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1. Independent and Joint‐GWAS for growth traits in Eucalyptus by assembling genome‐wide data for 3373 individuals across four breeding populations

Author:
Kirst, Matias,   et al.   ; Müller, Bárbara S. F.; de Almeida Filho, Janeo E.; Lima, Bruno M.; Garcia, Carla C.; Missiaggia, Alexandre; Aguiar, Aurelio M.; Takahashi, Elizabete; Gezan, Salvador A.; Silva‐Junior, Orzenil B.; Neves, Leandro G.; Grattapaglia, Dario;     Show all 12 Authors
Source:
Thenew phytologist 2019 v.221 no.2 pp. 818-833
ISSN:
0028-646X
Subject:
Eucalyptus; biosynthesis; cell walls; forest trees; genes; genome-wide association study; genomics; genotyping; growth traits; heritability; lignification; meta-analysis; models; phenotype; phenotypic variation; prediction; single nucleotide polymorphism; tree breeding; tree height
Abstract:
... Genome‐wide association studies (GWAS) in plants typically suffer from limited statistical power. An alternative to the logistical and cost challenge of increasing sample sizes is to gain power by meta‐analysis using information from independent studies. We carried out GWAS for growth traits with six single‐marker models and regional heritability mapping (RHM) in four Eucalyptus breeding populatio ...
DOI:
10.1111/nph.15449

2. Linking genome signatures of selection and adaptation in non-model plants: exploring potential and limitations in the angiosperm Amborella

Author:
Kirst, Matias,   et al.   ; Hodel, Richard GJ; Chandler, Luke M; Fahrenkrog, Annette M; Gitzendanner, Matthew A; Soltis, Douglas E; Soltis, Pamela S;     Show all 7 Authors
Source:
Current opinion in plant biology 2018 v.42 pp. 81-89
ISSN:
1369-5266
Subject:
Amborella trichopoda; crops; environmental factors; genes; genomics; loci; models; New Caledonia
Abstract:
... Selective sweeps may be caused by environmental conditions that select for a gene function or trait at one locus, causing reduced variation at neighboring sites due to linkage, with specific non-selected variants being swept along with the selected variant. For many species, genomic and environmental data are available to test hypotheses that environmental conditions are correlated with selected r ...
DOI:
10.1016/j.pbi.2018.04.003

3. Metabolic regulation of triacylglycerol accumulation in the green algae: identification of potential targets for engineering to improve oil yield

Author:
Kirst, Matias,   et al.   ; Goncalves, Elton C.; Wilkie, Ann C.; Rathinasabapathi, Bala;     Show all 4 Authors
Source:
Plant biotechnology journal 2016 v.14 no.8 pp. 1649-1660
ISSN:
1467-7644
Subject:
Chlorophyta; biochemical pathways; biofuels; carbon; cell division; lipid bodies; microalgae; oils; photosynthesis; triacylglycerols
Abstract:
... The great need for more sustainable alternatives to fossil fuels has increased our research interests in algal biofuels. Microalgal cells, characterized by high photosynthetic efficiency and rapid cell division, are an excellent source of neutral lipids as potential fuel stocks. Various stress factors, especially nutrient‐starvation conditions, induce an increased formation of lipid bodies filled ...
DOI:
10.1111/pbi.12523
PubMed:
26801206
PubMed Central:
PMC5066758

4. Overexpression of DEMETER, a DNA demethylase, promotes early apical bud maturation in poplar

Author:
Kirst, Matias,   et al.   ; Conde, Daniel; Moreno‐Cortés, Alicia; Dervinis, Christopher; Ramos‐Sánchez, José M.; Perales, Mariano; González‐Melendi, Pablo; Allona, Isabel;     Show all 8 Authors
Source:
Plant, cell and environment 2017 v.40 no.11 pp. 2806-2819
ISSN:
0140-7791
Subject:
Castanea sativa; Populus tremula; amino acid sequences; apical meristems; biosynthesis; buds; color; complementary DNA; dormancy; enzymes; flavonoids; gene expression regulation; genes; hybrids; methylation; perennials; phylogeny; sequence analysis; temperature; transgenic plants; trees; winter
Abstract:
... The transition from active growth to dormancy is critical for the survival of perennial plants. We identified a DEMETER‐like (CsDML) cDNA from a winter‐enriched cDNA subtractive library in chestnut (Castanea sativa Mill.), an economically and ecologically important species. Next, we characterized this DNA demethylase and its putative ortholog in the more experimentally tractable hybrid poplar (Pop ...
DOI:
10.1111/pce.13056

5. Chilling‐responsive DEMETER‐LIKE DNA demethylase mediates in poplar bud break

Author:
Kirst, Matias,   et al.   ; Conde, Daniel; Le Gac, Anne‐Laure; Perales, Mariano; Dervinis, Christopher; Maury, Stéphane; González‐Melendi, Pablo; Allona, Isabel;     Show all 8 Authors
Source:
Plant, cell and environment 2017 v.40 no.10 pp. 2236-2249
ISSN:
0140-7791
Subject:
DNA; DNA methylation; boreal forests; budbreak; dormancy; gene expression regulation; genetically modified organisms; perennials; spring; transcriptome; trees; vegetative growth; winter
Abstract:
... Annual dormancy‐growth cycle is a developmental and physiological process essential for the survival of deciduous trees in temperate and boreal forests. Seasonal control of shoot growth in woody perennials requires specific genetic programmes responding to environmental signals. The environmental‐controlled mechanisms that regulate the shift between winter dormancy and the growth‐promoting genetic ...
DOI:
10.1111/pce.13019

6. Comparison of Pyrolysis Mass Spectrometry and Near Infrared Spectroscopy for Genetic Analysis of Lignocellulose Chemical Composition in Populus

Author:
Kirst, Matias,   et al.   ; Zhang, Jianxing; Novaes, Evandro; Peter, Gary F.;     Show all 4 Authors
Source:
Forests 2014 v.5 no.3 pp. 466-481
ISSN:
1999-4907
Subject:
Populus; cellulose; chemical composition; genetic analysis; genetic correlation; greenhouses; heritability; lignin; lignocellulose; loci; mass spectrometry; models; near-infrared spectroscopy; nitrogen; prediction; pyrolysis; quantitative trait loci; statistics; trees; wood; xylan
Abstract:
... Genetic analysis of wood chemical composition is often limited by the cost and throughput of direct analytical methods. The speed and low cost of Fourier transform near infrared (FT-NIR) overcomes many of these limitations, but it is an indirect method relying on calibration models that are typically developed and validated with small sample sets. In this study, we used >1500 young greenhouse grow ...
DOI:
10.3390/f5030466

7. Integration of genetic, genomic and transcriptomic information identifies putative regulators of adventitious root formation in Populus

Author:
Kirst, Matias,   et al.   ; Ribeiro, Cintia L.; Silva, Cynthia M.; Drost, Derek R.; Novaes, Evandro; Novaes, Carolina R. D. B.; Dervinis, Christopher;     Show all 7 Authors
Source:
BMC plant biology 2016 v.16 no.1 pp. 66
ISSN:
1471-2229
Subject:
alleles; Populus deltoides; vegetative propagation; quantitative trait loci; linkage groups; adventitious roots; Populus trichocarpa; tryptophan synthase; phenotypic variation; gene expression regulation; tissues; glucosinolates; transcriptomics; Arabidopsis; models; woody plants; progeny; biomass; indole acetic acid; biosynthesis; absorption; tryptophan; time series analysis; crops
Abstract:
... BACKGROUND: Adventitious roots (AR) develop from tissues other than the primary root, in a process physiologically regulated by phytohormones. Adventitious roots provide structural support and contribute to water and nutrient absorption, and are critical for commercial vegetative propagation of several crops. Here we quantified the number of AR, root architectural traits and root biomass in cuttin ...
DOI:
10.1186/s12870-016-0753-0
PubMed:
26983547
PubMed Central:
PMC4793515

8. Genomic selection prediction models comparing sequence capture and SNP array genotyping methods

Author:
Kirst, Matias,   et al.   ; de Moraes, Bráulio Fabiano Xavier; dos Santos, Rodrigo Furtado; de Lima, Bruno Marco; Aguiar, Aurélio Mendes; Missiaggia, Alexandre Alves; da Costa Dias, Donizete; Rezende, Gabriel Dehon Peçanha Sampaio; Gonçalves, Flávia Maria Avelar; Acosta, Juan J.; Resende, Márcio F. R., Jr; Muñoz, Patricio R.;     Show all 12 Authors
Source:
Molecular breeding 2018 v.38 no.9 pp. 115
ISSN:
1380-3743
Subject:
Eucalyptus; gene frequency; genome; genomics; genotyping; growth traits; high-throughput nucleotide sequencing; linkage disequilibrium; marker-assisted selection; models; phenotype; prediction; single nucleotide polymorphism; trees; wood quality
Abstract:
... The successful application of genomic selection (GS) approaches is dependent on genetic makers derived from high-throughput and low-cost genotyping methods. Recent GS studies in trees have predominantly relied on SNP arrays as the source of genotyping, though this technology has a high entry cost. The recent development of alternative genotyping platforms, tailored to specific species and with low ...
DOI:
10.1007/s11032-018-0865-3
CHORUS:
10.1007/s11032-018-0865-3

9. Genetical genomics of Populus leaf shape variation

Author:
Kirst, Matias,   et al.   ; Drost, Derek R.; Puranik, Swati; Novaes, Evandro; Novaes, Carolina R.D.B.; Dervinis, Christopher; Gailing, Oliver;     Show all 7 Authors
Source:
BMC plant biology 2015 v.15 no.1 pp. 166
ISSN:
1471-2229
Subject:
Populus trichocarpa; alleles; auxins; brefeldin A; cell polarity; chromosome mapping; gene expression; genetic factors; genomics; guanosinetriphosphatase; leaf development; leaves; loci; models; mutagenesis; mutagens; nucleotide sequences; pedigree; plant organs; proteins; quantitative trait loci; transcriptomics
Abstract:
... BACKGROUND: Leaf morphology varies extensively among plant species and is under strong genetic control. Mutagenic screens in model systems have identified genes and established molecular mechanisms regulating leaf initiation, development, and shape. However, it is not known whether this diversity across plant species is related to naturally occurring variation at these genes. Quantitative trait lo ...
DOI:
10.1186/s12870-015-0557-7
PubMed:
26122556
PubMed Central:
PMC4486686

10. Genome‐wide association study reveals putative regulators of bioenergy traits in Populus deltoides

Author:
Kirst, Matias,   et al.   ; Fahrenkrog, Annette M.; Neves, Leandro G.; Resende, Márcio F. R., Jr; Vazquez, Ana I.; de los Campos, Gustavo; Dervinis, Christopher; Sykes, Robert; Davis, Mark; Davenport, Ruth; Barbazuk, William B.;     Show all 11 Authors
Source:
The new phytologist 2017 v.213 no.2 pp. 799-811
ISSN:
0028-646X
Subject:
Populus deltoides; bioenergy; bioenergy industry; feedstocks; forests; genes; genetic variation; genome-wide association study; phenotype; phenotypic variation; single nucleotide polymorphism; wood; North America
Abstract:
... Genome‐wide association studies (GWAS) have been used extensively to dissect the genetic regulation of complex traits in plants. These studies have focused largely on the analysis of common genetic variants despite the abundance of rare polymorphisms in several species, and their potential role in trait variation. Here, we conducted the first GWAS in Populus deltoides, a genetically diverse keysto ...
DOI:
10.1111/nph.14154

11. Spatial genetic structure, genetic diversity and pollen dispersal in a harvested population of Astrocaryum aculeatum in the Brazilian Amazon

Author:
Kirst, Matias,   et al.   ; Ramos, Santiago Linorio Ferreyra; Dequigiovanni, Gabriel; Sebbenn, Alexandre Magno; Lopes, Maria Teresa Gomes; Kageyama, Paulo Yoshio; de Macêdo, Jeferson Luis Vasconcelos; Veasey, Elizabeth Ann;     Show all 8 Authors
Source:
BMC genetics 2016 v.17 no.1 pp. 63
ISSN:
1471-2156
Subject:
Astrocaryum aculeatum; adults; alleles; farmers; fruits; gene pool; genetic variation; genotyping; indigenous species; mature plants; open pollination; parents; paternity; pollen; pollen flow; progeny; pulp; seed dispersal; seedlings; seeds; trees; tropics; Amazonia; Brazil
Abstract:
... BACKGROUND: Astrocaryum aculeatum is a palm tree species native to the tropical regions of South America, exploited commercially by local farmers for the pulp extracted from its fruits. The objective of this research was to compare the genetic diversity between adult plants and seedlings from open-pollinated seeds, quantify the pollen flow and dispersal, the spatial genetic structure, and the effe ...
DOI:
10.1186/s12863-016-0371-8
PubMed:
27108235
PubMed Central:
PMC4842287

12. Whole‐exome targeted sequencing of the uncharacterized pine genome

Author:
Kirst, Matias,   et al.   ; Neves, Leandro G.; Davis, John M.; Barbazuk, William B.;     Show all 4 Authors
Source:
The plant journal 2013 v.75 no.1 pp. 146-156
ISSN:
0960-7412
Subject:
Pinus elliottii; Pinus taeda; complementary DNA; conifers; diploidy; exons; expressed sequence tags; genomics; haploidy; introns; models; nucleic acid hybridization
Abstract:
... The large genome size of many species hinders the development and application of genomic tools to study them. For instance, loblolly pine (Pinus taeda L.), an ecologically and economically important conifer, has a large and yet uncharacterized genome of 21.7 Gbp. To characterize the pine genome, we performed exome capture and sequencing of 14 729 genes derived from an assembly of expressed sequenc ...
DOI:
10.1111/tpj.12193

13. Accelerating the domestication of forest trees in a changing world

Author:
Kirst, Matias,   et al.   ; Harfouche, Antoine; Meilan, Richard; Morgante, Michele; Boerjan, Wout; Sabatti, Maurizio; Scarascia Mugnozza, Giuseppe;     Show all 7 Authors
Source:
Trends in plant science 2012 v.17 no.2 pp. 64-72
ISSN:
1360-1385
Subject:
arable soils; biomass; climate change; domestication; forest trees; forests; fuels; genetic improvement; landowners; paper; population growth; society; wood
Abstract:
... In light of impending water and arable land shortages, population growth and climate change, it is more important than ever to examine how forest tree domestication can be accelerated to sustainably meet future demands for wood, biomass, paper, fuel and biomaterials. Because of long breeding cycles, tree domestication cannot be rapidly achieved through traditional genetic improvement methods alone ...
DOI:
10.1016/j.tplants.2011.11.005
PubMed:
22209522

14. Breeding for value in a changing world: past achievements and future prospects

Author:
Kirst, Matias,   et al.   ; White, Tim; Davis, John; Gezan, Salvador; Hulcr, Jiri; Jokela, Eric; Martin, Timothy A.; Peter, Gary; Powell, Greg; Smith, Jason;     Show all 10 Authors
Source:
New forests 2014 v.45 no.3 pp. 301-309
ISSN:
0169-4286
Subject:
breeding value; business enterprises; climate change; energy; foods; forest products; forests; globalization; markets; ownership; philosophy; planning; plantations; scientists; silviculture; teams; tree breeding; trees
Abstract:
... Large-scale tree improvement programs began in the 1950s. Tree improvement is now part of operational silviculture programs in many companies and countries around the world and tree breeding programs have produced very impressive results: (1) realized gains in plantations being established today of some 40–50 % in volume yield above unimproved material for many programs; (2) increased efficiencies ...
DOI:
10.1007/s11056-013-9400-x

15. Mapping Fusiform Rust Resistance Genes within a Complex Mating Design of Loblolly Pine

Author:
Kirst, Matias,   et al.   ; Quesada, Tania; Resende Jr., Marcio F.R.; Muñoz, Patricio; Wegrzyn, Jill L.; Neale, David B.; Peter, Gary F.; Gezan, Salvador A.; Nelson, C. Dana; Davis, John M.;     Show all 10 Authors
Source:
Forests 2014 v.5 no.2 pp. 347-362
ISSN:
1999-4907
Subject:
Bayesian theory; Cronartium quercuum; Pinus taeda; computer software; disease incidence; fusiform rust; genotype; inoculum; linkage groups; parents; pathogens; regression analysis; resistance genes; screening; single nucleotide polymorphism; trees; variance
Abstract:
... Fusiform rust resistance can involve gene-for-gene interactions where resistance (Fr) genes in the host interact with corresponding avirulence genes in the pathogen, Cronartium quercuum f.sp. fusiforme (Cqf). Here, we identify trees with Fr genes in a loblolly pine population derived from a complex mating design challenged with two Cqf inocula (one gall and 10 gall mixtures). We used single nucleo ...
DOI:
10.3390/f5020347

16. Discovering candidate genes that regulate resin canal number in Pinus taeda stems by integrating genetic analysis across environments, ages, and populations

Author:
Kirst, Matias,   et al.   ; Westbrook, Jared W.; Walker, Alejandro R.; Neves, Leandro G.; Munoz, Patricio; Resende, Marcio F. R., Jr; Neale, David B.; Wegrzyn, Jill L.; Huber, Dudley A.; Davis, John M.; Peter, Gary F.;     Show all 11 Authors
Source:
The new phytologist 2015 v.205 no.2 pp. 627-641
ISSN:
0028-646X
Subject:
Pinus elliottii; Pinus taeda; bark beetles; biofuels; feedstocks; genes; genetic variation; growth rings; marker-assisted selection; pedigree; quantitative trait loci; single nucleotide polymorphism; stems; terpenoids
Abstract:
... Genetically improving constitutive resin canal development in Pinus stems may enhance the capacity to synthesize terpenes for bark beetle resistance, chemical feedstocks, and biofuels. To discover genes that potentially regulate axial resin canal number (RCN), single nucleotide polymorphisms (SNPs) in 4027 genes were tested for association with RCN in two growth rings and three environments in a c ...
DOI:
10.1111/nph.13074
Chorus Open Access:
10.1111/nph.13074

17. Genomics of growth traits in forest trees

Author:
Kirst, Matias,   et al.   ; Grattapaglia, Dario; Plomion, Christophe; Sederoff, Ronald R;     Show all 4 Authors
Source:
Current opinion in plant biology 2009 v.12 no.2 pp. 148-156
ISSN:
1369-5266
Subject:
tree growth; quantitative trait loci; plant genetics; forest trees; genome; genomics
Abstract:
... Growth traits in trees are fundamental components of adaptation in a forest ecosystem and of productivity in planted forests. A number of processes determine tree growth, which are controlled by genetic and epigenetic factors that respond dynamically to environmental signals throughout centuries. Advances in genomics have allowed an increased comprehension of the complex mechanisms of tree growth ...
DOI:
10.1016/j.pbi.2008.12.008
PubMed:
19186096

18. Association and Linkage Analysis of Aluminum Tolerance Genes in Maize

Author:
Kirst, Matias,   et al.   ; Krill, Allison M.; Kochian, Leon V.; Buckler, Edward S.; Hoekenga, Owen A.; Zhang, Baohong;     Show all 6 Authors
ISSN:
1932-6203
Subject:
Zea mays; acid soils; alleles; aluminum; commodity foods; corn; genetic markers; genetic variation; inbred lines; malates; malic enzyme; marker-assisted selection; metal tolerance; nutrient solutions; pH; root growth; toxicity; Africa; South America
Abstract:
... Aluminum (Al) toxicity is a major worldwide constraint to crop productivity on acidic soils. Al becomes soluble at low pH, inhibiting root growth and severely reducing yields. Maize is an important staple food and commodity crop in acidic soil regions, especially in South America and Africa where these soils are very common. Al exclusion and intracellular tolerance have been suggested as two impor ...
DOI:
10.1371/journal.pone.0009958

19. Association and Linkage Analysis of Aluminum Tolerance Genes in Maize

Author:
Kirst, Matias,   et al.   ; Krill, Allison M.; Kochian, Leon V.; Buckler, Edward S.; Hoekenga, Owen A.; Zhang, Baohong;     Show all 6 Authors
ISSN:
1932-6203
Subject:
Zea mays; South America; Africa; toxicity; root growth; pH; nutrient solutions; marker-assisted selection; malates; inbred lines; genetic variation; genetic markers; commodity foods; alleles; acid soils; corn; metal tolerance; aluminum; genes; chromosome mapping; linkage groups; transporters; malic enzyme
Abstract:
... Aluminum (Al) toxicity is a major worldwide constraint to crop productivity on acidic soils. Al becomes soluble at low pH, inhibiting root growth and severely reducing yields. Maize is an important staple food and commodity crop in acidic soil regions, especially in South America and Africa where these soils are very common. Al exclusion and intracellular tolerance have been suggested as two impor ...
Handle:
10113/44678
DOI:
10.1371/journal.pone.0009958
PubMed:
20376361
PubMed Central:
PMC2848604

20. High-throughput SNP genotyping in the highly heterozygous genome of Eucalyptus: assay success, polymorphism and transferability across species

Author:
Kirst, Matias,   et al.   ; Grattapaglia, Dario; Silva-Junior, Orzenil B.; Lima, Bruno M. de; Faria, Danielle A.; Pappas, Georgios J.;     Show all 6 Authors
Source:
BMC Plant biology 2011 v.11
ISSN:
1471-2229
Subject:
marker-assisted selection; Eucalyptus; phylogeny; expressed sequence tags; heterozygosity; single nucleotide polymorphism; metagenomics; genotyping; databases; crops
Abstract:
... Background High-throughput SNP genotyping has become an essential requirement for molecular breeding and population genomics studies in plant species. Large scale SNP developments have been reported for several mainstream crops. A growing interest now exists to expand the speed and resolution of genetic analysis to outbred species with highly heterozygous genomes. When nucleotide diversity is high ...
DOI:
10.1186/1471-2229-11-65
PubMed:
21492434
PubMed Central:
PMC3090336