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High-density linkage mapping in a pine tree reveals a genomic region associated with inbreeding depression and provides clues to the extent and distribution of meiotic recombination

Chancerel, Emilie ; Lamy, Jean-Baptiste ; Lesur, Isabelle ; [et al.]

Springer Science and Business Media LLC ; 2013

In: BMC Biology Vol. 11, No. 1 ( 2013-12)

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In: BMC Biology, Springer Science and Business Media LLC, Vol. 11, No. 1 ( 2013-12)

Abstract: The availability of a large expressed sequence tags (EST) resource and recent advances in high-throughput genotyping technology have made it possible to develop highly multiplexed SNP arrays for multi-objective genetic applications, including the construction of meiotic maps. Such approaches are particularly useful in species with a large genome size, precluding the use of whole-genome shotgun assembly with current technologies. Results In this study, a 12 k-SNP genotyping array was developed for maritime pine from an extensive EST resource assembled into a unigene set. The offspring of three-generation outbred and inbred mapping pedigrees were then genotyped. The inbred pedigree consisted of a classical F2 population resulting from the selfing of a single inter-provenance (Landes x Corsica) hybrid tree, whereas the outbred pedigree (G2) resulted from a controlled cross of two intra-provenance (Landes x Landes) hybrid trees. This resulted in the generation of three linkage maps based on SNP markers: one from the parental genotype of the F2 population (1,131 markers in 1,708 centimorgan (cM)), and one for each parent of the G2 population (1,015 and 1,110 markers in 1,447 and 1,425 cM for the female and male parents, respectively). A comparison of segregation patterns in the progeny obtained from the two types of mating (inbreeding and outbreeding) led to the identification of a chromosomal region carrying an embryo viability locus with a semi-lethal allele. Following selfing and segregation, zygote mortality resulted in a deficit of Corsican homozygous genotypes in the F2 population. This dataset was also used to study the extent and distribution of meiotic recombination along the length of the chromosomes and the effect of sex and/or genetic background on recombination. The genetic background of trees in which meiotic recombination occurred was found to have a significant effect on the frequency of recombination. Furthermore, only a small proportion of the recombination hot- and cold-spots were common to all three genotypes, suggesting that the spatial pattern of recombination was genetically variable. Conclusion This study led to the development of classical genomic tools for this ecologically and economically important species. It also identified a chromosomal region bearing a semi-lethal recessive allele and demonstrated the genetic variability of recombination rate over the genome.

Type of Medium: Online Resource

ISSN: 1741-7007

URL: Article

DOI: 10.1186/1741-7007-11-50

Language: English

Publisher: Springer Science and Business Media LLC

Publication Date: 2013

detail.hit.zdb_id: 2133020-7

SSG: 12

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Decoding the oak genome: public release of sequence data, assembly, annotation and publication strategies

Plomion, Christophe ; Aury, Jean‐Marc ; Amselem, Joëlle ; [et al.]

Wiley ; 2016

In: Molecular Ecology Resources Vol. 16, No. 1 ( 2016-01), p. 254-265

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In: Molecular Ecology Resources, Wiley, Vol. 16, No. 1 ( 2016-01), p. 254-265

Abstract: The 1.5 Gbp/2C genome of pedunculate oak ( Quercus robur ) has been sequenced. A strategy was established for dealing with the challenges imposed by the sequencing of such a large, complex and highly heterozygous genome by a whole‐genome shotgun ( WGS ) approach, without the use of costly and time‐consuming methods, such as fosmid or BAC clone‐based hierarchical sequencing methods. The sequencing strategy combined short and long reads. Over 49 million reads provided by Roche 454 GS ‐ FLX technology were assembled into contigs and combined with shorter Illumina sequence reads from paired‐end and mate‐pair libraries of different insert sizes, to build scaffolds. Errors were corrected and gaps filled with Illumina paired‐end reads and contaminants detected, resulting in a total of 17 910 scaffolds ( 〉 2 kb) corresponding to 1.34 Gb. Fifty per cent of the assembly was accounted for by 1468 scaffolds (N50 of 260 kb). Initial comparison with the phylogenetically related Prunus persica gene model indicated that genes for 84.6% of the proteins present in peach (mean protein coverage of 90.5%) were present in our assembly. The second and third steps in this project are genome annotation and the assignment of scaffolds to the oak genetic linkage map. In accordance with the Bermuda and Fort Lauderdale agreements and the more recent Toronto Statement, the oak genome data have been released into public sequence repositories in advance of publication. In this presubmission paper, the oak genome consortium describes its principal lines of work and future directions for analyses of the nature, function and evolution of the oak genome.

Type of Medium: Online Resource

ISSN: 1755-098X , 1755-0998

URL: Issue

URL: Article

DOI: 10.1111/men.2016.16.issue-1

DOI: 10.1111/1755-0998.12425

Language: English

Publisher: Wiley

Publication Date: 2016

detail.hit.zdb_id: 2406833-0

SSG: 12

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High‐Throughput DNA sequencing of ancient wood

Wagner, Stefanie ; Lagane, Frédéric ; Seguin‐Orlando, Andaine ; [et al.]

Wiley ; 2018

In: Molecular Ecology Vol. 27, No. 5 ( 2018-03), p. 1138-1154

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In: Molecular Ecology, Wiley, Vol. 27, No. 5 ( 2018-03), p. 1138-1154

Abstract: Reconstructing the colonization and demographic dynamics that gave rise to extant forests is essential to forecasts of forest responses to environmental changes. Classical approaches to map how population of trees changed through space and time largely rely on pollen distribution patterns, with only a limited number of studies exploiting DNA molecules preserved in wooden tree archaeological and subfossil remains. Here, we advance such analyses by applying high‐throughput ( HTS ) DNA sequencing to wood archaeological and subfossil material for the first time, using a comprehensive sample of 167 European white oak waterlogged remains spanning a large temporal (from 550 to 9,800 years) and geographical range across Europe. The successful characterization of the endogenous DNA and exogenous microbial DNA of 140 (~83%) samples helped the identification of environmental conditions favouring long‐term DNA preservation in wood remains, and started to unveil the first trends in the DNA decay process in wood material. Additionally, the maternally inherited chloroplast haplotypes of 21 samples from three periods of forest human‐induced use (Neolithic, Bronze Age and Middle Ages) were found to be consistent with those of modern populations growing in the same geographic areas. Our work paves the way for further studies aiming at using ancient DNA preserved in wood to reconstruct the micro‐evolutionary response of trees to climate change and human forest management.

Type of Medium: Online Resource

ISSN: 0962-1083 , 1365-294X

URL: Issue

URL: Article

DOI: 10.1111/mec.2018.27.issue-5

DOI: 10.1111/mec.14514

RVK:

WA 15000

Language: English

Publisher: Wiley

Publication Date: 2018

detail.hit.zdb_id: 2020749-9

detail.hit.zdb_id: 1126687-9

SSG: 12

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Performance of genomic prediction within and across generations in maritime pine

Bartholomé, Jérôme ; Van Heerwaarden, Joost ; Isik, Fikret ; [et al.]

Springer Science and Business Media LLC ; 2016

In: BMC Genomics Vol. 17, No. 1 ( 2016-12)

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In: BMC Genomics, Springer Science and Business Media LLC, Vol. 17, No. 1 ( 2016-12)

Type of Medium: Online Resource

ISSN: 1471-2164

URL: Article

DOI: 10.1186/s12864-016-2879-8

Language: English

Publisher: Springer Science and Business Media LLC

Publication Date: 2016

detail.hit.zdb_id: 2041499-7

SSG: 12

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Oak genome reveals facets of long lifespan

Plomion, Christophe ; Aury, Jean-Marc ; Amselem, Joëlle ; [et al.]

Springer Science and Business Media LLC ; 2018

In: Nature Plants Vol. 4, No. 7 ( 2018-06-18), p. 440-452

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In: Nature Plants, Springer Science and Business Media LLC, Vol. 4, No. 7 ( 2018-06-18), p. 440-452

Abstract: Oaks are an important part of our natural and cultural heritage. Not only are they ubiquitous in our most common landscapes 1 but they have also supplied human societies with invaluable services, including food and shelter, since prehistoric times 2 . With 450 species spread throughout Asia, Europe and America 3 , oaks constitute a critical global renewable resource. The longevity of oaks (several hundred years) probably underlies their emblematic cultural and historical importance. Such long-lived sessile organisms must persist in the face of a wide range of abiotic and biotic threats over their lifespans. We investigated the genomic features associated with such a long lifespan by sequencing, assembling and annotating the oak genome. We then used the growing number of whole-genome sequences for plants (including tree and herbaceous species) to investigate the parallel evolution of genomic characteristics potentially underpinning tree longevity. A further consequence of the long lifespan of trees is their accumulation of somatic mutations during mitotic divisions of stem cells present in the shoot apical meristems. Empirical 4 and modelling 5 approaches have shown that intra-organismal genetic heterogeneity can be selected for 6 and provides direct fitness benefits in the arms race with short-lived pests and pathogens through a patchwork of intra-organismal phenotypes 7 . However, there is no clear proof that large-statured trees consist of a genetic mosaic of clonally distinct cell lineages within and between branches. Through this case study of oak, we demonstrate the accumulation and transmission of somatic mutations and the expansion of disease-resistance gene families in trees.

Type of Medium: Online Resource

ISSN: 2055-0278

URL: Article

DOI: 10.1038/s41477-018-0172-3

Language: English

Publisher: Springer Science and Business Media LLC

Publication Date: 2018

detail.hit.zdb_id: 2815502-6

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Linkage and Association Mapping for Two Major Traits Used in the Maritime Pine Breeding Program: Height Growth and Stem Straightness

Bartholomé, Jérôme ; Bink, Marco CAM ; van Heerwaarden, Joost ; [et al.]

Public Library of Science (PLoS) ; 2016

In: PLOS ONE Vol. 11, No. 11 ( 2016-11-2), p. e0165323-

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In: PLOS ONE, Public Library of Science (PLoS), Vol. 11, No. 11 ( 2016-11-2), p. e0165323-

Type of Medium: Online Resource

ISSN: 1932-6203

URL: Article

DOI: 10.1371/journal.pone.0165323

DOI: 10.1371/journal.pone.0165323.g001

DOI: 10.1371/journal.pone.0165323.g002

DOI: 10.1371/journal.pone.0165323.g003

DOI: 10.1371/journal.pone.0165323.g004

DOI: 10.1371/journal.pone.0165323.t001

DOI: 10.1371/journal.pone.0165323.t002

DOI: 10.1371/journal.pone.0165323.t003

DOI: 10.1371/journal.pone.0165323.t004

DOI: 10.1371/journal.pone.0165323.s001

DOI: 10.1371/journal.pone.0165323.s002

DOI: 10.1371/journal.pone.0165323.s003

DOI: 10.1371/journal.pone.0165323.s004

DOI: 10.1371/journal.pone.0165323.s005

DOI: 10.1371/journal.pone.0165323.s006

DOI: 10.1371/journal.pone.0165323.s007

DOI: 10.1371/journal.pone.0165323.s008

DOI: 10.1371/journal.pone.0165323.s009

DOI: 10.1371/journal.pone.0165323.s010

DOI: 10.1371/journal.pone.0165323.s011

DOI: 10.1371/journal.pone.0165323.s012

DOI: 10.1371/journal.pone.0165323.s013

DOI: 10.1371/journal.pone.0165323.s014

DOI: 10.1371/journal.pone.0165323.s015

DOI: 10.1371/journal.pone.0165323.s016

DOI: 10.1371/journal.pone.0165323.s017

Language: English

Publisher: Public Library of Science (PLoS)

Publication Date: 2016

detail.hit.zdb_id: 2267670-3

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The oak gene expression atlas: insights into Fagaceae genome evolution and the discovery of genes regulated during bud dormancy release

Lesur, Isabelle ; Le Provost, Grégoire ; Bento, Pascal ; [et al.]

Springer Science and Business Media LLC ; 2015

In: BMC Genomics Vol. 16, No. 1 ( 2015-12)

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In: BMC Genomics, Springer Science and Business Media LLC, Vol. 16, No. 1 ( 2015-12)

Type of Medium: Online Resource

ISSN: 1471-2164

URL: Article

DOI: 10.1186/s12864-015-1331-9

Language: English

Publisher: Springer Science and Business Media LLC

Publication Date: 2015

detail.hit.zdb_id: 2041499-7

SSG: 12

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Development and implementation of a highly-multiplexed SNP array for genetic mapping in maritime pine and comparative mapping with loblolly pine

Chancerel, Emilie ; Lepoittevin, Camille ; Le Provost, Grégoire ; [et al.]

Springer Science and Business Media LLC ; 2011

In: BMC Genomics Vol. 12, No. 1 ( 2011-12)

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In: BMC Genomics, Springer Science and Business Media LLC, Vol. 12, No. 1 ( 2011-12)

Abstract: Single nucleotide polymorphisms (SNPs) are the most abundant source of genetic variation among individuals of a species. New genotyping technologies allow examining hundreds to thousands of SNPs in a single reaction for a wide range of applications such as genetic diversity analysis, linkage mapping, fine QTL mapping, association studies, marker-assisted or genome-wide selection. In this paper, we evaluated the potential of highly-multiplexed SNP genotyping for genetic mapping in maritime pine ( Pinus pinaster Ait.), the main conifer used for commercial plantation in southwestern Europe. Results We designed a custom GoldenGate assay for 1,536 SNPs detected through the resequencing of gene fragments (707 in vitro SNPs/Indels) and from Sanger-derived Expressed Sequenced Tags assembled into a unigene set (829 in silico SNPs/Indels). Offspring from three-generation outbred (G2) and inbred (F2) pedigrees were genotyped. The success rate of the assay was 63.6% and 74.8% for in silico and in vitro SNPs, respectively. A genotyping error rate of 0.4% was further estimated from segregating data of SNPs belonging to the same gene. Overall, 394 SNPs were available for mapping. A total of 287 SNPs were integrated with previously mapped markers in the G2 parental maps, while 179 SNPs were localized on the map generated from the analysis of the F2 progeny. Based on 98 markers segregating in both pedigrees, we were able to generate a consensus map comprising 357 SNPs from 292 different loci. Finally, the analysis of sequence homology between mapped markers and their orthologs in a Pinus taeda linkage map, made it possible to align the 12 linkage groups of both species. Conclusions Our results show that the GoldenGate assay can be used successfully for high-throughput SNP genotyping in maritime pine, a conifer species that has a genome seven times the size of the human genome. This SNP-array will be extended thanks to recent sequencing effort using new generation sequencing technologies and will include SNPs from comparative orthologous sequences that were identified in the present study, providing a wider collection of anchor points for comparative genomics among the conifers.

Type of Medium: Online Resource

ISSN: 1471-2164

URL: Article

DOI: 10.1186/1471-2164-12-368

Language: English

Publisher: Springer Science and Business Media LLC

Publication Date: 2011

detail.hit.zdb_id: 2041499-7

SSG: 12

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De novo assembly of maritime pine transcriptome: implications for forest breeding and biotechnology

Canales, Javier ; Bautista, Rocio ; Label, Philippe ; [et al.]

Wiley ; 2014

In: Plant Biotechnology Journal Vol. 12, No. 3 ( 2014-04), p. 286-299

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In: Plant Biotechnology Journal, Wiley, Vol. 12, No. 3 ( 2014-04), p. 286-299

Abstract: Maritime pine ( P inus pinaster A it.) is a widely distributed conifer species in S outhwestern E urope and one of the most advanced models for conifer research. In the current work, comprehensive characterization of the maritime pine transcriptome was performed using a combination of two different next‐generation sequencing platforms, 454 and I llumina. De novo assembly of the transcriptome provided a catalogue of 26 020 unique transcripts in maritime pine trees and a collection of 9641 full‐length c DNA s. Quality of the transcriptome assembly was validated by RT ‐ PCR amplification of selected transcripts for structural and regulatory genes. Transcription factors and enzyme‐encoding transcripts were annotated. Furthermore, the available sequencing data permitted the identification of polymorphisms and the establishment of robust single nucleotide polymorphism ( SNP ) and simple‐sequence repeat ( SSR ) databases for genotyping applications and integration of translational genomics in maritime pine breeding programmes. All our data are freely available at S ustainpine DB , the P . pinaster expressional database. Results reported here on the maritime pine transcriptome represent a valuable resource for future basic and applied studies on this ecological and economically important pine species.

Type of Medium: Online Resource

ISSN: 1467-7644 , 1467-7652

URL: Issue

URL: Article

DOI: 10.1111/pbi.2014.12.issue-3

DOI: 10.1111/pbi.12136

Language: English

Publisher: Wiley

Publication Date: 2014

detail.hit.zdb_id: 2136367-5

SSG: 12

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Transcriptional profiling of bud dormancy induction and release in oak by next-generation sequencing

Ueno, Saneyoshi ; Klopp, Christophe ; Leplé, Jean Charles ; [et al.]

Springer Science and Business Media LLC ; 2013

In: BMC Genomics Vol. 14, No. 1 ( 2013-12)

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In: BMC Genomics, Springer Science and Business Media LLC, Vol. 14, No. 1 ( 2013-12)

Abstract: In temperate regions, the time lag between vegetative bud burst and bud set determines the duration of the growing season of trees (i.e. the duration of wood biomass production). Dormancy, the period during which the plant is not growing, allows trees to avoid cold injury resulting from exposure to low temperatures. An understanding of the molecular machinery controlling the shift between these two phenological states is of key importance in the context of climatic change. The objective of this study was to identify genes upregulated during endo- and ecodormancy, the two main stages of bud dormancy. Sessile oak is a widely distributed European white oak species. A forcing test on young trees was first carried out to identify the period most likely to correspond to these two stages. Total RNA was then extracted from apical buds displaying endo- and ecodormancy. This RNA was used for the generation of cDNA libraries, and in-depth transcriptome characterization was performed with 454 FLX pyrosequencing technology. Results Pyrosequencing produced a total of 495,915 reads. The data were cleaned, duplicated reads removed, and sequences were mapped onto the oak UniGene data. Digital gene expression analysis was performed, with both R statistics and the R-Bioconductor packages (edgeR and DESeq), on 6,471 contigs with read numbers ≥ 5 within any contigs. The number of sequences displaying significant differences in expression level (read abundance) between endo- and ecodormancy conditions ranged from 75 to 161, depending on the algorithm used. 13 genes displaying significant differences between conditions were selected for further analysis, and 11 of these genes, including those for glutathione-S-transferase (GST) and dehydrin xero2 (XERO2) were validated by quantitative PCR. Conclusions The identification and functional annotation of differentially expressed genes involved in the “response to abscisic acid”, “response to cold stress” and “response to oxidative stress” categories constitutes a major step towards characterization of the molecular network underlying vegetative bud dormancy, an important life history trait of long-lived organisms.

Type of Medium: Online Resource

ISSN: 1471-2164

URL: Article

DOI: 10.1186/1471-2164-14-236

Language: English

Publisher: Springer Science and Business Media LLC

Publication Date: 2013

detail.hit.zdb_id: 2041499-7

SSG: 12

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