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Delourme D, Brémaud L, Plazanet I, Pélissier P, Label P, Boizot N, Breton C, Durand S, Costa G. Transcriptomic monitoring of Douglas-fir heartwood formation. BMC Genom Data 2023; 24:69. [PMID: 37986039 PMCID: PMC10662504 DOI: 10.1186/s12863-023-01172-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 11/10/2023] [Indexed: 11/22/2023] Open
Abstract
OBJECTIVES Molecular cues linked to heartwood formation open new (complementary) perspectives to genetic breeding programs of Douglas-fir, a tree species largely cultivated in Europe for the natural durability and civil engineering properties of its wood. DATA DESCRIPTION RNAs from a single genotype of Douglas-fir, extracted from three distinct wood zones (outer sapwood, inner sapwood and transition zone) at four vegetative seasons to generate an extensive RNA-seq dataset used to apprehend the in-wood dynamic and seasonality of heartwood formation in this hardwood model species. Previously published data collected on somatic embryos of the same genotype could be merged with the present dataset to upgrade grade the Douglas-fir reference transcriptome.
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Affiliation(s)
- Didier Delourme
- Université de Limoges, LABCIS, UR 22722, 123 avenue Albert Thomas, Limoges, F-87060, France
| | - Laure Brémaud
- Université de Limoges, LABCIS, UR 22722, 123 avenue Albert Thomas, Limoges, F-87060, France
| | - Idelette Plazanet
- Université de Limoges, LABCIS, UR 22722, 123 avenue Albert Thomas, Limoges, F-87060, France
| | - Patrick Pélissier
- Université de Limoges, LABCIS, UR 22722, 123 avenue Albert Thomas, Limoges, F-87060, France
| | | | | | | | - Stéphanie Durand
- Université de Limoges, CAPTuR, UMR INSERM/CHU 1308, 2 Rue du Docteur Marcland, Limoges, F-87025, France
| | - Guy Costa
- Université de Limoges, LABCIS, UR 22722, 123 avenue Albert Thomas, Limoges, F-87060, France.
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2
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Velasco VME, Ferreira A, Zaman S, Noordermeer D, Ensminger I, Wegrzyn JL. A long-read and short-read transcriptomics approach provides the first high-quality reference transcriptome and genome annotation for Pseudotsuga menziesii (Douglas-fir). G3 (BETHESDA, MD.) 2023; 13:jkac304. [PMID: 36454025 PMCID: PMC10468028 DOI: 10.1093/g3journal/jkac304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 12/13/2021] [Accepted: 10/19/2022] [Indexed: 12/02/2022]
Abstract
Douglas-fir (Pseudotsuga menziesii) is native to western North America. It grows in a wide range of environmental conditions and is an important timber tree. Although there are several studies on the gene expression responses of Douglas-fir to abiotic cues, the absence of high-quality transcriptome and genome data is a barrier to further investigation. Like for most conifers, the available transcriptome and genome reference dataset for Douglas-fir remains fragmented and requires refinement. We aimed to generate a highly accurate, and complete reference transcriptome and genome annotation. We deep-sequenced the transcriptome of Douglas-fir needles from seedlings that were grown under nonstress control conditions or a combination of heat and drought stress conditions using long-read (LR) and short-read (SR) sequencing platforms. We used 2 computational approaches, namely de novo and genome-guided LR transcriptome assembly. Using the LR de novo assembly, we identified 1.3X more high-quality transcripts, 1.85X more "complete" genes, and 2.7X more functionally annotated genes compared to the genome-guided assembly approach. We predicted 666 long noncoding RNAs and 12,778 unique protein-coding transcripts including 2,016 putative transcription factors. We leveraged the LR de novo assembled transcriptome with paired-end SR and a published single-end SR transcriptome to generate an improved genome annotation. This was conducted with BRAKER2 and refined based on functional annotation, repetitive content, and transcriptome alignment. This high-quality genome annotation has 51,419 unique gene models derived from 322,631 initial predictions. Overall, our informatics approach provides a new reference Douglas-fir transcriptome assembly and genome annotation with considerably improved completeness and functional annotation.
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Affiliation(s)
| | - Alyssa Ferreira
- Department of Evolution and Ecology, University of
Connecticut, Storrs, CT 06269, USA
| | - Sumaira Zaman
- Department of Evolution and Ecology, University of
Connecticut, Storrs, CT 06269, USA
| | - Devin Noordermeer
- Department of Biology, University of Toronto,
Mississauga, ON L5L 1C8, Canada
- Graduate Department of Cell and Systems Biology, University of
Toronto, Toronto, ON M5S, Canada
| | - Ingo Ensminger
- Department of Biology, University of Toronto,
Mississauga, ON L5L 1C8, Canada
- Graduate Department of Cell and Systems Biology, University of
Toronto, Toronto, ON M5S, Canada
- Graduate Department of Ecology and Evolutionary Biology, University of
Toronto, Toronto, ON M5S, Canada
| | - Jill L Wegrzyn
- Department of Evolution and Ecology, University of
Connecticut, Storrs, CT 06269, USA
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3
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Elorriaga E, Klocko AL, Ma C, du Plessis M, An X, Myburg AA, Strauss SH. Genetic containment in vegetatively propagated forest trees: CRISPR disruption of LEAFY function in Eucalyptus gives sterile indeterminate inflorescences and normal juvenile development. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:1743-1755. [PMID: 33774917 PMCID: PMC8428835 DOI: 10.1111/pbi.13588] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 02/27/2021] [Accepted: 03/14/2021] [Indexed: 05/05/2023]
Abstract
Eucalyptus is among the most widely planted taxa of forest trees worldwide. However, its spread as an exotic or genetically engineered form can create ecological and social problems. To mitigate gene flow via pollen and seeds, we mutated the Eucalyptus orthologue of LEAFY (LFY) by transforming a Eucalyptus grandis × urophylla wild-type hybrid and two Flowering Locus T (FT) overexpressing (and flowering) lines with CRISPR Cas9 targeting its LFY orthologue, ELFY. We achieved high rates of elfy biallelic knockouts, often approaching 100% of transgene insertion events. Frameshift mutations and deletions removing conserved amino acids caused strong floral alterations, including indeterminacy in floral development and an absence of male and female gametes. These mutants were otherwise visibly normal and did not differ statistically from transgenic controls in juvenile vegetative growth rate or leaf morphology in greenhouse trials. Genes upstream or near to ELFY in the floral development pathway were overexpressed, whereas floral organ identity genes downstream of ELFY were severely depressed. We conclude that disruption of ELFY function appears to be a useful tool for sexual containment, without causing statistically significant or large adverse effects on juvenile vegetative growth or leaf morphology.
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Affiliation(s)
- Estefania Elorriaga
- Department of Forest Ecosystems and SocietyOregon State UniversityCorvallisORUSA
- Present address:
Department of Molecular and Structural BiochemistryNorth Carolina State UniversityRaleighNCUSA
| | - Amy L. Klocko
- Department of BiologyUniversity of Colorado Colorado SpringsColorado SpringsCOUSA
| | - Cathleen Ma
- Department of Forest Ecosystems and SocietyOregon State UniversityCorvallisORUSA
| | - Marc du Plessis
- Department of Zoology and EntomologyUniversity of PretoriaPretoriaSouth Africa
| | - Xinmin An
- Beijing Advanced Innovation Center for Tree Breeding by Molecular DesignNational Engineering Laboratory for Tree BreedingCollege of Biological Sciences and BiotechnologyBeijing Forestry UniversityBeijingChina
| | - Alexander A. Myburg
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI)University of PretoriaPretoriaSouth Africa
| | - Steven H. Strauss
- Department of Forest Ecosystems and SocietyOregon State UniversityCorvallisORUSA
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4
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George J, Schueler S, Grabner M, Karanitsch‐Ackerl S, Mayer K, Stierschneider M, Weissenbacher L, van Loo M. Looking for the needle in a downsized haystack: Whole-exome sequencing unravels genomic signals of climatic adaptation in Douglas-fir ( Pseudotsuga menziesii). Ecol Evol 2021; 11:8238-8253. [PMID: 34188883 PMCID: PMC8216971 DOI: 10.1002/ece3.7654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 04/14/2021] [Accepted: 04/21/2021] [Indexed: 11/24/2022] Open
Abstract
Conifers often occur along steep gradients of diverse climates throughout their natural ranges, which is expected to result in spatially varying selection to local climate conditions. However, signals of climatic adaptation can often be confounded, because unraveled clines covary with signals caused by neutral evolutionary processes such as gene flow and genetic drift. Consequently, our understanding of how selection and gene flow have shaped phenotypic and genotypic differentiation in trees is still limited.A 40-year-old common garden experiment comprising 16 Douglas-fir (Pseudotsuga menziesii) provenances from a north-to-south gradient of approx. 1,000 km was analyzed, and genomic information was obtained from exome capture, which resulted in an initial genomic dataset of >90,000 single nucleotide polymorphisms. We used a restrictive and conservative filtering approach, which permitted us to include only SNPs and individuals in environmental association analysis (EAA) that were free of potentially confounding effects (LD, relatedness among trees, heterozygosity deficiency, and deviations from Hardy-Weinberg proportions). We used four conceptually different genome scan methods based on FST outlier detection and gene-environment association in order to disentangle truly adaptive SNPs from neutral SNPs.We found that a relatively small proportion of the exome showed a truly adaptive signal (0.01%-0.17%) when population substructuring and multiple testing was accounted for. Nevertheless, the unraveled SNP candidates showed significant relationships with climate at provenance origins, which strongly suggests that they have featured adaptation in Douglas-fir along a climatic gradient. Two SNPs were independently found by three of the employed algorithms, and one of them is in close proximity to an annotated gene involved in circadian clock control and photoperiodism as was similarly found in Populus balsamifera. Synthesis. We conclude that despite neutral evolutionary processes, phenotypic and genomic signals of adaptation to climate are responsible for differentiation, which in particular explain disparity between the well-known coastal and interior varieties of Douglas-fir.
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Affiliation(s)
- Jan‐Peter George
- Faculty of Science & TechnologyTartu ObservatoryUniversity of TartuTartuEstonia
- Department of Forest Growth, Silviculture and Genetics/Unit of provenance research and breedingAustrian Research Centre for ForestsViennaAustria
| | - Silvio Schueler
- Department of Forest Growth, Silviculture and GeneticsAustrian Research Centre for ForestsViennaAustria
| | - Michael Grabner
- Institute of Wood Science and TechnologyUniversity of Natural Resources and Life Sciences (BOKU)TullnAustria
| | - Sandra Karanitsch‐Ackerl
- Institute of Wood Science and TechnologyUniversity of Natural Resources and Life Sciences (BOKU)TullnAustria
| | - Konrad Mayer
- Institute of Wood Science and TechnologyUniversity of Natural Resources and Life Sciences (BOKU)TullnAustria
| | | | - Lambert Weissenbacher
- Department of Forest Growth, Silviculture and Genetics/Unit of provenance research and breedingAustrian Research Centre for ForestsViennaAustria
| | - Marcela van Loo
- Department of Forest Growth, Silviculture and Genetics/Unit of provenance research and breedingAustrian Research Centre for ForestsViennaAustria
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Population Genetic Diversity and Structure of Ancient Tree Populations of Cryptomeria japonica var. sinensis Based on RAD-seq Data. FORESTS 2020. [DOI: 10.3390/f11111192] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Research highlights: Our study is the first to explore the genetic composition of ancient Cryptomeria trees across a distribution range in China. Background and objectives: Cryptomeria japonica var. sinensis is a native forest species of China; it is widely planted in the south of the country to create forests and for wood production. Unlike Cryptomeria in Japan, genetic Chinese Cryptomeria has seldom been studied, although there is ample evidence of its great ecological and economic value. Materials and methods: Because of overcutting, natural populations are rare in the wild. In this study, we investigated seven ancient tree populations to explore the genetic composition of Chinese Cryptomeria through ddRAD-seq technology. Results: The results reveal a lower genetic variation but higher genetic differentiation (Ho = 0.143, FST = 0.1204) than Japanese Cryptomeria (Ho = 0.245, FST = 0.0455). The 86% within-population variation is based on an analysis of molecular variance (AMOVA). Significant excess heterozygosity was detected in three populations and some outlier loci were found; these were considered to be the consequence of selection or chance. Structure analysis and dendrogram construction divided the seven ancient tree populations into four groups corresponding to the geographical provinces in which the populations are located, but there was no obvious correlation between genetic distance and geographic distance. A demographic history analysis conducted by a Stairway Plot showed that the effective population size of Chinese Cryptomeria had experienced a continuing decline from the mid-Pleistocene to the present. Our findings suggest that the strong genetic drift caused by climate fluctuation and intense anthropogenic disturbance together contributed to the current low diversity and structure. Considering the species’ unfavorable conservation status, strategies are urgently required to preserve the remaining genetic resources.
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6
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Perry A, Wachowiak W, Downing A, Talbot R, Cavers S. Development of a single nucleotide polymorphism array for population genomic studies in four European pine species. Mol Ecol Resour 2020; 20:1697-1705. [PMID: 32633888 DOI: 10.1111/1755-0998.13223] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 06/03/2020] [Accepted: 06/25/2020] [Indexed: 02/06/2023]
Abstract
Pines are some of the most ecologically and economically important tree species in the world, and many have enormous natural distributions or have been extensively planted. However, a lack of rapid genotyping capability is hampering progress in understanding the molecular basis of genetic variation in these species. Here, we deliver an efficient tool for genotyping thousands of single nucleotide polymorphism (SNP) markers across the genome that can be applied to genetic studies in pines. Polymorphisms from resequenced candidate genes and transcriptome sequences of P. sylvestris, P. mugo, P. uncinata, P. uliginosa and P. radiata were used to design a 49,829 SNP array (Axiom_PineGAP, Thermo Fisher). Over a third (34.68%) of the unigenes identified from the P. sylvestris transcriptome were represented on the array, which was used to screen samples of four pine species. The conversion rate for the array on all samples was 42% (N = 20,795 SNPs) and was similar for SNPs sourced from resequenced candidate gene and transcriptome sequences. The broad representation of gene ontology terms by unigenes containing converted SNPs reflected their coverage across the full transcriptome. Over a quarter of successfully converted SNPs were polymorphic among all species, and the data were successful in discriminating among the species and some individual populations. The SNP array provides a valuable new tool to advance genetic studies in these species and demonstrates the effectiveness of the technology for rapid genotyping in species with large and complex genomes.
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Affiliation(s)
- Annika Perry
- UK Centre for Ecology & Hydrology Edinburgh, Penicuik, UK
| | - Witold Wachowiak
- Institute of Environmental Biology, Faculty of Biology, Adam Mickiewicz University, Poznań, Poland
| | - Alison Downing
- Edinburgh Genomics, Ashworth Laboratories, University of Edinburgh, Edinburgh, UK
| | - Richard Talbot
- Edinburgh Genomics, Ashworth Laboratories, University of Edinburgh, Edinburgh, UK
| | - Stephen Cavers
- UK Centre for Ecology & Hydrology Edinburgh, Penicuik, UK
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7
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Linkage disequilibrium vs. pedigree: Genomic selection prediction accuracy in conifer species. PLoS One 2020; 15:e0232201. [PMID: 32520936 PMCID: PMC7286500 DOI: 10.1371/journal.pone.0232201] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 04/08/2020] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND The presupposition of genomic selection (GS) is that predictive accuracies should be based on population-wide linkage disequilibrium (LD). However, in species with large, highly complex genomes the limitation of marker density may preclude the ability to resolve LD accurately enough for GS. Here we investigate such an effect in two conifer species with ~ 20 Gbp genomes, Douglas-fir (Pseudotsuga menziesii Mirb. (Franco)) and Interior spruce (Picea glauca (Moench) Voss x Picea engelmannii Parry ex Engelm.). Random sampling of markers was performed to obtain SNP sets with totals in the range of 200-50,000, this was replicated 10 times. Ridge Regression Best Linear Unbiased Predictor (RR-BLUP) was deployed as the GS method to test these SNP sets, and 10-fold cross-validation was performed on 1,321 Douglas-fir trees, representing 37 full-sib F1 families and on 1,126 Interior spruce trees, representing 25 open-pollinated (half-sib) families. Both trials are located on 3 sites in British Columbia, Canada. RESULTS As marker number increased, so did GS predictive accuracy for both conifer species. However, a plateau in the gain of accuracy became apparent around 10,000-15,000 markers for both Douglas-fir and Interior spruce. Despite random marker selection, little variation in predictive accuracy was observed across replications. On average, Douglas-fir prediction accuracies were higher than those of Interior spruce, reflecting the difference between full- and half-sib families for Douglas-fir and Interior spruce populations, respectively, as well as their respective effective population size. CONCLUSIONS Although possibly advantageous within an advanced breeding population, reducing marker density cannot be recommended for carrying out GS in conifers. Significant LD between markers and putative causal variants was not detected using 50,000 SNPS, and GS was enabled only through the tracking of relatedness in the populations studied. Dramatically increasing marker density would enable said markers to better track LD with causal variants in these large, genetically diverse genomes; as well as providing a model that could be used across populations, breeding programs, and traits.
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Howe GT, Jayawickrama K, Kolpak SE, Kling J, Trappe M, Hipkins V, Ye T, Guida S, Cronn R, Cushman SA, McEvoy S. An Axiom SNP genotyping array for Douglas-fir. BMC Genomics 2020; 21:9. [PMID: 31900111 PMCID: PMC6942338 DOI: 10.1186/s12864-019-6383-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2019] [Accepted: 12/10/2019] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND In forest trees, genetic markers have been used to understand the genetic architecture of natural populations, identify quantitative trait loci, infer gene function, and enhance tree breeding. Recently, new, efficient technologies for genotyping thousands to millions of single nucleotide polymorphisms (SNPs) have finally made large-scale use of genetic markers widely available. These methods will be exceedingly valuable for improving tree breeding and understanding the ecological genetics of Douglas-fir, one of the most economically and ecologically important trees in the world. RESULTS We designed SNP assays for 55,766 potential SNPs that were discovered from previous transcriptome sequencing projects. We tested the array on ~ 2300 related and unrelated coastal Douglas-fir trees (Pseudotsuga menziesii var. menziesii) from Oregon and Washington, and 13 trees of interior Douglas-fir (P. menziesii var. glauca). As many as ~ 28 K SNPs were reliably genotyped and polymorphic, depending on the selected SNP call rate. To increase the number of SNPs and improve genome coverage, we developed protocols to 'rescue' SNPs that did not pass the default Affymetrix quality control criteria (e.g., 97% SNP call rate). Lowering the SNP call rate threshold from 97 to 60% increased the number of successful SNPs from 20,669 to 28,094. We used a subset of 395 unrelated trees to calculate SNP population genetic statistics for coastal Douglas-fir. Over a range of call rate thresholds (97 to 60%), the median call rate for SNPs in Hardy-Weinberg equilibrium ranged from 99.2 to 99.7%, and the median minor allele frequency ranged from 0.198 to 0.233. The successful SNPs also worked well on interior Douglas-fir. CONCLUSIONS Based on the original transcriptome assemblies and comparisons to version 1.0 of the Douglas-fir reference genome, we conclude that these SNPs can be used to genotype about 10 K to 15 K loci. The Axiom genotyping array will serve as an excellent foundation for studying the population genomics of Douglas-fir and for implementing genomic selection. We are currently using the array to construct a linkage map and test genomic selection in a three-generation breeding program for coastal Douglas-fir.
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Affiliation(s)
- Glenn T Howe
- Pacific Northwest Tree Improvement Research Cooperative, Department of Forest Ecosystems and Society, Oregon State University, Corvallis, OR, USA.
| | - Keith Jayawickrama
- Northwest Tree Improvement Cooperative, Department of Forest Ecosystems and Society, Oregon State University, Corvallis, OR, USA
| | - Scott E Kolpak
- Pacific Northwest Tree Improvement Research Cooperative, Department of Forest Ecosystems and Society, Oregon State University, Corvallis, OR, USA
| | - Jennifer Kling
- Pacific Northwest Tree Improvement Research Cooperative, Department of Forest Ecosystems and Society, Oregon State University, Corvallis, OR, USA
| | - Matt Trappe
- Northwest Tree Improvement Cooperative, Department of Forest Ecosystems and Society, Oregon State University, Corvallis, OR, USA
| | - Valerie Hipkins
- USDA Forest Service, National Forest Genetics Laboratory, Placerville, CA, USA
| | - Terrance Ye
- Northwest Tree Improvement Cooperative, Department of Forest Ecosystems and Society, Oregon State University, Corvallis, OR, USA
| | | | - Richard Cronn
- USDA Forest Service, Pacific Northwest Research Station, Corvallis, OR, USA
| | - Samuel A Cushman
- USDA Forest Service, Rocky Mountain Research Station, Flagstaff, AZ, USA
| | - Susan McEvoy
- Pacific Northwest Tree Improvement Research Cooperative, Department of Forest Ecosystems and Society, Oregon State University, Corvallis, OR, USA
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Utilization of Tissue Ploidy Level Variation in de Novo Transcriptome Assembly of Pinus sylvestris. G3-GENES GENOMES GENETICS 2019; 9:3409-3421. [PMID: 31427456 PMCID: PMC6778806 DOI: 10.1534/g3.119.400357] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Compared to angiosperms, gymnosperms lag behind in the availability of assembled and annotated genomes. Most genomic analyses in gymnosperms, especially conifer tree species, rely on the use of de novo assembled transcriptomes. However, the level of allelic redundancy and transcript fragmentation in these assembled transcriptomes, and their effect on downstream applications have not been fully investigated. Here, we assessed three assembly strategies for short-reads data, including the utility of haploid megagametophyte tissue during de novo assembly as single-allele guides, for six individuals and five different tissues in Pinus sylvestris. We then contrasted haploid and diploid tissue genotype calls obtained from the assembled transcriptomes to evaluate the extent of paralog mapping. The use of the haploid tissue during assembly increased its completeness without reducing the number of assembled transcripts. Our results suggest that current strategies that rely on available genomic resources as guidance to minimize allelic redundancy are less effective than the application of strategies that cluster redundant assembled transcripts. The strategy yielding the lowest levels of allelic redundancy among the assembled transcriptomes assessed here was the generation of SuperTranscripts with Lace followed by CD-HIT clustering. However, we still observed some levels of heterozygosity (multiple gene fragments per transcript reflecting allelic redundancy) in this assembled transcriptome on the haploid tissue, indicating that further filtering is required before using these assemblies for downstream applications. We discuss the influence of allelic redundancy when these reference transcriptomes are used to select regions for probe design of exome capture baits and for estimation of population genetic diversity.
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Telfer E, Graham N, Macdonald L, Li Y, Klápště J, Resende M, Neves LG, Dungey H, Wilcox P. A high-density exome capture genotype-by-sequencing panel for forestry breeding in Pinus radiata. PLoS One 2019; 14:e0222640. [PMID: 31568509 PMCID: PMC6768539 DOI: 10.1371/journal.pone.0222640] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 09/04/2019] [Indexed: 01/19/2023] Open
Abstract
Development of genome-wide resources for application in genomic selection or genome-wide association studies, in the absence of full reference genomes, present a challenge to the forestry industry, where longer breeding cycles could benefit from the accelerated selection possible through marker-based breeding value predictions. In particular, large conifer megagenomes require a strategy to reduce complexity, whilst ensuring genome-wide coverage is achieved. Using a transcriptome-based reference template, we have successfully developed a high density exome capture genotype-by-sequencing panel for radiata pine (Pinus radiata D.Don), capable of capturing in excess of 80,000 single nucleotide polymorphism (SNP) markers with a minor allele frequency above 0.03 in the population tested. This represents approximately 29,000 gene models from a core set of 48,914 probes. A set of 704 SNP markers capable of pedigree reconstruction and differentiating individual genotypes were tested within two full-sib mapping populations. While as few as 70 markers could reconstruct parentage in almost all cases, the impact of missing genotypes was noticeable in several offspring. Therefore, 60 sets of 110 randomly selected SNP markers were compared for both parentage reconstruction and clone differentiation. The performance in parentage reconstruction showed little variation over 60 iterations. However, there was notable variation in discriminatory power between closely related individuals, indicating a higher density SNP marker panel may be required to elucidate hidden relationships in complex pedigrees.
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Affiliation(s)
- Emily Telfer
- New Zealand Forest Research Institute LTD. trading as Scion, Rotorua, New Zealand
| | - Natalie Graham
- New Zealand Forest Research Institute LTD. trading as Scion, Rotorua, New Zealand
| | - Lucy Macdonald
- New Zealand Forest Research Institute LTD. trading as Scion, Rotorua, New Zealand
| | - Yongjun Li
- New Zealand Forest Research Institute LTD. trading as Scion, Rotorua, New Zealand
| | - Jaroslav Klápště
- New Zealand Forest Research Institute LTD. trading as Scion, Rotorua, New Zealand
| | - Marcio Resende
- Horticultural Sciences, University of Florida, Gainesville, FL, United States of America
- RAPiD Genomics LLC, Gainesville, FL, United States of America
| | | | - Heidi Dungey
- New Zealand Forest Research Institute LTD. trading as Scion, Rotorua, New Zealand
| | - Phillip Wilcox
- Department of Mathematics and Statistics, University of Otago, Dunedin, New Zealand
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11
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Chinese Fir Breeding in the High-Throughput Sequencing Era: Insights from SNPs. FORESTS 2019. [DOI: 10.3390/f10080681] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Knowledge on population diversity and structure is of fundamental importance for conifer breeding programs. In this study, we concentrated on the development and application of high-density single nucleotide polymorphism (SNP) markers through a high-throughput sequencing technique termed as specific-locus amplified fragment sequencing (SLAF-seq) for the economically important conifer tree species, Chinese fir (Cunninghamia lanceolata). Based on the SLAF-seq, we successfully established a high-density SNP panel consisting of 108,753 genomic SNPs from Chinese fir. This SNP panel facilitated us in gaining insight into the genetic base of the Chinese fir advance breeding population with 221 genotypes for its genetic variation, relationship and diversity, and population structure status. Overall, the present population appears to have considerable genetic variability. Most (94.15%) of the variability was attributed to the genetic differentiation of genotypes, very limited (5.85%) variation occurred on the population (sub-origin set) level. Correspondingly, low FST (0.0285–0.0990) values were seen for the sub-origin sets. When viewing the genetic structure of the population regardless of its sub-origin set feature, the present SNP data opened a new population picture where the advanced Chinese fir breeding population could be divided into four genetic sets, as evidenced by phylogenetic tree and population structure analysis results, albeit some difference in membership of the corresponding set (cluster vs. group). It also suggested that all the genetic sets were admixed clades revealing a complex relationship of the genotypes of this population. With a step wise pruning procedure, we captured a core collection (core 0.650) harboring 143 genotypes that maintains all the allele, diversity, and specific genetic structure of the whole population. This generalist core is valuable for the Chinese fir advanced breeding program and further genetic/genomic studies.
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12
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Thistlethwaite FR, Ratcliffe B, Klápště J, Porth I, Chen C, Stoehr MU, El-Kassaby YA. Genomic selection of juvenile height across a single-generational gap in Douglas-fir. Heredity (Edinb) 2019; 122:848-863. [PMID: 30631145 PMCID: PMC6781123 DOI: 10.1038/s41437-018-0172-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Revised: 11/24/2018] [Accepted: 11/26/2018] [Indexed: 11/30/2022] Open
Abstract
Here, we perform cross-generational GS analysis on coastal Douglas-fir (Pseudotsuga menziesii), reflecting trans-generational selective breeding application. A total of 1321 trees, representing 37 full-sib F1 families from 3 environments in British Columbia, Canada, were used as the training population for (1) EBVs (estimated breeding values) of juvenile height (HTJ) in the F1 generation predicting genomic EBVs of HTJ of 136 individuals in the F2 generation, (2) deregressed EBVs of F1 HTJ predicting deregressed genomic EBVs of F2 HTJ, (3) F1 mature height (HT35) predicting HTJ EBVs in F2, and (4) deregressed F1 HT35 predicting genomic deregressed HTJ EBVs in F2. Ridge regression best linear unbiased predictor (RR-BLUP), generalized ridge regression (GRR), and Bayes-B GS methods were used and compared to pedigree-based (ABLUP) predictions. GS accuracies for scenarios 1 (0.92, 0.91, and 0.91) and 3 (0.57, 0.56, and 0.58) were similar to their ABLUP counterparts (0.92 and 0.60, respectively) (using RR-BLUP, GRR, and Bayes-B). Results using deregressed values fell dramatically for both scenarios 2 and 4 which approached zero in many cases. Cross-generational GS validation of juvenile height in Douglas-fir produced predictive accuracies almost as high as that of ABLUP. Without capturing LD, GS cannot surpass the prediction of ABLUP. Here we tracked pedigree relatedness between training and validation sets. More markers or improved distribution of markers are required to capture LD in Douglas-fir. This is essential for accurate forward selection among siblings as markers that track pedigree are of little use for forward selection of individuals within controlled pollinated families.
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Affiliation(s)
- Frances R Thistlethwaite
- Department of Forest and Conservation Sciences, Faculty of Forestry, The University of British Columbia, 2424 Main Mall, Vancouver, BC, V6T 1Z4, Canada
| | - Blaise Ratcliffe
- Department of Forest and Conservation Sciences, Faculty of Forestry, The University of British Columbia, 2424 Main Mall, Vancouver, BC, V6T 1Z4, Canada
| | - Jaroslav Klápště
- Department of Forest and Conservation Sciences, Faculty of Forestry, The University of British Columbia, 2424 Main Mall, Vancouver, BC, V6T 1Z4, Canada
- Scion (New Zealand Forest Research Institute Ltd.), 49 Sala Street, Whakarewarewa, Rotorua, 3046, New Zealand
- Department of Genetics and Physiology of Forest Trees, Faculty of Forestry and Wood Sciences, Czech University of Life Sciences Prague, Praha 6, 165 21, Czech Republic
| | - Ilga Porth
- Département des sciences du bois et de la forêt, Université Laval, G1V 0A6, Québec, QC, Canada
| | - Charles Chen
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK, 74078-3035, USA
| | - Michael U Stoehr
- British Columbia Ministry of Forests, Lands and Natural Resource Operations, Victoria, BC, V8W 9C2, Canada
| | - Yousry A El-Kassaby
- Department of Forest and Conservation Sciences, Faculty of Forestry, The University of British Columbia, 2424 Main Mall, Vancouver, BC, V6T 1Z4, Canada.
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Azaiez A, Pavy N, Gérardi S, Laroche J, Boyle B, Gagnon F, Mottet MJ, Beaulieu J, Bousquet J. A catalog of annotated high-confidence SNPs from exome capture and sequencing reveals highly polymorphic genes in Norway spruce (Picea abies). BMC Genomics 2018; 19:942. [PMID: 30558528 PMCID: PMC6296092 DOI: 10.1186/s12864-018-5247-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 11/14/2018] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Norway spruce [Picea abies (L.) Karst.] is ecologically and economically one of the most important conifer worldwide. Our main goal was to develop a large catalog of annotated high confidence gene SNPs that should sustain the development of genomic tools for the conservation of natural and domesticated genetic diversity resources, and hasten tree breeding efforts in this species. RESULTS Targeted sequencing was achieved by capturing P. abies exome with probes previously designed from the sequenced transcriptome of white spruce (Picea glauca (Moench) Voss). Capture efficiency was high (74.5%) given a high level of exome conservation between the two species. Using stringent criteria, we delimited a set of 61,771 high-confidence SNPs across 13,543 genes. To validate SNPs, a high-throughput genotyping array was developed for a subset of 5571 predicted SNPs representing as many different gene loci, and was used to genotype over 1000 trees. The estimated true positive rate of the resource was 84.2%, which was comparable with the genotyping success rate obtained for P. abies control SNPs recycled from previous genotyping efforts. We also analyzed SNP abundance across various gene functional categories. Several GO terms and gene families involved in stress response were found over-represented in highly polymorphic genes. CONCLUSION The annotated high-confidence SNP catalog developed herein represents a valuable genomic resource, being representative of over 13 K genes distributed across the P. abies genome. This resource should serve a variety of population genomics and breeding applications in Norway spruce.
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Affiliation(s)
- Aïda Azaiez
- Canada Research Chair in Forest Genomics, Forest Research Centre, Université Laval, Québec, Québec G1V 0A6 Canada
- Institute of Integrative Biology and Systems, Université Laval, Québec, Québec G1V 0A6 Canada
| | - Nathalie Pavy
- Canada Research Chair in Forest Genomics, Forest Research Centre, Université Laval, Québec, Québec G1V 0A6 Canada
- Institute of Integrative Biology and Systems, Université Laval, Québec, Québec G1V 0A6 Canada
| | - Sébastien Gérardi
- Canada Research Chair in Forest Genomics, Forest Research Centre, Université Laval, Québec, Québec G1V 0A6 Canada
- Institute of Integrative Biology and Systems, Université Laval, Québec, Québec G1V 0A6 Canada
| | - Jérôme Laroche
- Institute of Integrative Biology and Systems, Université Laval, Québec, Québec G1V 0A6 Canada
| | - Brian Boyle
- Institute of Integrative Biology and Systems, Université Laval, Québec, Québec G1V 0A6 Canada
| | - France Gagnon
- Canada Research Chair in Forest Genomics, Forest Research Centre, Université Laval, Québec, Québec G1V 0A6 Canada
- Institute of Integrative Biology and Systems, Université Laval, Québec, Québec G1V 0A6 Canada
| | - Marie-Josée Mottet
- Direction de la recherche forestière, Ministère des Forêts, de la Faune et des Parcs du Québec, 2700 Einstein, Québec, Québec G1P 3W8 Canada
| | - Jean Beaulieu
- Canada Research Chair in Forest Genomics, Forest Research Centre, Université Laval, Québec, Québec G1V 0A6 Canada
- Institute of Integrative Biology and Systems, Université Laval, Québec, Québec G1V 0A6 Canada
| | - Jean Bousquet
- Canada Research Chair in Forest Genomics, Forest Research Centre, Université Laval, Québec, Québec G1V 0A6 Canada
- Institute of Integrative Biology and Systems, Université Laval, Québec, Québec G1V 0A6 Canada
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Reichman JR, Rygiewicz PT, Johnson MG, Bollman MA, Smith BM, Krantz QT, King CJ, Kovalcik KD, Andersen CP. Douglas-Fir ( Pseudotsuga menziesii (Mirb.) Franco) Transcriptome Profile Changes Induced by Diesel Emissions Generated with CeO 2 Nanoparticle Fuel Borne Catalyst. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2018; 52:10067-10077. [PMID: 30075627 PMCID: PMC6309902 DOI: 10.1021/acs.est.8b02169] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
It is important to understand molecular effects on plants exposed to compounds released from use of products containing engineered nanomaterials. Here, we present mRNA sequencing data on transcriptome impacts to Douglas-fir following 2 weeks of sublethal exposure to 30:1 diluted airborne emissions released from combustion of diesel fuel containing engineered CeO2 nanoparticle catalysts (DECe). Our hypothesis was that chamber exposure to DECe would induce distinct transcriptome changes in seedling needles compared with responses to conventional diesel exhaust (DE) or filtered DECe Gas Phase. Significantly increased uptake/binding of Ce in needles of DECe treated seedlings was 2.7X above background levels and was associated with altered gene expression patterns. All 225 Blast2GO gene ontologies (GOs) enriched by up-regulated DECe transcripts were nested within GOs for DE, however, 29 of 31 enriched GOs for down-regulated DECe transcripts were unique. MapMan analysis also identified three pathways enriched with DECe down-regulated transcripts. There was prominent representation of genes with attenuated expression in transferase, transporter, RNA regulation and protein degradation GOs and pathways. CeO2 nanoparticle additive decreased and shifted molecular impact of diesel emissions. Wide-spread use of such products and chronic environmental exposure to DECe may adversely affect plant physiology and development.
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Affiliation(s)
- Jay R. Reichman
- Western Ecology Division, National Health and Environmental Effects Laboratory, US Environmental Protection Agency, Corvallis, Oregon, 97333, USA
- Correspondence: Jay R. Reichman, Western Ecology Division, National Health and Environmental Effects Laboratory, US Environmental Protection Agency, Corvallis, Oregon, 97333, USA. Tel: 541-754-4643.
| | - Paul T. Rygiewicz
- Western Ecology Division, National Health and Environmental Effects Laboratory, US Environmental Protection Agency, Corvallis, Oregon, 97333, USA
| | - Mark G. Johnson
- Western Ecology Division, National Health and Environmental Effects Laboratory, US Environmental Protection Agency, Corvallis, Oregon, 97333, USA
| | - Michael A. Bollman
- Western Ecology Division, National Health and Environmental Effects Laboratory, US Environmental Protection Agency, Corvallis, Oregon, 97333, USA
| | - Bonnie M. Smith
- Western Ecology Division, National Health and Environmental Effects Laboratory, US Environmental Protection Agency, Corvallis, Oregon, 97333, USA
| | - Q. Todd Krantz
- Environmental Public Health Division, National Health and Environmental Effects Laboratory, US Environmental Protection Agency Research Triangle Park, North Carolina, 27711, USA
| | - Charly J. King
- Environmental Public Health Division, National Health and Environmental Effects Laboratory, US Environmental Protection Agency Research Triangle Park, North Carolina, 27711, USA
| | - Kasey D. Kovalcik
- Exposure Methods and Measurements Division, National Exposure Research Laboratory, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina 27711, United States
| | - Christian P. Andersen
- Western Ecology Division, National Health and Environmental Effects Laboratory, US Environmental Protection Agency, Corvallis, Oregon, 97333, USA
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Abstract
Conifers are the dominant plant species throughout the high latitude boreal forests as well as some lower latitude temperate forests of North America, Europe, and Asia. As such, they play an integral economic and ecological role across much of the world. This study focused on the characterization of needle transcriptomes from four ecologically important and understudied North American white pines within the Pinus subgenus Strobus. The populations of many Strobus species are challenged by native and introduced pathogens, native insects, and abiotic factors. RNA from the needles of western white pine (Pinus monticola), limber pine (Pinus flexilis), whitebark pine (Pinus albicaulis), and sugar pine (Pinus lambertiana) was sampled, Illumina short read sequenced, and de novo assembled. The assembled transcripts and their subsequent structural and functional annotations were processed through custom pipelines to contend with the challenges of non-model organism transcriptome validation. Orthologous gene family analysis of over 58,000 translated transcripts, implemented through Tribe-MCL, estimated the shared and unique gene space among the four species. This revealed 2025 conserved gene families, of which 408 were aligned to estimate levels of divergence and reveal patterns of selection. Specific candidate genes previously associated with drought tolerance and white pine blister rust resistance in conifers were investigated.
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Laricchia KM, Johnson MG, Ragone D, Williams EW, Zerega NJC, Wickett NJ. A transcriptome screen for positive selection in domesticated breadfruit and its wild relatives (Artocarpus spp.). AMERICAN JOURNAL OF BOTANY 2018; 105:915-926. [PMID: 29882953 DOI: 10.1002/ajb2.1095] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2017] [Accepted: 03/12/2018] [Indexed: 06/08/2023]
Abstract
PREMISE OF THE STUDY Underutilized crops, such as breadfruit (Artocarpus altilis, Moraceae) have the potential to improve global food security. Humans have artificially selected many cultivars of breadfruit since its domestication began approximately 3500 years ago. The goal of this research was to identify transcriptomic signals of positive selection and to develop genomic resources that may facilitate the development of improved breadfruit cultivars in the future. METHODS A reference transcriptome of breadfruit was assembled de novo and annotated. Twenty-four transcriptomes of breadfruit and its wild relatives were generated and analyzed to reveal signals of positive selection that may have resulted from local adaptation or natural selection. Emphasis was placed on MADS-box genes, which are important because they often regulate fruiting timing and structures, and on carotenoid biosynthesis genes, which can impact the nutritional quality of the fruit. KEY RESULTS Over 1000 genes showed signals of positive selection, and these genes were enriched for localization to plastids. Nucleotide sites and individuals under positive selection were discovered in MADS-box genes and carotenoid biosynthesis genes, with several sites located in cofactor or DNA-binding domains. A McDonald-Kreitman test comparing wild to cultivated samples revealed selection in one of the carotenoid biosynthesis genes, abscisic acid 8'-hydroxylase 3. CONCLUSIONS This research highlights some of the many genes that may have been intentionally or unintentionally selected for during the human-mediated dispersal of breadfruit and stresses the importance of conserving a varied germplasm collection. It has revealed candidate genes for further study and produced new genomic resources for breadfruit.
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Affiliation(s)
- Kristen M Laricchia
- Program in Plant Biology and Conservation, Northwestern University, Evanston, IL, 60208, USA
- Department of Plant Science, Chicago Botanic Garden, Glencoe, IL, 60022, USA
| | - Matthew G Johnson
- Department of Plant Science, Chicago Botanic Garden, Glencoe, IL, 60022, USA
| | - Diane Ragone
- Breadfruit Institute, National Tropical Botanical Garden, Kalaheo, HI, 96741, USA
| | - Evelyn W Williams
- Department of Plant Science, Chicago Botanic Garden, Glencoe, IL, 60022, USA
| | - Nyree J C Zerega
- Program in Plant Biology and Conservation, Northwestern University, Evanston, IL, 60208, USA
- Department of Plant Science, Chicago Botanic Garden, Glencoe, IL, 60022, USA
| | - Norman J Wickett
- Program in Plant Biology and Conservation, Northwestern University, Evanston, IL, 60208, USA
- Department of Plant Science, Chicago Botanic Garden, Glencoe, IL, 60022, USA
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Thistlethwaite FR, Ratcliffe B, Klápště J, Porth I, Chen C, Stoehr MU, El-Kassaby YA. Genomic prediction accuracies in space and time for height and wood density of Douglas-fir using exome capture as the genotyping platform. BMC Genomics 2017; 18:930. [PMID: 29197325 PMCID: PMC5712148 DOI: 10.1186/s12864-017-4258-5] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Accepted: 11/01/2017] [Indexed: 11/11/2022] Open
Abstract
Background Genomic selection (GS) can offer unprecedented gains, in terms of cost efficiency and generation turnover, to forest tree selective breeding; especially for late expressing and low heritability traits. Here, we used: 1) exome capture as a genotyping platform for 1372 Douglas-fir trees representing 37 full-sib families growing on three sites in British Columbia, Canada and 2) height growth and wood density (EBVs), and deregressed estimated breeding values (DEBVs) as phenotypes. Representing models with (EBVs) and without (DEBVs) pedigree structure. Ridge regression best linear unbiased predictor (RR-BLUP) and generalized ridge regression (GRR) were used to assess their predictive accuracies over space (within site, cross-sites, multi-site, and multi-site to single site) and time (age-age/ trait-trait). Results The RR-BLUP and GRR models produced similar predictive accuracies across the studied traits. Within-site GS prediction accuracies with models trained on EBVs were high (RR-BLUP: 0.79–0.91 and GRR: 0.80–0.91), and were generally similar to the multi-site (RR-BLUP: 0.83–0.91, GRR: 0.83–0.91) and multi-site to single-site predictive accuracies (RR-BLUP: 0.79–0.92, GRR: 0.79–0.92). Cross-site predictions were surprisingly high, with predictive accuracies within a similar range (RR-BLUP: 0.79–0.92, GRR: 0.78–0.91). Height at 12 years was deemed the earliest acceptable age at which accurate predictions can be made concerning future height (age-age) and wood density (trait-trait). Using DEBVs reduced the accuracies of all cross-validation procedures dramatically, indicating that the models were tracking pedigree (family means), rather than marker-QTL LD. Conclusions While GS models’ prediction accuracies were high, the main driving force was the pedigree tracking rather than LD. It is likely that many more markers are needed to increase the chance of capturing the LD between causal genes and markers.
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Affiliation(s)
- Frances R Thistlethwaite
- Department of Forest and Conservation Sciences, Faculty of Forestry, The University of British Columbia, 2424 Main Mall, Vancouver, BC, V6T 1Z4, Canada
| | - Blaise Ratcliffe
- Department of Forest and Conservation Sciences, Faculty of Forestry, The University of British Columbia, 2424 Main Mall, Vancouver, BC, V6T 1Z4, Canada
| | - Jaroslav Klápště
- Department of Forest and Conservation Sciences, Faculty of Forestry, The University of British Columbia, 2424 Main Mall, Vancouver, BC, V6T 1Z4, Canada.,Scion (New Zealand Forest Research Institute Ltd.), 49 Sala Street, Whakarewarewa, Rotorua, 3046, New Zealand.,Department of Genetics and Physiology of Forest Trees, Faculty of Forestry and Wood Sciences, Czech University of Life Sciences Prague, Kamycka 129, 165 21, Praha 6, Czech Republic
| | - Ilga Porth
- Département des sciences du bois et de la forêt, Université Laval, QC, Québec, G1V 0A6, Canada
| | - Charles Chen
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK, 74078-3035, USA
| | - Michael U Stoehr
- British Columbia Ministry of Forests, Lands and Natural Resource Operations, Victoria, BC, V8W 9C2, Canada
| | - Yousry A El-Kassaby
- Department of Forest and Conservation Sciences, Faculty of Forestry, The University of British Columbia, 2424 Main Mall, Vancouver, BC, V6T 1Z4, Canada.
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The Douglas-Fir Genome Sequence Reveals Specialization of the Photosynthetic Apparatus in Pinaceae. G3-GENES GENOMES GENETICS 2017; 7:3157-3167. [PMID: 28751502 PMCID: PMC5592940 DOI: 10.1534/g3.117.300078] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
A reference genome sequence for Pseudotsuga menziesii var. menziesii (Mirb.) Franco (Coastal Douglas-fir) is reported, thus providing a reference sequence for a third genus of the family Pinaceae. The contiguity and quality of the genome assembly far exceeds that of other conifer reference genome sequences (contig N50 = 44,136 bp and scaffold N50 = 340,704 bp). Incremental improvements in sequencing and assembly technologies are in part responsible for the higher quality reference genome, but it may also be due to a slightly lower exact repeat content in Douglas-fir vs. pine and spruce. Comparative genome annotation with angiosperm species reveals gene-family expansion and contraction in Douglas-fir and other conifers which may account for some of the major morphological and physiological differences between the two major plant groups. Notable differences in the size of the NDH-complex gene family and genes underlying the functional basis of shade tolerance/intolerance were observed. This reference genome sequence not only provides an important resource for Douglas-fir breeders and geneticists but also sheds additional light on the evolutionary processes that have led to the divergence of modern angiosperms from the more ancient gymnosperms.
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Cronn R, Dolan PC, Jogdeo S, Wegrzyn JL, Neale DB, St Clair JB, Denver DR. Transcription through the eye of a needle: daily and annual cyclic gene expression variation in Douglas-fir needles. BMC Genomics 2017; 18:558. [PMID: 28738815 PMCID: PMC5525293 DOI: 10.1186/s12864-017-3916-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Accepted: 06/30/2017] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Perennial growth in plants is the product of interdependent cycles of daily and annual stimuli that induce cycles of growth and dormancy. In conifers, needles are the key perennial organ that integrates daily and seasonal signals from light, temperature, and water availability. To understand the relationship between seasonal cycles and seasonal gene expression responses in conifers, we examined diurnal and circannual needle mRNA accumulation in Douglas-fir (Pseudotsuga menziesii) needles at diurnal and circannual scales. Using mRNA sequencing, we sampled 6.1 × 109 reads from 19 trees and constructed a de novo pan-transcriptome reference that includes 173,882 tree-derived transcripts. Using this reference, we mapped RNA-Seq reads from 179 samples that capture daily and annual variation. RESULTS We identified 12,042 diurnally-cyclic transcripts, 9299 of which showed homology to annotated genes from other plant genomes, including angiosperm core clock genes. Annual analysis revealed 21,225 circannual transcripts, 17,335 of which showed homology to annotated genes from other plant genomes. The timing of maximum gene expression is associated with light intensity at diurnal scales and photoperiod at annual scales, with approximately half of transcripts reaching maximum expression +/- 2 h from sunrise and sunset, and +/- 20 days from winter and summer solstices. Comparisons with published studies from other conifers shows congruent behavior in clock genes with Japanese cedar (Cryptomeria), and a significant preservation of gene expression patterns for 2278 putative orthologs from Douglas-fir during the summer growing season, and 760 putative orthologs from spruce (Picea) during the transition from fall to winter. CONCLUSIONS Our study highlight the extensive diurnal and circannual transcriptome variability demonstrated in conifer needles. At these temporal scales, 29% of expressed transcripts show a significant diurnal cycle, and 58.7% show a significant circannual cycle. Remarkably, thousands of genes reach their annual peak activity during winter dormancy. Our study establishes the fine-scale timing of daily and annual maximum gene expression for diverse needle genes in Douglas-fir, and it highlights the potential for using this information for evaluating hypotheses concerning the daily or seasonal timing of gene activity in temperate-zone conifers, and for identifying cyclic transcriptome components in other conifer species.
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Affiliation(s)
- Richard Cronn
- Pacific Northwest Research Station, USDA Forest Service, Corvallis, OR, 97331, USA.
| | - Peter C Dolan
- University of Minnesota - Morris, Morris, MN, 56267, USA
| | - Sanjuro Jogdeo
- Department of Integrative Biology, Oregon State University, Corvallis, OR, 97331, USA
| | - Jill L Wegrzyn
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, 06269, USA
| | - David B Neale
- Department of Plant Sciences, University of California - Davis, Davis, CA, 95616, USA
| | - J Bradley St Clair
- Pacific Northwest Research Station, USDA Forest Service, Corvallis, OR, 97331, USA
| | - Dee R Denver
- Department of Integrative Biology, Oregon State University, Corvallis, OR, 97331, USA
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Abstract
Transcriptomics technologies are the techniques used to study an organism's transcriptome, the sum of all of its RNA transcripts. The information content of an organism is recorded in the DNA of its genome and expressed through transcription. Here, mRNA serves as a transient intermediary molecule in the information network, whilst noncoding RNAs perform additional diverse functions. A transcriptome captures a snapshot in time of the total transcripts present in a cell. The first attempts to study the whole transcriptome began in the early 1990s, and technological advances since the late 1990s have made transcriptomics a widespread discipline. Transcriptomics has been defined by repeated technological innovations that transform the field. There are two key contemporary techniques in the field: microarrays, which quantify a set of predetermined sequences, and RNA sequencing (RNA-Seq), which uses high-throughput sequencing to capture all sequences. Measuring the expression of an organism's genes in different tissues, conditions, or time points gives information on how genes are regulated and reveals details of an organism's biology. It can also help to infer the functions of previously unannotated genes. Transcriptomic analysis has enabled the study of how gene expression changes in different organisms and has been instrumental in the understanding of human disease. An analysis of gene expression in its entirety allows detection of broad coordinated trends which cannot be discerned by more targeted assays.
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Affiliation(s)
- Rohan Lowe
- La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Australia
| | - Neil Shirley
- ARC Centre of Excellence in Plant Cell Walls, University of Adelaide, Adelaide, Australia
| | - Mark Bleackley
- La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Australia
| | - Stephen Dolan
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Thomas Shafee
- La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Australia
- * E-mail:
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Finch K, Espinoza E, Jones FA, Cronn R. Source identification of western Oregon Douglas-fir wood cores using mass spectrometry and random forest classification. APPLICATIONS IN PLANT SCIENCES 2017; 5:apps.1600158. [PMID: 28529831 PMCID: PMC5435404 DOI: 10.3732/apps.1600158] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/30/2016] [Accepted: 04/07/2017] [Indexed: 06/07/2023]
Abstract
PREMISE OF THE STUDY We investigated whether wood metabolite profiles from direct analysis in real time (time-of-flight) mass spectrometry (DART-TOFMS) could be used to determine the geographic origin of Douglas-fir wood cores originating from two regions in western Oregon, USA. METHODS Three annual ring mass spectra were obtained from 188 adult Douglas-fir trees, and these were analyzed using random forest models to determine whether samples could be classified to geographic origin, growth year, or growth year and geographic origin. Specific wood molecules that contributed to geographic discrimination were identified. RESULTS Douglas-fir mass spectra could be differentiated into two geographic classes with an accuracy between 70% and 76%. Classification models could not accurately classify sample mass spectra based on growth year. Thirty-two molecules were identified as key for classifying western Oregon Douglas-fir wood cores to geographic origin. DISCUSSION DART-TOFMS is capable of detecting minute but regionally informative differences in wood molecules over a small geographic scale, and these differences made it possible to predict the geographic origin of Douglas-fir wood with moderate accuracy. Studies involving DART-TOFMS, alone and in combination with other technologies, will be relevant for identifying the geographic origin of illegally harvested wood.
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Affiliation(s)
- Kristen Finch
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331 USA
| | - Edgard Espinoza
- National Fish and Wildlife Forensic Laboratory, Ashland, Oregon 97520 USA
| | - F. Andrew Jones
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331 USA
- Smithsonian Tropical Research Institute, Balboa, Ancon, Republic of Panama
| | - Richard Cronn
- USDA Forest Service Pacific Northwest Research Station, Corvallis, Oregon 97331 USA
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Pavy N, Lamothe M, Pelgas B, Gagnon F, Birol I, Bohlmann J, Mackay J, Isabel N, Bousquet J. A high-resolution reference genetic map positioning 8.8 K genes for the conifer white spruce: structural genomics implications and correspondence with physical distance. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 90:189-203. [PMID: 28090692 DOI: 10.1111/tpj.13478] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Revised: 12/23/2016] [Accepted: 01/03/2017] [Indexed: 05/21/2023]
Abstract
Over the last decade, extensive genetic and genomic resources have been developed for the conifer white spruce (Picea glauca, Pinaceae), which has one of the largest plant genomes (20 Gbp). Draft genome sequences of white spruce and other conifers have recently been produced, but dense genetic maps are needed to comprehend genome macrostructure, delineate regions involved in quantitative traits, complement functional genomic investigations, and assist the assembly of fragmented genomic sequences. A greatly expanded P. glauca composite linkage map was generated from a set of 1976 full-sib progeny, with the positioning of 8793 expressed genes. Regions with significant low or high gene density were identified. Gene family members tended to be mapped on the same chromosomes, with tandemly arrayed genes significantly biased towards specific functional classes. The map was integrated with transcriptome data surveyed across eight tissues. In total, 69 clusters of co-expressed and co-localising genes were identified. A high level of synteny was found with pine genetic maps, which should facilitate the transfer of structural information in the Pinaceae. Although the current white spruce genome sequence remains highly fragmented, dozens of scaffolds encompassing more than one mapped gene were identified. From these, the relationship between genetic and physical distances was examined and the genome-wide recombination rate was found to be much smaller than most estimates reported for angiosperm genomes. This gene linkage map shall assist the large-scale assembly of the next-generation white spruce genome sequence and provide a reference resource for the conifer genomics community.
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Affiliation(s)
- Nathalie Pavy
- Canada Research Chair in Forest Genomics, Forest Research Centre and Institute for Systems and Integrative Biology, Université Laval, Québec, QC, G1V 0A6, Canada
| | - Manuel Lamothe
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, 1055 du P.E.P.S., P.O. Box 10380, Stn. Sainte-Foy, Québec, QC, G1V 4C7, Canada
| | - Betty Pelgas
- Canada Research Chair in Forest Genomics, Forest Research Centre and Institute for Systems and Integrative Biology, Université Laval, Québec, QC, G1V 0A6, Canada
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, 1055 du P.E.P.S., P.O. Box 10380, Stn. Sainte-Foy, Québec, QC, G1V 4C7, Canada
| | - France Gagnon
- Canada Research Chair in Forest Genomics, Forest Research Centre and Institute for Systems and Integrative Biology, Université Laval, Québec, QC, G1V 0A6, Canada
| | - Inanç Birol
- Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, V5Z 4S6, Canada
| | - Joerg Bohlmann
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - John Mackay
- Canada Research Chair in Forest Genomics, Forest Research Centre and Institute for Systems and Integrative Biology, Université Laval, Québec, QC, G1V 0A6, Canada
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, 0X1 3RB, UK
| | - Nathalie Isabel
- Canada Research Chair in Forest Genomics, Forest Research Centre and Institute for Systems and Integrative Biology, Université Laval, Québec, QC, G1V 0A6, Canada
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, 1055 du P.E.P.S., P.O. Box 10380, Stn. Sainte-Foy, Québec, QC, G1V 4C7, Canada
| | - Jean Bousquet
- Canada Research Chair in Forest Genomics, Forest Research Centre and Institute for Systems and Integrative Biology, Université Laval, Québec, QC, G1V 0A6, Canada
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Little SA, Boyes IG, Donaleshen K, von Aderkas P, Ehlting J. A transcriptomic resource for Douglas-fir seed development and analysis of transcription during late megagametophyte development. PLANT REPRODUCTION 2016; 29:273-286. [PMID: 27699505 DOI: 10.1007/s00497-016-0291-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Accepted: 09/16/2016] [Indexed: 05/08/2023]
Abstract
Douglas-fir transcriptomics. Douglas-fir (Pseudotsuga menziesii (Mirb.) Franco) is economically important with extensive breeding programs and seed trade. However, the molecular genetics of its seed development are largely unknown. We developed a transcriptome resource covering key developmental stages of megagametophytes over time: prefertilization, fertilization, embryogenesis, and early, unfertilized abortion. RNA sequencing reads were assembled de novo into 105,505 predicted high-confidence transcripts derived from 34,521 predicted genes. Expression levels were estimated based on alignment of the original reads to the reference. Megagametophytes express a distinct set of genes compared to those of vegetative tissues. Transcripts related to signaling, protein turnover, and RNA biogenesis have lower expression values in vegetative tissues, whereas cell wall remodeling, solute transport, and seed storage protein transcripts have higher expression values in megagametophytes. Seed storage protein transcripts become very abundant in both pollinated and unpollinated megagametophytes over time, even in aborting ovules. However, the absence of protein storage bodies in unfertilized megagametophytes suggests extensive posttranscriptional mechanisms that either inhibit storage protein translation or their aggregation into protein bodies. This novel transcriptome resource provides a foundation for further important insights into conifer seed development.
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Affiliation(s)
- Stefan A Little
- Department of Biology, University of Victoria, Victoria, BC, V8W 3N5, Canada
- Laboratoire Écologie, Systématique, Évolution, CNRS UMR 8079, Université Paris-Sud, 91405, Orsay, France
| | - Ian G Boyes
- Department of Biology, University of Victoria, Victoria, BC, V8W 3N5, Canada
| | - Kate Donaleshen
- Department of Biology, University of Victoria, Victoria, BC, V8W 3N5, Canada
| | - Patrick von Aderkas
- Department of Biology, University of Victoria, Victoria, BC, V8W 3N5, Canada
| | - Jürgen Ehlting
- Department of Biology, University of Victoria, Victoria, BC, V8W 3N5, Canada.
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Hess M, Wildhagen H, Junker LV, Ensminger I. Transcriptome responses to temperature, water availability and photoperiod are conserved among mature trees of two divergent Douglas-fir provenances from a coastal and an interior habitat. BMC Genomics 2016; 17:682. [PMID: 27565139 PMCID: PMC5002200 DOI: 10.1186/s12864-016-3022-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Accepted: 08/16/2016] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Local adaptation and phenotypic plasticity are important components of plant responses to variations in environmental conditions. While local adaptation has been widely studied in trees, little is known about plasticity of gene expression in adult trees in response to ever changing environmental conditions in natural habitats. Here we investigate plasticity of gene expression in needle tissue between two Douglas-fir provenances represented by 25 adult trees using deep RNA sequencing (RNA-Seq). RESULTS Using linear mixed models we investigated the effect of temperature, soil water availability and photoperiod on the abundance of 59189 detected transcripts. Expression of more than 80 % of all identified transcripts revealed a response to variations in environmental conditions in the field. GO term overrepresentation analysis revealed gene expression responses to temperature, soil water availability and photoperiod that are highly conserved among many plant taxa. However, expression differences between the two Douglas-fir provenances were rather small compared to the expression differences observed between individual trees. Although the effect of environment on global transcript expression was high, the observed genotype by environment (GxE) interaction of gene expression was surprisingly low, since only 21 of all detected transcripts showed a GxE interaction. CONCLUSIONS The majority of the transcriptome responses in plant leaf tissue is driven by variations in environmental conditions. The small variation between individuals and populations suggests strong conservation of this response within Douglas-fir. Therefore we conclude that plastic transcriptome responses to variations in environmental conditions are only weakly affected by local adaptation in Douglas-fir.
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Affiliation(s)
- Moritz Hess
- Forest Research Institute of Baden-Württemberg (FVA), Wonnhaldestrasse 4, D-79100 Freiburg i. Brsg., Germany
- Institute for Biology III, Faculty of Biology, Albert Ludwigs University Freiburg, Schänzlestrasse 1, D-79104 Freiburg i. Brsg., Germany
- Present Address: Institute of Medical Biometry, Epidemiology and Informatics (IMBEI), University Medical Center Mainz, Obere Zahlbacher Strasse 69, 55131 Mainz, Germany
| | - Henning Wildhagen
- Forest Research Institute of Baden-Württemberg (FVA), Wonnhaldestrasse 4, D-79100 Freiburg i. Brsg., Germany
- Present Address: Department of Forest Botany and Tree Physiology, Büsgen-Institute, Georg-August-University Göttingen, Büsgenweg 2, D-37077 Göttingen, Germany
| | - Laura Verena Junker
- Forest Research Institute of Baden-Württemberg (FVA), Wonnhaldestrasse 4, D-79100 Freiburg i. Brsg., Germany
- Department of Biology, Graduate Programs in Cell & Systems Biology and Ecology & Evolutionary Biology, University of Toronto, 3359 Mississauga Road, Mississauga, ON L5L 1C6 Canada
| | - Ingo Ensminger
- Forest Research Institute of Baden-Württemberg (FVA), Wonnhaldestrasse 4, D-79100 Freiburg i. Brsg., Germany
- Department of Biology, Graduate Programs in Cell & Systems Biology and Ecology & Evolutionary Biology, University of Toronto, 3359 Mississauga Road, Mississauga, ON L5L 1C6 Canada
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Herraiz FJ, Blanca J, Ziarsolo P, Gramazio P, Plazas M, Anderson GJ, Prohens J, Vilanova S. The first de novo transcriptome of pepino (Solanum muricatum): assembly, comprehensive analysis and comparison with the closely related species S. caripense, potato and tomato. BMC Genomics 2016; 17:321. [PMID: 27142449 PMCID: PMC4855764 DOI: 10.1186/s12864-016-2656-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Accepted: 04/25/2016] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND Solanum sect. Basarthrum is phylogenetically very close to potatoes (Solanum sect. Petota) and tomatoes (Solanum sect. Lycopersicon), two groups with great economic importance, and for which Solanum sect. Basarthrum represents a tertiary gene pool for breeding. This section includes the important regional cultigen, the pepino (Solanum muricatum), and several wild species. Among the wild species, S. caripense is prominent due to its major involvement in the origin of pepino and its wide geographical distribution. Despite the value of the pepino as an emerging crop, and the potential for gene transfer from both the pepino and S. caripense to potatoes and tomatoes, there has been virtually no genomic study of these species. RESULTS Using Illumina HiSeq 2000, RNA-Seq was performed with a pool of three tissues (young leaf, flowers in pre-anthesis and mature fruits) from S. muricatum and S. caripense, generating almost 111,000,000 reads among the two species. A high quality de novo transcriptome was assembled from S. muricatum clean reads resulting in 75,832 unigenes with an average length of 704 bp. These unigenes were functionally annotated based on similarity of public databases. We used Blast2GO, to conduct an exhaustive study of the gene ontology, including GO terms, EC numbers and KEGG pathways. Pepino unigenes were compared to both potato and tomato genomes in order to determine their estimated relative position, and to infer gene prediction models. Candidate genes related to traits of interest in other Solanaceae were evaluated by presence or absence and compared with S. caripense transcripts. In addition, by studying five genes, the phylogeny of pepino and five other members of the family, Solanaceae, were studied. The comparison of S. caripense reads against S. muricatum assembled transcripts resulted in thousands of intra- and interspecific nucleotide-level variants. In addition, more than 1000 SSRs were identified in the pepino transcriptome. CONCLUSIONS This study represents the first genomic resource for the pepino. We suggest that the data will be useful not only for improvement of the pepino, but also for potato and tomato breeding and gene transfer. The high quality of the transcriptome presented here also facilitates comparative studies in the genus Solanum. The accurate transcript annotation will enable us to figure out the gene function of particular traits of interest. The high number of markers (SSR and nucleotide-level variants) obtained will be useful for breeding programs, as well as studies of synteny, diversity evolution, and phylogeny.
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Affiliation(s)
- Francisco J. Herraiz
- />Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Camino de Vera 14, 46022 Valencia Spain
| | - José Blanca
- />Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Camino de Vera 14, 46022 Valencia Spain
| | - Pello Ziarsolo
- />Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Camino de Vera 14, 46022 Valencia Spain
| | - Pietro Gramazio
- />Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Camino de Vera 14, 46022 Valencia Spain
| | - Mariola Plazas
- />Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Camino de Vera 14, 46022 Valencia Spain
| | - Gregory J. Anderson
- />Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06268-3043 USA
| | - Jaime Prohens
- />Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Camino de Vera 14, 46022 Valencia Spain
| | - Santiago Vilanova
- />Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Camino de Vera 14, 46022 Valencia Spain
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26
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Faivre-Rampant P, Zaina G, Jorge V, Giacomello S, Segura V, Scalabrin S, Guérin V, De Paoli E, Aluome C, Viger M, Cattonaro F, Payne A, PaulStephenRaj P, Le Paslier MC, Berard A, Allwright MR, Villar M, Taylor G, Bastien C, Morgante M. New resources for genetic studies in Populus nigra: genome-wide SNP discovery and development of a 12k Infinium array. Mol Ecol Resour 2016; 16:1023-36. [PMID: 26929265 DOI: 10.1111/1755-0998.12513] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Revised: 12/17/2015] [Accepted: 12/22/2015] [Indexed: 11/30/2022]
Abstract
Whole genome resequencing of 51 Populus nigra (L.) individuals from across Western Europe was performed using Illumina platforms. A total number of 1 878 727 SNPs distributed along the P. nigra reference sequence were identified. The SNP calling accuracy was validated with Sanger sequencing. SNPs were selected within 14 previously identified QTL regions, 2916 expressional candidate genes related to rust resistance, wood properties, water-use efficiency and bud phenology and 1732 genes randomly spread across the genome. Over 10 000 SNPs were selected for the construction of a 12k Infinium Bead-Chip array dedicated to association mapping. The SNP genotyping assay was performed with 888 P. nigra individuals. The genotyping success rate was 91%. Our high success rate was due to the discovery panel design and the stringent parameters applied for SNP calling and selection. In the same set of P. nigra genotypes, linkage disequilibrium throughout the genome decayed on average within 5-7 kb to half of its maximum value. As an application test, ADMIXTURE analysis was performed with a selection of 600 SNPs spread throughout the genome and 706 individuals collected along 12 river basins. The admixture pattern was consistent with genetic diversity revealed by neutral markers and the geographical distribution of the populations. These newly developed SNP resources and genotyping array provide a valuable tool for population genetic studies and identification of QTLs through natural-population based genetic association studies in P. nigra.
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Affiliation(s)
| | - G Zaina
- DI4A, University of Udine, via delle Scienze 206, 33100, Udine, Italy
| | - V Jorge
- INRA, UR 0588 AGPF, Centre INRA Val de Loire, 2163 avenue de la Pomme de Pin, CS 40001 - Ardon, 45075, Orléans, France
| | - S Giacomello
- IGA, Parco Scientifico e Tecnologico Luigi Danieli, via Jacopo Linussio 51, 33100, Udine, Italy
| | - V Segura
- INRA, UR 0588 AGPF, Centre INRA Val de Loire, 2163 avenue de la Pomme de Pin, CS 40001 - Ardon, 45075, Orléans, France
| | - S Scalabrin
- IGA, Parco Scientifico e Tecnologico Luigi Danieli, via Jacopo Linussio 51, 33100, Udine, Italy
| | - V Guérin
- INRA, UR 0588 AGPF, Centre INRA Val de Loire, 2163 avenue de la Pomme de Pin, CS 40001 - Ardon, 45075, Orléans, France
| | - E De Paoli
- IGA, Parco Scientifico e Tecnologico Luigi Danieli, via Jacopo Linussio 51, 33100, Udine, Italy
| | - C Aluome
- INRA, US1279 EPGV, CEA-IG/CNG, F-91057, Evry, France.,INRA, UR 0588 AGPF, Centre INRA Val de Loire, 2163 avenue de la Pomme de Pin, CS 40001 - Ardon, 45075, Orléans, France
| | - M Viger
- Centre For Biological Sciences, University of Southampton, Life Sciences, SO17 1BJ, Southampton, UK
| | - F Cattonaro
- IGA, Parco Scientifico e Tecnologico Luigi Danieli, via Jacopo Linussio 51, 33100, Udine, Italy
| | - A Payne
- Centre For Biological Sciences, University of Southampton, Life Sciences, SO17 1BJ, Southampton, UK
| | | | | | - A Berard
- INRA, US1279 EPGV, CEA-IG/CNG, F-91057, Evry, France
| | - M R Allwright
- Centre For Biological Sciences, University of Southampton, Life Sciences, SO17 1BJ, Southampton, UK
| | - M Villar
- INRA, UR 0588 AGPF, Centre INRA Val de Loire, 2163 avenue de la Pomme de Pin, CS 40001 - Ardon, 45075, Orléans, France
| | - G Taylor
- Centre For Biological Sciences, University of Southampton, Life Sciences, SO17 1BJ, Southampton, UK
| | - C Bastien
- INRA, UR 0588 AGPF, Centre INRA Val de Loire, 2163 avenue de la Pomme de Pin, CS 40001 - Ardon, 45075, Orléans, France
| | - M Morgante
- DI4A, University of Udine, via delle Scienze 206, 33100, Udine, Italy.,IGA, Parco Scientifico e Tecnologico Luigi Danieli, via Jacopo Linussio 51, 33100, Udine, Italy
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27
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Pavy N, Gagnon F, Deschênes A, Boyle B, Beaulieu J, Bousquet J. Development of highly reliable in silico SNP resource and genotyping assay from exome capture and sequencing: an example from black spruce (Picea mariana). Mol Ecol Resour 2015; 16:588-98. [PMID: 26391535 DOI: 10.1111/1755-0998.12468] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Revised: 06/30/2015] [Accepted: 08/21/2015] [Indexed: 11/29/2022]
Abstract
Picea mariana is a widely distributed boreal conifer across Canada and the subject of advanced breeding programmes for which population genomics and genomic selection approaches are being developed. Targeted sequencing was achieved after capturing P. mariana exome with probes designed from the sequenced transcriptome of Picea glauca, a distant relative. A high capture efficiency of 75.9% was reached although spruce has a complex and large genome including gene sequences interspersed by some long introns. The results confirmed the relevance of using probes from congeneric species to perform successfully interspecific exome capture in the genus Picea. A bioinformatics pipeline was developed including stringent criteria that helped detect a set of 97,075 highly reliable in silico SNPs. These SNPs were distributed across 14,909 genes. Part of an Infinium iSelect array was used to estimate the rate of true positives by validating 4267 of the predicted in silico SNPs by genotyping trees from P. mariana populations. The true positive rate was 96.2% for in silico SNPs, compared to a genotyping success rate of 96.7% for a set 1115 P. mariana control SNPs recycled from previous genotyping arrays. These results indicate the high success rate of the genotyping array and the relevance of the selection criteria used to delineate the new P. mariana in silico SNP resource. Furthermore, in silico SNPs were generally of medium to high frequency in natural populations, thus providing high informative value for future population genomics applications.
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Affiliation(s)
- Nathalie Pavy
- Canada Research Chair in Forest and Environmental Genomics, Centre for Forest Research, Université Laval, Québec, QC, G1V 0A6, Canada.,Institute of Systems and Integrative Biology, Université Laval, Québec, QC, G1V 0A6, Canada
| | - France Gagnon
- Canada Research Chair in Forest and Environmental Genomics, Centre for Forest Research, Université Laval, Québec, QC, G1V 0A6, Canada.,Institute of Systems and Integrative Biology, Université Laval, Québec, QC, G1V 0A6, Canada
| | - Astrid Deschênes
- Canada Research Chair in Forest and Environmental Genomics, Centre for Forest Research, Université Laval, Québec, QC, G1V 0A6, Canada.,Institute of Systems and Integrative Biology, Université Laval, Québec, QC, G1V 0A6, Canada
| | - Brian Boyle
- Institute of Systems and Integrative Biology, Université Laval, Québec, QC, G1V 0A6, Canada
| | - Jean Beaulieu
- Canada Research Chair in Forest and Environmental Genomics, Centre for Forest Research, Université Laval, Québec, QC, G1V 0A6, Canada.,Natural Resources Canada, Canadian Wood Fibre Centre, 1055 Rue du P.E.P.S., PO Box 10380, Station Sainte-Foy, Québec, QC, G1V 4C7, Canada
| | - Jean Bousquet
- Canada Research Chair in Forest and Environmental Genomics, Centre for Forest Research, Université Laval, Québec, QC, G1V 0A6, Canada.,Institute of Systems and Integrative Biology, Université Laval, Québec, QC, G1V 0A6, Canada
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28
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Plomion C, Bartholomé J, Lesur I, Boury C, Rodríguez-Quilón I, Lagraulet H, Ehrenmann F, Bouffier L, Gion JM, Grivet D, de Miguel M, de María N, Cervera MT, Bagnoli F, Isik F, Vendramin GG, González-Martínez SC. High-density SNP assay development for genetic analysis in maritime pine (Pinus pinaster). Mol Ecol Resour 2015; 16:574-87. [PMID: 26358548 DOI: 10.1111/1755-0998.12464] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Revised: 08/28/2015] [Accepted: 09/03/2015] [Indexed: 12/18/2022]
Abstract
Maritime pine provides essential ecosystem services in the south-western Mediterranean basin, where it covers around 4 million ha. Its scattered distribution over a range of environmental conditions makes it an ideal forest tree species for studies of local adaptation and evolutionary responses to climatic change. Highly multiplexed single nucleotide polymorphism (SNP) genotyping arrays are increasingly used to study genetic variation in living organisms and for practical applications in plant and animal breeding and genetic resource conservation. We developed a 9k Illumina Infinium SNP array and genotyped maritime pine trees from (i) a three-generation inbred (F2) pedigree, (ii) the French breeding population and (iii) natural populations from Portugal and the French Atlantic coast. A large proportion of the exploitable SNPs (2052/8410, i.e. 24.4%) segregated in the mapping population and could be mapped, providing the densest ever gene-based linkage map for this species. Based on 5016 SNPs, natural and breeding populations from the French gene pool exhibited similar level of genetic diversity. Population genetics and structure analyses based on 3981 SNP markers common to the Portuguese and French gene pools revealed high levels of differentiation, leading to the identification of a set of highly differentiated SNPs that could be used for seed provenance certification. Finally, we discuss how the validated SNPs could facilitate the identification of ecologically and economically relevant genes in this species, improving our understanding of the demography and selective forces shaping its natural genetic diversity, and providing support for new breeding strategies.
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Affiliation(s)
- C Plomion
- BIOGECO, UMR 1202, INRA, F-33610, Cestas, France.,BIOGECO, UMR 1202, University of Bordeaux, F-33400, Talence, France
| | - J Bartholomé
- BIOGECO, UMR 1202, INRA, F-33610, Cestas, France.,BIOGECO, UMR 1202, University of Bordeaux, F-33400, Talence, France
| | - I Lesur
- BIOGECO, UMR 1202, INRA, F-33610, Cestas, France.,HelixVenture, F-33700, Mérignac, France
| | - C Boury
- BIOGECO, UMR 1202, INRA, F-33610, Cestas, France.,BIOGECO, UMR 1202, University of Bordeaux, F-33400, Talence, France
| | | | - H Lagraulet
- BIOGECO, UMR 1202, INRA, F-33610, Cestas, France.,BIOGECO, UMR 1202, University of Bordeaux, F-33400, Talence, France
| | - F Ehrenmann
- BIOGECO, UMR 1202, INRA, F-33610, Cestas, France.,BIOGECO, UMR 1202, University of Bordeaux, F-33400, Talence, France
| | - L Bouffier
- BIOGECO, UMR 1202, INRA, F-33610, Cestas, France.,BIOGECO, UMR 1202, University of Bordeaux, F-33400, Talence, France
| | - J M Gion
- BIOGECO, UMR 1202, INRA, F-33610, Cestas, France.,UMR AGAP, CIRAD, F-33612, Cestas, France
| | - D Grivet
- Forest Research Centre, INIA, E-28040, Madrid, Spain
| | - M de Miguel
- BIOGECO, UMR 1202, INRA, F-33610, Cestas, France.,BIOGECO, UMR 1202, University of Bordeaux, F-33400, Talence, France
| | - N de María
- Forest Research Centre, INIA, E-28040, Madrid, Spain
| | - M T Cervera
- Forest Research Centre, INIA, E-28040, Madrid, Spain
| | - F Bagnoli
- Institute of Biosciences and Bioresources, National Research Council, Sesto Fiorentino (FI), Italy
| | - F Isik
- Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC, USA
| | - G G Vendramin
- Institute of Biosciences and Bioresources, National Research Council, Sesto Fiorentino (FI), Italy
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29
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Guo Y, Wiegert-Rininger KE, Vallejo VA, Barry CS, Warner RM. Transcriptome-enabled marker discovery and mapping of plastochron-related genes in Petunia spp. BMC Genomics 2015; 16:726. [PMID: 26400485 PMCID: PMC4581106 DOI: 10.1186/s12864-015-1931-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Accepted: 09/16/2015] [Indexed: 12/20/2022] Open
Abstract
Background Petunia (Petunia × hybrida), derived from a hybrid between P. axillaris and P. integrifolia, is one of the most economically important bedding plant crops and Petunia spp. serve as model systems for investigating the mechanisms underlying diverse mating systems and pollination syndromes. In addition, we have previously described genetic variation and quantitative trait loci (QTL) related to petunia development rate and morphology, which represent important breeding targets for the floriculture industry to improve crop production and performance. Despite the importance of petunia as a crop, the floriculture industry has been slow to adopt marker assisted selection to facilitate breeding strategies and there remains a limited availability of sequences and molecular markers from the genus compared to other economically important members of the Solanaceae family such as tomato, potato and pepper. Results Here we report the de novo assembly, annotation and characterization of transcriptomes from P. axillaris, P. exserta and P. integrifolia. Each transcriptome assembly was derived from five tissue libraries (callus, 3-week old seedlings, shoot apices, flowers of mixed developmental stages, and trichomes). A total of 74,573, 54,913, and 104,739 assembled transcripts were recovered from P. axillaris, P. exserta and P. integrifolia, respectively and following removal of multiple isoforms, 32,994 P. axillaris, 30,225 P. exserta, and 33,540 P. integrifolia high quality representative transcripts were extracted for annotation and expression analysis. The transcriptome data was mined for single nucleotide polymorphisms (SNP) and simple sequence repeat (SSR) markers, yielding 89,007 high quality SNPs and 2949 SSRs, respectively. 15,701 SNPs were computationally converted into user-friendly cleaved amplified polymorphic sequence (CAPS) markers and a subset of SNP and CAPS markers were experimentally verified. CAPS markers developed from plastochron-related homologous transcripts from P. axillaris were mapped in an interspecific Petunia population and evaluated for co-localization with QTL for development rate. Conclusions The high quality of the three Petunia spp. transcriptomes coupled with the utility of the SNP data will serve as a resource for further exploration of genetic diversity within the genus and will facilitate efforts to develop genetic and physical maps to aid the identification of QTL associated with traits of interest. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1931-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yufang Guo
- Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA
| | | | - Veronica A Vallejo
- Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA
| | - Cornelius S Barry
- Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA
| | - Ryan M Warner
- Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA.
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Bartholomé J, Mandrou E, Mabiala A, Jenkins J, Nabihoudine I, Klopp C, Schmutz J, Plomion C, Gion JM. High-resolution genetic maps of Eucalyptus improve Eucalyptus grandis genome assembly. THE NEW PHYTOLOGIST 2015; 206:1283-96. [PMID: 25385325 DOI: 10.1111/nph.13150] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Accepted: 09/29/2014] [Indexed: 05/21/2023]
Abstract
Genetic maps are key tools in genetic research as they constitute the framework for many applications, such as quantitative trait locus analysis, and support the assembly of genome sequences. The resequencing of the two parents of a cross between Eucalyptus urophylla and Eucalyptus grandis was used to design a single nucleotide polymorphism (SNP) array of 6000 markers evenly distributed along the E. grandis genome. The genotyping of 1025 offspring enabled the construction of two high-resolution genetic maps containing 1832 and 1773 markers with an average marker interval of 0.45 and 0.5 cM for E. grandis and E. urophylla, respectively. The comparison between genetic maps and the reference genome highlighted 85% of collinear regions. A total of 43 noncollinear regions and 13 nonsynthetic regions were detected and corrected in the new genome assembly. This improved version contains 4943 scaffolds totalling 691.3 Mb of which 88.6% were captured by the 11 chromosomes. The mapping data were also used to investigate the effect of population size and number of markers on linkage mapping accuracy. This study provides the most reliable linkage maps for Eucalyptus and version 2.0 of the E. grandis genome.
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Affiliation(s)
- Jérôme Bartholomé
- CIRAD, UMR AGAP, F-33612, Cestas, France
- INRA, UMR1202 BIOGECO, F-33610, Cestas, France
- BIOGECO, UMR 1202, Univ. Bordeaux, F-33600, Pessac, France
| | - Eric Mandrou
- INRA, UMR1202 BIOGECO, F-33610, Cestas, France
- BIOGECO, UMR 1202, Univ. Bordeaux, F-33600, Pessac, France
- Plate-forme Bio-informatique Genotoul, INRA, Biométrie et Intelligence Artificielle, BP 52627, 31326, Castanet-Tolosan Cedex, France
| | | | - Jerry Jenkins
- HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL, 35801, USA
| | - Ibouniyamine Nabihoudine
- Plate-forme Bio-informatique Genotoul, INRA, Biométrie et Intelligence Artificielle, BP 52627, 31326, Castanet-Tolosan Cedex, France
| | - Christophe Klopp
- Plate-forme Bio-informatique Genotoul, INRA, Biométrie et Intelligence Artificielle, BP 52627, 31326, Castanet-Tolosan Cedex, France
| | - Jeremy Schmutz
- HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL, 35801, USA
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA
| | - Christophe Plomion
- INRA, UMR1202 BIOGECO, F-33610, Cestas, France
- BIOGECO, UMR 1202, Univ. Bordeaux, F-33600, Pessac, France
| | - Jean-Marc Gion
- CIRAD, UMR AGAP, F-33612, Cestas, France
- INRA, UMR1202 BIOGECO, F-33610, Cestas, France
- BIOGECO, UMR 1202, Univ. Bordeaux, F-33600, Pessac, France
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Dasgupta MG, Dharanishanthi V, Agarwal I, Krutovsky KV. Development of genetic markers in Eucalyptus species by target enrichment and exome sequencing. PLoS One 2015; 10:e0116528. [PMID: 25602379 PMCID: PMC4300219 DOI: 10.1371/journal.pone.0116528] [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: 07/31/2014] [Accepted: 12/08/2014] [Indexed: 02/02/2023] Open
Abstract
The advent of next-generation sequencing has facilitated large-scale discovery, validation and assessment of genetic markers for high density genotyping. The present study was undertaken to identify markers in genes supposedly related to wood property traits in three Eucalyptus species. Ninety four genes involved in xylogenesis were selected for hybridization probe based nuclear genomic DNA target enrichment and exome sequencing. Genomic DNA was isolated from the leaf tissues and used for on-array probe hybridization followed by Illumina sequencing. The raw sequence reads were trimmed and high-quality reads were mapped to the E. grandis reference sequence and the presence of single nucleotide variants (SNVs) and insertions/ deletions (InDels) were identified across the three species. The average read coverage was 216X and a total of 2294 SNVs and 479 InDels were discovered in E. camaldulensis, 2383 SNVs and 518 InDels in E. tereticornis, and 1228 SNVs and 409 InDels in E. grandis. Additionally, SNV calling and InDel detection were conducted in pair-wise comparisons of E. tereticornis vs. E. grandis, E. camaldulensis vs. E. tereticornis and E. camaldulensis vs. E. grandis. This study presents an efficient and high throughput method on development of genetic markers for family– based QTL and association analysis in Eucalyptus.
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Affiliation(s)
- Modhumita Ghosh Dasgupta
- Division of Plant Biotechnology, Institute of Forest Genetics and Tree Breeding, P.B. No. 1061, R.S. Puram, Coimbatore–641002, India
- * E-mail:
| | - Veeramuthu Dharanishanthi
- Division of Plant Biotechnology, Institute of Forest Genetics and Tree Breeding, P.B. No. 1061, R.S. Puram, Coimbatore–641002, India
| | - Ishangi Agarwal
- Genotypic Technology Private Limited, #2/13, Balaji Complex, Poojari Layout, 80, Feet Road, R. M. V. 2nd Stage, Bangalore-560094, India
| | - Konstantin V. Krutovsky
- Department of Forest Genetics and Forest Tree Breeding, Büsgen Institute, Georg August University of Göttingen, Büsgenweg 2, D-37077 Göttingen, Germany
- Department of Ecosystem Science and Management, Texas A&M University, 2138 TAMU, College Station, TX 77843-2138, United States of America
- N.I. Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow 119333, Russia
- Genome Research and Education Center, Siberian Federal University, 50a/2 Akademgorodok, Krasnoyarsk 660036, Russia
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Liu JJ, Sniezko RA, Sturrock RN, Chen H. Western white pine SNP discovery and high-throughput genotyping for breeding and conservation applications. BMC PLANT BIOLOGY 2014; 14:380. [PMID: 25547170 PMCID: PMC4302426 DOI: 10.1186/s12870-014-0380-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Accepted: 12/11/2014] [Indexed: 05/10/2023]
Abstract
BACKGROUND Western white pine (WWP, Pinus monticola Douglas ex D. Don) is of high interest in forest breeding and conservation because of its high susceptibility to the invasive disease white pine blister rust (WPBR, caused by the fungus Cronartium ribicola J. C. Fisch). However, WWP lacks genomic resource development and is evolutionarily far away from plants with available draft genome sequences. Here we report a single nucleotide polymorphism (SNP) study by bulked segregation-based RNA-Seq analysis. RESULTS A collection of resistance germplasm was used for construction of cDNA libraries and SNP genotyping. Approximately 36-89 million 2 × 100-bp reads were obtained per library and de-novo assembly generated the first shoot-tip reference transcriptome containing a total of 54,661 unique transcripts. Bioinformatic SNP detection identified >100,000 high quality SNPs in three expressed candidate gene groups: Pinus highly conserved genes (HCGs), differential expressed genes (DEGs) in plant defense response, and resistance gene analogs (RGAs). To estimate efficiency of in-silico SNP discovery, genotyping assay was developed by using Sequenom iPlex and it unveiled SNP success rates from 40.1% to 61.1%. SNP clustering analyses consistently revealed distinct populations, each composed of multiple full-sib seed families by parentage assignment in the WWP germplasm collection. Linkage disequilibrium (LD) analysis identified six genes in significant association with major gene (Cr2) resistance, including three RGAs (two NBS-LRR genes and one receptor-like protein kinase -RLK gene), two HCGs, and one DEG. At least one SNP locus provided an excellent marker for Cr2 selection across P. monticola populations. CONCLUSIONS The WWP shoot tip transcriptome and those validated SNP markers provide novel genomic resources for genetic, evolutionary and ecological studies. SNP loci of those candidate genes associated with resistant phenotypes can be used as positional and functional variation sites for further characterization of WWP major gene resistance against C. ribicola. Our results demonstrate that integration of RNA-seq-based transcriptome analysis and high-throughput genotyping is an effective approach for discovery of a large number of nucleotide variations and for identification of functional gene variants associated with adaptive traits in a non-model species.
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Affiliation(s)
- Jun-Jun Liu
- />Pacific Forestry Centre, Canadian Forest Service, Natural Resources Canada, 506 West Burnside Road, Victoria, BC V8Z 1M5 Canada
| | - Richard A Sniezko
- />USDA Forest Service, Dorena Genetic Resource Center, 34963 Shoreview Road, Cottage Grove, OR 97424 USA
| | - Rona N Sturrock
- />Pacific Forestry Centre, Canadian Forest Service, Natural Resources Canada, 506 West Burnside Road, Victoria, BC V8Z 1M5 Canada
| | - Hao Chen
- />Pacific Forestry Centre, Canadian Forest Service, Natural Resources Canada, 506 West Burnside Road, Victoria, BC V8Z 1M5 Canada
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De La Torre AR, Birol I, Bousquet J, Ingvarsson PK, Jansson S, Jones SJM, Keeling CI, MacKay J, Nilsson O, Ritland K, Street N, Yanchuk A, Zerbe P, Bohlmann J. Insights into conifer giga-genomes. PLANT PHYSIOLOGY 2014; 166:1724-32. [PMID: 25349325 PMCID: PMC4256843 DOI: 10.1104/pp.114.248708] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Insights from sequenced genomes of major land plant lineages have advanced research in almost every aspect of plant biology. Until recently, however, assembled genome sequences of gymnosperms have been missing from this picture. Conifers of the pine family (Pinaceae) are a group of gymnosperms that dominate large parts of the world's forests. Despite their ecological and economic importance, conifers seemed long out of reach for complete genome sequencing, due in part to their enormous genome size (20-30 Gb) and the highly repetitive nature of their genomes. Technological advances in genome sequencing and assembly enabled the recent publication of three conifer genomes: white spruce (Picea glauca), Norway spruce (Picea abies), and loblolly pine (Pinus taeda). These genome sequences revealed distinctive features compared with other plant genomes and may represent a window into the past of seed plant genomes. This Update highlights recent advances, remaining challenges, and opportunities in light of the publication of the first conifer and gymnosperm genomes.
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Affiliation(s)
- Amanda R De La Torre
- Department of Ecology and Environmental Sciences (A.R.D.L.T., P.K.I.) and Umeå Plant Science Center, Department of Plant Physiology (P.K.I., S.J., O.N., N.S.), Umeå University, SE-901 87 Umea, Sweden;Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada V5Z 4S6 (I.B., S.J.M.J.);Canada Research Chair in Forest and Environmental Genomics (J.Bou.) and Center for Forest Research and Institute for Systems and Integrative Biology (J.Bou., J.M.), Université Laval, Quebec, Quebec, Canada G1V 0A6;Michael Smith Laboratories (C.I.K., P.Z., J.Boh.) and Department of Forest and Conservation Sciences (K.R., J.Boh.), University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4; andBritish Columbia Ministry of Forests, Lands, and Natural Resource Operations, Victoria, British Columbia, Canada V8W 9C2 (A.Y.)
| | - Inanc Birol
- Department of Ecology and Environmental Sciences (A.R.D.L.T., P.K.I.) and Umeå Plant Science Center, Department of Plant Physiology (P.K.I., S.J., O.N., N.S.), Umeå University, SE-901 87 Umea, Sweden;Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada V5Z 4S6 (I.B., S.J.M.J.);Canada Research Chair in Forest and Environmental Genomics (J.Bou.) and Center for Forest Research and Institute for Systems and Integrative Biology (J.Bou., J.M.), Université Laval, Quebec, Quebec, Canada G1V 0A6;Michael Smith Laboratories (C.I.K., P.Z., J.Boh.) and Department of Forest and Conservation Sciences (K.R., J.Boh.), University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4; andBritish Columbia Ministry of Forests, Lands, and Natural Resource Operations, Victoria, British Columbia, Canada V8W 9C2 (A.Y.)
| | - Jean Bousquet
- Department of Ecology and Environmental Sciences (A.R.D.L.T., P.K.I.) and Umeå Plant Science Center, Department of Plant Physiology (P.K.I., S.J., O.N., N.S.), Umeå University, SE-901 87 Umea, Sweden;Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada V5Z 4S6 (I.B., S.J.M.J.);Canada Research Chair in Forest and Environmental Genomics (J.Bou.) and Center for Forest Research and Institute for Systems and Integrative Biology (J.Bou., J.M.), Université Laval, Quebec, Quebec, Canada G1V 0A6;Michael Smith Laboratories (C.I.K., P.Z., J.Boh.) and Department of Forest and Conservation Sciences (K.R., J.Boh.), University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4; andBritish Columbia Ministry of Forests, Lands, and Natural Resource Operations, Victoria, British Columbia, Canada V8W 9C2 (A.Y.)
| | - Pär K Ingvarsson
- Department of Ecology and Environmental Sciences (A.R.D.L.T., P.K.I.) and Umeå Plant Science Center, Department of Plant Physiology (P.K.I., S.J., O.N., N.S.), Umeå University, SE-901 87 Umea, Sweden;Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada V5Z 4S6 (I.B., S.J.M.J.);Canada Research Chair in Forest and Environmental Genomics (J.Bou.) and Center for Forest Research and Institute for Systems and Integrative Biology (J.Bou., J.M.), Université Laval, Quebec, Quebec, Canada G1V 0A6;Michael Smith Laboratories (C.I.K., P.Z., J.Boh.) and Department of Forest and Conservation Sciences (K.R., J.Boh.), University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4; andBritish Columbia Ministry of Forests, Lands, and Natural Resource Operations, Victoria, British Columbia, Canada V8W 9C2 (A.Y.)
| | - Stefan Jansson
- Department of Ecology and Environmental Sciences (A.R.D.L.T., P.K.I.) and Umeå Plant Science Center, Department of Plant Physiology (P.K.I., S.J., O.N., N.S.), Umeå University, SE-901 87 Umea, Sweden;Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada V5Z 4S6 (I.B., S.J.M.J.);Canada Research Chair in Forest and Environmental Genomics (J.Bou.) and Center for Forest Research and Institute for Systems and Integrative Biology (J.Bou., J.M.), Université Laval, Quebec, Quebec, Canada G1V 0A6;Michael Smith Laboratories (C.I.K., P.Z., J.Boh.) and Department of Forest and Conservation Sciences (K.R., J.Boh.), University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4; andBritish Columbia Ministry of Forests, Lands, and Natural Resource Operations, Victoria, British Columbia, Canada V8W 9C2 (A.Y.)
| | - Steven J M Jones
- Department of Ecology and Environmental Sciences (A.R.D.L.T., P.K.I.) and Umeå Plant Science Center, Department of Plant Physiology (P.K.I., S.J., O.N., N.S.), Umeå University, SE-901 87 Umea, Sweden;Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada V5Z 4S6 (I.B., S.J.M.J.);Canada Research Chair in Forest and Environmental Genomics (J.Bou.) and Center for Forest Research and Institute for Systems and Integrative Biology (J.Bou., J.M.), Université Laval, Quebec, Quebec, Canada G1V 0A6;Michael Smith Laboratories (C.I.K., P.Z., J.Boh.) and Department of Forest and Conservation Sciences (K.R., J.Boh.), University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4; andBritish Columbia Ministry of Forests, Lands, and Natural Resource Operations, Victoria, British Columbia, Canada V8W 9C2 (A.Y.)
| | - Christopher I Keeling
- Department of Ecology and Environmental Sciences (A.R.D.L.T., P.K.I.) and Umeå Plant Science Center, Department of Plant Physiology (P.K.I., S.J., O.N., N.S.), Umeå University, SE-901 87 Umea, Sweden;Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada V5Z 4S6 (I.B., S.J.M.J.);Canada Research Chair in Forest and Environmental Genomics (J.Bou.) and Center for Forest Research and Institute for Systems and Integrative Biology (J.Bou., J.M.), Université Laval, Quebec, Quebec, Canada G1V 0A6;Michael Smith Laboratories (C.I.K., P.Z., J.Boh.) and Department of Forest and Conservation Sciences (K.R., J.Boh.), University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4; andBritish Columbia Ministry of Forests, Lands, and Natural Resource Operations, Victoria, British Columbia, Canada V8W 9C2 (A.Y.)
| | - John MacKay
- Department of Ecology and Environmental Sciences (A.R.D.L.T., P.K.I.) and Umeå Plant Science Center, Department of Plant Physiology (P.K.I., S.J., O.N., N.S.), Umeå University, SE-901 87 Umea, Sweden;Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada V5Z 4S6 (I.B., S.J.M.J.);Canada Research Chair in Forest and Environmental Genomics (J.Bou.) and Center for Forest Research and Institute for Systems and Integrative Biology (J.Bou., J.M.), Université Laval, Quebec, Quebec, Canada G1V 0A6;Michael Smith Laboratories (C.I.K., P.Z., J.Boh.) and Department of Forest and Conservation Sciences (K.R., J.Boh.), University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4; andBritish Columbia Ministry of Forests, Lands, and Natural Resource Operations, Victoria, British Columbia, Canada V8W 9C2 (A.Y.)
| | - Ove Nilsson
- Department of Ecology and Environmental Sciences (A.R.D.L.T., P.K.I.) and Umeå Plant Science Center, Department of Plant Physiology (P.K.I., S.J., O.N., N.S.), Umeå University, SE-901 87 Umea, Sweden;Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada V5Z 4S6 (I.B., S.J.M.J.);Canada Research Chair in Forest and Environmental Genomics (J.Bou.) and Center for Forest Research and Institute for Systems and Integrative Biology (J.Bou., J.M.), Université Laval, Quebec, Quebec, Canada G1V 0A6;Michael Smith Laboratories (C.I.K., P.Z., J.Boh.) and Department of Forest and Conservation Sciences (K.R., J.Boh.), University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4; andBritish Columbia Ministry of Forests, Lands, and Natural Resource Operations, Victoria, British Columbia, Canada V8W 9C2 (A.Y.)
| | - Kermit Ritland
- Department of Ecology and Environmental Sciences (A.R.D.L.T., P.K.I.) and Umeå Plant Science Center, Department of Plant Physiology (P.K.I., S.J., O.N., N.S.), Umeå University, SE-901 87 Umea, Sweden;Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada V5Z 4S6 (I.B., S.J.M.J.);Canada Research Chair in Forest and Environmental Genomics (J.Bou.) and Center for Forest Research and Institute for Systems and Integrative Biology (J.Bou., J.M.), Université Laval, Quebec, Quebec, Canada G1V 0A6;Michael Smith Laboratories (C.I.K., P.Z., J.Boh.) and Department of Forest and Conservation Sciences (K.R., J.Boh.), University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4; andBritish Columbia Ministry of Forests, Lands, and Natural Resource Operations, Victoria, British Columbia, Canada V8W 9C2 (A.Y.)
| | - Nathaniel Street
- Department of Ecology and Environmental Sciences (A.R.D.L.T., P.K.I.) and Umeå Plant Science Center, Department of Plant Physiology (P.K.I., S.J., O.N., N.S.), Umeå University, SE-901 87 Umea, Sweden;Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada V5Z 4S6 (I.B., S.J.M.J.);Canada Research Chair in Forest and Environmental Genomics (J.Bou.) and Center for Forest Research and Institute for Systems and Integrative Biology (J.Bou., J.M.), Université Laval, Quebec, Quebec, Canada G1V 0A6;Michael Smith Laboratories (C.I.K., P.Z., J.Boh.) and Department of Forest and Conservation Sciences (K.R., J.Boh.), University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4; andBritish Columbia Ministry of Forests, Lands, and Natural Resource Operations, Victoria, British Columbia, Canada V8W 9C2 (A.Y.)
| | - Alvin Yanchuk
- Department of Ecology and Environmental Sciences (A.R.D.L.T., P.K.I.) and Umeå Plant Science Center, Department of Plant Physiology (P.K.I., S.J., O.N., N.S.), Umeå University, SE-901 87 Umea, Sweden;Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada V5Z 4S6 (I.B., S.J.M.J.);Canada Research Chair in Forest and Environmental Genomics (J.Bou.) and Center for Forest Research and Institute for Systems and Integrative Biology (J.Bou., J.M.), Université Laval, Quebec, Quebec, Canada G1V 0A6;Michael Smith Laboratories (C.I.K., P.Z., J.Boh.) and Department of Forest and Conservation Sciences (K.R., J.Boh.), University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4; andBritish Columbia Ministry of Forests, Lands, and Natural Resource Operations, Victoria, British Columbia, Canada V8W 9C2 (A.Y.)
| | - Philipp Zerbe
- Department of Ecology and Environmental Sciences (A.R.D.L.T., P.K.I.) and Umeå Plant Science Center, Department of Plant Physiology (P.K.I., S.J., O.N., N.S.), Umeå University, SE-901 87 Umea, Sweden;Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada V5Z 4S6 (I.B., S.J.M.J.);Canada Research Chair in Forest and Environmental Genomics (J.Bou.) and Center for Forest Research and Institute for Systems and Integrative Biology (J.Bou., J.M.), Université Laval, Quebec, Quebec, Canada G1V 0A6;Michael Smith Laboratories (C.I.K., P.Z., J.Boh.) and Department of Forest and Conservation Sciences (K.R., J.Boh.), University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4; andBritish Columbia Ministry of Forests, Lands, and Natural Resource Operations, Victoria, British Columbia, Canada V8W 9C2 (A.Y.)
| | - Jörg Bohlmann
- Department of Ecology and Environmental Sciences (A.R.D.L.T., P.K.I.) and Umeå Plant Science Center, Department of Plant Physiology (P.K.I., S.J., O.N., N.S.), Umeå University, SE-901 87 Umea, Sweden;Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada V5Z 4S6 (I.B., S.J.M.J.);Canada Research Chair in Forest and Environmental Genomics (J.Bou.) and Center for Forest Research and Institute for Systems and Integrative Biology (J.Bou., J.M.), Université Laval, Quebec, Quebec, Canada G1V 0A6;Michael Smith Laboratories (C.I.K., P.Z., J.Boh.) and Department of Forest and Conservation Sciences (K.R., J.Boh.), University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4; andBritish Columbia Ministry of Forests, Lands, and Natural Resource Operations, Victoria, British Columbia, Canada V8W 9C2 (A.Y.)
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Karam MJ, Lefèvre F, Dagher-Kharrat MB, Pinosio S, Vendramin G. Genomic exploration and molecular marker development in a large and complex conifer genome using RADseq and mRNAseq. Mol Ecol Resour 2014; 15:601-12. [DOI: 10.1111/1755-0998.12329] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2014] [Revised: 08/30/2014] [Accepted: 09/05/2014] [Indexed: 01/05/2023]
Affiliation(s)
- M.-J. Karam
- INRA; UR 629 Ecologie des Forêts Méditerranéennes; URFM; Avignon France
| | - F. Lefèvre
- INRA; UR 629 Ecologie des Forêts Méditerranéennes; URFM; Avignon France
| | - M. Bou Dagher-Kharrat
- Laboratoire Caractérisation Génomique des Plantes; Département Sciences de la Vie et de la Terre; Faculté des Sciences; Campus Sciences et Technologies; Université Saint-Joseph; Mar Roukos Mkalles Lebanon
| | - S. Pinosio
- Istituto di Genomica Applicata (IGA); Udine Italy
- Institute of Biosciences and Bioresources; National Research Council; Florence Italy
| | - G.G. Vendramin
- Institute of Biosciences and Bioresources; National Research Council; Florence Italy
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Santos CA, Blanck DV, de Freitas PD. RNA-seq as a powerful tool for penaeid shrimp genetic progress. Front Genet 2014; 5:298. [PMID: 25221571 PMCID: PMC4147233 DOI: 10.3389/fgene.2014.00298] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2014] [Accepted: 08/11/2014] [Indexed: 11/27/2022] Open
Abstract
The sequences of all different RNA transcripts present in a cell or tissue that are related to the gene expression and its functional control represent what it is called a transcriptome. The transcripts vary between cells, tissues, ontogenetic and environmental conditions, and the knowledge that can be gained through them is of a solid relevance for genetic applications in aquaculture. Some of the techniques used in transcriptome studies, such as microarrays, are being replaced for next-generation sequencing approaches. RNA-seq emerges as a new possibility for the transcriptome complexity analysis as well as for the candidate genes and polymorphisms identification of penaeid species. Thus, it may also help to understand the determination of complex traits mechanisms and genetic improvement of stocks. In this review, it is first introduced an overview of transcriptome analysis by RNA-seq, followed by a discussion of how this approach may be applied in genetic progress within penaeid stocks.
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Affiliation(s)
- Camilla A Santos
- Laboratory of Molecular Biodiversity and Conservation, Department of Genetics and Evolution, Federal University of São Carlos São Carlos, Brazil
| | - Danielly V Blanck
- Laboratory of Molecular Biodiversity and Conservation, Department of Genetics and Evolution, Federal University of São Carlos São Carlos, Brazil
| | - Patrícia D de Freitas
- Laboratory of Molecular Biodiversity and Conservation, Department of Genetics and Evolution, Federal University of São Carlos São Carlos, Brazil
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Pavy N, Deschênes A, Blais S, Lavigne P, Beaulieu J, Isabel N, Mackay J, Bousquet J. The landscape of nucleotide polymorphism among 13,500 genes of the conifer picea glauca, relationships with functions, and comparison with medicago truncatula. Genome Biol Evol 2014; 5:1910-25. [PMID: 24065735 PMCID: PMC3814201 DOI: 10.1093/gbe/evt143] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Gene families differ in composition, expression, and chromosomal organization between conifers and angiosperms, but little is known regarding nucleotide polymorphism. Using various sequencing strategies, an atlas of 212k high-confidence single nucleotide polymorphisms (SNPs) with a validation rate of more than 92% was developed for the conifer white spruce (Picea glauca). Nonsynonymous and synonymous SNPs were annotated over the corresponding 13,498 white spruce genes representative of 2,457 known gene families. Patterns of nucleotide polymorphisms were analyzed by estimating the ratio of nonsynonymous to synonymous numbers of substitutions per site (A/S). A general excess of synonymous SNPs was expected and observed. However, the analysis from several perspectives enabled to identify groups of genes harboring an excess of nonsynonymous SNPs, thus potentially under positive selection. Four known gene families harbored such an excess: dehydrins, ankyrin-repeats, AP2/DREB, and leucine-rich repeat. Conifer-specific sequences were also generally associated with the highest A/S ratios. A/S values were also distributed asymmetrically across genes specifically expressed in megagametophytes, roots, or in both, harboring on average an excess of nonsynonymous SNPs. These patterns confirm that the breadth of gene expression is a contributing factor to the evolution of nucleotide polymorphism. The A/S ratios of Medicago truncatula genes were also analyzed: several gene families shared between P. glauca and M. truncatula data sets had similar excess of synonymous or nonsynonymous SNPs. However, a number of families with high A/S ratios were found specific to P. glauca, suggesting cases of divergent evolution at the functional level.
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Affiliation(s)
- Nathalie Pavy
- Canada Research Chair in Forest and Environmental Genomics, Centre for Forest Research and Institute for Systems and Integrative Biology, Université Laval, Québec, Canada
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Pinosio S, González-Martínez SC, Bagnoli F, Cattonaro F, Grivet D, Marroni F, Lorenzo Z, Pausas JG, Verdú M, Vendramin GG. First insights into the transcriptome and development of new genomic tools of a widespread circum-Mediterranean tree species, Pinus halepensis Mill. Mol Ecol Resour 2014; 14:846-56. [PMID: 24450970 DOI: 10.1111/1755-0998.12232] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2013] [Revised: 01/15/2014] [Accepted: 01/17/2014] [Indexed: 11/30/2022]
Abstract
Aleppo pine (Pinus halepensis Mill.) is a relevant conifer species for studying adaptive responses to drought and fire regimes in the Mediterranean region. In this study, we performed Illumina next-generation sequencing of two phenotypically divergent Aleppo pine accessions with the aims of (i) characterizing the transcriptome through Illumina RNA-Seq on trees phenotypically divergent for adaptive traits linked to fire adaptation and drought, (ii) performing a functional annotation of the assembled transcriptome, (iii) identifying genes with accelerated evolutionary rates, (iv) studying the expression levels of the annotated genes and (v) developing gene-based markers for population genomic and association genetic studies. The assembled transcriptome consisted of 48,629 contigs and covered about 54.6 Mbp. The comparison of Aleppo pine transcripts to Picea sitchensis protein-coding sequences resulted in the detection of 34,014 SNPs across species, with a Ka /Ks average value of 0.216, suggesting that the majority of the assembled genes are under negative selection. Several genes were differentially expressed across the two pine accessions with contrasted phenotypes, including a glutathione-s-transferase, a cellulose synthase and a cobra-like protein. A large number of new markers (3334 amplifiable SSRs and 28,236 SNPs) have been identified which should facilitate future population genomics and association genetics in this species. A 384-SNP Oligo Pool Assay for genotyping with the Illumina VeraCode technology has been designed which showed an high overall SNP conversion rate (76.6%). Our results showed that Illumina next-generation sequencing is a valuable technology to obtain an extensive overview on whole transcriptomes of nonmodel species with large genomes.
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Affiliation(s)
- S Pinosio
- Institute of Biosciences and Bioresources, National Research Council, Via Madonna del Piano 10, 50019, Sesto Fiorentino, Firenze, Italy; IGA Technology Services s.r.l., Via J. Linussio, 51, 33100, Udine, Italy
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Li MR, Wang XF, Zhang C, Wang HY, Shi FX, Xiao HX, Li LF. A simple strategy for development of single nucleotide polymorphisms from non-model species and its application in Panax. Int J Mol Sci 2013; 14:24581-91. [PMID: 24351835 PMCID: PMC3876129 DOI: 10.3390/ijms141224581] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2013] [Revised: 12/09/2013] [Accepted: 12/13/2013] [Indexed: 11/23/2022] Open
Abstract
Single nucleotide polymorphisms (SNPs) are widely employed in the studies of population genetics, molecular breeding and conservation genetics. In this study, we explored a simple route to develop SNPs from non-model species based on screening the library of single copy nuclear genes (SCNGs). Through application of this strategy in Panax, we identified 160 and 171 SNPs from P. quinquefolium and P. ginseng, respectively. Our results demonstrated that both P. ginseng and P. quinquefolium possessed a high level of nucleotide diversity. The number of haplotype per locus ranged from 1 to 12 for P. ginseng and from 1 to 9 for P. quinquefolium, respectively. The nucleotide diversity of total sites (πT) varied between 0.000 and 0.023 for P. ginseng and 0.000 and 0.035 for P. quinquefolium, respectively. These findings suggested that this approach is well suited for SNP discovery in non-model organisms and is easily employed in standard genetics laboratory studies.
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Affiliation(s)
- Ming Rui Li
- Key Laboratory of Molecular Epigenetics of Ministry of Education, Northeast Normal University, Changchun 130024, China; E-Mails: (M.R.L.); (X.F.W.); (C.Z.); (H.Y.W.); (F.X.S.)
| | - Xin Feng Wang
- Key Laboratory of Molecular Epigenetics of Ministry of Education, Northeast Normal University, Changchun 130024, China; E-Mails: (M.R.L.); (X.F.W.); (C.Z.); (H.Y.W.); (F.X.S.)
| | - Cui Zhang
- Key Laboratory of Molecular Epigenetics of Ministry of Education, Northeast Normal University, Changchun 130024, China; E-Mails: (M.R.L.); (X.F.W.); (C.Z.); (H.Y.W.); (F.X.S.)
| | - Hua Ying Wang
- Key Laboratory of Molecular Epigenetics of Ministry of Education, Northeast Normal University, Changchun 130024, China; E-Mails: (M.R.L.); (X.F.W.); (C.Z.); (H.Y.W.); (F.X.S.)
| | - Feng Xue Shi
- Key Laboratory of Molecular Epigenetics of Ministry of Education, Northeast Normal University, Changchun 130024, China; E-Mails: (M.R.L.); (X.F.W.); (C.Z.); (H.Y.W.); (F.X.S.)
| | - Hong Xing Xiao
- Key Laboratory of Molecular Epigenetics of Ministry of Education, Northeast Normal University, Changchun 130024, China; E-Mails: (M.R.L.); (X.F.W.); (C.Z.); (H.Y.W.); (F.X.S.)
| | - Lin Feng Li
- Key Laboratory of Molecular Epigenetics of Ministry of Education, Northeast Normal University, Changchun 130024, China; E-Mails: (M.R.L.); (X.F.W.); (C.Z.); (H.Y.W.); (F.X.S.)
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Neale DB, Langley CH, Salzberg SL, Wegrzyn JL. Open access to tree genomes: the path to a better forest. Genome Biol 2013; 14:120. [PMID: 23796049 PMCID: PMC3706761 DOI: 10.1186/gb-2013-14-6-120] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
An open-access culture and a well-developed comparative-genomics infrastructure must be developed in forest trees to derive the full potential of genome sequencing in this diverse group of plants that are the dominant species in much of the earth's terrestrial ecosystems.
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