477
Beilsmith K, Thoen M, Brachi B, Gloss A, Khan H, Bergelson J (2019) Genome-wide associations
studies on the phyllosphere microbiome: embracing complexity in host-microbe interactions.
Plant J. 97:164–181
Bernardo R (2008) Molecular markers and selection for complex traits in plants: Learning from the
last 20 years. Crop Sci 48:1649–1664
Bessega C, Pometti C, Miller J, Watts R, Saidman B, Vilardi J (2013) New microsatellite loci for
Prosopis alba and P. chilensis (Fabaceae). Appl Plant Sci 1:1200324
Birol I, Raymond A, Jackman S, Pleasance S, Coope R, Taylor G et al (2013) Assembling the
20 Gb white spruce (Picea glauca) genome from whole-genome shotgun sequencing data.
Bioinformatics. https://doi.org/10.1093/bioinformatics/btt178
Blott S, Kim J, Moisio S, Schmidt-Kuntzel A, Cornet A et al (2003) Molecular dissection of a
quantitative trait locus: a phenylalanine-to-tyrosine substitution in the transmembrane domain
of the bovine growth hormone receptor is associated with a major effect on milk yield and
composition. Genetics 163:253–266
Botstein D, Risch N (2003) Discovering genotypes underlying human phenotypes: past successes
for mendelian disease, future approaches for complex disease. Nat Genet 33(Suppl):228–237
Brachi B, Morris G, Borevitz J (2011) Genome-wide association studies in plants: the missing
heritability is in the field. Genome Biol 12:232
Brousseau L, Tinaut A, Duret C, Lang T, Garnier-Gere P, Scotti I (2014) High-throughput transcriptome sequencing and preliminary functional analysis in four Neotropical tree species.
BMC Genomics 15:238
Budde K, Heuertz M, Hernández-Serrano A, Pausas J, Vendramin G, Verdú M, González-Martínez
S (2014) In situ genetic association for serotiny, a fire-related trait, in Mediterranean maritime
pine (Pinus pinaster Aiton). New Phytol 201:230–241
Canales J, Bautista R, Label P, Gómez Maldonado J, Lesur I, Fernández Pozo N et al (2014) De
novo assembly of maritime pine transcriptome: Implications for forest breeding and biotechnology. Plant Biotechnol J 12:286–299
Cappa E, Marco de Lima B, da Silva-Junior O, Garcia C, Mansfield S, Grattapaglia D (2019)
Improving genomic prediction of growth and wood traits in Eucalyptus using phenotypes from
non-genotyped trees by single-step GBLUP. Plant Sci 84:9–15
Catchen J, Hohenlohe P, Bassham S, Amores A, Cresko WA (2013) Stacks: an analysis tool set for
population genomics. Mol Ecol 22:3124–3140
Chang S, Puryear J, Cairney J (1993) A simple and efficient method for isolating RNA from pine
trees. Plant Mol Biol Rep 11:113–116
Chhetri H, Macaya-Sanz D, Kainer D, Biswal A, Evans L, Chen J et al (2019) Multi-trait genomewide association analysis of Populus trichocarpa identifies key polymorphisms controlling
morphological and physiological traits. New Phytol 223:293–309
Chinwalla A, Cook L, Delehaunty K, Fewell G, Fulton L, Fulton R et al (2002) Initial sequencing
and comparative analysis of the mouse genome. Nature 420:520–562
Collevatti R, Novaes E, Silva-Junior O, Vieira L, Lima-Ribeiro M, Grattapaglia D (2019) A
genome-wide scan shows evidence for local adaptation in a widespread keystone Neotropical
forest tree. Heredity 123:117–137
Conesa A, Madrigal P, Tarazona S, Gomez-Cabrero D, Cervera A, McPherson A et al (2016) A
survey of best practices for RNA-seq data analysis. Genome Biol 17:13
Davey J, Hohenlohe P, Etter P, Boone J, Catchen J, Blaxter L (2011) Genome-wide genetic marker
discovery and genotyping using next-generation sequencing. Nat Rev Genet. 12:499–510
De Pristo M, Banks E, Poplin R, Garimella K, Maguire J, Hartl C et al (2011) A framework for
variation discovery and genotyping using next-generation DNA sequencing data. Nat Genet
43:491–498
De Villemereuil P, Gaggiotti O, Mouterde M, Till-Bottraud I (2016) Common garden experiments
in the genomic era: new perspectives and opportunities. Heredity 116:249–254
Du Q, Lu W, Quan M, Xiao L, Song F, Li P, Zhou D, Xie J, Wang L, Zhang D (2018) GenomeWide Association Studies to Improve Wood Properties: Challenges and Prospects. Front Plant
Sci 9:1912
17 Application of High-Throughput Sequencing Technologies in Native Forest Tree…
Beilsmith K, Thoen M, Brachi B, Gloss A, Khan H, Bergelson J (2019) Genome-wide associations
studies on the phyllosphere microbiome: embracing complexity in host-microbe interactions.
Plant J. 97:164–181
Bernardo R (2008) Molecular markers and selection for complex traits in plants: Learning from the
last 20 years. Crop Sci 48:1649–1664
Bessega C, Pometti C, Miller J, Watts R, Saidman B, Vilardi J (2013) New microsatellite loci for
Prosopis alba and P. chilensis (Fabaceae). Appl Plant Sci 1:1200324
Birol I, Raymond A, Jackman S, Pleasance S, Coope R, Taylor G et al (2013) Assembling the
20 Gb white spruce (Picea glauca) genome from whole-genome shotgun sequencing data.
Bioinformatics. https://doi.org/10.1093/bioinformatics/btt178
Blott S, Kim J, Moisio S, Schmidt-Kuntzel A, Cornet A et al (2003) Molecular dissection of a
quantitative trait locus: a phenylalanine-to-tyrosine substitution in the transmembrane domain
of the bovine growth hormone receptor is associated with a major effect on milk yield and
composition. Genetics 163:253–266
Botstein D, Risch N (2003) Discovering genotypes underlying human phenotypes: past successes
for mendelian disease, future approaches for complex disease. Nat Genet 33(Suppl):228–237
Brachi B, Morris G, Borevitz J (2011) Genome-wide association studies in plants: the missing
heritability is in the field. Genome Biol 12:232
Brousseau L, Tinaut A, Duret C, Lang T, Garnier-Gere P, Scotti I (2014) High-throughput transcriptome sequencing and preliminary functional analysis in four Neotropical tree species.
BMC Genomics 15:238
Budde K, Heuertz M, Hernández-Serrano A, Pausas J, Vendramin G, Verdú M, González-Martínez
S (2014) In situ genetic association for serotiny, a fire-related trait, in Mediterranean maritime
pine (Pinus pinaster Aiton). New Phytol 201:230–241
Canales J, Bautista R, Label P, Gómez Maldonado J, Lesur I, Fernández Pozo N et al (2014) De
novo assembly of maritime pine transcriptome: Implications for forest breeding and biotechnology. Plant Biotechnol J 12:286–299
Cappa E, Marco de Lima B, da Silva-Junior O, Garcia C, Mansfield S, Grattapaglia D (2019)
Improving genomic prediction of growth and wood traits in Eucalyptus using phenotypes from
non-genotyped trees by single-step GBLUP. Plant Sci 84:9–15
Catchen J, Hohenlohe P, Bassham S, Amores A, Cresko WA (2013) Stacks: an analysis tool set for
population genomics. Mol Ecol 22:3124–3140
Chang S, Puryear J, Cairney J (1993) A simple and efficient method for isolating RNA from pine
trees. Plant Mol Biol Rep 11:113–116
Chhetri H, Macaya-Sanz D, Kainer D, Biswal A, Evans L, Chen J et al (2019) Multi-trait genomewide association analysis of Populus trichocarpa identifies key polymorphisms controlling
morphological and physiological traits. New Phytol 223:293–309
Chinwalla A, Cook L, Delehaunty K, Fewell G, Fulton L, Fulton R et al (2002) Initial sequencing
and comparative analysis of the mouse genome. Nature 420:520–562
Collevatti R, Novaes E, Silva-Junior O, Vieira L, Lima-Ribeiro M, Grattapaglia D (2019) A
genome-wide scan shows evidence for local adaptation in a widespread keystone Neotropical
forest tree. Heredity 123:117–137
Conesa A, Madrigal P, Tarazona S, Gomez-Cabrero D, Cervera A, McPherson A et al (2016) A
survey of best practices for RNA-seq data analysis. Genome Biol 17:13
Davey J, Hohenlohe P, Etter P, Boone J, Catchen J, Blaxter L (2011) Genome-wide genetic marker
discovery and genotyping using next-generation sequencing. Nat Rev Genet. 12:499–510
De Pristo M, Banks E, Poplin R, Garimella K, Maguire J, Hartl C et al (2011) A framework for
variation discovery and genotyping using next-generation DNA sequencing data. Nat Genet
43:491–498
De Villemereuil P, Gaggiotti O, Mouterde M, Till-Bottraud I (2016) Common garden experiments
in the genomic era: new perspectives and opportunities. Heredity 116:249–254
Du Q, Lu W, Quan M, Xiao L, Song F, Li P, Zhou D, Xie J, Wang L, Zhang D (2018) GenomeWide Association Studies to Improve Wood Properties: Challenges and Prospects. Front Plant
Sci 9:1912
17 Application of High-Throughput Sequencing Technologies in Native Forest Tree…