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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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High-Throughput Resequencing of Maize Landraces at Genomic Regions Associated with Flowering Time. PLoS One 2017; 12:e0168910. [PMID: 28045987 PMCID: PMC5207663 DOI: 10.1371/journal.pone.0168910] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Accepted: 12/08/2016] [Indexed: 12/17/2022] Open
Abstract
Despite the reduction in the price of sequencing, it remains expensive to sequence and assemble whole, complex genomes of multiple samples for population studies, particularly for large genomes like those of many crop species. Enrichment of target genome regions coupled with next generation sequencing is a cost-effective strategy to obtain sequence information for loci of interest across many individuals, providing a less expensive approach to evaluating sequence variation at the population scale. Here we evaluate amplicon-based enrichment coupled with semiconductor sequencing on a validation set consisting of three maize inbred lines, two hybrids and 19 landrace accessions. We report the use of a multiplexed panel of 319 PCR assays that target 20 candidate loci associated with photoperiod sensitivity in maize while requiring 25 ng or less of starting DNA per sample. Enriched regions had an average on-target sequence read depth of 105 with 98% of the sequence data mapping to the maize ‘B73’ reference and 80% of the reads mapping to the target interval. Sequence reads were aligned to B73 and 1,486 and 1,244 variants were called using SAMtools and GATK, respectively. Of the variants called by both SAMtools and GATK, 30% were not previously reported in maize. Due to the high sequence read depth, heterozygote genotypes could be called with at least 92.5% accuracy in hybrid materials using GATK. The genetic data are congruent with previous reports of high total genetic diversity and substantial population differentiation among maize landraces. In conclusion, semiconductor sequencing of highly multiplexed PCR reactions is a cost-effective strategy for resequencing targeted genomic loci in diverse maize materials.
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Mei W, Liu S, Schnable JC, Yeh CT, Springer NM, Schnable PS, Barbazuk WB. A Comprehensive Analysis of Alternative Splicing in Paleopolyploid Maize. FRONTIERS IN PLANT SCIENCE 2017; 8:694. [PMID: 28539927 PMCID: PMC5423905 DOI: 10.3389/fpls.2017.00694] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Accepted: 04/18/2017] [Indexed: 05/19/2023]
Abstract
Identifying and characterizing alternative splicing (AS) enables our understanding of the biological role of transcript isoform diversity. This study describes the use of publicly available RNA-Seq data to identify and characterize the global diversity of AS isoforms in maize using the inbred lines B73 and Mo17, and a related species, sorghum. Identification and characterization of AS within maize tissues revealed that genes expressed in seed exhibit the largest differential AS relative to other tissues examined. Additionally, differences in AS between the two genotypes B73 and Mo17 are greatest within genes expressed in seed. We demonstrate that changes in the level of alternatively spliced transcripts (intron retention and exon skipping) do not solely reflect differences in total transcript abundance, and we present evidence that intron retention may act to fine-tune gene expression across seed development stages. Furthermore, we have identified temperature sensitive AS in maize and demonstrate that drought-induced changes in AS involve distinct sets of genes in reproductive and vegetative tissues. Examining our identified AS isoforms within B73 × Mo17 recombinant inbred lines (RILs) identified splicing QTL (sQTL). The 43.3% of cis-sQTL regulated junctions are actually identified as alternatively spliced junctions in our analysis, while 10 Mb windows on each side of 48.2% of trans-sQTLs overlap with splicing related genes. Using sorghum as an out-group enabled direct examination of loss or conservation of AS between homeologous genes representing the two subgenomes of maize. We identify several instances where AS isoforms that are conserved between one maize homeolog and its sorghum ortholog are absent from the second maize homeolog, suggesting that these AS isoforms may have been lost after the maize whole genome duplication event. This comprehensive analysis provides new insights into the complexity of AS in maize.
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Affiliation(s)
- Wenbin Mei
- Department of Biology, University of Florida, GainesvilleFL, USA
| | - Sanzhen Liu
- Department of Agronomy, Iowa State University, AmesIA, USA
- Department of Plant Pathology, Kansas State University, ManhattanKS, USA
| | - James C. Schnable
- Department of Agronomy and Horticulture, University of Nebraska–Lincoln, LincolnNE, USA
| | - Cheng-Ting Yeh
- Department of Agronomy, Iowa State University, AmesIA, USA
| | - Nathan M. Springer
- Department of Plant Biology, Microbial and Plant Genomics Institute, University of Minnesota, Saint PaulMN, USA
| | - Patrick S. Schnable
- Department of Agronomy, Iowa State University, AmesIA, USA
- Center for Plant Genomics, Iowa State University, AmesIA, USA
| | - William B. Barbazuk
- Department of Biology, University of Florida, GainesvilleFL, USA
- Genetics Institute, University of Florida, GainesvilleFL, USA
- *Correspondence: William B. Barbazuk,
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104
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Schaefer RJ, Michno JM, Myers CL. Unraveling gene function in agricultural species using gene co-expression networks. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2017; 1860:53-63. [DOI: 10.1016/j.bbagrm.2016.07.016] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Revised: 07/23/2016] [Accepted: 07/25/2016] [Indexed: 10/21/2022]
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105
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Suryawanshi V, Talke IN, Weber M, Eils R, Brors B, Clemens S, Krämer U. Between-species differences in gene copy number are enriched among functions critical for adaptive evolution in Arabidopsis halleri. BMC Genomics 2016; 17:1034. [PMID: 28155655 PMCID: PMC5259951 DOI: 10.1186/s12864-016-3319-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Background Gene copy number divergence between species is a form of genetic polymorphism that contributes significantly to both genome size and phenotypic variation. In plants, copy number expansions of single genes were implicated in cultivar- or species-specific tolerance of high levels of soil boron, aluminium or calamine-type heavy metals, respectively. Arabidopsis halleri is a zinc- and cadmium-hyperaccumulating extremophile species capable of growing on heavy-metal contaminated, toxic soils. In contrast, its non-accumulating sister species A. lyrata and the closely related reference model species A. thaliana exhibit merely basal metal tolerance. Results For a genome-wide assessment of the role of copy number divergence (CND) in lineage-specific environmental adaptation, we conducted cross-species array comparative genome hybridizations of three plant species and developed a global signal scaling procedure to adjust for sequence divergence. In A. halleri, transition metal homeostasis functions are enriched twofold among the genes detected as copy number expanded. Moreover, biotic stress functions including mostly disease Resistance (R) gene-related genes are enriched twofold among genes detected as copy number reduced, when compared to the abundance of these functions among all genes. Conclusions Our results provide genome-wide support for a link between evolutionary adaptation and CND in A. halleri as shown previously for Heavy metal ATPase4. Moreover our results support the hypothesis that elemental defences, which result from the hyperaccumulation of toxic metals, allow the reduction of classical defences against biotic stress as a trade-off. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3319-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Vasantika Suryawanshi
- Department of Plant Physiology, Ruhr University Bochum, Universitätsstrasse 150, Bochum, 44801, Germany.,BioQuant, University of Heidelberg, Im Neuenheimer Feld 267, Heidelberg, 69120, Germany
| | - Ina N Talke
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, Potsdam, 14476, Germany
| | - Michael Weber
- Department of Plant Physiology, University of Bayreuth, Universitätsstrasse 30, Bayreuth, 95447, Germany
| | - Roland Eils
- Division of Theoretical Bioinformatics, DKFZ, Im Neuenheimer Feld 280, Heidelberg, 69121, Germany.,BioQuant, University of Heidelberg, Im Neuenheimer Feld 267, Heidelberg, 69120, Germany.,Institute of Pharmacy and Molecular Biotechnology, University of Heidelberg, Im Neuenheimer Feld 364, Heidelberg, 69120, Germany
| | - Benedikt Brors
- Division of Theoretical Bioinformatics, DKFZ, Im Neuenheimer Feld 280, Heidelberg, 69121, Germany
| | - Stephan Clemens
- Department of Plant Physiology, University of Bayreuth, Universitätsstrasse 30, Bayreuth, 95447, Germany
| | - Ute Krämer
- Department of Plant Physiology, Ruhr University Bochum, Universitätsstrasse 150, Bochum, 44801, Germany. .,BioQuant, University of Heidelberg, Im Neuenheimer Feld 267, Heidelberg, 69120, Germany.
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106
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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: 255] [Impact Index Per Article: 31.9] [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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107
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Hirsch CN, Hirsch CD, Brohammer AB, Bowman MJ, Soifer I, Barad O, Shem-Tov D, Baruch K, Lu F, Hernandez AG, Fields CJ, Wright CL, Koehler K, Springer NM, Buckler E, Buell CR, de Leon N, Kaeppler SM, Childs KL, Mikel MA. Draft Assembly of Elite Inbred Line PH207 Provides Insights into Genomic and Transcriptome Diversity in Maize. THE PLANT CELL 2016; 28:2700-2714. [PMID: 27803309 PMCID: PMC5155341 DOI: 10.1105/tpc.16.00353] [Citation(s) in RCA: 115] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Revised: 10/19/2016] [Accepted: 10/31/2016] [Indexed: 05/18/2023]
Abstract
Intense artificial selection over the last 100 years has produced elite maize (Zea mays) inbred lines that combine to produce high-yielding hybrids. To further our understanding of how genome and transcriptome variation contribute to the production of high-yielding hybrids, we generated a draft genome assembly of the inbred line PH207 to complement and compare with the existing B73 reference sequence. B73 is a founder of the Stiff Stalk germplasm pool, while PH207 is a founder of Iodent germplasm, both of which have contributed substantially to the production of temperate commercial maize and are combined to make heterotic hybrids. Comparison of these two assemblies revealed over 2500 genes present in only one of the two genotypes and 136 gene families that have undergone extensive expansion or contraction. Transcriptome profiling revealed extensive expression variation, with as many as 10,564 differentially expressed transcripts and 7128 transcripts expressed in only one of the two genotypes in a single tissue. Genotype-specific genes were more likely to have tissue/condition-specific expression and lower transcript abundance. The availability of a high-quality genome assembly for the elite maize inbred PH207 expands our knowledge of the breadth of natural genome and transcriptome variation in elite maize inbred lines across heterotic pools.
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Affiliation(s)
- Candice N Hirsch
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108
| | - Cory D Hirsch
- Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota 55108
| | - Alex B Brohammer
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108
| | - Megan J Bowman
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824
| | - Ilya Soifer
- Calico Labs, San Francisco, California 94080
| | | | | | | | - Fei Lu
- Instiute for Genome Diversity, Cornell University, Ithaca, New York 14850
| | - Alvaro G Hernandez
- Roy J. Carver Biotechnology Center, University of Illinois, Urbana, Illinois 61801
| | - Christopher J Fields
- Roy J. Carver Biotechnology Center, University of Illinois, Urbana, Illinois 61801
| | - Chris L Wright
- Roy J. Carver Biotechnology Center, University of Illinois, Urbana, Illinois 61801
| | | | - Nathan M Springer
- Department of Plant Biology, University of Minnesota, St. Paul, Minnesota 55108
| | - Edward Buckler
- Instiute for Genome Diversity, Cornell University, Ithaca, New York 14850
- U.S. Department of Agriculture/Agricultural Research Services, Ithaca, New York 14850
| | - C Robin Buell
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824
- DOE Great Lakes Bioenergy Research Center, East Lansing, Michigan 48824
| | - Natalia de Leon
- Department of Agronomy, University of Wisconsin-Madison, Madison, Wisconsin 53706
- DOE Great Lakes Bioenergy Research Center, Madison, Wisconsin 53706
| | - Shawn M Kaeppler
- Department of Agronomy, University of Wisconsin-Madison, Madison, Wisconsin 53706
- DOE Great Lakes Bioenergy Research Center, Madison, Wisconsin 53706
| | - Kevin L Childs
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824
- Center for Genomics-Enabled Plant Sciences, Michigan State University, East Lansing, Michigan 48824
| | - Mark A Mikel
- Roy J. Carver Biotechnology Center, University of Illinois, Urbana, Illinois 61801
- Department of Crop Sciences, University of Illinois, Urbana, Illinois 61801
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108
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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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109
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Niederhuth CE, Schmitz RJ. Putting DNA methylation in context: from genomes to gene expression in plants. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2016; 1860:149-156. [PMID: 27590871 DOI: 10.1016/j.bbagrm.2016.08.009] [Citation(s) in RCA: 84] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2016] [Revised: 08/20/2016] [Accepted: 08/23/2016] [Indexed: 12/26/2022]
Abstract
Plant DNA methylation is its own language, interpreted by the cell to maintain silencing of transposons, facilitate chromatin structure, and to ensure proper expression of some genes. Just as in any language, context is important. Rather than being a simple "on-off switch", DNA methylation has a range of "meanings" dependent upon the underlying sequence and its location in the genome. Differences in the sequence context of individual sites are established, maintained, and interpreted by differing molecular pathways. Varying patterns of methylation within genes and surrounding sequences are associated with a continuous range of expression differences, from silencing to constitutive expression. These often-subtle differences have been pieced together from years of effort, but have taken off with the advent of methods for assessing methylation across entire genomes. Recognizing these patterns and identifying underlying causes is essential for understanding the function of DNA methylation and its systems-wide contribution to a range of processes in plant genomes. This article is part of a Special Issue entitled: Plant Gene Regulatory Mechanisms and Networks, edited by Dr. Erich Grotewold and Dr. Nathan Springer.
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Affiliation(s)
- Chad E Niederhuth
- Department of Genetics, The University of Georgia, Athens, GA, 30602, USA
| | - Robert J Schmitz
- Department of Genetics, The University of Georgia, Athens, GA, 30602, 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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111
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Haberer G, Mayer KF, Spannagl M. The big five of the monocot genomes. CURRENT OPINION IN PLANT BIOLOGY 2016; 30:33-40. [PMID: 26866569 DOI: 10.1016/j.pbi.2016.01.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Revised: 01/14/2016] [Accepted: 01/21/2016] [Indexed: 06/05/2023]
Abstract
Monocots represent a monophyletic clade of the angiosperms that - based on fossil and molecular records - originated at around the Early Cretaceous from aquatic and wetland ancestors. Among their members are important crops including maize, wheat, rice, sorghum and barley, accounting for the major source for the daily calorie uptake by humans. Reflecting this importance, the partly large and complex genomes of these plants were major targets for ambitious and innovative sequencing projects, which will be discussed in this review article.
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Affiliation(s)
- Georg Haberer
- Plant Genome and Systems Biology/PGSB, Helmholtz Center Munich - German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Klaus Fx Mayer
- Plant Genome and Systems Biology/PGSB, Helmholtz Center Munich - German Research Center for Environmental Health, 85764 Neuherberg, Germany.
| | - Manuel Spannagl
- Plant Genome and Systems Biology/PGSB, Helmholtz Center Munich - German Research Center for Environmental Health, 85764 Neuherberg, Germany
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112
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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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113
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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: 139] [Impact Index Per Article: 17.4] [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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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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115
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Maize pan-transcriptome provides novel insights into genome complexity and quantitative trait variation. Sci Rep 2016; 6:18936. [PMID: 26729541 PMCID: PMC4733048 DOI: 10.1038/srep18936] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Accepted: 12/01/2015] [Indexed: 11/12/2022] Open
Abstract
Gene expression variation largely contributes to phenotypic diversity and constructing pan-transcriptome is considered necessary for species with complex genomes. However, the regulation mechanisms and functional consequences of pan-transcriptome is unexplored systematically. By analyzing RNA-seq data from 368 maize diverse inbred lines, we identified almost one-third nuclear genes under expression presence and absence variation, which tend to play regulatory roles and are likely regulated by distant eQTLs. The ePAV was directly used as “genotype” to perform GWAS for 15 agronomic phenotypes and 526 metabolic traits to efficiently explore the associations between transcriptomic and phenomic variations. Through a modified assembly strategy, 2,355 high-confidence novel sequences with total 1.9 Mb lengths were found absent within reference genome. Ten randomly selected novel sequences were fully validated with genomic PCR, including another two NBS_LRR candidates potentially affect flavonoids and disease-resistance. A simulation analysis suggested that the pan-transcriptome of the maize whole kernel is approaching a maximum value of 63,000 genes, and through developing two test-cross populations and surveying several most important yield traits, the dispensable genes were shown to contribute to heterosis. Novel perspectives and resources to discover maize quantitative trait variations were provided to better understand the kernel regulation networks and to enhance maize breeding.
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116
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Song J, Yang X, Resende MFR, Neves LG, Todd J, Zhang J, Comstock JC, Wang J. Natural Allelic Variations in Highly Polyploidy Saccharum Complex. FRONTIERS IN PLANT SCIENCE 2016; 7:804. [PMID: 27375658 PMCID: PMC4896942 DOI: 10.3389/fpls.2016.00804] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2016] [Accepted: 05/23/2016] [Indexed: 05/20/2023]
Abstract
Sugarcane (Saccharum spp.) is an important sugar and biofuel crop with high polyploid and complex genomes. The Saccharum complex, comprised of Saccharum genus and a few related genera, are important genetic resources for sugarcane breeding. A large amount of natural variation exists within the Saccharum complex. Though understanding their allelic variation has been challenging, it is critical to dissect allelic structure and to identify the alleles controlling important traits in sugarcane. To characterize natural variations in Saccharum complex, a target enrichment sequencing approach was used to assay 12 representative germplasm accessions. In total, 55,946 highly efficient probes were designed based on the sorghum genome and sugarcane unigene set targeting a total of 6 Mb of the sugarcane genome. A pipeline specifically tailored for polyploid sequence variants and genotype calling was established. BWA-mem and sorghum genome approved to be an acceptable aligner and reference for sugarcane target enrichment sequence analysis, respectively. Genetic variations including 1,166,066 non-redundant SNPs, 150,421 InDels, 919 gene copy number variations, and 1,257 gene presence/absence variations were detected. SNPs from three different callers (Samtools, Freebayes, and GATK) were compared and the validation rates were nearly 90%. Based on the SNP loci of each accession and their ploidy levels, 999,258 single dosage SNPs were identified and most loci were estimated as largely homozygotes. An average of 34,397 haplotype blocks for each accession was inferred. The highest divergence time among the Saccharum spp. was estimated as 1.2 million years ago (MYA). Saccharum spp. diverged from Erianthus and Sorghum approximately 5 and 6 MYA, respectively. The target enrichment sequencing approach provided an effective way to discover and catalog natural allelic variation in highly polyploid or heterozygous genomes.
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Affiliation(s)
- Jian Song
- Agronomy Department, University of FloridaGainesville, FL, USA
- College of Life Sciences, Dezhou UniversityDezhou, China
| | - Xiping Yang
- Agronomy Department, University of FloridaGainesville, FL, USA
| | | | | | - James Todd
- Sugarcane Research Unit, United States Department of Agriculture-Agricultural Research ServiceHouma, LA, USA
- Sugarcane Field Station, United States Department of Agriculture-Agricultural Research Service, Canal PointFL, USA
| | - Jisen Zhang
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry UniversityFuzhou, China
| | - Jack C. Comstock
- Sugarcane Field Station, United States Department of Agriculture-Agricultural Research Service, Canal PointFL, USA
| | - Jianping Wang
- Agronomy Department, University of FloridaGainesville, FL, USA
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry UniversityFuzhou, China
- Plant Molecular and Biology Program, Genetics Institute, University of FloridaGainesville, FL, USA
- *Correspondence: Jianping Wang,
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117
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Cardone MF, Bergamini C, D'Addabbo P, Alkan C, Catacchio CR, Anaclerio F, Chiatante G, Marra A, Giannuzzi G, Perniola R, Ventura M, Antonacci D. Genomics technologies to study structural variations in the grapevine genome. BIO WEB OF CONFERENCES 2016. [DOI: 10.1051/bioconf/20160701016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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118
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Evans J, Crisovan E, Barry K, Daum C, Jenkins J, Kunde-Ramamoorthy G, Nandety A, Ngan CY, Vaillancourt B, Wei CL, Schmutz J, Kaeppler SM, Casler MD, Buell CR. Diversity and population structure of northern switchgrass as revealed through exome capture sequencing. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 84:800-15. [PMID: 26426343 DOI: 10.1111/tpj.13041] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Revised: 08/31/2015] [Accepted: 09/03/2015] [Indexed: 05/11/2023]
Abstract
Panicum virgatum L. (switchgrass) is a polyploid, perennial grass species that is native to North America, and is being developed as a future biofuel feedstock crop. Switchgrass is present primarily in two ecotypes: a northern upland ecotype, composed of tetraploid and octoploid accessions, and a southern lowland ecotype, composed of primarily tetraploid accessions. We employed high-coverage exome capture sequencing (~2.4 Tb) to genotype 537 individuals from 45 upland and 21 lowland populations. From these data, we identified ~27 million single-nucleotide polymorphisms (SNPs), of which 1 590 653 high-confidence SNPs were used in downstream analyses of diversity within and between the populations. From the 66 populations, we identified five primary population groups within the upland and lowland ecotypes, a result that was further supported through genetic distance analysis. We identified conserved, ecotype-restricted, non-synonymous SNPs that are predicted to affect the protein function of CONSTANS (CO) and EARLY HEADING DATE 1 (EHD1), key genes involved in flowering, which may contribute to the phenotypic differences between the two ecotypes. We also identified, relative to the near-reference Kanlow population, 17 228 genes present in more copies than in the reference genome (up-CNVs), 112 630 genes present in fewer copies than in the reference genome (down-CNVs) and 14 430 presence/absence variants (PAVs), affecting a total of 9979 genes, including two upland-specific CNV clusters. In total, 45 719 genes were affected by an SNP, CNV, or PAV across the panel, providing a firm foundation to identify functional variation associated with phenotypic traits of interest for biofuel feedstock production.
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Affiliation(s)
- Joseph Evans
- DOE Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI, 48824, USA
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA
| | - Emily Crisovan
- DOE Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI, 48824, USA
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA
| | - Kerrie Barry
- Department of Energy, Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Chris Daum
- Department of Energy, Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Jerry Jenkins
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | | | - Aruna Nandety
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, 73019, USA
| | - Chew Yee Ngan
- Department of Energy, Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Brieanne Vaillancourt
- DOE Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI, 48824, USA
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA
| | - Chia-Lin Wei
- Department of Energy, Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Jeremy Schmutz
- Department of Energy, Joint Genome Institute, Walnut Creek, CA, 94598, USA
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | - Shawn M Kaeppler
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, 1575 Linden Drive, Madison, WI, 53706, USA
- Department of Agronomy, University of Wisconsin-Madison, 1575 Linden Drive, Madison, WI, 53706, USA
| | - Michael D Casler
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, 1575 Linden Drive, Madison, WI, 53706, USA
- USDA-ARS, U.S. Dairy Forage Research Center, 1925 Linden Dr., Madison, WI, 53706-1108, USA
| | - Carol Robin Buell
- DOE Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI, 48824, USA
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA
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Li C, Li Y, Bradbury PJ, Wu X, Shi Y, Song Y, Zhang D, Rodgers-Melnick E, Buckler ES, Zhang Z, Li Y, Wang T. Construction of high-quality recombination maps with low-coverage genomic sequencing for joint linkage analysis in maize. BMC Biol 2015; 13:78. [PMID: 26390990 PMCID: PMC4578237 DOI: 10.1186/s12915-015-0187-4] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2014] [Accepted: 09/02/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND A genome-wide association study (GWAS) is the foremost strategy used for finding genes that control human diseases and agriculturally important traits, but it often reports false positives. In contrast, its complementary method, linkage analysis, provides direct genetic confirmation, but with limited resolution. A joint approach, using multiple linkage populations, dramatically improves resolution and statistical power. For example, this approach has been used to confirm that many complex traits, such as flowering time controlling adaptation in maize, are controlled by multiple genes with small effects. In addition, genotyping by sequencing (GBS) at low coverage not only produces genotyping errors, but also results in large datasets, making the use of high-throughput sequencing technologies computationally inefficient or unfeasible. RESULTS In this study, we converted raw SNPs into effective recombination bins. The reduced bins not only retain the original information, but also correct sequencing errors from low-coverage genomic sequencing. To further increase the statistical power and resolution, we merged a new temperate maize nested association mapping (NAM) population derived in China (CN-NAM) with the existing maize NAM population developed in the US (US-NAM). Together, the two populations contain 36 families and 7,000 recombinant inbred lines (RILs). One million SNPs were generated for all the RILs with GBS at low coverage. We developed high-quality recombination maps for each NAM population to correct genotyping errors and improve the computational efficiency of the joint linkage analysis. The original one million SNPs were reduced to 4,932 and 5,296 recombination bins with average interval distances of 0.34 cM and 0.28 cM for CN-NAM and US-NAM, respectively. The quantitative trait locus (QTL) mapping for flowering time (days to tasseling) indicated that the high-density, recombination bin map improved resolution of QTL mapping by 50 % compared with that using a medium-density map. We also demonstrated that combining the CN-NAM and US-NAM populations improves the power to detect QTL by 50 % compared to single NAM population mapping. Among the QTLs mapped by joint usage of the US-NAM and CN-NAM maps, 25 % of the QTLs overlapped with known flowering-time genes in maize. CONCLUSION This study provides directions and resources for the research community, especially maize researchers, for future studies using the recombination bin strategy for joint linkage analysis. Available resources include efficient usage of low-coverage genomic sequencing, detailed positions for genes controlling maize flowering, and recombination bin maps and flowering- time data for both CN and US NAMs. Maize researchers even have the opportunity to grow both CN and US NAM populations to study the traits of their interest, as the seeds of both NAM populations are available from the seed repository in China and the US.
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Affiliation(s)
- Chunhui Li
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yongxiang Li
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Peter J Bradbury
- USA Department of Agriculture-Agricultural Research Service, New York, USA
| | - Xun Wu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yunsu Shi
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yanchun Song
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Dengfeng Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | | | - Edward S Buckler
- Institute for Genomic Diversity, Cornell University, Ithaca, NY, USA. .,USA Department of Agriculture-Agricultural Research Service, New York, USA.
| | - Zhiwu Zhang
- Institute for Genomic Diversity, Cornell University, Ithaca, NY, USA. .,Department of Crop and Soil Sciences, Washington State University, Pullman, WA, USA.
| | - Yu Li
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.
| | - Tianyu Wang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.
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120
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Abstract
A multiparent advanced-generation intercross population of maize has been developed to help plant geneticists identify sequence variants affecting important agricultural traits.
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Affiliation(s)
- James B Holland
- USDA-ARS Plant Science Research Unit, Department of Crop Science, North Carolina State University, Raleigh, NC, 27695-7620, USA.
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121
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Bachère E, Rosa RD, Schmitt P, Poirier AC, Merou N, Charrière GM, Destoumieux-Garzón D. The new insights into the oyster antimicrobial defense: Cellular, molecular and genetic view. FISH & SHELLFISH IMMUNOLOGY 2015; 46:50-64. [PMID: 25753917 DOI: 10.1016/j.fsi.2015.02.040] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Revised: 02/24/2015] [Accepted: 02/26/2015] [Indexed: 06/04/2023]
Abstract
Oysters are sessile filter feeders that live in close association with abundant and diverse communities of microorganisms that form the oyster microbiota. In such an association, cellular and molecular mechanisms have evolved to maintain oyster homeostasis upon stressful conditions including infection and changing environments. We give here cellular and molecular insights into the Crassostrea gigas antimicrobial defense system with focus on antimicrobial peptides and proteins (AMPs). This review highlights the central role of the hemocytes in the modulation and control of oyster antimicrobial response. As vehicles for AMPs and other antimicrobial effectors, including reactive oxygen species (ROS), and together with epithelia, hemocytes provide the oyster with local defense reactions instead of systemic humoral ones. These reactions are largely based on phagocytosis but also, as recently described, on the extracellular release of antimicrobial histones (ETosis) which is triggered by ROS. Thus, ROS can signal danger and activate cellular responses in the oyster. From the current literature, AMP production/release could serve similar functions. We provide also new lights on the oyster genetic background that underlies a great diversity of AMP sequences but also an extraordinary individual polymorphism of AMP gene expression. We discuss here how this polymorphism could generate new immune functions, new pathogen resistances or support individual adaptation to environmental stresses.
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Affiliation(s)
- Evelyne Bachère
- Ifremer, UMR 5244, IHPE Interaction Host Pathogen Environment, UPVD, CNRS, Université de Montpellier, CC 80, F-34095 Montpellier, France.
| | - Rafael Diego Rosa
- Ifremer, UMR 5244, IHPE Interaction Host Pathogen Environment, UPVD, CNRS, Université de Montpellier, CC 80, F-34095 Montpellier, France; Laboratory of Immunology Applied to Aquaculture, Department of Cell Biology, Embryology and Genetics, Federal University of Santa Catarina, 88040-900 Florianópolis, SC, Brazil
| | - Paulina Schmitt
- Ifremer, UMR 5244, IHPE Interaction Host Pathogen Environment, UPVD, CNRS, Université de Montpellier, CC 80, F-34095 Montpellier, France; Laboratorio de Genética e Inmunología Molecular, Instituto de Biología, Pontificia Universidad, Católica de Valparaíso, Avenida Universidad 330, 2373223 Valparaíso, Chile
| | - Aurore C Poirier
- Ifremer, UMR 5244, IHPE Interaction Host Pathogen Environment, UPVD, CNRS, Université de Montpellier, CC 80, F-34095 Montpellier, France
| | - Nicolas Merou
- Ifremer, UMR 5244, IHPE Interaction Host Pathogen Environment, UPVD, CNRS, Université de Montpellier, CC 80, F-34095 Montpellier, France
| | - Guillaume M Charrière
- Ifremer, UMR 5244, IHPE Interaction Host Pathogen Environment, UPVD, CNRS, Université de Montpellier, CC 80, F-34095 Montpellier, France
| | - Delphine Destoumieux-Garzón
- Ifremer, UMR 5244, IHPE Interaction Host Pathogen Environment, UPVD, CNRS, Université de Montpellier, CC 80, F-34095 Montpellier, France
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122
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Wang Y, Drader T, Tiwari VK, Dong L, Kumar A, Huo N, Ghavami F, Iqbal MJ, Lazo GR, Leonard J, Gill BS, Kianian SF, Luo MC, Gu YQ. Development of a D genome specific marker resource for diploid and hexaploid wheat. BMC Genomics 2015; 16:646. [PMID: 26315263 PMCID: PMC4552153 DOI: 10.1186/s12864-015-1852-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Accepted: 08/17/2015] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND Mapping and map-based cloning of genes that control agriculturally and economically important traits remain great challenges for plants with complex highly repetitive genomes such as those within the grass tribe, Triticeae. Mapping limitations in the Triticeae are primarily due to low frequencies of polymorphic gene markers and poor genetic recombination in certain genetic regions. Although the abundance of repetitive sequence may pose common problems in genome analysis and sequence assembly of large and complex genomes, they provide repeat junction markers with random and unbiased distribution throughout chromosomes. Hence, development of a high-throughput mapping technology that combine both gene-based and repeat junction-based markers is needed to generate maps that have better coverage of the entire genome. RESULTS In this study, the available genomics resource of the diploid Aegilop tauschii, the D genome donor of bread wheat, were used to develop genome specific markers that can be applied for mapping in modern hexaploid wheat. A NimbleGen array containing both gene-based and repeat junction probe sequences derived from Ae. tauschii was developed and used to map the Chinese Spring nullisomic-tetrasomic lines and deletion bin lines of the D genome chromosomes. Based on these mapping data, we have now anchored 5,171 repeat junction probes and 10,892 gene probes, corresponding to 5,070 gene markers, to the delineated deletion bins of the D genome. The order of the gene-based markers within the deletion bins of the Chinese Spring can be inferred based on their positions on the Ae. tauschii genetic map. Analysis of the probe sequences against the Chinese Spring chromosome sequence assembly database facilitated mapping of the NimbleGen probes to the sequence contigs and allowed assignment or ordering of these sequence contigs within the deletion bins. The accumulated length of anchored sequence contigs is about 155 Mb, representing ~ 3.2 % of the D genome. A specific database was developed to allow user to search or BLAST against the probe sequence information and to directly download PCR primers for mapping specific genetic loci. CONCLUSIONS In bread wheat, aneuploid stocks have been extensively used to assign markers linked with genes/traits to chromosomes, chromosome arms, and their specific bins. Through this study, we added thousands of markers to the existing wheat chromosome bin map, representing a significant step forward in providing a resource to navigate the wheat genome. The database website ( http://probes.pw.usda.gov/ATRJM/ ) provides easy access and efficient utilization of the data. The resources developed herein can aid map-based cloning of traits of interest and the sequencing of the D genome of hexaploid wheat.
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Affiliation(s)
- Yi Wang
- Western Regional Research Center, USDA-ARS, Albany, CA, 94710, USA. .,Department of Plant Sciences, University of California, Davis, CA, 95616, USA.
| | - Thomas Drader
- Western Regional Research Center, USDA-ARS, Albany, CA, 94710, USA.
| | - Vijay K Tiwari
- Department of Crop and Soil Science, Oregon State University, Corvallis, OR, 97331, USA. .,Wheat Genetic Resource Center, Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA.
| | - Lingli Dong
- Western Regional Research Center, USDA-ARS, Albany, CA, 94710, USA. .,Department of Plant Sciences, University of California, Davis, CA, 95616, USA.
| | - Ajay Kumar
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58108, USA. ajay.kumar.2.@ndsu.edu
| | - Naxin Huo
- Western Regional Research Center, USDA-ARS, Albany, CA, 94710, USA.,Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Farhad Ghavami
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58108, USA.,Molecular Breeding and Genomics Technology Laboratory, BioDiagnostics Inc., River Falls, WI, 54022, USA
| | - M Javed Iqbal
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58108, USA
| | - Gerard R Lazo
- Western Regional Research Center, USDA-ARS, Albany, CA, 94710, USA.
| | - Jeff Leonard
- Department of Crop and Soil Science, Oregon State University, Corvallis, OR, 97331, USA.
| | - Bikram S Gill
- Wheat Genetic Resource Center, Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA.
| | | | - Ming-Cheng Luo
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA.
| | - Yong Q Gu
- Western Regional Research Center, USDA-ARS, Albany, CA, 94710, USA.
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Muraya MM, Schmutzer T, Ulpinnis C, Scholz U, Altmann T. Targeted Sequencing Reveals Large-Scale Sequence Polymorphism in Maize Candidate Genes for Biomass Production and Composition. PLoS One 2015; 10:e0132120. [PMID: 26151830 PMCID: PMC4495061 DOI: 10.1371/journal.pone.0132120] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Accepted: 06/10/2015] [Indexed: 12/30/2022] Open
Abstract
A major goal of maize genomic research is to identify sequence polymorphisms responsible for phenotypic variation in traits of economic importance. Large-scale detection of sequence variation is critical for linking genes, or genomic regions, to phenotypes. However, due to its size and complexity, it remains expensive to generate whole genome sequences of sufficient coverage for divergent maize lines, even with access to next generation sequencing (NGS) technology. Because methods involving reduction of genome complexity, such as genotyping-by-sequencing (GBS), assess only a limited fraction of sequence variation, targeted sequencing of selected genomic loci offers an attractive alternative. We therefore designed a sequence capture assay to target 29 Mb genomic regions and surveyed a total of 4,648 genes possibly affecting biomass production in 21 diverse inbred maize lines (7 flints, 14 dents). Captured and enriched genomic DNA was sequenced using the 454 NGS platform to 19.6-fold average depth coverage, and a broad evaluation of read alignment and variant calling methods was performed to select optimal procedures for variant discovery. Sequence alignment with the B73 reference and de novo assembly identified 383,145 putative single nucleotide polymorphisms (SNPs), of which 42,685 were non-synonymous alterations and 7,139 caused frameshifts. Presence/absence variation (PAV) of genes was also detected. We found that substantial sequence variation exists among genomic regions targeted in this study, which was particularly evident within coding regions. This diversification has the potential to broaden functional diversity and generate phenotypic variation that may lead to new adaptations and the modification of important agronomic traits. Further, annotated SNPs identified here will serve as useful genetic tools and as candidates in searches for phenotype-altering DNA variation. In summary, we demonstrated that sequencing of captured DNA is a powerful approach for variant discovery in maize genes.
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Affiliation(s)
- Moses M. Muraya
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstraße 3, D-06466, Stadt Seeland, Germany
- Department of Plant Science, Chuka University, P.O. Box, 109–60400, Chuka, Kenya
| | - Thomas Schmutzer
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstraße 3, D-06466, Stadt Seeland, Germany
- * E-mail:
| | - Chris Ulpinnis
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstraße 3, D-06466, Stadt Seeland, Germany
| | - Uwe Scholz
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstraße 3, D-06466, Stadt Seeland, Germany
| | - Thomas Altmann
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstraße 3, D-06466, Stadt Seeland, Germany
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124
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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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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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126
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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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Rosa RD, Alonso P, Santini A, Vergnes A, Bachère E. High polymorphism in big defensin gene expression reveals presence-absence gene variability (PAV) in the oyster Crassostrea gigas. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2015; 49:231-238. [PMID: 25482648 DOI: 10.1016/j.dci.2014.12.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Revised: 11/28/2014] [Accepted: 12/01/2014] [Indexed: 06/04/2023]
Abstract
We report here the first evidence in an invertebrate, the oyster Crassostrea gigas, of a phenomenon of Presence-Absence Variation (PAV) affecting immune-related genes. We previously evidenced an extraordinary interindividual variability in the basal mRNA abundances of oyster immune genes including those coding for a family of antimicrobial peptides, the big defensins (Cg-BigDef). Cg-BigDef is a diverse family composed of three members: Cg-BigDef1 to -3. Here, we show that besides a high polymorphism in Cg-BigDef mRNA expression, not all individual oysters express simultaneously the three Cg-BigDefs. Moreover, in numerous individuals, no expression of Cg-BigDefs could be detected. Further investigation at the genomic level revealed that in individuals in which the transcription of one or all Cg-BigDefs was absent the corresponding Cg-bigdef gene was missing. In our experiments, no correlation was found between Cg-bigdef PAV and oyster capacity to survive Vibrio infections. The discovery of P-A immune genes in oysters leads to reconsider the role that the immune system plays in the individual adaptation to survive environmental, biotic and abiotic stresses.
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Affiliation(s)
- Rafael D Rosa
- Ifremer, CNRS, Université Montpellier 2, IRD, Université Montpellier 1, UMR5119 - Ecology of Coastal Marine Systems, Place Eugène Bataillon, CC80, 34095 Montpellier, France.
| | - Pascal Alonso
- Ifremer, CNRS, Université Montpellier 2, IRD, Université Montpellier 1, UMR5119 - Ecology of Coastal Marine Systems, Place Eugène Bataillon, CC80, 34095 Montpellier, France
| | - Adrien Santini
- Ifremer, CNRS, Université Montpellier 2, IRD, Université Montpellier 1, UMR5119 - Ecology of Coastal Marine Systems, Place Eugène Bataillon, CC80, 34095 Montpellier, France
| | - Agnès Vergnes
- Ifremer, CNRS, Université Montpellier 2, IRD, Université Montpellier 1, UMR5119 - Ecology of Coastal Marine Systems, Place Eugène Bataillon, CC80, 34095 Montpellier, France
| | - Evelyne Bachère
- Ifremer, CNRS, Université Montpellier 2, IRD, Université Montpellier 1, UMR5119 - Ecology of Coastal Marine Systems, Place Eugène Bataillon, CC80, 34095 Montpellier, France
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Soto JC, Ortiz JF, Perlaza-Jiménez L, Vásquez AX, Lopez-Lavalle LAB, Mathew B, Léon J, Bernal AJ, Ballvora A, López CE. A genetic map of cassava (Manihot esculenta Crantz) with integrated physical mapping of immunity-related genes. BMC Genomics 2015; 16:190. [PMID: 25887443 PMCID: PMC4417308 DOI: 10.1186/s12864-015-1397-4] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2014] [Accepted: 02/24/2015] [Indexed: 03/19/2023] Open
Abstract
BACKGROUND Cassava, Manihot esculenta Crantz, is one of the most important crops world-wide representing the staple security for more than one billion of people. The development of dense genetic and physical maps, as the basis for implementing genetic and molecular approaches to accelerate the rate of genetic gains in breeding program represents a significant challenge. A reference genome sequence for cassava has been made recently available and community efforts are underway for improving its quality. Cassava is threatened by several pathogens, but the mechanisms of defense are far from being understood. Besides, there has been a lack of information about the number of genes related to immunity as well as their distribution and genomic organization in the cassava genome. RESULTS A high dense genetic map of cassava containing 2,141 SNPs has been constructed. Eighteen linkage groups were resolved with an overall size of 2,571 cM and an average distance of 1.26 cM between markers. More than half of mapped SNPs (57.4%) are located in coding sequences. Physical mapping of scaffolds of cassava whole genome sequence draft using the mapped markers as anchors resulted in the orientation of 687 scaffolds covering 45.6% of the genome. One hundred eighty nine new scaffolds are anchored to the genetic cassava map leading to an extension of the present cassava physical map with 30.7 Mb. Comparative analysis using anchor markers showed strong co-linearity to previously reported cassava genetic and physical maps. In silico based searching for conserved domains allowed the annotation of a repertory of 1,061 cassava genes coding for immunity-related proteins (IRPs). Based on physical map of the corresponding sequencing scaffolds, unambiguous genetic localization was possible for 569 IRPs. CONCLUSIONS This is the first study reported so far of an integrated high density genetic map using SNPs with integrated genetic and physical localization of newly annotated immunity related genes in cassava. These data build a solid basis for future studies to map and associate markers with single loci or quantitative trait loci for agronomical important traits. The enrichment of the physical map with novel scaffolds is in line with the efforts of the cassava genome sequencing consortium.
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Affiliation(s)
- Johana Carolina Soto
- Manihot Biotec Laboratory, Biology Department, Universidad Nacional de Colombia, Bogotá, Colombia.
| | - Juan Felipe Ortiz
- Manihot Biotec Laboratory, Biology Department, Universidad Nacional de Colombia, Bogotá, Colombia. .,Present address Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA.
| | - Laura Perlaza-Jiménez
- Laboratory of Mycology and Plant Pathology, Universidad de los Andes, Bogotá, Colombia. .,Present address Max Planck Institute for Molecular Plant Physiology, Potsdam-Golm, Germany.
| | - Andrea Ximena Vásquez
- Manihot Biotec Laboratory, Biology Department, Universidad Nacional de Colombia, Bogotá, Colombia.
| | | | - Boby Mathew
- INRES-Plant Breeding University of Bonn, Bonn, Germany.
| | - Jens Léon
- INRES-Plant Breeding University of Bonn, Bonn, Germany.
| | - Adriana Jimena Bernal
- Laboratory of Mycology and Plant Pathology, Universidad de los Andes, Bogotá, Colombia.
| | - Agim Ballvora
- INRES-Plant Breeding University of Bonn, Bonn, Germany.
| | - Camilo Ernesto López
- Manihot Biotec Laboratory, Biology Department, Universidad Nacional de Colombia, Bogotá, Colombia.
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Abstract
Maize occupies dual roles as both (a) one of the big-three grain species (along with rice and wheat) responsible for providing more than half of the calories consumed around the world, and (b) a model system for plant genetics and cytogenetics dating back to the origin of the field of genetics in the early twentieth century. The long history of genetic investigation in this species combined with modern genomic and quantitative genetic data has provided particular insight into the characteristics of genes linked to phenotypes and how these genes differ from many other sequences in plant genomes that are not easily distinguishable based on molecular data alone. These recent results suggest that the number of genes in plants that make significant contributions to phenotype may be lower than the number of genes defined by current molecular criteria, and also indicate that syntenic conservation has been underemphasized as a marker for gene function.
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Affiliation(s)
- James C Schnable
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, Nebraska 68583;
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131
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A maize wall-associated kinase confers quantitative resistance to head smut. Nat Genet 2014; 47:151-7. [PMID: 25531751 DOI: 10.1038/ng.3170] [Citation(s) in RCA: 220] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2014] [Accepted: 12/01/2014] [Indexed: 11/08/2022]
Abstract
Head smut is a systemic disease in maize caused by the soil-borne fungus Sporisorium reilianum that poses a grave threat to maize production worldwide. A major head smut quantitative resistance locus, qHSR1, has been detected on maize chromosome bin2.09. Here we report the map-based cloning of qHSR1 and the molecular mechanism of qHSR1-mediated resistance. Sequential fine mapping and transgenic complementation demonstrated that ZmWAK is the gene within qHSR1 conferring quantitative resistance to maize head smut. ZmWAK spans the plasma membrane, potentially serving as a receptor-like kinase to perceive and transduce extracellular signals. ZmWAK was highly expressed in the mesocotyl of seedlings where it arrested biotrophic growth of the endophytic S. reilianum. Impaired expression in the mesocotyl compromised ZmWAK-mediated resistance. Deletion of the ZmWAK locus appears to have occurred after domestication and spread among maize germplasm, and the ZmWAK kinase domain underwent functional constraints during maize evolution.
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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: 370] [Impact Index Per Article: 37.0] [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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Paschold A, Larson NB, Marcon C, Schnable JC, Yeh CT, Lanz C, Nettleton D, Piepho HP, Schnable PS, Hochholdinger F. Nonsyntenic genes drive highly dynamic complementation of gene expression in maize hybrids. THE PLANT CELL 2014; 26:3939-48. [PMID: 25315323 PMCID: PMC4247586 DOI: 10.1105/tpc.114.130948] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Revised: 09/05/2014] [Accepted: 09/24/2014] [Indexed: 05/19/2023]
Abstract
Maize (Zea mays) displays an exceptional level of structural genomic diversity, which is likely unique among higher eukaryotes. In this study, we surveyed how the genetic divergence of two maize inbred lines affects the transcriptomic landscape in four different primary root tissues of their F1-hybrid progeny. An extreme instance of complementation was frequently observed: genes that were expressed in only one parent but in both reciprocal hybrids. This single-parent expression (SPE) pattern was detected for 2341 genes with up to 1287 SPE patterns per tissue. As a consequence, the number of active genes in hybrids exceeded that of their parents in each tissue by >400. SPE patterns are highly dynamic, as illustrated by their excessive degree of tissue specificity (80%). The biological significance of this type of complementation is underpinned by the observation that a disproportionally high number of SPE genes (75 to 82%) is nonsyntenic, as opposed to all expressed genes (36%). These genes likely evolved after the last whole-genome duplication and are therefore younger than the syntenic genes. In summary, SPE genes shape the remarkable gene expression plasticity between root tissues and complementation in maize hybrids, resulting in a tissue-specific increase of active genes in F1-hybrids compared with their inbred parents.
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Affiliation(s)
- Anja Paschold
- Institute of Crop Science and Resource Conservation, Crop Functional Genomics, University of Bonn, 53113 Bonn, Germany
| | - Nick B Larson
- Department of Statistics, Iowa State University, Ames, Iowa 50011-1210
| | - Caroline Marcon
- Institute of Crop Science and Resource Conservation, Crop Functional Genomics, University of Bonn, 53113 Bonn, Germany
| | - James C Schnable
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, Nebraska 68588
| | - Cheng-Ting Yeh
- Department of Agronomy and Center for Plant Genomics, Iowa State University, Ames, Iowa 50011-3650
| | - Christa Lanz
- Department of Molecular Biology, Max-Planck-Institute for Developmental Biology, 72076 Tuebingen, Germany
| | - Dan Nettleton
- Department of Statistics, Iowa State University, Ames, Iowa 50011-1210
| | - Hans-Peter Piepho
- Institute for Crop Science, Biostatistics Unit, University of Hohenheim, 70599 Stuttgart, Germany
| | - Patrick S Schnable
- Department of Agronomy and Center for Plant Genomics, Iowa State University, Ames, Iowa 50011-3650
| | - Frank Hochholdinger
- Institute of Crop Science and Resource Conservation, Crop Functional Genomics, University of Bonn, 53113 Bonn, Germany
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135
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Linkage disequilibrium with linkage analysis of multiline crosses reveals different multiallelic QTL for hybrid performance in the flint and dent heterotic groups of maize. Genetics 2014; 198:1717-34. [PMID: 25271305 DOI: 10.1534/genetics.114.169367] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Multiparental designs combined with dense genotyping of parents have been proposed as a way to increase the diversity and resolution of quantitative trait loci (QTL) mapping studies, using methods combining linkage disequilibrium information with linkage analysis (LDLA). Two new nested association mapping designs adapted to European conditions were derived from the complementary dent and flint heterotic groups of maize (Zea mays L.). Ten biparental dent families (N = 841) and 11 biparental flint families (N = 811) were genotyped with 56,110 single nucleotide polymorphism markers and evaluated as test crosses with the central line of the reciprocal design for biomass yield, plant height, and precocity. Alleles at candidate QTL were defined as (i) parental alleles, (ii) haplotypic identity by descent, and (iii) single-marker groupings. Between five and 16 QTL were detected depending on the model, trait, and genetic group considered. In the flint design, a major QTL (R(2) = 27%) with pleiotropic effects was detected on chromosome 10, whereas other QTL displayed milder effects (R(2) < 10%). On average, the LDLA models detected more QTL but generally explained lower percentages of variance, consistent with the fact that most QTL display complex allelic series. Only 15% of the QTL were common to the two designs. A joint analysis of the two designs detected between 15 and 21 QTL for the five traits. Of these, between 27 for silking date and 41% for tasseling date were significant in both groups. Favorable allelic effects detected in both groups open perspectives for improving biomass production.
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136
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Abstract
Nucleotide diversity is greater in maize than in most organisms studied to date, so allelic pairs in a hybrid tend to be highly polymorphic. Most recombination events between such pairs of maize polymorphic alleles are crossovers. However, intragenic recombination events not associated with flanking marker exchange, corresponding to noncrossover gene conversions, predominate between alleles derived from the same progenitor. In these dimorphic heterozygotes, the two alleles differ only at the two mutant sites between which recombination is being measured. To investigate whether gene conversion at the bz locus is polarized, two large diallel crossing matrices involving mutant sites spread across the bz gene were performed and more than 2,500 intragenic recombinants were scored. In both diallels, around 90% of recombinants could be accounted for by gene conversion. Furthermore, conversion exhibited a striking polarity, with sites located within 150 bp of the start and stop codons converting more frequently than sites located in the middle of the gene. The implications of these findings are discussed with reference to recent data from genome-wide studies in other plants.
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137
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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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138
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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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139
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Kim J, Matsuba Y, Ning J, Schilmiller AL, Hammar D, Jones AD, Pichersky E, Last RL. Analysis of natural and induced variation in tomato glandular trichome flavonoids identifies a gene not present in the reference genome. THE PLANT CELL 2014; 26:3272-85. [PMID: 25128240 PMCID: PMC4176439 DOI: 10.1105/tpc.114.129460] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2014] [Revised: 07/25/2014] [Accepted: 07/31/2014] [Indexed: 05/20/2023]
Abstract
Flavonoids are ubiquitous plant aromatic specialized metabolites found in a variety of cell types and organs. Methylated flavonoids are detected in secreting glandular trichomes of various Solanum species, including the cultivated tomato (Solanum lycopersicum). Inspection of the sequenced S. lycopersicum Heinz 1706 reference genome revealed a close homolog of Solanum habrochaites MOMT1 3'/5' myricetin O-methyltransferase gene, but this gene (Solyc06g083450) is missing the first exon, raising the question of whether cultivated tomato has a distinct 3' or 3'/5' O-methyltransferase. A combination of mining genome and cDNA sequences from wild tomato species and S. lycopersicum cultivar M82 led to the identification of Sl-MOMT4 as a 3' O-methyltransferase. In parallel, three independent ethyl methanesulfonate mutants in the S. lycopersicum cultivar M82 background were identified as having reduced amounts of di- and trimethylated myricetins and increased monomethylated myricetin. Consistent with the hypothesis that Sl-MOMT4 is a 3' O-methyltransferase gene, all three myricetin methylation defective mutants were found to have defects in MOMT4 sequence, transcript accumulation, or 3'-O-methyltransferase enzyme activity. Surprisingly, no MOMT4 sequence is found in the Heinz 1706 reference genome sequence, and this cultivar accumulates 3-methyl myricetin and is deficient in 3'-methyl myricetins, demonstrating variation in this gene among cultivated tomato varieties.
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Affiliation(s)
- Jeongwoon Kim
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824 Department of Energy Plant Research Laboratory, Michigan State University, East Lansing, Michigan 48824
| | - Yuki Matsuba
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109
| | - Jing Ning
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824
| | - Anthony L Schilmiller
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824
| | - Dagan Hammar
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109
| | - A Daniel Jones
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824 Department of Chemistry, Michigan State University, East Lansing, Michigan 48824
| | - Eran Pichersky
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109
| | - Robert L Last
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824 Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824
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140
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Abstract
Grain produced from cereal crops is a primary source of human food and animal feed worldwide. To understand the genetic basis of seed-size variation, a grain yield component, we conducted a genome-wide scan to detect evidence of selection in the maize Krug Yellow Dent long-term divergent seed-size selection experiment. Previous studies have documented significant phenotypic divergence between the populations. Allele frequency estimates for ∼3 million single nucleotide polymorphisms (SNPs) in the base population and selected populations were estimated from pooled whole-genome resequencing of 48 individuals per population. Using FST values across sliding windows, 94 divergent regions with a median of six genes per region were identified. Additionally, 2729 SNPs that reached fixation in both selected populations with opposing fixed alleles were identified, many of which clustered in two regions of the genome. Copy-number variation was highly prevalent between the selected populations, with 532 total regions identified on the basis of read-depth variation and comparative genome hybridization. Regions important for seed weight in natural variation were identified in the maize nested association mapping population. However, the number of regions that overlapped with the long-term selection experiment did not exceed that expected by chance, possibly indicating unique sources of variation between the two populations. The results of this study provide insights into the genetic elements underlying seed-size variation in maize and could also have applications for other cereal crops.
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141
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Discovering functional modules across diverse maize transcriptomes using COB, the Co-expression Browser. PLoS One 2014; 9:e99193. [PMID: 24922320 PMCID: PMC4055606 DOI: 10.1371/journal.pone.0099193] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Accepted: 05/12/2014] [Indexed: 01/13/2023] Open
Abstract
Tools that provide improved ability to relate genotype to phenotype have the potential to accelerate breeding for desired traits and to improve our understanding of the molecular variants that underlie phenotypes. The availability of large-scale gene expression profiles in maize provides an opportunity to advance our understanding of complex traits in this agronomically important species. We built co-expression networks based on genome-wide expression data from a variety of maize accessions as well as an atlas of different tissues and developmental stages. We demonstrate that these networks reveal clusters of genes that are enriched for known biological function and contain extensive structure which has yet to be characterized. Furthermore, we found that co-expression networks derived from developmental or tissue atlases as compared to expression variation across diverse accessions capture unique functions. To provide convenient access to these networks, we developed a public, web-based Co-expression Browser (COB), which enables interactive queries of the genome-wide networks. We illustrate the utility of this system through two specific use cases: one in which gene-centric queries are used to provide functional context for previously characterized metabolic pathways, and a second where lists of genes produced by mapping studies are further resolved and validated using co-expression networks.
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142
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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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143
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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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144
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Epstein B, Sadowsky MJ, Tiffin P. Selection on horizontally transferred and duplicated genes in sinorhizobium (ensifer), the root-nodule symbionts of medicago. Genome Biol Evol 2014; 6:1199-209. [PMID: 24803571 PMCID: PMC4040998 DOI: 10.1093/gbe/evu090] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Structural variation, including variation in gene copy number and presence or absence of genes, is a widespread and important source of genomic variation. We used whole-genome DNA sequences from 48 strains of Sinorhizobium (recently renamed Ensifer), including 20 strains of Sinorhizobium meliloti and 12 strains of S. medicae that were the focus of the analyses, to study the fitness effects of new structural variants created by duplication and horizontal gene transfer. We find that derived duplicated and horizontally transferred (HT) genes segregate at lower frequency than synonymous and nonsynonymous nucleotide variants in S. meliloti and S. medicae. Furthermore, the relative frequencies of different types of variants are more similar in S. medicae than in S. meliloti, the species with the larger effective population size. These results are consistent with the hypothesis that most duplications and HT genes have deleterious effects. Diversity of duplications, as measured by segregating duplicated genes per gene, is greater than nucleotide diversity, consistent with a high rate of duplication. Our results suggest that the vast majority of structural variants found among closely related bacterial strains are short-lived and unlikely to be involved in species-wide adaptation.
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Affiliation(s)
- Brendan Epstein
- Department of Plant Biology, University of MinnesotaSchool of Biological Sciences, Washington State University
| | - Michael J Sadowsky
- Department of Soil, Water, and Climate, University of MinnesotaBioTechnology Institute, Saint Paul, MN
| | - Peter Tiffin
- Department of Plant Biology, University of Minnesota
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145
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Diez CM, Meca E, Tenaillon MI, Gaut BS. Three groups of transposable elements with contrasting copy number dynamics and host responses in the maize (Zea mays ssp. mays) genome. PLoS Genet 2014; 10:e1004298. [PMID: 24743518 PMCID: PMC3990487 DOI: 10.1371/journal.pgen.1004298] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2013] [Accepted: 02/21/2014] [Indexed: 12/19/2022] Open
Abstract
Most angiosperm nuclear DNA is repetitive and derived from silenced transposable elements (TEs). TE silencing requires substantial resources from the plant host, including the production of small interfering RNAs (siRNAs). Thus, the interaction between TEs and siRNAs is a critical aspect of both the function and the evolution of plant genomes. Yet the co-evolutionary dynamics between these two entities remain poorly characterized. Here we studied the organization of TEs within the maize (Zea mays ssp mays) genome, documenting that TEs fall within three groups based on the class and copy numbers. These groups included DNA elements, low copy RNA elements and higher copy RNA elements. The three groups varied statistically in characteristics that included length, location, age, siRNA expression and 24∶22 nucleotide (nt) siRNA targeting ratios. In addition, the low copy retroelements encompassed a set of TEs that had previously been shown to decrease expression within a 24 nt siRNA biogenesis mutant (mop1). To investigate the evolutionary dynamics of the three groups, we estimated their abundance in two landraces, one with a genome similar in size to that of the maize reference and the other with a 30% larger genome. For all three accessions, we assessed TE abundance as well as 22 nt and 24 nt siRNA content within leaves. The high copy number retroelements are under targeted similarly by siRNAs among accessions, appear to be born of a rapid bust of activity, and may be currently transpositionally dead or limited. In contrast, the lower copy number group of retrolements are targeted more dynamically and have had a long and ongoing history of transposition in the maize genome. Because transposable elements (TEs) constitute most angiosperm nuclear DNA, the interaction between TEs and their host genome is a key component for understanding the function and evolution of plant genomes. The diversity of the host response has been studied a great deal, including the biogenesis of small interfering RNAs (siRNAs) that target TEs for epigenetic modifications. However, little is known about variation in TE content among closely related genomes and whether siRNA expression tracks this variation. To that end, we surveyed both the copy number and the siRNA targeting of more than 1500 distinct TE subfamilies in the B73 maize reference genome. These surveys indicated that TE subfamilies fall naturally into three distinctive groups based on their class and copy number, but these groups also differ with respect to their location in the genome, their age, their expression and their siRNA regulation. The presence and consistency of these TE groups was also assessed in two genetically distant maize landraces with contrasting genome sizes. The variation in siRNA targeting across different TE groups and families, as well as the lack of correlation between TE and siRNA abundances, argues for the existence of multiple mechanisms and strategies for TE silencing.
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Affiliation(s)
- Concepcion M. Diez
- Dept. of Ecology and Evolutionary Biology, UC Irvine, Irvine, California, United States of America
- Departamento de Agronomía, Universidad de Córdoba, Campus de Excelencia Internacional Agroalimentario, ceiA3, Cordoba, Spain
| | - Esteban Meca
- Department of Mathematics, UC Irvine, Irvine, California, United States of America
| | - Maud I. Tenaillon
- CNRS, UMR de Génétique Végétale, INRA/CNRS/Univ Paris-Sud/AgroParisTech, Ferme du Moulon, Gif-sur-Yvette, France
| | - Brandon S. Gaut
- Dept. of Ecology and Evolutionary Biology, UC Irvine, Irvine, California, United States of America
- * E-mail:
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146
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Wang H, Nettleton D, Ying K. Copy number variation detection using next generation sequencing read counts. BMC Bioinformatics 2014; 15:109. [PMID: 24731174 PMCID: PMC4021345 DOI: 10.1186/1471-2105-15-109] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2013] [Accepted: 04/02/2014] [Indexed: 12/11/2022] Open
Abstract
Background A copy number variation (CNV) is a difference between genotypes in the number of copies of a genomic region. Next generation sequencing (NGS) technologies provide sensitive and accurate tools for detecting genomic variations that include CNVs. However, statistical approaches for CNV identification using NGS are limited. We propose a new methodology for detecting CNVs using NGS data. This method (henceforth denoted by m-HMM) is based on a hidden Markov model with emission probabilities that are governed by mixture distributions. We use the Expectation-Maximization (EM) algorithm to estimate the parameters in the model. Results A simulation study demonstrates that our proposed m-HMM approach has greater power for detecting copy number gains and losses relative to existing methods. Furthermore, application of our m-HMM to DNA sequencing data from the two maize inbred lines B73 and Mo17 to identify CNVs that may play a role in creating phenotypic differences between these inbred lines provides results concordant with previous array-based efforts to identify CNVs. Conclusions The new m-HMM method is a powerful and practical approach for identifying CNVs from NGS data.
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Affiliation(s)
- Heng Wang
- Lyman Briggs College, Michigan State University, East Lansing, USA.
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147
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Marroni F, Pinosio S, Morgante M. Structural variation and genome complexity: is dispensable really dispensable? CURRENT OPINION IN PLANT BIOLOGY 2014; 18:31-6. [PMID: 24548794 DOI: 10.1016/j.pbi.2014.01.003] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2013] [Revised: 01/08/2014] [Accepted: 01/26/2014] [Indexed: 05/18/2023]
Abstract
Structural variants (SVs) such as copy number variants (CNVs) and presence/absence variants (PAVs) substantially contribute to genetic variation and have an important effect on phenotypic diversity. Since unbalanced SVs are by definition sequences present only in some individuals, they have therefore been referred to as dispensable genome and are not necessary for survival, even though they may provide an important contribution to phenotypic diversity within the species. However, some multi-copy sequences of the dispensable genomes (e.g., multigene families) may be needed in a given proportion by each individual, thus belonging to a conditionally dispensable portion of the pan-genome. Another interesting aspect reported by recent studies is that the rate at which SVs are formed might be influenced by the mating system and by common environmental stresses. In conclusion the dispensable genome plays an important role in genome evolution and in the complex interplay between the genome and the environment.
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Affiliation(s)
- Fabio Marroni
- Dipartimento di Scienze Agrarie e Ambientali, Università di Udine, 33100 Udine, Italy; Istituto di Genomica Applicata (IGA), 33100 Udine, Italy
| | - Sara Pinosio
- Institute of Biosciences and Bioresources, National Research Council, Via Madonna del Piano 10, 50019 Sesto Fiorentino (Firenze), Italy; Istituto di Genomica Applicata (IGA), 33100 Udine, Italy
| | - Michele Morgante
- Dipartimento di Scienze Agrarie e Ambientali, Università di Udine, 33100 Udine, Italy; Istituto di Genomica Applicata (IGA), 33100 Udine, Italy.
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148
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Lin K, Zhang N, Severing EI, Nijveen H, Cheng F, Visser RGF, Wang X, de Ridder D, Bonnema G. Beyond genomic variation--comparison and functional annotation of three Brassica rapa genomes: a turnip, a rapid cycling and a Chinese cabbage. BMC Genomics 2014; 15:250. [PMID: 24684742 PMCID: PMC4230417 DOI: 10.1186/1471-2164-15-250] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2013] [Accepted: 02/25/2014] [Indexed: 11/10/2022] Open
Abstract
Background Brassica rapa is an economically important crop species. During its long breeding history, a large number of morphotypes have been generated, including leafy vegetables such as Chinese cabbage and pakchoi, turnip tuber crops and oil crops. Results To investigate the genetic variation underlying this morphological variation, we re-sequenced, assembled and annotated the genomes of two B. rapa subspecies, turnip crops (turnip) and a rapid cycling. We then analysed the two resulting genomes together with the Chinese cabbage Chiifu reference genome to obtain an impression of the B. rapa pan-genome. The number of genes with protein-coding changes between the three genotypes was lower than that among different accessions of Arabidopsis thaliana, which can be explained by the smaller effective population size of B. rapa due to its domestication. Based on orthology to a number of non-brassica species, we estimated the date of divergence among the three B. rapa morphotypes at approximately 250,000 YA, far predating Brassica domestication (5,000-10,000 YA). Conclusions By analysing genes unique to turnip we found evidence for copy number differences in peroxidases, pointing to a role for the phenylpropanoid biosynthesis pathway in the generation of morphological variation. The estimated date of divergence among three B. rapa morphotypes implies that prior to domestication there was already considerably divergence among B. rapa genotypes. Our study thus provides two new B. rapa reference genomes, delivers a set of computer tools to analyse the resulting pan-genome and uses these to shed light on genetic drivers behind the rich morphological variation found in B. rapa. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-250) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Guusje Bonnema
- Laboratory of Plant Breeding, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands.
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149
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Vitte C, Fustier MA, Alix K, Tenaillon MI. The bright side of transposons in crop evolution. Brief Funct Genomics 2014; 13:276-95. [PMID: 24681749 DOI: 10.1093/bfgp/elu002] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The past decades have revealed an unexpected yet prominent role of so-called 'junk DNA' in the regulation of gene expression, thereby challenging our view of the mechanisms underlying phenotypic evolution. In particular, several mechanisms through which transposable elements (TEs) participate in functional genome diversity have been depicted, bringing to light the 'TEs bright side'. However, the relative contribution of those mechanisms and, more generally, the importance of TE-based polymorphisms on past and present phenotypic variation in crops species remain poorly understood. Here, we review current knowledge on both issues, and discuss how analyses of massively parallel sequencing data combined with statistical methodologies and functional validations will help unravelling the impact of TEs on crop evolution in a near future.
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150
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Makino T, McLysaght A, Kawata M. Genome-wide deserts for copy number variation in vertebrates. Nat Commun 2014; 4:2283. [PMID: 23917329 DOI: 10.1038/ncomms3283] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2013] [Accepted: 07/10/2013] [Indexed: 01/14/2023] Open
Abstract
Most copy number variations are neutral, but some are deleterious and associated with various human diseases. Copy number variations are distributed non-randomly in vertebrate genomes, and it was recently reported that ohnologs, which are duplicated genes derived from whole genome duplication, are refractory to copy number variations. However, it is unclear what genomic factors affect the deleterious effects of copy number variations and the biological significance of the biased genomic distribution of copy number variations remains poorly understood. Here we show that non-ohnologs neighbouring ohnologs are unlikely to have copy number variations, resulting in ohnolog-rich regions in vertebrate genomes being copy number variation deserts. Our results suggest that the genomic location of ohnologs is a determining factor in the retention of copy number variations and that the dosage-balanced ohnologs are likely to cause the deleterious effects of copy number variations in these regions. We propose that investigating copy number variation of genes in regions that are typically copy number variation deserts is an efficient means to find disease-related copy number variations.
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Affiliation(s)
- Takashi Makino
- Department of Ecology and Evolutionary Biology, Graduate School of Life Sciences, Tohoku University, 6-3, Aramaki Aza Aoba, Aoba-ku 980-8578, Japan.
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