Brassica species against these pathogens. Insights into the relationships between the pathogen and its Brassica host, the unique host resistance mechanisms and how these affect resistance outcomes is also presented. We discuss challenges in identification and deployment of R genes in B. napus in relation to highly specific genetic interactions between host subpopulations and pathogen pathotypes and emphasize the need for common or shared techniques and research materials or tighter collaboration between researchers to reconcile the inconsistencies in the research outcomes. Using current genomics tools, we provide examples of how characterization and cloning of R genes in B. napus can be carried out more effectively. Lastly, we put forward strategies to breed resistant cultivars through introgressions supported by genomic approaches and suggest prospects that can be implemented in the future for a better, pathogen-resistant B. napus.
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Affiliation(s)
- Ting Xiang Neik
- School of Biological Sciences, University of Western Australia, Perth, WA, Australia
| | - Martin J. Barbetti
- School of Agriculture and Environment and Institute of Agriculture, University of Western Australia, Perth, WA, Australia
| | - Jacqueline Batley
- School of Biological Sciences, University of Western Australia, Perth, WA, Australia
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55
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Seidl MF, Thomma BPHJ. Transposable Elements Direct The Coevolution between Plants and Microbes. Trends Genet 2017; 33:842-851. [PMID: 28800915 DOI: 10.1016/j.tig.2017.07.003] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 06/24/2017] [Accepted: 07/14/2017] [Indexed: 12/31/2022]
Abstract
Transposable elements are powerful drivers of genome evolution in many eukaryotes. Although they are mostly considered as 'selfish' genetic elements, increasing evidence suggests that they contribute to genetic variability; particularly under stress conditions. Over the past few years, the role of transposable elements during host-microbe interactions has been recognised. It has been proposed that many pathogenic microbes have evolved a 'two-speed' genome with regions that show increased variability and that are enriched in transposable elements and pathogenicity-related genes. Plants similarly display structured genomes with transposable-element-rich regions that mediate accelerated evolution. Immune receptor genes typically reside in such regions. Various mechanisms have recently been identified through which transposable elements contribute to the coevolution between plants and their associated microbes.
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Affiliation(s)
- Michael F Seidl
- Laboratory of Phytopathology, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands; Both authors contributed equally.
| | - Bart P H J Thomma
- Laboratory of Phytopathology, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands; Both authors contributed equally.
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56
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Rasheed A, Hao Y, Xia X, Khan A, Xu Y, Varshney RK, He Z. Crop Breeding Chips and Genotyping Platforms: Progress, Challenges, and Perspectives. MOLECULAR PLANT 2017; 10:1047-1064. [PMID: 28669791 DOI: 10.1016/j.molp.2017.06.008] [Citation(s) in RCA: 219] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Revised: 05/29/2017] [Accepted: 06/19/2017] [Indexed: 05/18/2023]
Abstract
There is a rapidly rising trend in the development and application of molecular marker assays for gene mapping and discovery in field crops and trees. Thus far, more than 50 SNP arrays and 15 different types of genotyping-by-sequencing (GBS) platforms have been developed in over 25 crop species and perennial trees. However, much less effort has been made on developing ultra-high-throughput and cost-effective genotyping platforms for applied breeding programs. In this review, we discuss the scientific bottlenecks in existing SNP arrays and GBS technologies and the strategies to develop targeted platforms for crop molecular breeding. We propose that future practical breeding platforms should adopt automated genotyping technologies, either array or sequencing based, target functional polymorphisms underpinning economic traits, and provide desirable prediction accuracy for quantitative traits, with universal applications under wide genetic backgrounds in crops. The development of such platforms faces serious challenges at both the technological level due to cost ineffectiveness, and the knowledge level due to large genotype-phenotype gaps in crop plants. It is expected that such genotyping platforms will be achieved in the next ten years in major crops in consideration of (a) rapid development in gene discovery of important traits, (b) deepened understanding of quantitative traits through new analytical models and population designs, (c) integration of multi-layer -omics data leading to identification of genes and pathways responsible for important breeding traits, and (d) improvement in cost effectiveness of large-scale genotyping. Crop breeding chips and genotyping platforms will provide unprecedented opportunities to accelerate the development of cultivars with desired yield potential, quality, and enhanced adaptation to mitigate the effects of climate change.
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Affiliation(s)
- Awais Rasheed
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China; International Maize and Wheat Improvement Center (CIMMYT), c/o CAAS, Beijing 100081, China
| | - Yuanfeng Hao
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China
| | - Xianchun Xia
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China
| | - Awais Khan
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Geneva, NY, USA
| | - Yunbi Xu
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China; International Maize and Wheat Improvement Center (CIMMYT), c/o CAAS, Beijing 100081, China
| | - Rajeev K Varshney
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502324, India
| | - Zhonghu He
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China; International Maize and Wheat Improvement Center (CIMMYT), c/o CAAS, Beijing 100081, China.
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57
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Di Donato A, Andolfo G, Ferrarini A, Delledonne M, Ercolano MR. Investigation of orthologous pathogen recognition gene-rich regions in solanaceous species. Genome 2017; 60:850-859. [PMID: 28742982 DOI: 10.1139/gen-2016-0217] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Pathogen receptor proteins such as receptor-like protein (RLP), receptor-like kinase (RLK), and nucleotide-binding leucine-rich repeat (NLR) play a leading role in plant immunity activation. The genome architecture of such genes has been extensively investigated in several plant species. However, we still know little about their elaborate reorganization that arose during the plant speciation process. Using recently released pepper and eggplant genome sequences, we were able to identify 1097 pathogen recognition genes (PRGs) in the cultivated pepper Zunla-1 and 775 in the eggplant line Nakate-Shinkuro. The retrieved genes were analysed for their tendency to cluster, using different methods to infer the means of grouping. Orthologous relationships among clustering loci were found, and interesting reshuffling within given loci was observed for each analysed species. The information obtained was integrated into a comparative map to highlight the evolutionary dynamics in which the PRG loci were involved. Diversification of 14 selected PRG-rich regions was also explored using a DNA target-enrichment approach. A large number of gene variants were found as well as rearrangements of sequences encoding single protein domain and changes in chromosome gene order among species. Gene duplication and transposition activity have clearly influenced plant genome R-gene architecture and diversification. Our findings contribute to addressing several biological questions concerning the parallel evolution that occurred between genomes of the family Solanaceae. Moreover, the integration of different methods proved a powerful approach to reconstruct the evolutionary history in plant families and to transfer important biology findings among plant genomes.
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Affiliation(s)
- A Di Donato
- a Dipartimento di Agraria, Università di Napoli 'Federico II', Via Università 100, 80055 Portici, Italy
| | - G Andolfo
- a Dipartimento di Agraria, Università di Napoli 'Federico II', Via Università 100, 80055 Portici, Italy
| | - A Ferrarini
- b Dipartimento di Biotecnologie, Università degli Studi di Verona, Strada le Grazie, 15, 37134 Verona, Italy
| | - M Delledonne
- b Dipartimento di Biotecnologie, Università degli Studi di Verona, Strada le Grazie, 15, 37134 Verona, Italy
| | - M R Ercolano
- a Dipartimento di Agraria, Università di Napoli 'Federico II', Via Università 100, 80055 Portici, Italy
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58
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Rutter MT, Wieckowski YM, Murren CJ, Strand AE. Fitness effects of mutation: testing genetic redundancy in Arabidopsis thaliana. J Evol Biol 2017; 30:1124-1135. [PMID: 28387971 DOI: 10.1111/jeb.13081] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Accepted: 03/09/2017] [Indexed: 01/05/2023]
Abstract
Screens of organisms with disruptive mutations in a single gene often fail to detect phenotypic consequences for the majority of mutants. One explanation for this phenomenon is that the presence of paralogous loci provides genetic redundancy. However, it is also possible that the assayed traits are affected by few loci, that effects could be subtle or that phenotypic effects are restricted to certain environments. We assayed a set of T-DNA insertion mutant lines of Arabidopsis thaliana to determine the frequency with which mutation affected fitness-related phenotypes. We found that between 8% and 42% of the assayed lines had altered fitness from the wild type. Furthermore, many of these lines exhibited fitness greater than the wild type. In a second experiment, we grew a subset of the lines in multiple environments and found whether a T-DNA insert increased or decreased fitness traits depended on the assay environment. Overall, our evidence contradicts the hypothesis that genetic redundancy is a common phenomenon in A. thaliana for fitness traits. Evidence for redundancy from prior screens of knockout mutants may often be an artefact of the design of the phenotypic assays which have focused on less complex phenotypes than fitness and have used single environments. Finally, our study adds to evidence that beneficial mutations may represent a significant component of the mutational spectrum of A. thaliana.
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Affiliation(s)
- M T Rutter
- Department of Biology, College of Charleston, Charleston, SC, USA
| | - Y M Wieckowski
- Department of Biology, College of Charleston, Charleston, SC, USA
| | - C J Murren
- Department of Biology, College of Charleston, Charleston, SC, USA
| | - A E Strand
- Department of Biology, College of Charleston, Charleston, SC, USA
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59
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Dobbels AA, Michno JM, Campbell BW, Virdi KS, Stec AO, Muehlbauer GJ, Naeve SL, Stupar RM. An Induced Chromosomal Translocation in Soybean Disrupts a KASI Ortholog and Is Associated with a High-Sucrose and Low-Oil Seed Phenotype. G3 (BETHESDA, MD.) 2017; 7:1215-1223. [PMID: 28235823 PMCID: PMC5386870 DOI: 10.1534/g3.116.038596] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Accepted: 02/11/2017] [Indexed: 12/15/2022]
Abstract
Mutagenesis is a useful tool in many crop species to induce heritable genetic variability for trait improvement and gene discovery. In this study, forward screening of a soybean fast neutron (FN) mutant population identified an individual that produced seed with nearly twice the amount of sucrose (8.1% on dry matter basis) and less than half the amount of oil (8.5% on dry matter basis) as compared to wild type. Bulked segregant analysis (BSA), comparative genomic hybridization, and genome resequencing were used to associate the seed composition phenotype with a reciprocal translocation between chromosomes 8 and 13. In a backcross population, the translocation perfectly cosegregated with the seed composition phenotype and exhibited non-Mendelian segregation patterns. We hypothesize that the translocation is responsible for the altered seed composition by disrupting a β-ketoacyl-[acyl carrier protein] synthase 1 (KASI) ortholog. KASI is a core fatty acid synthesis enzyme that is involved in the conversion of sucrose into oil in developing seeds. This finding may lead to new research directions for developing soybean cultivars with modified carbohydrate and oil seed composition.
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Affiliation(s)
- Austin A Dobbels
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108
| | - Jean-Michel Michno
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108
| | - Benjamin W Campbell
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108
| | - Kamaldeep S Virdi
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108
| | - Adrian O Stec
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108
| | - Gary J Muehlbauer
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108
- Department of Plant Biology, University of Minnesota, St. Paul, Minnesota 55108
| | - Seth L Naeve
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108
| | - Robert M Stupar
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108
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60
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Sedivy EJ, Wu F, Hanzawa Y. Soybean domestication: the origin, genetic architecture and molecular bases. THE NEW PHYTOLOGIST 2017; 214:539-553. [PMID: 28134435 DOI: 10.1111/nph.14418] [Citation(s) in RCA: 108] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2016] [Accepted: 11/28/2016] [Indexed: 05/20/2023]
Abstract
Domestication provides an important model for the study of evolution, and information learned from domestication research aids in the continued improvement of crop species. Recent progress in de novo assembly and whole-genome resequencing of wild and cultivated soybean genomes, in addition to new archeological discoveries, sheds light on the origin of this important crop and provides a clearer view on the modes of artificial selection that drove soybean domestication and diversification. This novel genomic information enables the search for polymorphisms that underlie variation in agronomic traits and highlights genes that exhibit a signature of selection, leading to the identification of a number of candidate genes that may have played important roles in soybean domestication, diversification and improvement. These discoveries provide a novel point of comparison on the evolutionary bases of important agronomic traits among different crop species.
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Affiliation(s)
- Eric J Sedivy
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Faqiang Wu
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Yoshie Hanzawa
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
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61
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Samelak-Czajka A, Marszalek-Zenczak M, Marcinkowska-Swojak M, Kozlowski P, Figlerowicz M, Zmienko A. MLPA-Based Analysis of Copy Number Variation in Plant Populations. FRONTIERS IN PLANT SCIENCE 2017; 8:222. [PMID: 28270823 PMCID: PMC5318451 DOI: 10.3389/fpls.2017.00222] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Accepted: 02/06/2017] [Indexed: 05/18/2023]
Abstract
Copy number variants (CNVs) are intraspecies duplications/deletions of large DNA segments (>1 kb). A growing number of reports highlight the functional and evolutionary impact of CNV in plants, increasing the need for appropriate tools that enable locus-specific CNV genotyping on a population scale. Multiplex ligation-dependent probe amplification (MLPA) is considered a gold standard in genotyping CNV in humans. Consequently, numerous commercial MLPA assays for CNV-related human diseases have been created. We routinely genotype complex multiallelic CNVs in human and plant genomes using the modified MLPA procedure based on fully synthesized oligonucleotide probes (90-200 nt), which greatly simplifies the design process and allows for the development of custom assays. Here, we present a step-by-step protocol for gene-specific MLPA probe design, multiplexed assay setup and data analysis in a copy number genotyping experiment in plants. As a case study, we present the results of a custom assay designed to genotype the copy number status of 12 protein coding genes in a population of 80 Arabidopsis accessions. The genes were pre-selected based on whole genome sequencing data and are localized in the genomic regions that display different levels of population-scale variation (non-variable, biallelic, or multiallelic, as well as CNVs overlapping whole genes or their fragments). The presented approach is suitable for population-scale validation of the CNV regions inferred from whole genome sequencing data analysis and for focused analysis of selected genes of interest. It can also be very easily adopted for any plant species, following optimization of the template amount and design of the appropriate control probes, according to the general guidelines presented in this paper.
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Affiliation(s)
- Anna Samelak-Czajka
- Institute of Computing Science, Faculty of Computing, Poznan University of TechnologyPoznan, Poland
| | - Malgorzata Marszalek-Zenczak
- Department of Molecular and Systems Biology, Institute of Bioorganic Chemistry, Polish Academy of SciencesPoznan, Poland
| | | | - Piotr Kozlowski
- Department of Molecular Genetics, Institute of Bioorganic Chemistry, Polish Academy of SciencesPoznan, Poland
| | - Marek Figlerowicz
- Institute of Computing Science, Faculty of Computing, Poznan University of TechnologyPoznan, Poland
- Department of Molecular and Systems Biology, Institute of Bioorganic Chemistry, Polish Academy of SciencesPoznan, Poland
| | - Agnieszka Zmienko
- Institute of Computing Science, Faculty of Computing, Poznan University of TechnologyPoznan, Poland
- Department of Molecular and Systems Biology, Institute of Bioorganic Chemistry, Polish Academy of SciencesPoznan, Poland
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62
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Prunier J, Caron S, MacKay J. CNVs into the wild: screening the genomes of conifer trees (Picea spp.) reveals fewer gene copy number variations in hybrids and links to adaptation. BMC Genomics 2017; 18:97. [PMID: 28100184 PMCID: PMC5241962 DOI: 10.1186/s12864-016-3458-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Accepted: 12/22/2016] [Indexed: 12/31/2022] Open
Abstract
Background Copy number variations (CNVs) have been linked to different phenotypes in human, including many diseases. A genome-scale understanding of CNVs is available in a few plants but none are wild species, leaving a knowledge gap regarding their genome biology and evolutionary role. We developed a reliable CNV detection method for species lacking contiguous reference genome. We selected multiple probes within 14,078 gene sequences and developed comparative genome hybridization on arrays. Gene CNVs were assessed in three full-sib families from species with 20 Gb genomes, i.e., white and black spruce, and interior spruce - a natural hybrid. Results We discovered hundreds of gene CNVs in each species, 3612 in total, which were enriched in functions related to stress and defense responses and narrow expression profiles, indicating a potential role in adaptation. The number of shared CNVs was in accordance with the degree of relatedness between individuals and species. The genetically mapped subset of these genes showed a wide distribution across the genome, implying numerous structural variations. The hybrid family presented significantly fewer CNVs, suggesting that the admixture of two species within one genome reduces the occurrence of CNVs. Conclusions The approach we developed is of particular interest in non-model species lacking a reference genome. Our findings point to a role for CNVs in adaptation. Their reduced abundance in the hybrid may limit genetic variability and evolvability of hybrids. We propose that CNVs make a qualitatively distinct contribution to adaptation which could be important for short term change. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3458-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Julien Prunier
- Institute for System and Integrative Biology (IBIS), Université Laval, Quebec, QC, G1V 0A6, Canada. .,Centre for Forest Research, Université Laval, Quebec, QC, G1V 0A6, Canada.
| | - Sébastien Caron
- Institute for System and Integrative Biology (IBIS), Université Laval, Quebec, QC, G1V 0A6, Canada
| | - John MacKay
- Centre for Forest Research, Université Laval, Quebec, QC, G1V 0A6, Canada.,Department of Plant Sciences, University of Oxford, Oxford, OX1 3RB, UK
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Contreras-Moreira B, Cantalapiedra CP, García-Pereira MJ, Gordon SP, Vogel JP, Igartua E, Casas AM, Vinuesa P. Analysis of Plant Pan-Genomes and Transcriptomes with GET_HOMOLOGUES-EST, a Clustering Solution for Sequences of the Same Species. FRONTIERS IN PLANT SCIENCE 2017; 8:184. [PMID: 28261241 PMCID: PMC5306281 DOI: 10.3389/fpls.2017.00184] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Accepted: 01/30/2017] [Indexed: 05/22/2023]
Abstract
The pan-genome of a species is defined as the union of all the genes and non-coding sequences found in all its individuals. However, constructing a pan-genome for plants with large genomes is daunting both in sequencing cost and the scale of the required computational analysis. A more affordable alternative is to focus on the genic repertoire by using transcriptomic data. Here, the software GET_HOMOLOGUES-EST was benchmarked with genomic and RNA-seq data of 19 Arabidopsis thaliana ecotypes and then applied to the analysis of transcripts from 16 Hordeum vulgare genotypes. The goal was to sample their pan-genomes and classify sequences as core, if detected in all accessions, or accessory, when absent in some of them. The resulting sequence clusters were used to simulate pan-genome growth, and to compile Average Nucleotide Identity matrices that summarize intra-species variation. Although transcripts were found to under-estimate pan-genome size by at least 10%, we concluded that clusters of expressed sequences can recapitulate phylogeny and reproduce two properties observed in A. thaliana gene models: accessory loci show lower expression and higher non-synonymous substitution rates than core genes. Finally, accessory sequences were observed to preferentially encode transposon components in both species, plus disease resistance genes in cultivated barleys, and a variety of protein domains from other families that appear frequently associated with presence/absence variation in the literature. These results demonstrate that pan-genome analyses are useful to explore germplasm diversity.
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Affiliation(s)
- Bruno Contreras-Moreira
- Estación Experimental de Aula Dei - Consejo Superior de Investigaciones CientíficasZaragoza, Spain; Fundación ARAIDZaragoza, Spain
| | - Carlos P Cantalapiedra
- Estación Experimental de Aula Dei - Consejo Superior de Investigaciones Científicas Zaragoza, Spain
| | - María J García-Pereira
- Estación Experimental de Aula Dei - Consejo Superior de Investigaciones Científicas Zaragoza, Spain
| | | | - John P Vogel
- DOE Joint Genome Institute, Walnut Creek CA, USA
| | - Ernesto Igartua
- Estación Experimental de Aula Dei - Consejo Superior de Investigaciones Científicas Zaragoza, Spain
| | - Ana M Casas
- Estación Experimental de Aula Dei - Consejo Superior de Investigaciones Científicas Zaragoza, Spain
| | - Pablo Vinuesa
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México Cuernavaca, Mexico
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64
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The pangenome of an agronomically important crop plant Brassica oleracea. Nat Commun 2016; 7:13390. [PMID: 27834372 PMCID: PMC5114598 DOI: 10.1038/ncomms13390] [Citation(s) in RCA: 253] [Impact Index Per Article: 31.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Accepted: 09/28/2016] [Indexed: 02/07/2023] Open
Abstract
There is an increasing awareness that as a result of structural variation, a reference sequence representing a genome of a single individual is unable to capture all of the gene repertoire found in the species. A large number of genes affected by presence/absence and copy number variation suggest that it may contribute to phenotypic and agronomic trait diversity. Here we show by analysis of the Brassica oleracea pangenome that nearly 20% of genes are affected by presence/absence variation. Several genes displaying presence/absence variation are annotated with functions related to major agronomic traits, including disease resistance, flowering time, glucosinolate metabolism and vitamin biosynthesis. Brassica oleracea is a single species that includes diverse crops such as cabbage, broccoli and Brussels sprouts. Here, the authors identify genes not captured in existing B. oleracea reference genomes by the assembly of a pangenome and show variations in gene content that may be related to important agronomic traits
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Zmienko A, Samelak-Czajka A, Kozlowski P, Szymanska M, Figlerowicz M. Arabidopsis thaliana population analysis reveals high plasticity of the genomic region spanning MSH2, AT3G18530 and AT3G18535 genes and provides evidence for NAHR-driven recurrent CNV events occurring in this location. BMC Genomics 2016; 17:893. [PMID: 27825302 PMCID: PMC5101643 DOI: 10.1186/s12864-016-3221-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Accepted: 10/27/2016] [Indexed: 12/28/2022] Open
Abstract
Background Intraspecies copy number variations (CNVs), defined as unbalanced structural variations of specific genomic loci, ≥1 kb in size, are present in the genomes of animals and plants. A growing number of examples indicate that CNVs may have functional significance and contribute to phenotypic diversity. In the model plant Arabidopsis thaliana at least several hundred protein-coding genes might display CNV; however, locus-specific genotyping studies in this plant have not been conducted. Results We analyzed the natural CNVs in the region overlapping MSH2 gene that encodes the DNA mismatch repair protein, and AT3G18530 and AT3G18535 genes that encode poorly characterized proteins. By applying multiplex ligation-dependent probe amplification and droplet digital PCR we genotyped those genes in 189 A. thaliana accessions. We found that AT3G18530 and AT3G18535 were duplicated (2–14 times) in 20 and deleted in 101 accessions. MSH2 was duplicated in 12 accessions (up to 12-14 copies) but never deleted. In all but one case, the MSH2 duplications were associated with those of AT3G18530 and AT3G18535. Considering the structure of the CNVs, we distinguished 5 genotypes for this region, determined their frequency and geographical distribution. We defined the CNV breakpoints in 35 accessions with AT3G18530 and AT3G18535 deletions and tandem duplications and showed that they were reciprocal events, resulting from non-allelic homologous recombination between 99 %-identical sequences flanking these genes. The widespread geographical distribution of the deletions supported by the SNP and linkage disequilibrium analyses of the genomic sequence confirmed the recurrent nature of this CNV. Conclusions We characterized in detail for the first time the complex multiallelic CNV in Arabidopsis genome. The region encoding MSH2, AT3G18530 and AT3G18535 genes shows enormous variation of copy numbers among natural ecotypes, being a remarkable example of high Arabidopsis genome plasticity. We provided the molecular insight into the mechanism underlying the recurrent nature of AT3G18530-AT3G18535 duplications/deletions. We also performed the first direct comparison of the two leading experimental methods, suitable for assessing the DNA copy number status. Our comprehensive case study provides foundation information for further analyses of CNV evolution in Arabidopsis and other plants, and their possible use in plant breeding. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3221-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Agnieszka Zmienko
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland.,Institute of Computing Science, Poznan University of Technology, Piotrowo 2, 60-965, Poznan, Poland
| | - Anna Samelak-Czajka
- Institute of Computing Science, Poznan University of Technology, Piotrowo 2, 60-965, Poznan, Poland
| | - Piotr Kozlowski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland
| | - Maja Szymanska
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland
| | - Marek Figlerowicz
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland. .,Institute of Computing Science, Poznan University of Technology, Piotrowo 2, 60-965, Poznan, Poland.
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Cardone MF, D'Addabbo P, Alkan C, Bergamini C, Catacchio CR, Anaclerio F, Chiatante G, Marra A, Giannuzzi G, Perniola R, Ventura M, Antonacci D. Inter-varietal structural variation in grapevine genomes. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2016; 88:648-661. [PMID: 27419916 DOI: 10.1111/tpj.13274] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Revised: 07/12/2016] [Accepted: 07/13/2016] [Indexed: 05/10/2023]
Abstract
Grapevine (Vitis vinifera L.) is one of the world's most important crop plants, which is of large economic value for fruit and wine production. There is much interest in identifying genomic variations and their functional effects on inter-varietal, phenotypic differences. Using an approach developed for the analysis of human and mammalian genomes, which combines high-throughput sequencing, array comparative genomic hybridization, fluorescent in situ hybridization and quantitative PCR, we created an inter-varietal atlas of structural variations and single nucleotide variants (SNVs) for the grapevine genome analyzing four economically and genetically relevant table grapevine varieties. We found 4.8 million SNVs and detected 8% of the grapevine genome to be affected by genomic variations. We identified more than 700 copy number variation (CNV) regions and more than 2000 genes subjected to CNV as potential candidates for phenotypic differences between varieties.
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Affiliation(s)
- Maria Francesca Cardone
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria (CREA)-Unità di ricerca per l'uva da tavola e la vitivinicoltura in ambiente mediterraneo, Research Unit for viticulture and enology in Southern Italy, Turi (BA), Italy
| | - Pietro D'Addabbo
- Dipartimento di Biologia, Università degli Studi di Bari 'Aldo Moro', Bari, Italy
| | - Can Alkan
- Department of Computer Engineering, Bilkent University, Ankara, TR-06800, Turkey
| | - Carlo Bergamini
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria (CREA)-Unità di ricerca per l'uva da tavola e la vitivinicoltura in ambiente mediterraneo, Research Unit for viticulture and enology in Southern Italy, Turi (BA), Italy
| | | | - Fabio Anaclerio
- Dipartimento di Biologia, Università degli Studi di Bari 'Aldo Moro', Bari, Italy
| | - Giorgia Chiatante
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria (CREA)-Unità di ricerca per l'uva da tavola e la vitivinicoltura in ambiente mediterraneo, Research Unit for viticulture and enology in Southern Italy, Turi (BA), Italy
- Dipartimento di Biologia, Università degli Studi di Bari 'Aldo Moro', Bari, Italy
| | - Annamaria Marra
- Dipartimento di Biologia, Università degli Studi di Bari 'Aldo Moro', Bari, Italy
| | - Giuliana Giannuzzi
- Dipartimento di Biologia, Università degli Studi di Bari 'Aldo Moro', Bari, Italy
- Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland
| | - Rocco Perniola
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria (CREA)-Unità di ricerca per l'uva da tavola e la vitivinicoltura in ambiente mediterraneo, Research Unit for viticulture and enology in Southern Italy, Turi (BA), Italy
| | - Mario Ventura
- Dipartimento di Biologia, Università degli Studi di Bari 'Aldo Moro', Bari, Italy
| | - Donato Antonacci
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria (CREA)-Unità di ricerca per l'uva da tavola e la vitivinicoltura in ambiente mediterraneo, Research Unit for viticulture and enology in Southern Italy, Turi (BA), Italy
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Francia E, Morcia C, Pasquariello M, Mazzamurro V, Milc JA, Rizza F, Terzi V, Pecchioni N. Copy number variation at the HvCBF4-HvCBF2 genomic segment is a major component of frost resistance in barley. PLANT MOLECULAR BIOLOGY 2016; 92:161-75. [PMID: 27338258 DOI: 10.1007/s11103-016-0505-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Accepted: 06/02/2016] [Indexed: 05/27/2023]
Abstract
A family of CBF transcription factors plays a major role in reconfiguring the plant transcriptome in response to low-freezing temperature in temperate cereals. In barley, more than 13 HvCBF genes map coincident with the major QTL FR-H2 suggesting them as candidates to explain the function of the locus. Variation in copy number (CNV) of specific HvCBFs was assayed in a panel of 41 barley genotypes using RT-qPCR. Taking advantage of an accurate phenotyping that combined Fv/Fm and field survival, resistance-associated variants within FR-H2 were identified. Genotypes with an increased copy number of HvCBF4 and HvCBF2 (at least ten and eight copies, respectively) showed greater frost resistance. A CAPS marker able to distinguish the CBF2A, CBF2B and CBF2A/B forms was developed and showed that all the higher-ranking genotypes in term of resistance harbour only CBF2A, while other resistant winter genotypes harbour also CBF2B, although at a lower CNV. In addition to the major involvement of the HvCBF4-HvCBF2 genomic segment in the proximal cluster of CBF elements, a negative role of HvCBF3 in the distal cluster was identified. Multiple linear regression models taking into account allelic variation at FR-H1/VRN-H1 explained 0.434 and 0.550 (both at p < 0.001) of the phenotypic variation for Fv/Fm and field survival respectively, while no interaction effect between CNV at the HvCBFs and FR-H1/VRN-H1 was found. Altogether our data suggest a major involvement of the CBF genes located in the proximal cluster, with no apparent involvement of the central cluster contrary to what was reported for wheat.
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Affiliation(s)
- Enrico Francia
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Amendola 2, Pad.Besta, 42122, Reggio Emilia, Italy.
- Center for Genome Research (CGR), University of Modena and Reggio Emilia, Via Campi 287, 41125, Modena, Italy.
| | - Caterina Morcia
- Genomics Research Centre (GPG), Council for Agricultural Research and Economics, Via San Protaso 302, 29017, Fiorenzuola d'Arda, Italy
| | - Marianna Pasquariello
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Amendola 2, Pad.Besta, 42122, Reggio Emilia, Italy
- Department of Crop Genetics, John Innes Centre (JIC), Norwich Research Park, Norwich, NR4 7UH, UK
| | - Valentina Mazzamurro
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Amendola 2, Pad.Besta, 42122, Reggio Emilia, Italy
| | - Justyna Anna Milc
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Amendola 2, Pad.Besta, 42122, Reggio Emilia, Italy
- Center for Genome Research (CGR), University of Modena and Reggio Emilia, Via Campi 287, 41125, Modena, Italy
| | - Fulvia Rizza
- Genomics Research Centre (GPG), Council for Agricultural Research and Economics, Via San Protaso 302, 29017, Fiorenzuola d'Arda, Italy
| | - Valeria Terzi
- Genomics Research Centre (GPG), Council for Agricultural Research and Economics, Via San Protaso 302, 29017, Fiorenzuola d'Arda, Italy
| | - Nicola Pecchioni
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Amendola 2, Pad.Besta, 42122, Reggio Emilia, Italy
- Center for Genome Research (CGR), University of Modena and Reggio Emilia, Via Campi 287, 41125, Modena, Italy
- Cereal Research Centre, Council for Agricultural Research and Economics, 71122, Foggia, Italy
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Campbell BW, Hofstad AN, Sreekanta S, Fu F, Kono TJY, O'Rourke JA, Vance CP, Muehlbauer GJ, Stupar RM. Fast neutron-induced structural rearrangements at a soybean NAP1 locus result in gnarled trichomes. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2016; 129:1725-38. [PMID: 27282876 PMCID: PMC4983299 DOI: 10.1007/s00122-016-2735-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Accepted: 05/28/2016] [Indexed: 05/20/2023]
Abstract
KEY MESSAGE Three adjacent and distinct sequence rearrangements were identified at a NAP1 locus in a soybean mutant. Genetic dissection and validation revealed the function of this gene in soybean trichome development. A soybean (Glycine max (L.) Merr.) gnarled trichome mutant, exhibiting stunted trichomes compared to wild-type, was identified in a fast neutron mutant population. Genetic mapping using whole genome sequencing-based bulked segregant analysis identified a 26.6 megabase interval on chromosome 20 that co-segregated with the phenotype. Comparative genomic hybridization analysis of the mutant indicated that the chromosome 20 interval included a small structural variant within the coding region of a soybean ortholog (Glyma.20G019300) of Arabidopsis Nck-Associated Protein 1 (NAP1), a regulator of actin nucleation during trichome morphogenesis. Sequence analysis of the candidate allele revealed multiple rearrangements within the coding region, including two deletions (approximately 1-2 kb each), a translocation, and an inversion. Further analyses revealed that the mutant allele perfectly co-segregated with the phenotype, and a wild-type soybean NAP1 transgene functionally complemented an Arabidopsis nap1 mutant. In addition, mapping and exon sequencing of NAP1 in a spontaneous soybean gnarled trichome mutant (T31) identified a frame shift mutation resulting in a truncation of the coding region. These data indicate that the soybean NAP1 gene is essential for proper trichome development and show the utility of the soybean fast neutron population for forward genetic approaches for identifying genes.
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Affiliation(s)
- Benjamin W Campbell
- Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN, 55108, USA
| | - Anna N Hofstad
- Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN, 55108, USA
| | - Suma Sreekanta
- Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN, 55108, USA
| | - Fengli Fu
- Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN, 55108, USA
| | - Thomas J Y Kono
- Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN, 55108, USA
| | - Jamie A O'Rourke
- USDA-ARS, Corn Insects and Crop Genetics Research, Iowa State University, Ames, IA, 50011, USA
| | - Carroll P Vance
- Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN, 55108, USA
| | - Gary J Muehlbauer
- Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN, 55108, USA
- Department of Plant Biology, University of Minnesota, Saint Paul, MN, 55108, USA
| | - Robert M Stupar
- Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN, 55108, USA.
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Pinosio S, Giacomello S, Faivre-Rampant P, Taylor G, Jorge V, Le Paslier MC, Zaina G, Bastien C, Cattonaro F, Marroni F, Morgante M. Characterization of the Poplar Pan-Genome by Genome-Wide Identification of Structural Variation. Mol Biol Evol 2016; 33:2706-19. [PMID: 27499133 PMCID: PMC5026262 DOI: 10.1093/molbev/msw161] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Many recent studies have emphasized the important role of structural variation (SV) in determining human genetic and phenotypic variation. In plants, studies aimed at elucidating the extent of SV are still in their infancy. Evidence has indicated a high presence and an active role of SV in driving plant genome evolution in different plant species. With the aim of characterizing the size and the composition of the poplar pan-genome, we performed a genome-wide analysis of structural variation in three intercrossable poplar species: Populus nigra, Populus deltoides, and Populus trichocarpa. We detected a total of 7,889 deletions and 10,586 insertions relative to the P. trichocarpa reference genome, covering respectively 33.2 Mb and 62.9 Mb of genomic sequence, and 3,230 genes affected by copy number variation (CNV). The majority of the detected variants are inter-specific in agreement with a recent origin following separation of species. Insertions and deletions (INDELs) were preferentially located in low-gene density regions of the poplar genome and were, for the majority, associated with the activity of transposable elements. Genes affected by SV showed lower-than-average expression levels and higher levels of dN/dS, suggesting that they are subject to relaxed selective pressure or correspond to pseudogenes. Functional annotation of genes affected by INDELs showed over-representation of categories associated with transposable elements activity, while genes affected by genic CNVs showed enrichment in categories related to resistance to stress and pathogens. This study provides a genome-wide catalogue of SV and the first insight on functional and structural properties of the poplar pan-genome.
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Affiliation(s)
- Sara Pinosio
- Istituto di Bioscienze e Biorisorse, Consiglio Nazionale delle Ricerche, Sesto Fiorentino, Firenze, Italy Istituto di Genomica Applicata (IGA), Udine, Italy
| | - Stefania Giacomello
- Istituto di Genomica Applicata (IGA), Udine, Italy Dipartimento di Scienze Agro-alimentari, Università di Udine, Ambientali e Animali (DI4A), Udine, Italy
| | | | - Gail Taylor
- School of Biological Sciences, University of Southampton, Southampton, United Kingdom
| | - Veronique Jorge
- INRA, UR 0588 AGPF, Centre INRA Val de Loire, Orléans, France
| | | | - Giusi Zaina
- Dipartimento di Scienze Agro-alimentari, Università di Udine, Ambientali e Animali (DI4A), Udine, Italy
| | | | | | - Fabio Marroni
- Istituto di Genomica Applicata (IGA), Udine, Italy Dipartimento di Scienze Agro-alimentari, Università di Udine, Ambientali e Animali (DI4A), Udine, Italy
| | - Michele Morgante
- Istituto di Genomica Applicata (IGA), Udine, Italy Dipartimento di Scienze Agro-alimentari, Università di Udine, Ambientali e Animali (DI4A), Udine, Italy
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Using Genotyping by Sequencing to Map Two Novel Anthracnose Resistance Loci in Sorghum bicolor. G3-GENES GENOMES GENETICS 2016; 6:1935-46. [PMID: 27194807 PMCID: PMC4938647 DOI: 10.1534/g3.116.030510] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Colletotrichum sublineola is an aggressive fungal pathogen that causes anthracnose in sorghum [Sorghum bicolor (L.) Moench]. The obvious symptoms of anthracnose are leaf blight and stem rot. Sorghum, the fifth most widely grown cereal crop in the world, can be highly susceptible to the disease, most notably in hot and humid environments. In the southeastern United States the acreage of sorghum has been increasing steadily in recent years, spurred by growing interest in producing biofuels, bio-based products, and animal feed. Resistance to anthracnose is, therefore, of paramount importance for successful sorghum production in this region. To identify anthracnose resistance loci present in the highly resistant cultivar ‘Bk7’, a biparental mapping population of F3:4 and F4:5 sorghum lines was generated by crossing ‘Bk7’ with the susceptible inbred ‘Early Hegari-Sart’. Lines were phenotyped in three environments and in two different years following natural infection. The population was genotyped by sequencing. Following a stringent custom filtering protocol, totals of 5186 and 2759 informative SNP markers were identified in the two populations. Segregation data and association analysis identified resistance loci on chromosomes 7 and 9, with the resistance alleles derived from ‘Bk7’. Both loci contain multiple classes of defense-related genes based on sequence similarity and gene ontologies. Genetic analysis following an independent selection experiment of lines derived from a cross between ‘Bk7’ and sweet sorghum ‘Mer81-4’ narrowed the resistance locus on chromosome 9 substantially, validating this QTL. As observed in other species, sorghum appears to have regions of clustered resistance genes. Further characterization of these regions will facilitate the development of novel germplasm with resistance to anthracnose and other diseases.
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Redekar NR, Clevinger EM, Laskar MA, Biyashev RM, Ashfield T, Jensen RV, Jeong SC, Tolin SA, Saghai Maroof MA. Candidate Gene Sequence Analyses toward Identifying -Type Resistance to. THE PLANT GENOME 2016; 9. [PMID: 27898808 DOI: 10.3835/plantgenome2015.09.0088] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Accepted: 02/22/2016] [Indexed: 05/25/2023]
Abstract
is one of three genetic loci conferring strain-specific resistance to (SMV). The locus has been mapped to a 154-kb region on chromosome 14, containing a cluster of five nucleotide-binding leucine-rich repeat (NB-LRR) resistance genes. High sequence similarity between the candidate genes challenges fine mapping of the locus. Among the five, Glyma14g38533 showed the highest transcript abundance in 1 to 3 h of SMV-G7 inoculation. Comparative sequence analyses were conducted with the five candidate NB-LRR genes from susceptible (-type) soybean [ (L.) Merr.] cultivar Williams 82, resistant (-type) cultivar Hwangkeum, and resistant lines L29 and RRR. Sequence comparisons revealed that Glyma14g38533 had far more polymorphisms than the other candidate genes. Interestingly, Glyma14g38533 gene from -type lines exhibited 150 single-nucleotide polymorphism (SNP and six insertion-deletion (InDel) markers relative to -type line, Furthermore, the polymorphisms identified in three -type lines were highly conserved. Several polymorphisms were validated in 18 -type resistant and six -type susceptible lines and were found associated with their disease response. The majority of the polymorphisms were located in LRR domain encoding region, which is involved in pathogen recognition via protein-protein interactions. These findings associating Glyma14g38533 with -type resistance to SMV suggest it is the most likely candidate gene for .
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Anderson JE, Michno JM, Kono TJY, Stec AO, Campbell BW, Curtin SJ, Stupar RM. Genomic variation and DNA repair associated with soybean transgenesis: a comparison to cultivars and mutagenized plants. BMC Biotechnol 2016; 16:41. [PMID: 27176220 PMCID: PMC4866027 DOI: 10.1186/s12896-016-0271-z] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Accepted: 05/04/2016] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND The safety of mutagenized and genetically transformed plants remains a subject of scrutiny. Data gathered and communicated on the phenotypic and molecular variation induced by gene transfer technologies will provide a scientific-based means to rationally address such concerns. In this study, genomic structural variation (e.g. large deletions and duplications) and single nucleotide polymorphism rates were assessed among a sample of soybean cultivars, fast neutron-derived mutants, and five genetically transformed plants developed through Agrobacterium based transformation methods. RESULTS On average, the number of genes affected by structural variations in transgenic plants was one order of magnitude less than that of fast neutron mutants and two orders of magnitude less than the rates observed between cultivars. Structural variants in transgenic plants, while rare, occurred adjacent to the transgenes, and at unlinked loci on different chromosomes. DNA repair junctions at both transgenic and unlinked sites were consistent with sequence microhomology across breakpoints. The single nucleotide substitution rates were modest in both fast neutron and transformed plants, exhibiting fewer than 100 substitutions genome-wide, while inter-cultivar comparisons identified over one-million single nucleotide polymorphisms. CONCLUSIONS Overall, these patterns provide a fresh perspective on the genomic variation associated with high-energy induced mutagenesis and genetically transformed plants. The genetic transformation process infrequently results in novel genetic variation and these rare events are analogous to genetic variants occurring spontaneously, already present in the existing germplasm, or induced through other types of mutagenesis. It remains unclear how broadly these results can be applied to other crops or transformation methods.
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Affiliation(s)
- Justin E Anderson
- Department of Agronomy & Plant Genetics, University of Minnesota, 1991 Upper Buford Circle, 411 Borlaug Hall, St. Paul, MN 55108, USA
| | - Jean-Michel Michno
- Department of Agronomy & Plant Genetics, University of Minnesota, 1991 Upper Buford Circle, 411 Borlaug Hall, St. Paul, MN 55108, USA
| | - Thomas J Y Kono
- Department of Agronomy & Plant Genetics, University of Minnesota, 1991 Upper Buford Circle, 411 Borlaug Hall, St. Paul, MN 55108, USA
| | - Adrian O Stec
- Department of Agronomy & Plant Genetics, University of Minnesota, 1991 Upper Buford Circle, 411 Borlaug Hall, St. Paul, MN 55108, USA
| | - Benjamin W Campbell
- Department of Agronomy & Plant Genetics, University of Minnesota, 1991 Upper Buford Circle, 411 Borlaug Hall, St. Paul, MN 55108, USA
| | - Shaun J Curtin
- Department of Agronomy & Plant Genetics, University of Minnesota, 1991 Upper Buford Circle, 411 Borlaug Hall, St. Paul, MN 55108, USA
| | - Robert M Stupar
- Department of Agronomy & Plant Genetics, University of Minnesota, 1991 Upper Buford Circle, 411 Borlaug Hall, St. Paul, MN 55108, USA.
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Genes and Small RNA Transcripts Exhibit Dosage-Dependent Expression Pattern in Maize Copy-Number Alterations. Genetics 2016; 203:1133-47. [PMID: 27129738 DOI: 10.1534/genetics.116.188235] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Accepted: 04/04/2016] [Indexed: 12/18/2022] Open
Abstract
Copy-number alterations are widespread in animal and plant genomes, but their immediate impact on gene expression is still unclear. In animals, copy-number alterations usually exhibit dosage effects, except for sex chromosomes which tend to be dosage compensated. In plants, genes within small duplications (<100 kb) often exhibit dosage-dependent expression, whereas large duplications (>50 Mb) are more often dosage compensated. However, little or nothing is known about expression in moderately-sized (1-50 Mb) segmental duplications, and about the response of small RNAs to dosage change. Here, we compared maize (Zea mays) plants with two, three, and four doses of a 14.6-Mb segment of chromosome 1 that contains ∼300 genes. Plants containing the duplicated segment exhibit dosage-dependent effects on ear length and flowering time. Transcriptome analyses using GeneChip and RNA-sequencing methods indicate that most expressed genes and unique small RNAs within the duplicated segments exhibit dosage-dependent transcript levels. We conclude that dosage effect is the predominant regulatory response for both genes and unique small RNA transcripts in the segmental dosage series we tested. To our knowledge this is the first analysis of small RNA expression in plant gene dosage variants. Because segmental duplications comprise a significant proportion of eukaryotic genomes, these findings provide important new insight into the regulation of genes and small RNAs in response to dosage changes.
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74
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Zhang F, Xu T, Mao L, Yan S, Chen X, Wu Z, Chen R, Luo X, Xie J, Gao S. Genome-wide analysis of Dongxiang wild rice (Oryza rufipogon Griff.) to investigate lost/acquired genes during rice domestication. BMC PLANT BIOLOGY 2016; 16:103. [PMID: 27118394 PMCID: PMC4845489 DOI: 10.1186/s12870-016-0788-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Accepted: 04/18/2016] [Indexed: 05/03/2023]
Abstract
BACKGROUND It is widely accepted that cultivated rice (Oryza sativa L.) was domesticated from common wild rice (Oryza rufipogon Griff.). Compared to other studies which concentrate on rice origin, this study is to genetically elucidate the substantially phenotypic and physiological changes from wild rice to cultivated rice at the whole genome level. RESULTS Instead of comparing two assembled genomes, this study directly compared the Dongxiang wild rice (DXWR) Illumina sequencing reads with the Nipponbare (O. sativa) complete genome without assembly of the DXWR genome. Based on the results from the comparative genomics analysis, structural variations (SVs) between DXWR and Nipponbare were determined to locate deleted genes which could have been acquired by Nipponbare during rice domestication. To overcome the limit of the SV detection, the DXWR transcriptome was also sequenced and compared with the Nipponbare transcriptome to discover the genes which could have been lost in DXWR during domestication. Both 1591 Nipponbare-acquired genes and 206 DXWR-lost transcripts were further analyzed using annotations from multiple sources. The NGS data are available in the NCBI SRA database with ID SRP070627. CONCLUSIONS These results help better understanding the domestication from wild rice to cultivated rice at the whole genome level and provide a genomic data resource for rice genetic research or breeding. One finding confirmed transposable elements contribute greatly to the genome evolution from wild rice to cultivated rice. Another finding suggested the photophosphorylation and oxidative phosphorylation system in cultivated rice could have adapted to environmental changes simultaneously during domestication.
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Affiliation(s)
- Fantao Zhang
- />College of Life Sciences, Jiangxi Normal University, Nanchang, Jiangxi 330022 P. R. China
| | - Tao Xu
- />College of Animal Science and Veterinary Medicine, Shanxi Agricultural University, Taigu, Shanxi 030801 P. R. China
| | - Linyong Mao
- />Department of Biochemistry and Molecular Biology, College of Medicine, Howard University, Washington DC, WA 20059 USA
| | - Shuangyong Yan
- />Tianjin Institute of Crop Research, Tianjin Academy of Agricultural Sciences, Tianjin, 300381 P. R. China
| | - Xiwen Chen
- />College of Life Sciences, Nankai University, Tianjin, 300071 P. R. China
| | - Zhenfeng Wu
- />School of Mathematical Sciences, Nankai University, Tianjin, 300071 P. R. China
| | - Rui Chen
- />Tianjin Institute of Agricultural Quality Standard and Testing Technology, Tianjin Academy of Agricultural Sciences, Tianjin, 300381 P. R. China
| | - Xiangdong Luo
- />College of Life Sciences, Jiangxi Normal University, Nanchang, Jiangxi 330022 P. R. China
| | - Jiankun Xie
- />College of Life Sciences, Jiangxi Normal University, Nanchang, Jiangxi 330022 P. R. China
| | - Shan Gao
- />College of Life Sciences, Nankai University, Tianjin, 300071 P. R. China
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75
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Golicz AA, Batley J, Edwards D. Towards plant pangenomics. PLANT BIOTECHNOLOGY JOURNAL 2016; 14:1099-105. [PMID: 26593040 DOI: 10.1111/pbi.12499] [Citation(s) in RCA: 136] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2015] [Revised: 09/18/2015] [Accepted: 10/04/2015] [Indexed: 05/05/2023]
Abstract
As an increasing number of genome sequences become available for a wide range of species, there is a growing understanding that the genome of a single individual is insufficient to represent the gene diversity within a whole species. Many studies examine the sequence diversity within genes, and this allelic variation is an important source of phenotypic variation which can be selected for by man or nature. However, the significant gene presence/absence variation that has been observed within species and the impact of this variation on traits is only now being studied in detail. The sum of the genes for a species is termed the pangenome, and the determination and characterization of the pangenome is a requirement to understand variation within a species. In this review, we explore the current progress in pangenomics as well as methods and approaches for the characterization of pangenomes for a wide range of plant species.
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Affiliation(s)
- Agnieszka A Golicz
- School of Agriculture and Food Sciences, University of Queensland, St. Lucia, QLD, Australia
- School of Plant Biology, University of Western Australia, Perth, WA, Australia
| | - Jacqueline Batley
- School of Agriculture and Food Sciences, University of Queensland, St. Lucia, QLD, Australia
- School of Plant Biology, University of Western Australia, Perth, WA, Australia
| | - David Edwards
- School of Agriculture and Food Sciences, University of Queensland, St. Lucia, QLD, Australia
- School of Plant Biology, University of Western Australia, Perth, WA, Australia
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76
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Young ND, Zhou P, Silverstein KA. Exploring structural variants in environmentally sensitive gene families. CURRENT OPINION IN PLANT BIOLOGY 2016; 30:19-24. [PMID: 26855303 DOI: 10.1016/j.pbi.2015.12.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Revised: 12/22/2015] [Accepted: 12/28/2015] [Indexed: 06/05/2023]
Abstract
Environmentally sensitive plant gene families like NBS-LRRs, receptor kinases, defensins and others, are known to be highly variable. However, most existing strategies for discovering and describing structural variation in complex gene families provide incomplete and imperfect results. The move to de novo genome assemblies for multiple accessions or individuals within a species is enabling more comprehensive and accurate insights about gene family variation. Earlier array-based genome hybridization and sequence-based read mapping methods were limited by their reliance on a reference genome and by misplacement of paralogous sequences. Variant discovery based on de novo genome assemblies overcome the problems arising from a reference genome and reduce sequence misplacement. As de novo genome sequencing moves to the use of longer reads, artifacts will be minimized, intact tandem gene clusters will be constructed accurately, and insights into rapid evolution will become feasible.
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Affiliation(s)
- Nevin Dale Young
- Department of Plant Pathology, 495 Borlaug Hall, University of Minnesota, St. Paul, MN 55108, USA; Department of Plant Biology, 220 BioScience Building, University of Minnesota, St. Paul, MN 55108, USA.
| | - Peng Zhou
- Department of Plant Pathology, 495 Borlaug Hall, University of Minnesota, St. Paul, MN 55108, USA; Minnesota Supercomputer Institute, University of Minnesota, Minneapolis, MN 55455, USA
| | - Kevin At Silverstein
- Minnesota Supercomputer Institute, University of Minnesota, Minneapolis, MN 55455, USA
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77
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Bai Z, Chen J, Liao Y, Wang M, Liu R, Ge S, Wing RA, Chen M. The impact and origin of copy number variations in the Oryza species. BMC Genomics 2016; 17:261. [PMID: 27025496 PMCID: PMC4812662 DOI: 10.1186/s12864-016-2589-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2015] [Accepted: 03/15/2016] [Indexed: 02/16/2023] Open
Abstract
Background Copy number variation (CNV), a complex genomic rearrangement, has been extensively studied in humans and other organisms. In plants, CNVs of several genes were found to be responsible for various important traits; however, the cause and consequence of CNVs remains largely unknown. Recently released next-generation sequencing (NGS) data provide an opportunity for a genome-wide study of CNVs in rice. Results Here, by an NGS-based approach, we generated a CNV map comprising 9,196 deletions compared to the reference genome ‘Nipponbare’. Using Oryza glaberrima as the outgroup, 80 % of the CNV events turned out to be insertions in Nipponbare. There were 2,806 annotated genes affected by these CNV events. We experimentally validated 28 functional CNV genes including OsMADS56, BPH14, OsDCL2b and OsMADS30, implying that CNVs might have contributed to phenotypic variations in rice. Most CNV genes were found to be located in non-co-linear positions by comparison to O. glaberrima. One of the origins of these non-co-linear genes was genomic duplications caused by transposon activity or double-strand break repair. Comprehensive analysis of mutation mechanisms suggested an abundance of CNVs formed by non-homologous end-joining and mobile element insertion. Conclusions This study showed the impact and origin of copy number variations in rice on a genomic scale. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2589-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Zetao Bai
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jinfeng Chen
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yi Liao
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Meijiao Wang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Rong Liu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Song Ge
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Rod A Wing
- Arizona Genomics Institute, School of Plant Science, University of Arizona, Tucson, AZ, 85721, USA
| | - Mingsheng Chen
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.
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78
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Llinares-López F, Grimm DG, Bodenham DA, Gieraths U, Sugiyama M, Rowan B, Borgwardt K. Genome-wide detection of intervals of genetic heterogeneity associated with complex traits. Bioinformatics 2015; 31:i240-9. [PMID: 26072488 PMCID: PMC4559912 DOI: 10.1093/bioinformatics/btv263] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Motivation: Genetic heterogeneity, the fact that several sequence variants give rise to the same phenotype, is a phenomenon that is of the utmost interest in the analysis of complex phenotypes. Current approaches for finding regions in the genome that exhibit genetic heterogeneity suffer from at least one of two shortcomings: (i) they require the definition of an exact interval in the genome that is to be tested for genetic heterogeneity, potentially missing intervals of high relevance, or (ii) they suffer from an enormous multiple hypothesis testing problem due to the large number of potential candidate intervals being tested, which results in either many false positives or a lack of power to detect true intervals. Results: Here, we present an approach that overcomes both problems: it allows one to automatically find all contiguous sequences of single nucleotide polymorphisms in the genome that are jointly associated with the phenotype. It also solves both the inherent computational efficiency problem and the statistical problem of multiple hypothesis testing, which are both caused by the huge number of candidate intervals. We demonstrate on Arabidopsis thaliana genome-wide association study data that our approach can discover regions that exhibit genetic heterogeneity and would be missed by single-locus mapping. Conclusions: Our novel approach can contribute to the genome-wide discovery of intervals that are involved in the genetic heterogeneity underlying complex phenotypes. Availability and implementation: The code can be obtained at: http://www.bsse.ethz.ch/mlcb/research/bioinformatics-and-computational-biology/sis.html. Contact:felipe.llinares@bsse.ethz.ch Supplementary information:Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Felipe Llinares-López
- Machine Learning and Computational Biology Lab, Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland, The Institute of Scientific and Industrial Research, Osaka University, Osaka, Japan, JST, PRESTO, Japan and Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Dominik G Grimm
- Machine Learning and Computational Biology Lab, Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland, The Institute of Scientific and Industrial Research, Osaka University, Osaka, Japan, JST, PRESTO, Japan and Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Dean A Bodenham
- Machine Learning and Computational Biology Lab, Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland, The Institute of Scientific and Industrial Research, Osaka University, Osaka, Japan, JST, PRESTO, Japan and Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Udo Gieraths
- Machine Learning and Computational Biology Lab, Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland, The Institute of Scientific and Industrial Research, Osaka University, Osaka, Japan, JST, PRESTO, Japan and Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Mahito Sugiyama
- Machine Learning and Computational Biology Lab, Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland, The Institute of Scientific and Industrial Research, Osaka University, Osaka, Japan, JST, PRESTO, Japan and Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany Machine Learning and Computational Biology Lab, Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland, The Institute of Scientific and Industrial Research, Osaka University, Osaka, Japan, JST, PRESTO, Japan and Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Beth Rowan
- Machine Learning and Computational Biology Lab, Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland, The Institute of Scientific and Industrial Research, Osaka University, Osaka, Japan, JST, PRESTO, Japan and Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Karsten Borgwardt
- Machine Learning and Computational Biology Lab, Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland, The Institute of Scientific and Industrial Research, Osaka University, Osaka, Japan, JST, PRESTO, Japan and Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
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79
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Hayes JE, Pallotta M, Garcia M, Öz MT, Rongala J, Sutton T. Diversity in boron toxicity tolerance of Australian barley (Hordeum vulgare L.) genotypes. BMC PLANT BIOLOGY 2015; 15:231. [PMID: 26410221 PMCID: PMC4584011 DOI: 10.1186/s12870-015-0607-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Accepted: 09/06/2015] [Indexed: 05/18/2023]
Abstract
BACKGROUND Boron (B) is an important micronutrient for plant growth, but is toxic when levels are too high. This commonly occurs in environments with alkaline soils and relatively low rainfall, including many of the cereal growing regions of southern Australia. Four major genetic loci controlling tolerance to high soil B have been identified in the landrace barley, Sahara 3771. Genes underlying two of the loci encode the B transporters HvBot1 and HvNIP2;1. RESULTS We investigated sequence and expression level diversity in HvBot1 and HvNIP2;1 across barley germplasm, and identified five novel coding sequence alleles for HvBot1. Lines were identified containing either single or multiple copies of the Sahara HvBot1 allele. We established that only the tandemly duplicated Sahara allele conferred B tolerance, and this duplicated allele was found only in a set of nine lines accessioned in Australian collections as Sahara 3763-3771. HvNIP2;1 coding sequences were highly conserved across barley germplasm. We identified the likely causative SNP in the 5'UTR of Sahara HvNIP2;1, and propose that the creation of a small upstream open reading frame interferes with HvNIP2;1 translation in Sahara 3771. Similar to HvBot1, the tolerant HvNIP2;1 allele was unique to the Sahara barley accessions. We identified a new source of the 2H B tolerance allele controlling leaf symptom development, in the landrace Ethiopia 756. CONCLUSIONS Ethiopia 756, as well as the cultivar Sloop Vic which carries both the 2H and HvBot1 B tolerance alleles derived from Sahara 3771, may be valuable as alternative parents in breeding programs targeted to high soil B environments. There is significant diversity in B toxicity tolerance among contemporary Australian barley varieties but this is not related to variation at any of the four known B tolerance loci, indicating that novel, as yet undiscovered, sources of tolerance exist.
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Affiliation(s)
- Julie E Hayes
- Australian Centre for Plant Functional Genomics and The University of Adelaide, Adelaide, South Australia, Australia.
| | - Margaret Pallotta
- Australian Centre for Plant Functional Genomics and The University of Adelaide, Adelaide, South Australia, Australia.
| | - Melissa Garcia
- Australian Centre for Plant Functional Genomics and The University of Adelaide, Adelaide, South Australia, Australia.
| | - Mehmet Tufan Öz
- Australian Centre for Plant Functional Genomics and The University of Adelaide, Adelaide, South Australia, Australia.
- Present address: University of Florida Agronomy Department, Gainesville, Florida, USA.
| | - Jay Rongala
- Australian Centre for Plant Functional Genomics and The University of Adelaide, Adelaide, South Australia, Australia.
| | - Tim Sutton
- Australian Centre for Plant Functional Genomics and The University of Adelaide, Adelaide, South Australia, Australia.
- Present address: South Australian Research and Development Institute, Adelaide, South Australia, Australia.
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80
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Sanseverino W, Hénaff E, Vives C, Pinosio S, Burgos-Paz W, Morgante M, Ramos-Onsins SE, Garcia-Mas J, Casacuberta JM. Transposon Insertions, Structural Variations, and SNPs Contribute to the Evolution of the Melon Genome. Mol Biol Evol 2015; 32:2760-74. [PMID: 26174143 DOI: 10.1093/molbev/msv152] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
The availability of extensive databases of crop genome sequences should allow analysis of crop variability at an unprecedented scale, which should have an important impact in plant breeding. However, up to now the analysis of genetic variability at the whole-genome scale has been mainly restricted to single nucleotide polymorphisms (SNPs). This is a strong limitation as structural variation (SV) and transposon insertion polymorphisms are frequent in plant species and have had an important mutational role in crop domestication and breeding. Here, we present the first comprehensive analysis of melon genetic diversity, which includes a detailed analysis of SNPs, SV, and transposon insertion polymorphisms. The variability found among seven melon varieties representing the species diversity and including wild accessions and highly breed lines, is relatively high due in part to the marked divergence of some lineages. The diversity is distributed nonuniformly across the genome, being lower at the extremes of the chromosomes and higher in the pericentromeric regions, which is compatible with the effect of purifying selection and recombination forces over functional regions. Additionally, this variability is greatly reduced among elite varieties, probably due to selection during breeding. We have found some chromosomal regions showing a high differentiation of the elite varieties versus the rest, which could be considered as strongly selected candidate regions. Our data also suggest that transposons and SV may be at the origin of an important fraction of the variability in melon, which highlights the importance of analyzing all types of genetic variability to understand crop genome evolution.
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Affiliation(s)
- Walter Sanseverino
- Institut de Recerca i Tecnologia Agroalimentàries, Centre for Research in Agricultural Genomics CSIC-IRTA-UAB-UB, Barcelona, Spain
| | - Elizabeth Hénaff
- Centre for Research in Agricultural Genomics CSIC-IRTA-UAB-UB, Barcelona, Spain
| | - Cristina Vives
- Centre for Research in Agricultural Genomics CSIC-IRTA-UAB-UB, Barcelona, Spain
| | - Sara Pinosio
- Dipartimento di szience agrarie e ambientali, Università degli studi di Udine, Udine, Italy
| | - William Burgos-Paz
- Centre for Research in Agricultural Genomics CSIC-IRTA-UAB-UB, Barcelona, Spain
| | - Michele Morgante
- Dipartimento di szience agrarie e ambientali, Università degli studi di Udine, Udine, Italy
| | | | - Jordi Garcia-Mas
- Institut de Recerca i Tecnologia Agroalimentàries, Centre for Research in Agricultural Genomics CSIC-IRTA-UAB-UB, Barcelona, Spain
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81
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Copy number variation at the GL7 locus contributes to grain size diversity in rice. Nat Genet 2015; 47:944-8. [PMID: 26147619 DOI: 10.1038/ng.3346] [Citation(s) in RCA: 336] [Impact Index Per Article: 37.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2015] [Accepted: 06/01/2015] [Indexed: 12/16/2022]
Abstract
Copy number variants (CNVs) are associated with changes in gene expression levels and contribute to various adaptive traits. Here we show that a CNV at the Grain Length on Chromosome 7 (GL7) locus contributes to grain size diversity in rice (Oryza sativa L.). GL7 encodes a protein homologous to Arabidopsis thaliana LONGIFOLIA proteins, which regulate longitudinal cell elongation. Tandem duplication of a 17.1-kb segment at the GL7 locus leads to upregulation of GL7 and downregulation of its nearby negative regulator, resulting in an increase in grain length and improvement of grain appearance quality. Sequence analysis indicates that allelic variants of GL7 and its negative regulator are associated with grain size diversity and that the CNV at the GL7 locus was selected for and used in breeding. Our work suggests that pyramiding beneficial alleles of GL7 and other yield- and quality-related genes may improve the breeding of elite rice varieties.
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82
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Liu JZ, Graham MA, Pedley KF, Whitham SA. Gaining insight into soybean defense responses using functional genomics approaches. Brief Funct Genomics 2015; 14:283-90. [PMID: 25832523 DOI: 10.1093/bfgp/elv009] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2023] Open
Abstract
Soybean pathogens significantly impact yield, resulting in over $4 billion dollars in lost revenue annually in the United States. Despite the deployment of improved soybean cultivars, pathogens continue to evolve to evade plant defense responses. Thus, there is an urgent need to identify and characterize gene networks controlling defense responses to harmful pathogens. In this review, we focus on major advances that have been made in identifying the genes and gene networks regulating defense responses with an emphasis on soybean-pathogen interactions that have been amenable to gene function analyses using gene silencing technologies. Further we describe new research striving to identify genes involved in durable broad-spectrum resistance. Finally, we consider future prospects for functional genomic studies in soybean and demonstrate that understanding soybean disease and stress tolerance will be expedited at an unprecedented pace.
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83
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Zhang Z, Mao L, Chen H, Bu F, Li G, Sun J, Li S, Sun H, Jiao C, Blakely R, Pan J, Cai R, Luo R, Van de Peer Y, Jacobsen E, Fei Z, Huang S. Genome-Wide Mapping of Structural Variations Reveals a Copy Number Variant That Determines Reproductive Morphology in Cucumber. THE PLANT CELL 2015; 27:1595-604. [PMID: 26002866 PMCID: PMC4498199 DOI: 10.1105/tpc.114.135848] [Citation(s) in RCA: 84] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Revised: 03/26/2015] [Accepted: 04/30/2015] [Indexed: 05/18/2023]
Abstract
Structural variations (SVs) represent a major source of genetic diversity. However, the functional impact and formation mechanisms of SVs in plant genomes remain largely unexplored. Here, we report a nucleotide-resolution SV map of cucumber (Cucumis sativas) that comprises 26,788 SVs based on deep resequencing of 115 diverse accessions. The largest proportion of cucumber SVs was formed through nonhomologous end-joining rearrangements, and the occurrence of SVs is closely associated with regions of high nucleotide diversity. These SVs affect the coding regions of 1676 genes, some of which are associated with cucumber domestication. Based on the map, we discovered a copy number variation (CNV) involving four genes that defines the Female (F) locus and gives rise to gynoecious cucumber plants, which bear only female flowers and set fruit at almost every node. The CNV arose from a recent 30.2-kb duplication at a meiotically unstable region, likely via microhomology-mediated break-induced replication. The SV set provides a snapshot of structural variations in plants and will serve as an important resource for exploring genes underlying key traits and for facilitating practical breeding in cucumber.
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Affiliation(s)
- Zhonghua Zhang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing 100081, China
| | - Linyong Mao
- Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, New York 14853
| | - Huiming Chen
- Hunan Vegetable Research Institute, Hunan Academy of Agricultural Sciences, Changsha 410125, China
| | - Fengjiao Bu
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing 100081, China Agricultural Genomic Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Guangcun Li
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing 100081, China Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Jinjing Sun
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing 100081, China
| | - Shuai Li
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing 100081, China
| | - Honghe Sun
- Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, New York 14853
| | - Chen Jiao
- Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, New York 14853
| | - Rachel Blakely
- Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, New York 14853
| | - Junsong Pan
- Shanghai Jiaotong University, Shanghai 200240, China
| | - Run Cai
- Shanghai Jiaotong University, Shanghai 200240, China
| | - Ruibang Luo
- Department of Computer Science, University of Hong Kong, Hong Kong 999077, China
| | - Yves Van de Peer
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium Genomics Research Institute, University of Pretoria, Pretoria 0028, South Africa
| | - Evert Jacobsen
- Deparment of Plant Sciences, Laboratory of Plant Breeding, Wageningen University and Research Centre, 6700AA Wageningen, The Netherlands
| | - Zhangjun Fei
- Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, New York 14853 USDA-ARS Robert W. Holley Center for Agriculture and Health, Ithaca, New York 14853
| | - Sanwen Huang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing 100081, China Agricultural Genomic Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
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de Boer JM, Datema E, Tang X, Borm TJA, Bakker EH, van Eck HJ, van Ham RCHJ, de Jong H, Visser RGF, Bachem CWB. Homologues of potato chromosome 5 show variable collinearity in the euchromatin, but dramatic absence of sequence similarity in the pericentromeric heterochromatin. BMC Genomics 2015; 16:374. [PMID: 25958312 PMCID: PMC4470070 DOI: 10.1186/s12864-015-1578-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Accepted: 04/24/2015] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND In flowering plants it has been shown that de novo genome assemblies of different species and genera show a significant drop in the proportion of alignable sequence. Within a plant species, however, it is assumed that different haplotypes of the same chromosome align well. In this paper we have compared three de novo assemblies of potato chromosome 5 and report on the sequence variation and the proportion of sequence that can be aligned. RESULTS For the diploid potato clone RH89-039-16 (RH) we produced two linkage phase controlled and haplotype-specific assemblies of chromosome 5 based on BAC-by-BAC sequencing, which were aligned to each other and compared to the 52 Mb chromosome 5 reference sequence of the doubled monoploid clone DM 1-3 516 R44 (DM). We identified 17.0 Mb of non-redundant sequence scaffolds derived from euchromatic regions of RH and 38.4 Mb from the pericentromeric heterochromatin. For 32.7 Mb of the RH sequences the correct position and order on chromosome 5 was determined, using genetic markers, fluorescence in situ hybridisation and alignment to the DM reference genome. This ordered fraction of the RH sequences is situated in the euchromatic arms and in the heterochromatin borders. In the euchromatic regions, the sequence collinearity between the three chromosomal homologs is good, but interruption of collinearity occurs at nine gene clusters. Towards and into the heterochromatin borders, absence of collinearity due to structural variation was more extensive and was caused by hemizygous and poorly aligning regions of up to 450 kb in length. In the most central heterochromatin, a total of 22.7 Mb sequence from both RH haplotypes remained unordered. These RH sequences have very few syntenic regions and represent a non-alignable region between the RH and DM heterochromatin haplotypes of chromosome 5. CONCLUSIONS Our results show that among homologous potato chromosomes large regions are present with dramatic loss of sequence collinearity. This stresses the need for more de novo reference assemblies in order to capture genome diversity in this crop. The discovery of three highly diverged pericentric heterochromatin haplotypes within one species is a novelty in plant genome analysis. The possible origin and cytogenetic implication of this heterochromatin haplotype diversity are discussed.
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Affiliation(s)
- Jan M de Boer
- Wageningen UR Plant Breeding, Wageningen University and Research Centre, Droevendaalsesteeg 1, 6708PB, Wageningen, The Netherlands. .,Current address: Averis Seeds B.V., Valtherblokken Zuid 40, 7876 TC, Valthermond, The Netherlands.
| | - Erwin Datema
- Wageningen University and Research Centre, Applied Bioinformatics, Plant Research International, Droevendaalsesteeg 1, 6708PB, Wageningen, The Netherlands. .,Current address: KeyGene N.V., P.O. Box 216, 6700, Wageningen, The Netherlands.
| | - Xiaomin Tang
- Laboratory of Genetics, Wageningen University, Droevendaalsesteeg 1, 6708PB, Wageningen, The Netherlands. .,Current address: Department of Biology, Colorado State University, Fort Collins, USA.
| | - Theo J A Borm
- Wageningen UR Plant Breeding, Wageningen University and Research Centre, Droevendaalsesteeg 1, 6708PB, Wageningen, The Netherlands.
| | - Erin H Bakker
- Laboratory of Nematology, Wageningen University, Droevendaalsesteeg 1, 6708PB, Wageningen, The Netherlands.
| | - Herman J van Eck
- Wageningen UR Plant Breeding, Wageningen University and Research Centre, Droevendaalsesteeg 1, 6708PB, Wageningen, The Netherlands.
| | - Roeland C H J van Ham
- Wageningen University and Research Centre, Applied Bioinformatics, Plant Research International, Droevendaalsesteeg 1, 6708PB, Wageningen, The Netherlands. .,Current address: KeyGene N.V., P.O. Box 216, 6700, Wageningen, The Netherlands.
| | - Hans de Jong
- Laboratory of Genetics, Wageningen University, Droevendaalsesteeg 1, 6708PB, Wageningen, The Netherlands.
| | - Richard G F Visser
- Wageningen UR Plant Breeding, Wageningen University and Research Centre, Droevendaalsesteeg 1, 6708PB, Wageningen, The Netherlands.
| | - Christian W B Bachem
- Wageningen UR Plant Breeding, Wageningen University and Research Centre, Droevendaalsesteeg 1, 6708PB, Wageningen, The Netherlands.
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High-resolution genetic mapping of maize pan-genome sequence anchors. Nat Commun 2015; 6:6914. [PMID: 25881062 PMCID: PMC4411285 DOI: 10.1038/ncomms7914] [Citation(s) in RCA: 139] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Accepted: 03/11/2015] [Indexed: 12/15/2022] Open
Abstract
In addition to single-nucleotide polymorphisms, structural variation is abundant in many plant genomes. The structural variation across a species can be represented by a 'pan-genome', which is essential to fully understand the genetic control of phenotypes. However, the pan-genome's complexity hinders its accurate assembly via sequence alignment. Here we demonstrate an approach to facilitate pan-genome construction in maize. By performing 18 trillion association tests we map 26 million tags generated by reduced representation sequencing of 14,129 maize inbred lines. Using machine-learning models we select 4.4 million accurately mapped tags as sequence anchors, 1.1 million of which are presence/absence variations. Structural variations exhibit enriched association with phenotypic traits, indicating that it is a significant source of adaptive variation in maize. The ability to efficiently map ultrahigh-density pan-genome sequence anchors enables fine characterization of structural variation and will advance both genetic research and breeding in many crops.
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86
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Jiang L, Lv Y, Li T, Zhao H, Zhang T. Identification and characterization of presence/absence variation in maize genotype Mo17. Genes Genomics 2015. [DOI: 10.1007/s13258-015-0272-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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87
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Shen X, Liu ZQ, Mocoeur A, Xia Y, Jing HC. PAV markers in Sorghum bicolour: genome pattern, affected genes and pathways, and genetic linkage map construction. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2015; 128:623-37. [PMID: 25634103 PMCID: PMC4361761 DOI: 10.1007/s00122-015-2458-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2014] [Accepted: 01/06/2015] [Indexed: 05/23/2023]
Abstract
KEY MESSAGE 5,511 genic small-size PAVs in sorghum were identified and examined, including the pattern and the function enrichment of PAV genes. 325 PAV markers were developed to construct a genetic map. Presence/absence variants (PAVs) correlate closely to the phenotypic variation, by impacting plant genome sizes and the adaption to the environment. To shed more light on their genome-wide patterns, functions and the possibility of using them as molecular markers, we generated next generation genome sequencing data for four sorghum inbred lines and used associated bioinformatic pipelines to identify small-size PAVs (40-10 kb). Five thousand five hundreds and eleven genic PAVs (40-10 kb) were identified and found to affect 3,238 genes. These PAVs were mainly distributed on the sub-telomeric regions, but the highest proportions occurred in the vicinity of the centromeric regions. One of the prominent features of the PAVs is the high occurrence of long terminal repeats retrotransposons and DNA transposons. PAVs caused various alterations to gene structure, primarily including the coding sequence variants, intron variants, transcript ablation, and initiator codon changes. The genes affected by PAVs were significantly enriched in those involved in stress responses and protein modification. We used 325 PAVs polymorphic between two sorghum inbred lines Ji2731 and E-Tian, together with 49 SSR markers, and constructed a genetic map, which consisted of 10 linkage groups corresponding to the 10 chromosomes of sorghum and spanned 1,430.3 cM in length covering 97% of the physical genome. The resources reported here should be useful for genetic study and breeding of sorghum and related species.
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Affiliation(s)
- Xin Shen
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Zhi-Quan Liu
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093 China
| | - Anne Mocoeur
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093 China
- Department of Plant and Environment, Faculty of Sciences, University of Copenhagen, 1871 Frederiksberg, Denmark
| | - Yan Xia
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093 China
| | - Hai-Chun Jing
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093 China
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Lee TG, Kumar I, Diers BW, Hudson ME. Evolution and selection of Rhg1, a copy-number variant nematode-resistance locus. Mol Ecol 2015; 24:1774-91. [PMID: 25735447 PMCID: PMC4413360 DOI: 10.1111/mec.13138] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Revised: 02/25/2015] [Accepted: 02/27/2015] [Indexed: 11/29/2022]
Abstract
The soybean cyst nematode (SCN) resistance locus Rhg1 is a tandem repeat of a 31.2 kb unit of the soybean genome. Each 31.2-kb unit contains four genes. One allele of Rhg1, Rhg1-b, is responsible for protecting most US soybean production from SCN. Whole-genome sequencing was performed, and PCR assays were developed to investigate allelic variation in sequence and copy number of the Rhg1 locus across a population of soybean germplasm accessions. Four distinct sequences of the 31.2-kb repeat unit were identified, and some Rhg1 alleles carry up to three different types of repeat unit. The total number of copies of the repeat varies from 1 to 10 per haploid genome. Both copy number and sequence of the repeat correlate with the resistance phenotype, and the Rhg1 locus shows strong signatures of selection. Significant linkage disequilibrium in the genome outside the boundaries of the repeat allowed the Rhg1 genotype to be inferred using high-density single nucleotide polymorphism genotyping of 15 996 accessions. Over 860 germplasm accessions were found likely to possess Rhg1 alleles. The regions surrounding the repeat show indications of non-neutral evolution and high genetic variability in populations from different geographic locations, but without evidence of fixation of the resistant genotype. A compelling explanation of these results is that balancing selection is in operation at Rhg1.
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Affiliation(s)
- Tong Geon Lee
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
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89
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Ladics GS, Bartholomaeus A, Bregitzer P, Doerrer NG, Gray A, Holzhauser T, Jordan M, Keese P, Kok E, Macdonald P, Parrott W, Privalle L, Raybould A, Rhee SY, Rice E, Romeis J, Vaughn J, Wal JM, Glenn K. Genetic basis and detection of unintended effects in genetically modified crop plants. Transgenic Res 2015; 24:587-603. [PMID: 25716164 PMCID: PMC4504983 DOI: 10.1007/s11248-015-9867-7] [Citation(s) in RCA: 74] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2015] [Accepted: 02/14/2015] [Indexed: 11/26/2022]
Abstract
In January 2014, an international meeting sponsored by the International Life Sciences Institute/Health and Environmental Sciences Institute and the Canadian Food Inspection Agency titled “Genetic Basis of Unintended Effects in Modified Plants” was held in Ottawa, Canada, bringing together over 75 scientists from academia, government, and the agro-biotech industry. The objectives of the meeting were to explore current knowledge and identify areas requiring further study on unintended effects in plants and to discuss how this information can inform and improve genetically modified (GM) crop risk assessments. The meeting featured presentations on the molecular basis of plant genome variability in general, unintended changes at the molecular and phenotypic levels, and the development and use of hypothesis-driven evaluations of unintended effects in assessing conventional and GM crops. The development and role of emerging “omics” technologies in the assessment of unintended effects was also discussed. Several themes recurred in a number of talks; for example, a common observation was that no system for genetic modification, including conventional methods of plant breeding, is without unintended effects. Another common observation was that “unintended” does not necessarily mean “harmful”. This paper summarizes key points from the information presented at the meeting to provide readers with current viewpoints on these topics.
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Affiliation(s)
- Gregory S. Ladics
- DuPont Pioneer Agricultural Biotechnology, DuPont Experimental Station, 200 Powder Mill Road, Wilmington, DE 19803 USA
| | - Andrew Bartholomaeus
- Therapeutics Research Centre, School of Medicine, Queensland University, Brisbane, QLD 4072 Australia
- Faculty of Health, School of Pharmacy, University of Canberra, Locked Bag 1, Canberra, ACT 2601 Australia
| | - Phil Bregitzer
- National Small Grains Germplasm Research Facility, US Department of Agriculture – Agricultural Research Service, 1691 S. 2700 W., Aberdeen, ID 83210 USA
| | - Nancy G. Doerrer
- ILSI Health and Environmental Sciences Institute, 1156 15th St., NW, Suite 200, Washington, DC 20005 USA
| | - Alan Gray
- Centre for Ecology and Hydrology, CEH Wallingford, Crowmarsh Gifford, Wallingford, Oxfordshire OX10 8BB UK
| | - Thomas Holzhauser
- Division of Allergology, Paul-Ehrlich-Institut, Paul-Ehrlich-Strasse 51-59, 63225 Langen, Germany
| | - Mark Jordan
- Cereal Research Centre, Agriculture and Agri-Food Canada, 101 Route 100, Morden, MB R6M 1Y5 Canada
| | - Paul Keese
- Office of the Gene Technology Regulator, Australian Government, MDP54, GPO Box 9848, Canberra, ACT 2601 Australia
| | - Esther Kok
- RIKILT Wageningen UR, P.O. Box 230, 6700 AE Wageningen, The Netherlands
| | - Phil Macdonald
- Canadian Food Inspection Agency, 1400 Merivale Rd, Ottawa, ON K1A 0Y9 Canada
| | - Wayne Parrott
- Center for Applied Genetic Technologies, University of Georgia, 111 Riverbend Road, Athens, GA 30602 USA
| | - Laura Privalle
- Bayer CropScience, 407 Davis Drive, Morrisville, NC 27560 USA
| | - Alan Raybould
- Syngenta Ltd, Jealott’s Hill International Research Centre, Bracknell, RG42 6EY UK
- Present Address: Syngenta Crop Protection AG, Schwarzwaldallee 215, 4058 Basel, Switzerland
| | - Seung Yon Rhee
- Department of Plant Biology, Carnegie Institution for Science, 260 Panama St., Stanford, CA 94305 USA
| | - Elena Rice
- Monsanto Company, 700 Chesterfield Pkwy W., CC5A, Chesterfield, MO 63017 USA
| | - Jörg Romeis
- Agroscope, Institute for Sustainability Sciences ISS, Reckenholzstr. 191, 8046 Zurich, Switzerland
| | - Justin Vaughn
- University of Georgia, 111 Riverbend Road, Athens, GA 30602 USA
| | - Jean-Michel Wal
- Dept. SVS, AgroParisTech, 16 rue Claude Bernard, 75231 Paris, France
| | - Kevin Glenn
- Monsanto Company, 800 N. Lindbergh Blvd, U4NA, St. Louis, MO 63167 USA
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González VM, Aventín N, Centeno E, Puigdomènech P. Interspecific and intraspecific gene variability in a 1-Mb region containing the highest density of NBS-LRR genes found in the melon genome. BMC Genomics 2014; 15:1131. [PMID: 25523007 PMCID: PMC4378003 DOI: 10.1186/1471-2164-15-1131] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2014] [Accepted: 12/12/2014] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Plant NBS-LRR -resistance genes tend to be found in clusters, which have been shown to be hot spots of genome variability. In melon, half of the 81 predicted NBS-LRR genes group in nine clusters, and a 1 Mb region on linkage group V contains the highest density of R-genes and presence/absence gene polymorphisms found in the melon genome. This region is known to contain the locus of Vat, an agronomically important gene that confers resistance to aphids. However, the presence of duplications makes the sequencing and annotation of R-gene clusters difficult, usually resulting in multi-gapped sequences with higher than average errors. RESULTS A 1-Mb sequence that contains the largest NBS-LRR gene cluster found in melon was improved using a strategy that combines Illumina paired-end mapping and PCR-based gap closing. Unknown sequence was decreased by 70% while about 3,000 SNPs and small indels were corrected. As a result, the annotations of 18 of a total of 23 NBS-LRR genes found in this region were modified, including additional coding sequences, amino acid changes, correction of splicing boundaries, or fussion of ORFs in common transcription units. A phylogeny analysis of the R-genes and their comparison with syntenic sequences in other cucurbits point to a pattern of local gene amplifications since the diversification of cucurbits from other families, and through speciation within the family. A candidate Vat gene is proposed based on the sequence similarity between a reported Vat gene from a Korean melon cultivar and a sequence fragment previously absent in the unrefined sequence. CONCLUSIONS A sequence refinement strategy allowed substantial improvement of a 1 Mb fragment of the melon genome and the re-annotation of the largest cluster of NBS-LRR gene homologues found in melon. Analysis of the cluster revealed that resistance genes have been produced by sequence duplication in adjacent genome locations since the divergence of cucurbits from other close families, and through the process of speciation within the family a candidate Vat gene was also identified using sequence previously unavailable, which demonstrates the advantages of genome assembly refinements when analyzing complex regions such as those containing clusters of highly similar genes.
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Affiliation(s)
| | | | | | - Pere Puigdomènech
- Molecular Genetics Department, Center for Research in Agricultural Genomics CRAG (CSIC-IRTA-UAB-UB), Campus UAB, Edifici CRAG, Bellaterra (Cerdanyola del Vallès), 08193 Barcelona, Spain.
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91
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Campbell BW, Mani D, Curtin SJ, Slattery RA, Michno JM, Ort DR, Schaus PJ, Palmer RG, Orf JH, Stupar RM. Identical substitutions in magnesium chelatase paralogs result in chlorophyll-deficient soybean mutants. G3 (BETHESDA, MD.) 2014; 5:123-31. [PMID: 25452420 PMCID: PMC4291463 DOI: 10.1534/g3.114.015255] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/24/2014] [Accepted: 11/27/2014] [Indexed: 12/16/2022]
Abstract
The soybean [Glycine max (L.) Merr.] chlorophyll-deficient line MinnGold is a spontaneous mutant characterized by yellow foliage. Map-based cloning and transgenic complementation revealed that the mutant phenotype is caused by a nonsynonymous nucleotide substitution in the third exon of a Mg-chelatase subunit gene (ChlI1a) on chromosome 13. This gene was selected as a candidate for a different yellow foliage mutant, T219H (Y11y11), that had been previously mapped to chromosome 13. Although the phenotypes of MinnGold and T219H are clearly distinct, sequencing of ChlI1a in T219H identified a different nonsynonymous mutation in the third exon, only six base pairs from the MinnGold mutation. This information, along with previously published allelic tests, were used to identify and clone a third yellow foliage mutation, CD-5, which was previously mapped to chromosome 15. This mutation was identified in the ChlI1b gene, a paralog of ChlI1a. Sequencing of the ChlI1b allele in CD-5 identified a nonsynonymous substitution in the third exon that confers an identical amino acid change as the T219H substitution at ChlI1a. Protein sequence alignments of the two Mg-chelatase subunits indicated that the sites of amino acid modification in MinnGold, T219H, and CD-5 are highly conserved among photosynthetic species. These results suggest that amino acid alterations in this critical domain may create competitive inhibitory interactions between the mutant and wild-type ChlI1a and ChlI1b proteins.
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Affiliation(s)
- Benjamin W Campbell
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108
| | - Dhananjay Mani
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108
| | - Shaun J Curtin
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108
| | - Rebecca A Slattery
- Department of Plant Biology, University of Illinois, Urbana, Illinois 61801
| | - Jean-Michel Michno
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108
| | - Donald R Ort
- Department of Plant Biology, University of Illinois, Urbana, Illinois 61801 US Department of Agriculture/Agricultural Research Service, Global Change and Photosynthesis Research Unit, Urbana, Illinois 61801
| | - Philip J Schaus
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108
| | - Reid G Palmer
- Department of Agronomy, Iowa State University, Ames, Iowa 50011
| | - James H Orf
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108
| | - Robert M Stupar
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108
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Schnell J, Steele M, Bean J, Neuspiel M, Girard C, Dormann N, Pearson C, Savoie A, Bourbonnière L, Macdonald P. A comparative analysis of insertional effects in genetically engineered plants: considerations for pre-market assessments. Transgenic Res 2014; 24:1-17. [PMID: 25344849 PMCID: PMC4274372 DOI: 10.1007/s11248-014-9843-7] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2014] [Accepted: 10/16/2014] [Indexed: 01/20/2023]
Abstract
During genetic engineering, DNA is inserted into a plant’s genome, and such insertions are often accompanied by the insertion of additional DNA, deletions and/or rearrangements. These genetic changes are collectively known as insertional effects, and they have the potential to give rise to unintended traits in plants. In addition, there are many other genetic changes that occur in plants both spontaneously and as a result of conventional breeding practices. Genetic changes similar to insertional effects occur in plants, namely as a result of the movement of transposable elements, the repair of double-strand breaks by non-homologous end-joining, and the intracellular transfer of organelle DNA. Based on this similarity, insertional effects should present a similar level of risk as these other genetic changes in plants, and it is within the context of these genetic changes that insertional effects must be considered. Increased familiarity with genetic engineering techniques and advances in molecular analysis techniques have provided us with a greater understanding of the nature and impact of genetic changes in plants, and this can be used to refine pre-market assessments of genetically engineered plants and food and feeds derived from genetically engineered plants.
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Affiliation(s)
- Jaimie Schnell
- Plant and Biotechnology Risk Assessment Unit, Canadian Food Inspection Agency, 1400 Merivale Road, Ottawa, ON, K1A 0Y9, Canada,
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Li YH, Zhou G, Ma J, Jiang W, Jin LG, Zhang Z, Guo Y, Zhang J, Sui Y, Zheng L, Zhang SS, Zuo Q, Shi XH, Li YF, Zhang WK, Hu Y, Kong G, Hong HL, Tan B, Song J, Liu ZX, Wang Y, Ruan H, Yeung CKL, Liu J, Wang H, Zhang LJ, Guan RX, Wang KJ, Li WB, Chen SY, Chang RZ, Jiang Z, Jackson SA, Li R, Qiu LJ. De novo assembly of soybean wild relatives for pan-genome analysis of diversity and agronomic traits. Nat Biotechnol 2014; 32:1045-52. [PMID: 25218520 DOI: 10.1038/nbt.2979] [Citation(s) in RCA: 368] [Impact Index Per Article: 36.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2013] [Accepted: 07/02/2014] [Indexed: 12/13/2022]
Abstract
Wild relatives of crops are an important source of genetic diversity for agriculture, but their gene repertoire remains largely unexplored. We report the establishment and analysis of a pan-genome of Glycine soja, the wild relative of cultivated soybean Glycine max, by sequencing and de novo assembly of seven phylogenetically and geographically representative accessions. Intergenomic comparisons identified lineage-specific genes and genes with copy number variation or large-effect mutations, some of which show evidence of positive selection and may contribute to variation of agronomic traits such as biotic resistance, seed composition, flowering and maturity time, organ size and final biomass. Approximately 80% of the pan-genome was present in all seven accessions (core), whereas the rest was dispensable and exhibited greater variation than the core genome, perhaps reflecting a role in adaptation to diverse environments. This work will facilitate the harnessing of untapped genetic diversity from wild soybean for enhancement of elite cultivars.
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Affiliation(s)
- Ying-hui Li
- 1] The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China. [2] Key Laboratory of Crop Gene Resource and Germplasm Enhancement (MOA), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China. [3] Key Laboratory of Soybean Biology (Beijing) (MOA), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China. [4]
| | - Guangyu Zhou
- 1] Novogene Bioinformatics Institute, Beijing, P.R. China. [2] [3]
| | - Jianxin Ma
- 1] Department of Agronomy, Purdue University, West Lafayette, Indiana, USA. [2]
| | - Wenkai Jiang
- 1] Novogene Bioinformatics Institute, Beijing, P.R. China. [2]
| | - Long-guo Jin
- 1] The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China. [2] Key Laboratory of Crop Gene Resource and Germplasm Enhancement (MOA), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China. [3] Key Laboratory of Soybean Biology (Beijing) (MOA), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China
| | - Zhouhao Zhang
- Novogene Bioinformatics Institute, Beijing, P.R. China
| | - Yong Guo
- 1] The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China. [2] Key Laboratory of Crop Gene Resource and Germplasm Enhancement (MOA), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China. [3] Key Laboratory of Soybean Biology (Beijing) (MOA), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China
| | - Jinbo Zhang
- Novogene Bioinformatics Institute, Beijing, P.R. China
| | - Yi Sui
- 1] The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China. [2] Key Laboratory of Crop Gene Resource and Germplasm Enhancement (MOA), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China. [3] Key Laboratory of Soybean Biology (Beijing) (MOA), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China
| | | | - Shan-shan Zhang
- 1] The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China. [2] Key Laboratory of Crop Gene Resource and Germplasm Enhancement (MOA), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China. [3] Key Laboratory of Soybean Biology (Beijing) (MOA), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China
| | - Qiyang Zuo
- Novogene Bioinformatics Institute, Beijing, P.R. China
| | - Xue-hui Shi
- 1] The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China. [2] Key Laboratory of Crop Gene Resource and Germplasm Enhancement (MOA), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China. [3] Key Laboratory of Soybean Biology (Beijing) (MOA), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China
| | - Yan-fei Li
- 1] The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China. [2] Key Laboratory of Crop Gene Resource and Germplasm Enhancement (MOA), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China. [3] Key Laboratory of Soybean Biology (Beijing) (MOA), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China
| | - Wan-ke Zhang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, P.R. China
| | - Yiyao Hu
- Novogene Bioinformatics Institute, Beijing, P.R. China
| | - Guanyi Kong
- Novogene Bioinformatics Institute, Beijing, P.R. China
| | - Hui-long Hong
- 1] The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China. [2] Key Laboratory of Crop Gene Resource and Germplasm Enhancement (MOA), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China. [3] Key Laboratory of Soybean Biology (Beijing) (MOA), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China
| | - Bing Tan
- 1] The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China. [2] Key Laboratory of Crop Gene Resource and Germplasm Enhancement (MOA), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China. [3] Key Laboratory of Soybean Biology (Beijing) (MOA), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China
| | - Jian Song
- 1] The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China. [2] Key Laboratory of Crop Gene Resource and Germplasm Enhancement (MOA), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China. [3] Key Laboratory of Soybean Biology (Beijing) (MOA), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China
| | - Zhang-xiong Liu
- 1] The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China. [2] Key Laboratory of Crop Gene Resource and Germplasm Enhancement (MOA), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China. [3] Key Laboratory of Soybean Biology (Beijing) (MOA), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China
| | - Yaoshen Wang
- Novogene Bioinformatics Institute, Beijing, P.R. China
| | - Hang Ruan
- Novogene Bioinformatics Institute, Beijing, P.R. China
| | | | - Jian Liu
- Novogene Bioinformatics Institute, Beijing, P.R. China
| | - Hailong Wang
- Novogene Bioinformatics Institute, Beijing, P.R. China
| | - Li-juan Zhang
- 1] The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China. [2] Key Laboratory of Crop Gene Resource and Germplasm Enhancement (MOA), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China. [3] Key Laboratory of Soybean Biology (Beijing) (MOA), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China
| | - Rong-xia Guan
- 1] The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China. [2] Key Laboratory of Crop Gene Resource and Germplasm Enhancement (MOA), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China. [3] Key Laboratory of Soybean Biology (Beijing) (MOA), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China
| | - Ke-jing Wang
- 1] The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China. [2] Key Laboratory of Crop Gene Resource and Germplasm Enhancement (MOA), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China. [3] Key Laboratory of Soybean Biology (Beijing) (MOA), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China
| | - Wen-bin Li
- Key Laboratory of Soybean Biology in Chinese Ministry of Education, Northeast Agricultural University, Harbin, P.R. China
| | - Shou-yi Chen
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, P.R. China
| | - Ru-zhen Chang
- 1] The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China. [2] Key Laboratory of Crop Gene Resource and Germplasm Enhancement (MOA), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China. [3] Key Laboratory of Soybean Biology (Beijing) (MOA), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China
| | - Zhi Jiang
- Novogene Bioinformatics Institute, Beijing, P.R. China
| | - Scott A Jackson
- Center for Applied Genetic Technologies, University of Georgia, Athens, Georgia, USA
| | - Ruiqiang Li
- 1] Novogene Bioinformatics Institute, Beijing, P.R. China. [2] Peking-Tsinghua Center for Life Sciences, Biodynamic Optical Imaging Center, and School of Life Sciences, Peking University, Beijing, P.R. China
| | - Li-juan Qiu
- 1] The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China. [2] Key Laboratory of Crop Gene Resource and Germplasm Enhancement (MOA), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China. [3] Key Laboratory of Soybean Biology (Beijing) (MOA), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China
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94
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Wang Y, Lu J, Chen S, Shu L, Palmer RG, Xing G, Li Y, Yang S, Yu D, Zhao T, Gai J. Exploration of presence/absence variation and corresponding polymorphic markers in soybean genome. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2014; 56:1009-19. [PMID: 24751174 DOI: 10.1111/jipb.12208] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2014] [Accepted: 04/17/2014] [Indexed: 05/26/2023]
Abstract
This study was designed to reveal the genome-wide distribution of presence/absence variation (PAV) and to establish a database of polymorphic PAV markers in soybean. The 33 soybean whole-genome sequences were compared to each other with that of Williams 82 as a reference genome. A total of 33,127 PAVs were detected and 28,912 PAV markers with their primer sequences were designed as the database NJAUSoyPAV_1.0. The PAVs scattered on whole genome while only 518 (1.8%) overlapped with simple sequence repeats (SSRs) in BARCSOYSSR_1.0 database. In a random sample of 800 PAVs, 713 (89.13%) showed polymorphism among the 12 differential genotypes. Using 126 PAVs and 108 SSRs to test a Chinese soybean germplasm collection composed of 828 Glycine soja Sieb. et Zucc. and Glycine max (L.) Merr. accessions, the per locus allele number and its variation appeared less in PAVs than in SSRs. The distinctness among alleles/bands of PCR (polymerase chain reaction) products showed better in PAVs than in SSRs, potential in accurate marker-assisted allele selection. The association mapping results showed SSR + PAV was more powerful than any single marker systems. The NJAUSoyPAV_1.0 database has enriched the source of PCR markers, and may fit the materials with a range of per locus allele numbers, if jointly used with SSR markers.
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Affiliation(s)
- Yufeng Wang
- Soybean Research Institute/National Center for Soybean Improvement/MOA Key Laboratory for Biology and Genetic Improvement of Soybean (General)/National Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
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95
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Evans J, Kim J, Childs KL, Vaillancourt B, Crisovan E, Nandety A, Gerhardt DJ, Richmond TA, Jeddeloh JA, Kaeppler SM, Casler MD, Buell CR. Nucleotide polymorphism and copy number variant detection using exome capture and next-generation sequencing in the polyploid grass Panicum virgatum. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2014; 79:993-1008. [PMID: 24947485 PMCID: PMC4309430 DOI: 10.1111/tpj.12601] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2014] [Revised: 05/31/2014] [Accepted: 06/09/2014] [Indexed: 05/23/2023]
Abstract
Switchgrass (Panicum virgatum) is a polyploid, outcrossing grass species native to North America and has recently been recognized as a potential biofuel feedstock crop. Significant phenotypic variation including ploidy is present across the two primary ecotypes of switchgrass, referred to as upland and lowland switchgrass. The tetraploid switchgrass genome is approximately 1400 Mbp, split between two subgenomes, with significant repetitive sequence content limiting the efficiency of re-sequencing approaches for determining genome diversity. To characterize genetic diversity in upland and lowland switchgrass as a first step in linking genotype to phenotype, we designed an exome capture probe set based on transcript assemblies that represent approximately 50 Mb of annotated switchgrass exome sequences. We then evaluated and optimized the probe set using solid phase comparative genome hybridization and liquid phase exome capture followed by next-generation sequencing. Using the optimized probe set, we assessed variation in the exomes of eight switchgrass genotypes representing tetraploid lowland and octoploid upland cultivars to benchmark our exome capture probe set design. We identified ample variation in the switchgrass genome including 1,395,501 single nucleotide polymorphisms (SNPs), 8173 putative copy number variants and 3336 presence/absence variants. While the majority of the SNPs (84%) detected was bi-allelic, a substantial number was tri-allelic with limited occurrence of tetra-allelic polymorphisms consistent with the heterozygous and polyploid nature of the switchgrass genome. Collectively, these data demonstrate the efficacy of exome capture for discovery of genome variation in a polyploid species with a large, repetitive and heterozygous genome.
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Affiliation(s)
- Joseph Evans
- Department of Energy Great Lakes Bioenergy Research Center, Michigan State UniversityEast Lansing, MI, 48824, USA
- Department of Plant Biology, Michigan State UniversityEast Lansing, MI, 48824, USA
| | - Jeongwoon Kim
- Department of Energy Great Lakes Bioenergy Research Center, Michigan State UniversityEast Lansing, MI, 48824, USA
- Department of Plant Biology, Michigan State UniversityEast Lansing, MI, 48824, USA
| | - Kevin L Childs
- Department of Energy Great Lakes Bioenergy Research Center, Michigan State UniversityEast Lansing, MI, 48824, USA
- Department of Plant Biology, Michigan State UniversityEast Lansing, MI, 48824, USA
| | - Brieanne Vaillancourt
- Department of Energy Great Lakes Bioenergy Research Center, Michigan State UniversityEast Lansing, MI, 48824, USA
- Department of Plant Biology, Michigan State UniversityEast Lansing, MI, 48824, USA
| | - Emily Crisovan
- Department of Energy Great Lakes Bioenergy Research Center, Michigan State UniversityEast Lansing, MI, 48824, USA
- Department of Plant Biology, Michigan State UniversityEast Lansing, MI, 48824, USA
| | - Aruna Nandety
- Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-MadisonMadison, WI, 53706, USA
- US Dairy Forage Research Center, USDA-ARS1925 Linden Dr., Madison, WI, 53706-1108, USA
| | | | | | | | - Shawn M Kaeppler
- Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-MadisonMadison, WI, 53706, USA
- Department of Agronomy, University of Wisconsin-Madison1575 Linden Drive, Madison, WI, 53706, USA
| | - Michael D Casler
- Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-MadisonMadison, WI, 53706, USA
- US Dairy Forage Research Center, USDA-ARS1925 Linden Dr., Madison, WI, 53706-1108, USA
| | - C Robin Buell
- Department of Energy Great Lakes Bioenergy Research Center, Michigan State UniversityEast Lansing, MI, 48824, USA
- Department of Plant Biology, Michigan State UniversityEast Lansing, MI, 48824, USA
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96
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Flagel LE, Willis JH, Vision TJ. The standing pool of genomic structural variation in a natural population of Mimulus guttatus. Genome Biol Evol 2014; 6:53-64. [PMID: 24336482 PMCID: PMC3914686 DOI: 10.1093/gbe/evt199] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Major unresolved questions in evolutionary genetics include determining the contributions of different mutational sources to the total pool of genetic variation in a species, and understanding how these different forms of genetic variation interact with natural selection. Recent work has shown that structural variants (SVs) (insertions, deletions, inversions, and transpositions) are a major source of genetic variation, often outnumbering single nucleotide variants in terms of total bases affected. Despite the near ubiquity of SVs, major questions about their interaction with natural selection remain. For example, how does the allele frequency spectrum of SVs differ when compared with single nucleotide variants? How often do SVs affect genes, and what are the consequences? To begin to address these questions, we have systematically identified and characterized a large set of submicroscopic insertion and deletion (indel) variants (between 1 and 200 kb in length) among ten inbred lines from a single natural population of the plant species Mimulus guttatus. After extensive computational filtering, we focused on a set of 4,142 high-confidence indels that showed an experimental validation rate of 73%. All but one of these indels were less than 200 kb. Although the largest were generally at lower frequencies in the population, a surprising number of large indels are at intermediate frequencies. Although indels overlapping with genes were much rarer than expected by chance, approximately 600 genes were affected by an indel. Nucleotide-binding site leucine-rich repeat (NBS–LRR) defense response genes were the most enriched among the gene families affected. Most indels associated with genes were rare and appeared to be under purifying selection, though we do find four high-frequency derived insertion alleles that show signatures of recent positive selection.
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97
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Gordon SP, Priest H, Des Marais DL, Schackwitz W, Figueroa M, Martin J, Bragg JN, Tyler L, Lee CR, Bryant D, Wang W, Messing J, Manzaneda AJ, Barry K, Garvin DF, Budak H, Tuna M, Mitchell-Olds T, Pfender WF, Juenger TE, Mockler TC, Vogel JP. Genome diversity in Brachypodium distachyon: deep sequencing of highly diverse inbred lines. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2014; 79:361-74. [PMID: 24888695 DOI: 10.1111/tpj.12569] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2013] [Revised: 05/20/2014] [Accepted: 05/23/2014] [Indexed: 05/08/2023]
Abstract
Brachypodium distachyon is small annual grass that has been adopted as a model for the grasses. Its small genome, high-quality reference genome, large germplasm collection, and selfing nature make it an excellent subject for studies of natural variation. We sequenced six divergent lines to identify a comprehensive set of polymorphisms and analyze their distribution and concordance with gene expression. Multiple methods and controls were utilized to identify polymorphisms and validate their quality. mRNA-Seq experiments under control and simulated drought-stress conditions, identified 300 genes with a genotype-dependent treatment response. We showed that large-scale sequence variants had extremely high concordance with altered expression of hundreds of genes, including many with genotype-dependent treatment responses. We generated a deep mRNA-Seq dataset for the most divergent line and created a de novo transcriptome assembly. This led to the discovery of >2400 previously unannotated transcripts and hundreds of genes not present in the reference genome. We built a public database for visualization and investigation of sequence variants among these widely used inbred lines.
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Affiliation(s)
- Sean P Gordon
- USDA-ARS Western Regional Research Center, 800 Buchanan St., Albany, CA, 94710, USA
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98
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Abstract
Multiple disease resistance has important implications for plant fitness, given the selection pressure that many pathogens exert directly on natural plant populations and indirectly via crop improvement programs. Evidence of a locus conditioning resistance to multiple pathogens was found in bin 1.06 of the maize genome with the allele from inbred line "Tx303" conditioning quantitative resistance to northern leaf blight (NLB) and qualitative resistance to Stewart's wilt. To dissect the genetic basis of resistance in this region and to refine candidate gene hypotheses, we mapped resistance to the two diseases. Both resistance phenotypes were localized to overlapping regions, with the Stewart's wilt interval refined to a 95.9-kb segment containing three genes and the NLB interval to a 3.60-Mb segment containing 117 genes. Regions of the introgression showed little to no recombination, suggesting structural differences between the inbred lines Tx303 and "B73," the parents of the fine-mapping population. We examined copy number variation across the region using next-generation sequencing data, and found large variation in read depth in Tx303 across the region relative to the reference genome of B73. In the fine-mapping region, association mapping for NLB implicated candidate genes, including a putative zinc finger and pan1. We tested mutant alleles and found that pan1 is a susceptibility gene for NLB and Stewart's wilt. Our data strongly suggest that structural variation plays an important role in resistance conditioned by this region, and pan1, a gene conditioning susceptibility for NLB, may underlie the QTL.
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99
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Abstract
Differences between plant genomes range from single nucleotide polymorphisms to large-scale duplications, deletions and rearrangements. The large polymorphisms are termed structural variants (SVs). SVs have received significant attention in human genetics and were found to be responsible for various chronic diseases. However, little effort has been directed towards understanding the role of SVs in plants. Many recent advances in plant genetics have resulted from improvements in high-resolution technologies for measuring SVs, including microarray-based techniques, and more recently, high-throughput DNA sequencing. In this review we describe recent reports of SV in plants and describe the genomic technologies currently used to measure these SVs.
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100
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Anderson JE, Kantar MB, Kono TY, Fu F, Stec AO, Song Q, Cregan PB, Specht JE, Diers BW, Cannon SB, McHale LK, Stupar RM. A roadmap for functional structural variants in the soybean genome. G3 (BETHESDA, MD.) 2014; 4:1307-18. [PMID: 24855315 PMCID: PMC4455779 DOI: 10.1534/g3.114.011551] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/10/2014] [Accepted: 05/20/2014] [Indexed: 01/25/2023]
Abstract
Gene structural variation (SV) has recently emerged as a key genetic mechanism underlying several important phenotypic traits in crop species. We screened a panel of 41 soybean (Glycine max) accessions serving as parents in a soybean nested association mapping population for deletions and duplications in more than 53,000 gene models. Array hybridization and whole genome resequencing methods were used as complementary technologies to identify SV in 1528 genes, or approximately 2.8%, of the soybean gene models. Although SV occurs throughout the genome, SV enrichment was noted in families of biotic defense response genes. Among accessions, SV was nearly eightfold less frequent for gene models that have retained paralogs since the last whole genome duplication event, compared with genes that have not retained paralogs. Increases in gene copy number, similar to that described at the Rhg1 resistance locus, account for approximately one-fourth of the genic SV events. This assessment of soybean SV occurrence presents a target list of genes potentially responsible for rapidly evolving and/or adaptive traits.
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Affiliation(s)
- Justin E Anderson
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108
| | - Michael B Kantar
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108 Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada, V6T 1Z4
| | - Thomas Y Kono
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108
| | - Fengli Fu
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108
| | - Adrian O Stec
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108
| | - Qijian Song
- United States Department of Agriculture, Agricultural Research Service, Soybean Genomics and Improvement Lab, Beltsville, Maryland 20705
| | - Perry B Cregan
- United States Department of Agriculture, Agricultural Research Service, Soybean Genomics and Improvement Lab, Beltsville, Maryland 20705
| | - James E Specht
- Agronomy and Horticulture Department, University of Nebraska, Lincoln, Nebraska 68583
| | - Brian W Diers
- Department of Crop Sciences, University of Illinois, Urbana, Illinois 61801
| | - Steven B Cannon
- United States Department of Agriculture, Agricultural Research Service, Corn Insects and Crop Genetics Research Unit, Ames, Iowa 50011
| | - Leah K McHale
- Department of Horticulture and Crop Science, The Ohio State University, Columbus, Ohio 43210
| | - Robert M Stupar
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108
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