461
identify genome variation like SNP and the development of genotyping platforms.
Neale and Wheeler (2019) completed and updated the review specifically for conifers. In López de Heredia and Vázquez-Poletti (2016), bioinformatics tools that are
needed for the analysis of RNA-Seq data from forest trees are pointed out taking
into account difficulties in de novo transcriptome assembly due to the high level of
heterozygosity, large genome size particularly in conifers and annotation difficulties
when based on intensively studied crops or herbs.
Recently, Estravis-Barcala et al. (2019) reviewed RNA-Seq works directed to
study abiotic stress responses in trees, with focus on temperature and drought
stresses. In the article, authors provide information about sequencing methods, bioinformatics tools employed, type of stress analysed, source of RNA and differentially Gene Ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes
(KEGG) pathways overrepresented in each species/stress. Alternatively, highthroughput genotyping methods, such as RADSeq, ddRADSeq or GBS, offer powerful ways to generate genome-wide SNPs. They have been applied in several tree
species for a diversity of research objectives such as linkage mapping, QTL analysis, markers development, phylogenetics, hybridization and introgression, phylogeography, genome scan, landscape genomics, genomic selection, association
mapping, parentage analysis, dispersal distance estimation, species delimitation,
heritability, population genetics and seed zone delineation (reviewed in Parchman
et al. 2018).
In Eucalyptus dunnii, Aguirre et al. (2019) have published a detailed protocol of
an optimized ddRADseq, which can be applied to other non-model plant species.
Applying the technique GBS in two individuals of a breeding population of E. dunnii and a de novo analysis (Stacks 1.48 pipeline, Catchen et al. 2013), 25,778 SNPs
in 14,423 genomic regions and 55 polymorphic SSRs were identified (Aguirre et al.
2019). Similarly, ddRADSeq is being applied to study phenotype-genotype association in Nothofagus alpina (Arias Rios, El Mujtar, Marchelli, in progress).
17.3 Genomic Strategies to Accelerate Tree Breeding
The development of forest tree breeding programmes faces multiple challenges,
such as long breeding cycles, late flowering, emerging diseases and a constantly
changing environment (Grattapaglia et al. 2018). Some of these challenges were
simplified thanks to the development of DNA markers in the late 1980s and their
subsequent application in marker-assisted selection (MAS) (Lande and Thompson
1990; Neale and Williams 1991; Strauss et al. 1992; Williams and Neale 1992).
The main benefit of the use of molecular markers in forestry programmes was
reflected especially in the last decades, in the change from a traditional phenotypebased to a genotype-based selection. This allows delivering genetically improved
material to the forestry sector (Grattapaglia et al. 2018). However, one crucial problem of MAS is that it is not suitable for complex traits that are controlled by a large
17 Application of High-Throughput Sequencing Technologies in Native Forest Tree…
identify genome variation like SNP and the development of genotyping platforms.
Neale and Wheeler (2019) completed and updated the review specifically for conifers. In López de Heredia and Vázquez-Poletti (2016), bioinformatics tools that are
needed for the analysis of RNA-Seq data from forest trees are pointed out taking
into account difficulties in de novo transcriptome assembly due to the high level of
heterozygosity, large genome size particularly in conifers and annotation difficulties
when based on intensively studied crops or herbs.
Recently, Estravis-Barcala et al. (2019) reviewed RNA-Seq works directed to
study abiotic stress responses in trees, with focus on temperature and drought
stresses. In the article, authors provide information about sequencing methods, bioinformatics tools employed, type of stress analysed, source of RNA and differentially Gene Ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes
(KEGG) pathways overrepresented in each species/stress. Alternatively, highthroughput genotyping methods, such as RADSeq, ddRADSeq or GBS, offer powerful ways to generate genome-wide SNPs. They have been applied in several tree
species for a diversity of research objectives such as linkage mapping, QTL analysis, markers development, phylogenetics, hybridization and introgression, phylogeography, genome scan, landscape genomics, genomic selection, association
mapping, parentage analysis, dispersal distance estimation, species delimitation,
heritability, population genetics and seed zone delineation (reviewed in Parchman
et al. 2018).
In Eucalyptus dunnii, Aguirre et al. (2019) have published a detailed protocol of
an optimized ddRADseq, which can be applied to other non-model plant species.
Applying the technique GBS in two individuals of a breeding population of E. dunnii and a de novo analysis (Stacks 1.48 pipeline, Catchen et al. 2013), 25,778 SNPs
in 14,423 genomic regions and 55 polymorphic SSRs were identified (Aguirre et al.
2019). Similarly, ddRADSeq is being applied to study phenotype-genotype association in Nothofagus alpina (Arias Rios, El Mujtar, Marchelli, in progress).
17.3 Genomic Strategies to Accelerate Tree Breeding
The development of forest tree breeding programmes faces multiple challenges,
such as long breeding cycles, late flowering, emerging diseases and a constantly
changing environment (Grattapaglia et al. 2018). Some of these challenges were
simplified thanks to the development of DNA markers in the late 1980s and their
subsequent application in marker-assisted selection (MAS) (Lande and Thompson
1990; Neale and Williams 1991; Strauss et al. 1992; Williams and Neale 1992).
The main benefit of the use of molecular markers in forestry programmes was
reflected especially in the last decades, in the change from a traditional phenotypebased to a genotype-based selection. This allows delivering genetically improved
material to the forestry sector (Grattapaglia et al. 2018). However, one crucial problem of MAS is that it is not suitable for complex traits that are controlled by a large
17 Application of High-Throughput Sequencing Technologies in Native Forest Tree…