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David B Neale - One of the best experts on this subject based on the ideXlab platform.
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a consensus genetic map for Pinus taeda and Pinus elliottii and extent of linkage disequilibrium in two genotype phenotype discovery populations of Pinus taeda
G3: Genes Genomes Genetics, 2015Co-Authors: Jared W Westbrook, David B Neale, Vikram E Chhatre, Srikar Chamala, Leandro G Neves, Patricio R Munoz, Pedro J Martinezgarcia, Matias Kirst, Keithanne Mockaitis, Dana C NelsonAbstract:A consensus genetic map for Pinus taeda (loblolly pine) and Pinus elliottii (slash pine) was constructed by merging three previously published P. taeda maps with a map from a pseudo-backcross between P. elliottii and P. taeda. The consensus map positioned 3856 markers via genotyping of 1251 individuals from four pedigrees. It is the densest linkage map for a conifer to date. Average marker spacing was 0.6 cM and total map length was 2305 cM. Functional predictions of mapped genes were improved by aligning expressed sequence tags used for marker discovery to full-length P. taeda transcripts. Alignments to the P. taeda genome mapped 3305 scaffold sequences onto 12 linkage groups. The consensus genetic map was used to compare the genome-wide linkage disequilibrium in a population of distantly related P. taeda individuals (ADEPT2) used for association genetic studies and a multiple-family pedigree used for genomic selection (CCLONES). The prevalence and extent of LD was greater in CCLONES as compared to ADEPT2; however, extended LD with LGs or between LGs was rare in both populations. The average squared correlations, r2, between SNP alleles less than 1 cM apart were less than 0.05 in both populations and r2 did not decay substantially with genetic distance. The consensus map and analysis of linkage disequilibrium establish a foundation for comparative association mapping and genomic selection in P. taeda and P. elliottii.
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association genetics of the loblolly pine Pinus taeda pinaceae metabolome
New Phytologist, 2012Co-Authors: Andrew J Eckert, Barry Goldfarb, Jill L Wegrzyn, Patrick W Cumbie, Dudley A Huber, Vladimir Tolstikov, Oliver Fiehn, David B NealeAbstract:The metabolome of a plant comprises all small molecule metabolites, which are produced during cellular processes. The genetic basis for metabolites in nonmodel plants is unknown, despite frequently observed correlations between metabolite concentrations and stress responses. A quantitative genetic analysis of metabolites in a nonmodel plant species is thus warranted. Here, we use standard association genetic methods to correlate 3563 single nucleotide polymorphisms (SNPs) to concentrations of 292 metabolites measured in a single loblolly pine (Pinus taeda) association population. A total of 28 single locus associations were detected, representing 24 and 20 unique SNPs and metabolites, respectively. Multilocus Bayesian mixed linear models identified 2998 additional associations for a total of 1617 unique SNPs associated to 255 metabolites. These SNPs explained sizeable fractions of metabolite heritabilities when considered jointly (56.6% on average) and had lower minor allele frequencies and magnitudes of population structure as compared with random SNPs. Modest sets of SNPs (n = 1-23) explained sizeable portions of genetic effects for many metabolites, thus highlighting the importance of multi-SNP models to association mapping, and exhibited patterns of polymorphism consistent with being linked to targets of natural selection. The implications for association mapping in forest trees are discussed.
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back to nature ecological genomics of loblolly pine Pinus taeda pinaceae
Molecular Ecology, 2010Co-Authors: Andrew J Eckert, Andrew D Bower, Santiago C Gonzalezmartinez, Jill L Wegrzyn, Graham Coop, David B NealeAbstract:Genetic variation is often arrayed in latitudinal or altitudinal clines, reflecting either adaptation along environmental gradients, migratory routes, or both. For forest trees, climate is one of the most important drivers of adaptive phenotypic traits. Correlations of single and multilocus genotypes with environmental gradients have been identified for a variety of forest trees. These correlations are interpreted normally as evidence of natural selection. Here, we use a genome-wide dataset of single nucleotide polymorphisms (SNPs) typed from 1730 loci in 682 loblolly pine (Pinus taeda L.) trees sampled from 54 local populations covering the full-range of the species to examine allelic correlations to five multivariate measures of climate. Applications of a Bayesian generalized linear mixed model, where the climate variable was a fixed effect and an estimated variance– covariance matrix controlled random effects due to shared population history, identified several well-supported SNPs associating to principal components corresponding to geography, temperature, growing degree-days, precipitation and aridity. Functional annotation of those genes with putative orthologs in Arabidopsis revealed a diverse set of abiotic stress response genes ranging from transmembrane proteins to proteins involved in sugar metabolism. Many of these SNPs also had large allele frequency differences among populations (FST = 0.10–0.35). These results illustrate a first step towards a ecosystem perspective of population genomics for non-model organisms, but also highlight the need for further integration of the methodologies employed in spatial statistics, population genetics and climate modeling during scans for signatures of natural selection from genomic data.
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anchored reference loci in loblolly pine Pinus taeda l for integrating pine genomics
Genetics, 2001Co-Authors: Garth R Brown, Edward E Kadel, Daniel L Bassoni, Kristine L Kiehne, Berhanu Temesgen, J P Van Buijtenen, Mitchell M Sewell, Kimberly A Marshall, David B NealeAbstract:Anchored reference loci provide a framework for comparative mapping. They are landmarks to denote conserved chromosomal segments, allowing the synthesis of genetic maps from multiple sources. We evaluated 90 expressed sequence tag polymorphisms (ESTPs) from loblolly pine (Pinus taeda L.) for this function. Primer sets were assayed for amplification and polymorphism in six pedigrees, representing two subgenera of Pinus and a distant member of the Pinaceae, Douglas-fir (Pseudotsuga menziesii [Mirb.] Franco). On average, 89% of primer sets amplified in four species of subgenus Pinus, 49% in one species of subgenus Strobus, and 22% in Douglas-fir. Polymorphisms were detected for 37-61% of the ESTPs within each pedigree. Comparative mapping in loblolly and slash pine (P. elliottii Englm.) revealed that ESTPs mapped to the same location. Disrupted synteny or significant disruptions in colinearity were not detected. Thirty-five ESTPs met criteria established for anchor loci. The majority of those that did not meet these criteria were excluded when map location was known in only a single species. Anchor loci provide a unifying tool for the community, facilitating the creation of a "generic" pine map and serving as a foundation for studies on genome organization and evolution.
Anjos, Viviane Ferreira Dos - One of the best experts on this subject based on the ideXlab platform.
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Utiliza??o de marcadores SSR (Simple Sequence Repeats) na an?lise da diversidade gen?tica de matrizes de Pinus taeda Linnaeus
UFVJM, 2018Co-Authors: Anjos, Viviane Ferreira DosAbstract:Ap?s sua introdu??o em 1948, o cultivo de Pinus taeda L. ocorre nas regi?es sul e sudeste do Brasil e tem por finalidade, basicamente, abastecer os setores de celulose de fibras longas, pain?is reconstitu?dos, constru??o civil, ind?stria moveleira e servir como fonte de energia (lenha industrial). Diante da sua import?ncia econ?mica, pesquisadores buscam ferramentas que auxiliem no aumento da qualidade e da produtividade dos plantios e com isso, passaram a fazer uso dos marcadores moleculares, a fim de obter informa??es a respeito principalmente da diversidade gen?tica entre os indiv?duos que comp?em a popula??o de sele??o. Assim, com vistas a contribuir com o programa de melhoramento do Pinus taeda, utilizou-se marcadores moleculares microssat?lites (SSR) para detectar a exist?ncia de polimorfismos entre 124 plantas de um pomar de sementes. Para o desenvolvimento do estudo, foi realizada a extra??o do DNA gen?mico total do material vegetal (ac?culas) das 124 plantas de Pinus taeda, que ap?s esse processo, foram amplificados por 5 pares de iniciadores microssat?lites espec?ficos para a esp?cie. Os produtos da PCR foram separados em gel de poliacrilamida n?o desnaturante a 6%, corado com nitrato de prata e analisados visualmente, e em gel de agarose a 3%, corado com Brometo de Et?deo. Os marcadores moleculares microssat?lites utilizados permitiram analisar a diversidade gen?tica das plantas de Pinus taeda avaliadas. As informa??es de diversidade obtidas poder?o auxiliar no processo de melhoramento gen?tico da esp?cie. A depender do objetivo do programa de melhoramento, a popula??o e sua diversidade poder?o ser manipuladas, mediante cruzamentos e sele??es devidamente direcionados.Coordena??o de Aperfei?oamento de Pessoal de N?vel Superior (CAPES)Disserta??o (Mestrado) ? Programa de P?s-Gradua??o em Ci?ncia Florestal, Universidade Federal dos Vales do Jequitinhonha e Mucuri, 2018.After its introduction in 1948, the cultivation of Pinus taeda L. occurs in the southern and southeastern regions of Brazil and its main purpose is to supply the long fiber cellulose, reconstituted panels, civil construction, furniture industry and serve as sources of energy (industrial firewood). Due to their economic importance, researchers are looking for tools that help increase the quality and productivity of the plantations and, with this, they started to make use of molecular markers, in order to obtain information about mainly the genetic diversity among the individuals that compose the population of selection. Thus, in order to contribute to the Pinus taeda breeding program, microsatellite molecular markers (SSR) were used to detect the existence of polymorphisms among 124 plants of a seed orchard. For the development of the study, total genomic DNA was extracted from the plant material (needles) of the 124 plants of Pinus taeda, which were amplified by 5 pairs of microsatellite primers specific to the species. The PCR products were separated on a 6% non-denaturing polyacrylamide gel, stained with silver nitrate and visually analyzed, and on a 3% agarose gel stained with Ethidium Bromide. The microsatellite molecular markers used allowed to analyze the genetic diversity of the Pinus taeda plants evaluated. The diversity information obtained may help in the process of genetic improvement of the species. Depending on the objective of the breeding program, the population and its diversity can be manipulated through crossings and selections
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Utiliza??o de marcadores SSR (Simple Sequence Repeats) na an?lise da diversidade gen?tica de matrizes de Pinus taeda Linnaeus
UFVJM, 2018Co-Authors: Anjos, Viviane Ferreira DosAbstract:Submitted by Jos? Henrique Henrique (jose.neves@ufvjm.edu.br) on 2019-02-01T18:25:58Z No. of bitstreams: 2 license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) viviane_ferreira_anjos.pdf: 955893 bytes, checksum: 59ddc9cb28b9b3d67f2088979c39eb45 (MD5)Approved for entry into archive by Rodrigo Martins Cruz (rodrigo.cruz@ufvjm.edu.br) on 2019-03-07T16:49:00Z (GMT) No. of bitstreams: 2 license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) viviane_ferreira_anjos.pdf: 955893 bytes, checksum: 59ddc9cb28b9b3d67f2088979c39eb45 (MD5)Made available in DSpace on 2019-03-07T16:49:00Z (GMT). No. of bitstreams: 2 license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) viviane_ferreira_anjos.pdf: 955893 bytes, checksum: 59ddc9cb28b9b3d67f2088979c39eb45 (MD5) Previous issue date: 2018Coordena??o de Aperfei?oamento de Pessoal de N?vel Superior (CAPES)Ap?s sua introdu??o em 1948, o cultivo de Pinus taeda L. ocorre nas regi?es sul e sudeste do Brasil e tem por finalidade, basicamente, abastecer os setores de celulose de fibras longas, pain?is reconstitu?dos, constru??o civil, ind?stria moveleira e servir como fonte de energia (lenha industrial). Diante da sua import?ncia econ?mica, pesquisadores buscam ferramentas que auxiliem no aumento da qualidade e da produtividade dos plantios e com isso, passaram a fazer uso dos marcadores moleculares, a fim de obter informa??es a respeito principalmente da diversidade gen?tica entre os indiv?duos que comp?em a popula??o de sele??o. Assim, com vistas a contribuir com o programa de melhoramento do Pinus taeda, utilizou-se marcadores moleculares microssat?lites (SSR) para detectar a exist?ncia de polimorfismos entre 124 plantas de um pomar de sementes. Para o desenvolvimento do estudo, foi realizada a extra??o do DNA gen?mico total do material vegetal (ac?culas) das 124 plantas de Pinus taeda, que ap?s esse processo, foram amplificados por 5 pares de iniciadores microssat?lites espec?ficos para a esp?cie. Os produtos da PCR foram separados em gel de poliacrilamida n?o desnaturante a 6%, corado com nitrato de prata e analisados visualmente, e em gel de agarose a 3%, corado com Brometo de Et?deo. Os marcadores moleculares microssat?lites utilizados permitiram analisar a diversidade gen?tica das plantas de Pinus taeda avaliadas. As informa??es de diversidade obtidas poder?o auxiliar no processo de melhoramento gen?tico da esp?cie. A depender do objetivo do programa de melhoramento, a popula??o e sua diversidade poder?o ser manipuladas, mediante cruzamentos e sele??es devidamente direcionados.Disserta??o (Mestrado) ? Programa de P?s-Gradua??o em Ci?ncia Florestal, Universidade Federal dos Vales do Jequitinhonha e Mucuri, 2018.After its introduction in 1948, the cultivation of Pinus taeda L. occurs in the southern and southeastern regions of Brazil and its main purpose is to supply the long fiber cellulose, reconstituted panels, civil construction, furniture industry and serve as sources of energy (industrial firewood). Due to their economic importance, researchers are looking for tools that help increase the quality and productivity of the plantations and, with this, they started to make use of molecular markers, in order to obtain information about mainly the genetic diversity among the individuals that compose the population of selection. Thus, in order to contribute to the Pinus taeda breeding program, microsatellite molecular markers (SSR) were used to detect the existence of polymorphisms among 124 plants of a seed orchard. For the development of the study, total genomic DNA was extracted from the plant material (needles) of the 124 plants of Pinus taeda, which were amplified by 5 pairs of microsatellite primers specific to the species. The PCR products were separated on a 6% non-denaturing polyacrylamide gel, stained with silver nitrate and visually analyzed, and on a 3% agarose gel stained with Ethidium Bromide. The microsatellite molecular markers used allowed to analyze the genetic diversity of the Pinus taeda plants evaluated. The diversity information obtained may help in the process of genetic improvement of the species. Depending on the objective of the breeding program, the population and its diversity can be manipulated through crossings and selections
Jill L Wegrzyn - One of the best experts on this subject based on the ideXlab platform.
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unique features of the loblolly pine Pinus taeda l megagenome revealed through sequence annotation
Genetics, 2014Co-Authors: Jill L Wegrzyn, Pedro J Martinezgarcia, John D Liechty, Kristian Stevens, Carol A Loopstra, Hans A Vasquezgross, William M Dougherty, Brian Y Lin, Jacob J Zieve, Carson HoltAbstract:The largest genus in the conifer family Pinaceae is Pinus, with over 100 species. The size and complexity of their genomes (∼20–40 Gb, 2n = 24) have delayed the arrival of a well-annotated reference sequence. In this study, we present the annotation of the first whole-genome shotgun assembly of loblolly pine (Pinus taeda L.), which comprises 20.1 Gb of sequence. The MAKER-P annotation pipeline combined evidence-based alignments and ab initio predictions to generate 50,172 gene models, of which 15,653 are classified as high confidence. Clustering these gene models with 13 other plant species resulted in 20,646 gene families, of which 1554 are predicted to be unique to conifers. Among the conifer gene families, 159 are composed exclusively of loblolly pine members. The gene models for loblolly pine have the highest median and mean intron lengths of 24 fully sequenced plant genomes. Conifer genomes are full of repetitive DNA, with the most significant contributions from long-terminal-repeat retrotransposons. In depth analysis of the tandem and interspersed repetitive content yielded a combined estimate of 82%.
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association genetics of the loblolly pine Pinus taeda pinaceae metabolome
New Phytologist, 2012Co-Authors: Andrew J Eckert, Barry Goldfarb, Jill L Wegrzyn, Patrick W Cumbie, Dudley A Huber, Vladimir Tolstikov, Oliver Fiehn, David B NealeAbstract:The metabolome of a plant comprises all small molecule metabolites, which are produced during cellular processes. The genetic basis for metabolites in nonmodel plants is unknown, despite frequently observed correlations between metabolite concentrations and stress responses. A quantitative genetic analysis of metabolites in a nonmodel plant species is thus warranted. Here, we use standard association genetic methods to correlate 3563 single nucleotide polymorphisms (SNPs) to concentrations of 292 metabolites measured in a single loblolly pine (Pinus taeda) association population. A total of 28 single locus associations were detected, representing 24 and 20 unique SNPs and metabolites, respectively. Multilocus Bayesian mixed linear models identified 2998 additional associations for a total of 1617 unique SNPs associated to 255 metabolites. These SNPs explained sizeable fractions of metabolite heritabilities when considered jointly (56.6% on average) and had lower minor allele frequencies and magnitudes of population structure as compared with random SNPs. Modest sets of SNPs (n = 1-23) explained sizeable portions of genetic effects for many metabolites, thus highlighting the importance of multi-SNP models to association mapping, and exhibited patterns of polymorphism consistent with being linked to targets of natural selection. The implications for association mapping in forest trees are discussed.
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back to nature ecological genomics of loblolly pine Pinus taeda pinaceae
Molecular Ecology, 2010Co-Authors: Andrew J Eckert, Andrew D Bower, Santiago C Gonzalezmartinez, Jill L Wegrzyn, Graham Coop, David B NealeAbstract:Genetic variation is often arrayed in latitudinal or altitudinal clines, reflecting either adaptation along environmental gradients, migratory routes, or both. For forest trees, climate is one of the most important drivers of adaptive phenotypic traits. Correlations of single and multilocus genotypes with environmental gradients have been identified for a variety of forest trees. These correlations are interpreted normally as evidence of natural selection. Here, we use a genome-wide dataset of single nucleotide polymorphisms (SNPs) typed from 1730 loci in 682 loblolly pine (Pinus taeda L.) trees sampled from 54 local populations covering the full-range of the species to examine allelic correlations to five multivariate measures of climate. Applications of a Bayesian generalized linear mixed model, where the climate variable was a fixed effect and an estimated variance– covariance matrix controlled random effects due to shared population history, identified several well-supported SNPs associating to principal components corresponding to geography, temperature, growing degree-days, precipitation and aridity. Functional annotation of those genes with putative orthologs in Arabidopsis revealed a diverse set of abiotic stress response genes ranging from transmembrane proteins to proteins involved in sugar metabolism. Many of these SNPs also had large allele frequency differences among populations (FST = 0.10–0.35). These results illustrate a first step towards a ecosystem perspective of population genomics for non-model organisms, but also highlight the need for further integration of the methodologies employed in spatial statistics, population genetics and climate modeling during scans for signatures of natural selection from genomic data.
Afonso Figueiredo Filho - One of the best experts on this subject based on the ideXlab platform.
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modelos de afilamento para Pinus taeda por classes de idade
Floresta e Ambiente, 2013Co-Authors: Sintia Valerio Kohler, Henrique Soares Koehler, Afonso Figueiredo FilhoAbstract:O objetivo deste trabalho foi ajustar modelos de afilamento para Pinus taeda utilizando-se dados de analise de tronco de 120 arvores amostradas em povoamentos localizados no Estado de Santa Catarina. Os polinomios de quinto grau e de potencias inteiras e fracionarias foram ajustados para dados sem estratificacao e estratificando-os em classes de idade, avaliando a necessidade ou nao de desenvolver modelos por classe de idade. Foi realizada a validacao e aplicado um teste de identidade sobre o modelo de melhor ajuste, a fim de verificar a necessidade de estratificacao dos dados. O polinomio de potencias inteiras e fracionarias foi selecionado para as estimativas dos diâmetros nas diferentes alturas do fuste. As equacoes de afilamento obtidas para as classes de idades apresentaram certa superioridade em relacao a equacao geral, sugerindo que, ao se trabalhar com dados em classes de idade, pode-se obter maior precisao nas estimativas dos diâmetros ao longo do tronco.
Andrew J Eckert - One of the best experts on this subject based on the ideXlab platform.
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association genetics of the loblolly pine Pinus taeda pinaceae metabolome
New Phytologist, 2012Co-Authors: Andrew J Eckert, Barry Goldfarb, Jill L Wegrzyn, Patrick W Cumbie, Dudley A Huber, Vladimir Tolstikov, Oliver Fiehn, David B NealeAbstract:The metabolome of a plant comprises all small molecule metabolites, which are produced during cellular processes. The genetic basis for metabolites in nonmodel plants is unknown, despite frequently observed correlations between metabolite concentrations and stress responses. A quantitative genetic analysis of metabolites in a nonmodel plant species is thus warranted. Here, we use standard association genetic methods to correlate 3563 single nucleotide polymorphisms (SNPs) to concentrations of 292 metabolites measured in a single loblolly pine (Pinus taeda) association population. A total of 28 single locus associations were detected, representing 24 and 20 unique SNPs and metabolites, respectively. Multilocus Bayesian mixed linear models identified 2998 additional associations for a total of 1617 unique SNPs associated to 255 metabolites. These SNPs explained sizeable fractions of metabolite heritabilities when considered jointly (56.6% on average) and had lower minor allele frequencies and magnitudes of population structure as compared with random SNPs. Modest sets of SNPs (n = 1-23) explained sizeable portions of genetic effects for many metabolites, thus highlighting the importance of multi-SNP models to association mapping, and exhibited patterns of polymorphism consistent with being linked to targets of natural selection. The implications for association mapping in forest trees are discussed.
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back to nature ecological genomics of loblolly pine Pinus taeda pinaceae
Molecular Ecology, 2010Co-Authors: Andrew J Eckert, Andrew D Bower, Santiago C Gonzalezmartinez, Jill L Wegrzyn, Graham Coop, David B NealeAbstract:Genetic variation is often arrayed in latitudinal or altitudinal clines, reflecting either adaptation along environmental gradients, migratory routes, or both. For forest trees, climate is one of the most important drivers of adaptive phenotypic traits. Correlations of single and multilocus genotypes with environmental gradients have been identified for a variety of forest trees. These correlations are interpreted normally as evidence of natural selection. Here, we use a genome-wide dataset of single nucleotide polymorphisms (SNPs) typed from 1730 loci in 682 loblolly pine (Pinus taeda L.) trees sampled from 54 local populations covering the full-range of the species to examine allelic correlations to five multivariate measures of climate. Applications of a Bayesian generalized linear mixed model, where the climate variable was a fixed effect and an estimated variance– covariance matrix controlled random effects due to shared population history, identified several well-supported SNPs associating to principal components corresponding to geography, temperature, growing degree-days, precipitation and aridity. Functional annotation of those genes with putative orthologs in Arabidopsis revealed a diverse set of abiotic stress response genes ranging from transmembrane proteins to proteins involved in sugar metabolism. Many of these SNPs also had large allele frequency differences among populations (FST = 0.10–0.35). These results illustrate a first step towards a ecosystem perspective of population genomics for non-model organisms, but also highlight the need for further integration of the methodologies employed in spatial statistics, population genetics and climate modeling during scans for signatures of natural selection from genomic data.