Genetic mapping of expressed sequence tag polymorphism (ESTP) markers in loblolly pine (Pinus taeda L.)

Temesgen, Berhanu; Brown, Garth; Harry, David E.; Kinlaw, Claire S.; Sewell, Mitchell M.; Neale, David B.

doi:10.1007/s001220051695

Cited by 72 publications

(46 citation statements)

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“…Only selection on polymorphic genes involved in the traits will provide genetic gains from breeding population. Genetic mapping with genes of known function [17] and the test of their possible co-localisation with QTLs should be investigated. Comparative genome mapping will also allow to suspect QTLs in some genomic regions from results obtained in other species [17].…”

Section: Discussionmentioning

confidence: 99%

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Localisation of genomic regions controlling microdensitometric parameters of wood characteristics in hybrid larches

Arcade

Faivre-Rampant

Pâques³

et al. 2002

Ann. For. Sci.

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-The use of wood quality components in forest trees selection is hampered by long delays before phenotypic evaluation. Marker-assisted selection opens new possibilities since selection becomes feasible even before trait expression. In the present study, we have analysed 224 13-year-old hybrid larches derived from eight progenies from a single female parent in order to localise genomic regions controlling several wood traits. Traits were assessed on radial cores by microdensitometry, a method that provides estimates of wood density and radial growth and avoids tree destruction. Measurements were assessed individually on six consecutive rings. QTL detection was achieved by ANOVA using 68 AFLP markers distributed on average each 20 cM along larch genome. Significant QTLs for at least two out of six studied years are distributed on seven linkage groups. Applications towards marker-assisted selection are discussed. QTL / wood quality / microdensitometry / wood density / LarixRésumé -Localisation des régions du génome contrôlant des composantes microdensitométriques de la qualité du bois chez des mélèzes hybrides. Les paramètres de qualité du bois sont peu pris en compte dans l'amélioration des arbres forestiers en raison des délais d'évaluation très longs. La sélection assistée par marqueurs ouvre de nouvelles perspectives en rendant possible une sélection précoce pour des caractères à expression tardive. Dans ce travail, nous avons analysé huit descendances de mélèze hybride (Larix decidua × L. kaempferi) issues d'un même parent et comportant 224 arbres âgés de 13 ans, afin de localiser sur une carte génétique les régions du génome qui contrôlent divers paramètres de qualité du bois. Ces paramètres ont été mesurés sur des carottes de bois par microdensitométrie. Cette méthode permet d'évaluer, de façon non destructrice, de nombreuses composantes de la densité du bois et également de la croissance radiale. Les mesures sont effectuées sur six cernes consécutifs. La localisation des QTL a été menée à l'aide de 68 marqueurs AFLP distants en moyenne de 20 cM et par analyse de variance. Les QTL significatifs pour au moins deux des six années analysées se répartissent sur sept groupes de liaison. Les applications de ces résultats sont discutées essentiellement dans les perspectives de la sélection assistée par marqueurs. QTL / qualité du bois / microdensitométrie / densité du bois / Larix

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Section: Discussionmentioning

confidence: 99%

“…Genetic mapping with genes of known function [17] and the test of their possible co-localisation with QTLs should be investigated. Comparative genome mapping will also allow to suspect QTLs in some genomic regions from results obtained in other species [17]. Marker-assisted selection efficiency will be further tested in forest tree species.…”

Section: Discussionmentioning

confidence: 99%

Localisation of genomic regions controlling microdensitometric parameters of wood characteristics in hybrid larches

Arcade

Faivre-Rampant

Pâques³

et al. 2002

Ann. For. Sci.

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“…PCR amplification was performed using primer pairs designed from these loci [20][21][22]26], which targeted the intron and/or 3' un-translated region [20] of the selected gene fragments. Of the screened 21 primer pairs, 15 (71%) produced single and clear PCR products ranging from 211 to 918 bp (Table 2); while the remaining 6 (29%) were produced multiple PCR products or no PCR amplifications.…”

Section: Resultsmentioning

confidence: 99%

“…The extracted DNA was further purified by MagneSil-Red (Promega) based on the manufacturer's instructions. Based on previously published low-copy anchored loci in Pinaceae [20][21][22]26], 21 loci were initially screened. PCR reactions were performed in a total volume of 10 L containing 1 × PCR buffer (Invitrogen), 1.5 mM MgCl 2 , 0.2 mM each dNTP, approximately 20 ng of template DNA and 0.25 U Platinum Taq DNA polymerase (Invitrogen).…”

Section: Sample and Dna Extractionmentioning

confidence: 99%

“…The large genome size of pines (22-37 pg/2C; [18]) hinders the development and application of low-copy anchor loci for nucleotide diversity and phylogenetic analysis [19]. However, despite this problem, efforts to develop low-copy anchor loci have been directed toward P. taeda L. and P. pinaster Aiton which revealed a large number of low-copy anchor loci that show orthology across pine species [20][21][22][23]. Because these conifer anchor loci show strong evidence for positional orthology, they are promising candidates for nucleotide diversity and phylogenetic analysis in other pine species [21].…”

Section: Introductionmentioning

confidence: 99%

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Nucleotide Diversities and Genetic Relationship in the Three Japanese Pine Species; Pinus thunbergii, Pinus densiflora, and Pinus luchuensis

Suharyanto

Shiraishi

2011

Diversity

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Abstract:The nucleotide diversities and genetic relationship in the three Japanese pine species, P. thunbergii, P. densiflora, and P. luchuensis, were measured using low-copy anchor loci in Pinaceae. The average nucleotide diversity among these three Japanese pines revealed that P. thunbergii was the highest (6.05 × 10 −3 ), followed by P. densiflora (5.27 × 10 −3 ) and P. luchuensis (5.02 × 10 −3 ). In comparison to other conifer species, it was concluded that the pines possessed an intermediate level of nucleotide diversity. The Heat shock protein (HSP) gene in P. thunbergii, Phenylalanine tRNA synthetase, RuBP carboxylase, and Disease resistance response protein 206 genes in P. densiflora were significantly deviated from standard neutral models. Some of these genes were related to stress or pathogen/defense response. As the samples used in this study were collected from natural populations that showed specific characteristics of being resistant to pine wilt nematode, it was hypothesized that the initial selection was an important factor in discriminating the deviation from neutrality models. Phylogenetic reconstruction revealed that the three Japanese pines were split into two lineages corresponding to P. densiflora and P. thunbergii-P. luchuensis. The latter lineage was differentiated further into two clades; P. thunbergii and P. luchuensis. The result concludes that the three Japanese pines are closely related and P. thunbergii is genetically closer to P. luchuensis, than P. densiflora. OPEN ACCESSDiversity 2011, 3 122

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Landscapes, Genomics and Transgenic Conifers

Williams¹

2006

Managing Forest Ecosystems

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Aims & Scope:Well-managed forests and woodlands are a renewable resource, producing essential raw material with minimum waste and energy use. Rich in habitat and species diversity, forests may contribute to increased ecosystem stability. They can absorb the effects of unwanted deposition and other disturbances and protect neighbouring ecosystems by maintaining stable nutrient and energy cycles and by preventing soil degradation and erosion. They provide much-needed recreation and their continued existence contributes to stabilizing rural communities.Forests are managed for timber production and species, habitat and process conservation. A subtle shift from multiple-use management to ecosystems management is being observed and the new ecological perspective of multi-functional forest management is based on the principles of ecosystem diversity, stability and elasticity, and the dynamic equilibrium of primary and secondary production.Making full use of new technology is one of the challenges facing forest management today. Resource information must be obtained with a limited budget. This requires better timing of resource assessment activities and improved use of multiple data sources. Sound ecosystems management, like any other management activity, relies on effective forecasting and operational control.The aim of the book series Managing Forest Ecosystems is to present state-of-the-art research results relating to the practice of forest management. Contributions are solicited from prominent authors. Each reference book, monograph or proceedings volume will be focused to deal with a specific context. Typical issues of the series are: resource assessment techniques, evaluating sustainability for even-aged and uneven-aged forests, multi-objective management, predicting forest development, optimizing forest management, biodiversity management and monitoring, risk assessment and economic analysis.The titles published in this series are listed at the end of this volume. All Rights ReservedNo part of this work may be reproduced, stored in a retrieval system, or transmitted in any form or by any means, electronic, mechanical, photocopying, microfilming, recording or otherwise, without written permission from the Publisher, with the exception of any material supplied specifically for the purpose of being entered and executed on a computer system, for exclusive use by the purchaser of the work.Printed in the Netherlands.

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Genetic mapping of expressed sequence tag polymorphism (ESTP) markers in loblolly pine (Pinus taeda L.)

Cited by 72 publications

References 26 publications

Localisation of genomic regions controlling microdensitometric parameters of wood characteristics in hybrid larches

Localisation of genomic regions controlling microdensitometric parameters of wood characteristics in hybrid larches

Nucleotide Diversities and Genetic Relationship in the Three Japanese Pine Species; Pinus thunbergii, Pinus densiflora, and Pinus luchuensis

Landscapes, Genomics and Transgenic Conifers

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