High-throughput gene and SNP discovery in Eucalyptus grandis, an uncharacterized genome

Novaes, Evandro; Drost, Derek R.; Farmerie, William G.; Pappas, George J.; Grattapaglia, Dário; Sederoff, Ronald R.; Kirst, Matias

doi:10.1186/1471-2164-9-312

Cited by 431 publications

(472 citation statements)

References 39 publications

(46 reference statements)

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“…Eucalypts are preferentially outcrossing with late-acting post-zygotic selfincompatibility resulting in outcrossing rates that can exceed 90% 1 , high levels of nucleotide variation 23,24 and accumulation of genetic load and expression of inbreeding depression 4 . A microsatellite survey of BRASUZ1 and its inbred siblings indicated putative hotspots of genetic load (Supplementary Information section 4).…”

Section: Genetic Load and Heterozygositymentioning

confidence: 99%

The genome of Eucalyptus grandis

Myburg¹,

Grattapaglia²,

Tuskan³

et al. 2014

Nature

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Eucalypts are the world's most widely planted hardwood trees. Their outstanding diversity, adaptability and growth have made them a global renewable resource of fibre and energy. We sequenced and assembled .94% of the 640-megabase genome of Eucalyptus grandis. Of 36,376 predicted protein-coding genes, 34% occur in tandem duplications, the largest proportion thus far in plant genomes. Eucalyptus also shows the highest diversity of genes for specialized metabolites such as terpenes that act as chemical defence and provide unique pharmaceutical oils. Genome sequencing of the E. grandis sister species E. globulus and a set of inbred E. grandis tree genomes reveals dynamic genome evolution and hotspots of inbreeding depression. The E. grandis genome is the first reference for the eudicot order Myrtales and is placed here sister to the eurosids. This resource expands our understanding of the unique biology of large woody perennials and provides a powerful tool to accelerate comparative biology, breeding and biotechnology.A major opportunity for a sustainable energy and biomaterials economy in many parts of the world lies in a better understanding of the molecular basis of superior growth and adaptation in woody plants. Part of this opportunity involves species of Eucalyptus L'Hér, a genus of woody perennials native to Australia 1 . The remarkable adaptability of eucalypts coupled with their fast growth and superior wood properties has driven their rapid adoption for plantation forestry in more than 100 countries across six continents (.20 million ha) 2 , making eucalypts the most widely planted hardwood forest trees in the world. The subtropical E. grandis and the temperate E. globulus stand out as targets of breeding programmes worldwide. Planted eucalypts provide key renewable resources for the production of pulp, paper, biomaterials and bioenergy, while mitigating human pressures on native forests 3 . Eucalypts also have a large diversity and high concentration of essential oils (mixtures of mono-and sesquiterpenes), many of which have ecological functions as well as medicinal and industrial uses. Predominantly outcrossers 1 with hermaphroditic animal-pollinated flowers, eucalypts are highly heterozygous and display pre-and postzygotic barriers to selfing to reduce inbreeding depression for fitness and survival 4 .To mitigate the challenge of assembling a highly heterozygous genome, we sequenced the genome of 'BRASUZ1', a 17-year-old E. grandis genotype derived from one generation of selfing. The availability of annotated forest tree genomes from two separately evolving rosid lineages, Eucalyptus (order Myrtales) and Populus (order Malpighiales 5 ), in combination with genomes from domesticated woody plants (for example, Vitis, Prunus, Citrus), provides a comparative foundation for addressing

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Section: Genetic Load and Heterozygositymentioning

confidence: 99%

The genome of Eucalyptus grandis

Myburg¹,

Grattapaglia²,

Tuskan³

et al. 2014

Nature

Self Cite

740

750

View full text Add to dashboard Cite

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“…The resulting ESTs are aligned the gene-enriched sequences to identify SNPs (Barbazuk et al 2007). This approach can be successful even in cases for which reference genomic sequences are not available (Novaes et al 2008;Buggs et al 2009). Once identified, SNPs are converted into genetic markers and are used to genotype the mapping population and build a genetic map.…”

Section: Conversion Of Putative Snps To Genetic Markersmentioning

confidence: 99%

High-Throughput Genetic Mapping of Mutants via Quantitative Single Nucleotide Polymorphism Typing

Liu

Chen²,

Makarevitch

et al. 2010

Genetics

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Advances in next-generation sequencing technology have facilitated the discovery of single nucleotide polymorphisms (SNPs). Sequenom-based SNP-typing assays were developed for 1359 maize SNPs identified via comparative next-generation transcriptomic sequencing. Approximately 75% of these SNPs were successfully converted into genetic markers that can be scored reliably and used to generate a SNPbased genetic map by genotyping recombinant inbred lines from the intermated B73 3 Mo17 population. The quantitative nature of Sequenom-based SNP assays led to the development of a time-and costefficient strategy to genetically map mutants via quantitative bulked segregant analysis. This strategy was used to rapidly map the loci associated with several dozen recessive mutants. Because a mutant can be mapped using as few as eight multiplexed sets of SNP assays on a bulk of as few as 20 mutant F 2 individuals, this strategy is expected to be widely adopted for mapping in many species. W ITH the availability of a sequenced genome it is feasibletoundertakechromosomewalking projects to clone genes responsible for mutant phenotypes (Alleman et al. 2006;Briggs et al. 2007;Menzel et al. 2007;Song et al. 2007) and quantitative trait loci (QTL) (Glazier et al. 2002;Korstanje and Paigen 2002;Salvi et al. 2007). However, it can be logistically difficult and time-consuming to map mutants with current technologies. A high-throughput system to map phenotypic mutants would be very useful in converting the wealth of phenotypic mutants into an understanding of the molecular basis.Single nucleotide polymorphisms (SNPs) can be converted into genetic markers that are scored in mapping populations using various high-throughput SNP-typing technologies ( Maize (Zea mays L.) is an important model organism with substantial economic value. In this species, SNPs occur at a rate of one per 28-214 bp (Tenaillon et al. 2001;Barbazuk et al. 2007). Using our 454-based SNP discovery pipeline, we identified .7000 putative SNPs, .85% (94/ 110) of which could be validated via Sanger sequencing (Barbazuk et al. 2007). Here, we report the analysis of 1359 of these putative SNPs. Approximately 75% of the tested SNPs could be converted into genetic markers, and only 3% were deemed to be false positives. These SNP-based markers were used to construct a genetic map that can be used to address diverse biological questions. Finally, we apply the combination of quantitative SNP typing and bulked segregant analysis (BSA) (Michelmore et al. 1991) to efficiently map phenotypic mutants. MATERIALS AND METHODSGenetic materials: Using a high-throughput protocol (Dietrich et al. 2002) (Table S1, supporting information), the 25 non-B73 parents of the nested association mapping (NAM) population , and mutant and non-mutant pools of DNAs for BSA. For BSA, tissues from all mutant (or non-mutant) individuals from within the same F 2 family were pooled, and a single DNA isolation was performed or DNA was isolated from each individual and then equal amounts from each individ...

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“…Like DArT, they are largely bi-allelic, but, similarly, their high abundance should ameliorate this limitation. Published accounts of the SNP resource are still rare for eucalypts, but sequencing of the transcriptome and resequencing genome fractions or genes using conventional or next-generation sequencing has confirmed that large numbers of SNPs will be available (Külheim et al 2009;Novaes et al 2008;Poke et al 2003). Assay methods have been used that accommodate the complexity of SNP genotyping in the highly heterozygous eucalypt genome (Sexton et al 2010b), although at a relatively low throughput of less than 100 multiplexed SNPs.…”

Section: Molecular Marker Resourcesmentioning

confidence: 99%