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RESEARCH ARTICLE Open Access

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by María-dolores Vélez , Enrique Sáez-laguna , Luis-manuel Díaz , Jose-antonio Mancha , María-carmen Barbero , Carmen Collada , Carmen Díaz-sala , Ismael Ar , María-teresa Cervera

Citations

492	García-Gómez JM, Terol J, Talón M, Robles M. Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics - Conesa, Gotz (Show Context) Citation Context ...ancerel et al. de Miguel et al. BMC Genomics 2014, 15:464 Page 4 of 19 http://www.biomedcentral.com/1471-2164/15/464 [20,82]. Functional annotation for SNP array C was obtained with Blast2GO software =-=[89]-=-. For high-scoring segment pair (HSP) a restrictive E−20 e-value was chosen finding in a Blastx search against a set of 88,516 reference proteins from UniProt (http://www.uniprot.org/). In order to up...
239	The estimation of map distance from recombination values. Annals of Eugenics12,172^175. - Kosambi - 1944 (Show Context) Citation Context ...the software JoinMap® v4.1 [84] with the CP population type and using a recombination fraction < 0.35 and a LOD > 3 as mapping parameters. Map distances were calculated using Kosambi mapping function =-=[85]-=-. For map building a goodness-of-fit jump threshold of 5 was established. JoinMap suggests three genetic maps with increasing number of markers (map1, map2 and map3). In map2, new markers were added b...
180	A plant DNA minipreparation: Version II. Plant Mol Biol Rep. - SL, Wood, et al. - 1983 (Show Context) Citation Context ...fication of microsatellite polymorphic loci (SAMPL) and single nucleotide polymorphism (SNP) markers. Different DNA extraction methods were used in needles: a modified protocol from Dellaporta et al. =-=[78]-=- for nSSRs, SAMPLs and SNP array D (detailed below); the commercial kit Invisorb DNA plants HTS 96 kit (Invitek GmbH, Berlin, Germany) for SNP arrays A and C (detailed below) and the commercial kit DN...
111	Genetic linkage maps of Eucalyptus grandis and Eucalyptus urophylla using a pseudotestcross: Mapping strategy and RAPD markers. - Grattapaglia, Sederoff - 1994 (Show Context) Citation Context ...omatically scored. Construction of dense linkage maps For the construction of two genetic maps, one for each progenitor (Gal1056 and Oria6), the “two-way-pseudotestcross” mapping strategy was applied =-=[83]-=-. The consensus map for the cross, combining markers informative for both parents, was also developed (GxO). Linkage analyses and map estimations were performed using the regression mapping algorithm ...
51	Principles of Stable Isotope Geochemistry, Prentice-Hall, Upper Saddle River, - Sharp - 2007 (Show Context) Citation Context ...PDZ Europa 20–20 continuous flow isotope ratio mass spectrometer (Sercon Ltd., Cheshire, UK) at Stable Isotope Facility UC Davis, California, USA. The isotopic composition of 13C (‰) was expressed as =-=[77]-=-: δ13C Rs −Rb Rb 1000 Where Rs and Rb refer to the 13C/12C ratio in the sample and in the Pee Dee Belemnite standard, respectively. Broad-sense heritability estimates and genetic correlations were...
39	Ooijen JW: JoinMap® 4. Software for the calculation of genetic linkage maps in experimental populations - Van - 2006 (Show Context) Citation Context ...ng markers informative for both parents, was also developed (GxO). Linkage analyses and map estimations were performed using the regression mapping algorithm implemented in the software JoinMap® v4.1 =-=[84]-=- with the CP population type and using a recombination fraction < 0.35 and a LOD > 3 as mapping parameters. Map distances were calculated using Kosambi mapping function [85]. For map building a goodne...
38	A (2011) Forest tree genomics: Growing resources and applications - DB, Kremer (Show Context) Citation Context ...de available in this article, unless otherwise stated. de Miguel et al. BMC Genomics 2014, 15:464 http://www.biomedcentral.com/1471-2164/15/464 power of association studies is higher than QTL mapping =-=[9]-=-. However, the rapid decay in linkage disequilibrium of conifers [10] makes the development of genome wide association studies in these species laborious and advocates in favor of candidate gene appro...
37	The genetics and genomics of drought response in Populus - NR, Skogstrom, et al. - 2006 (Show Context) Citation Context ...ster in conservation, afforestation or breeding programs. QTL and association studies of drought tolerance traits have been developed in several tree species, such as P. taeda [23,63,64], Populus sp. =-=[19,65,66]-=- or Quercus robur [43,67]. Several QTL and association studies in P. pinaster have analyzed the molecular basis of different processes related to growth or wood quality traits [68-73], terpenes [74] a...
30	LB: Effects of genotyping errors, missing values and segregation distortion in molecular marker data on the construction of linkage maps. Heredity 2003 - CA, Broadfoot (Show Context) Citation Context ...e-point of measurement (14 days without watering) respectively. de Miguel et al. BMC Genomics 2014, 15:464 Page 10 of 19 http://www.biomedcentral.com/1471-2164/15/464 the construction of linkage maps =-=[99]-=-. In this study it was achieved by the thorough genotypic data integrity obtained by using highly stringent thresholds to consider SNPs for mapping. Also, the position of the SNPs genotyped in fewer i...
29	High-resolution genetic mapping of complex traits - Kruglyak, ES - 1995 (Show Context) Citation Context ...d molecular characterization of the progeny and construction of genetic maps [47]. The power to resolve the location of a QTL is related to the size of the studied population and the mapping coverage =-=[48]-=-. Additionally, forest tree species are characterized by long generation times which hinder development of backcross or three-generation pedigrees by controlled crosses. On the other hand, replication...
28	Likely effects of climate change on growth of Quercus ilex, Pinus halepensis, Pinus pinaster, Pinus sylvestris and Fagus sylvatica forests in the Mediterranean region. Forest Ecology and Management 162 - Sabaté, Gracia, et al. - 2002 (Show Context) Citation Context ...terranean region with a high ecological and socio-economical value [56-58]. Although P. pinaster shows evidence of drought adaptation [59,60], recurrent or severe drought periods can limit its growth =-=[61,62]-=-. Understanding the molecular basis of drought tolerance is of high importance for a suitable management of the available genetic resources of P. pinaster in conservation, afforestation or breeding pr...
27	Partitioning stomatal and non-stomatal limitations to photosynthesis,” - Jones - 2005
26	Photosynthesis and drought: can we make meta‐ bolic connections from available data? - Pinheiro, Chaves - 2011 (Show Context) Citation Context ...iew of its implication in survival, growth and biomass production. However, carbon uptake in response to drought is a complex process with many mechanisms acting in coordination in final CO2 fixation =-=[2]-=-. From stomatal and mesophyll resistances to diffusion of CO2 to biochemical processes within chloroplast, complex mechanisms are involved in net carbon fixation [2-5]. The functional bases that contr...
26	Enhancing genetic mapping of complex genomes through the design of highly-multiplexed SNP arrays: application to the large and unsequenced genomes of white spruce and black spruce. - Pavy, Pelgas, et al. - 2008
25	Los bosques ibericos: una interpretacion geobotanica. 4ª ed rev. - Blanco, Casado, et al. - 2005
25	Reefer JE: A maximum likelihood method for estimating genome length using genetic linkage data. Genetics - Chakravarti, LK - 1991 (Show Context) Citation Context ...e length was calculated as the sum of all mapped marker intervals. Estimated genome length was determined from the partial linkage data according to Hulbert et al. [86] modified by Chakravarti et al. =-=[87]-=- (Method 3). To estimate genome length using framework maps, a minimum LOD score of three was chosen. Observed map coverage was calculated as the ratio of total genome length to estimated genome lengt...
23	Resolution of quantitative traits into Mendelian factors by using a complete linkage map of restriction fragment length polymorphisms. - AH, ES, et al. - 1988 (Show Context) Citation Context ...sed on the photochemical machinery. QTL studies involve development of a segregant progeny for target traits, phenotypic and molecular characterization of the progeny and construction of genetic maps =-=[47]-=-. The power to resolve the location of a QTL is related to the size of the studied population and the mapping coverage [48]. Additionally, forest tree species are characterized by long generation time...
22	Soybean Response to Water: A QTL Analysis of Drought Tolerance. - Specht, Chase, et al. - 2001
21	JQ: Genome-scale transcriptome analysis of the desert poplar. Populus euphratica. Tree Physiology - Qiu, Ma, et al. - 2011
20	A white spruce gene catalog for conifer genome analyses. - Rigault, Boyle, et al. - 2011
19	Mesophyll diffusion conductance to CO2: An unappreciated central player in photosynthesis. - Flexas, M, et al. - 2012 (Show Context) Citation Context ...to biochemical processes within chloroplast, complex mechanisms are involved in net carbon fixation [2-5]. The functional bases that control carbon uptake under water stress have been largely studied =-=[6,7]-=-, but less information is available about its genetic regulation. Complex functional trait dissection can be achieved through two approaches: association studies and QTL (Quantitative Trait Loci) mapp...
19	Genomics and bioinformatics resources for crop improvement. - Mochida, Shinozaki - 2010 (Show Context) Citation Context ...fication of candidate genes underlying QTL was difficult due to the use of anonymous markers and limited sequences with functional information, and thus restricted the approach to model plant species =-=[12]-=-. Nowadays, gene-based markers are easily developed and much more functional information is available for a wide range of organisms [13-18], allowing to integrate functional annotation with QTL studie...
19	The role of ecophysiological models in QTL analysis: the example of specific leaf area in barley. - Yin, MJ, et al. - 1999 (Show Context) Citation Context ...r hand, replication of each genotype is needed for a reliable phenotypic evaluation [49], especially when working with physiological parameters that are extremely sensible to environmental conditions =-=[41,50,51]-=-. Mediterranean species are particularly threatened by drought [52-54], especially in the context of climatic change predictions [55]. Pinus pinaster Ait. is an important conifer in Mediterranean regi...
17	Quantitative traits in plants: beyond the QTL - Paran, Zamir - 2003 (Show Context) Citation Context ...eration times which hinder development of backcross or three-generation pedigrees by controlled crosses. On the other hand, replication of each genotype is needed for a reliable phenotypic evaluation =-=[49]-=-, especially when working with physiological parameters that are extremely sensible to environmental conditions [41,50,51]. Mediterranean species are particularly threatened by drought [52-54], especi...
16	De novo sequencing and analysis of root transcriptome using 454 pyrosequencing to discover putative genes associated with drought tolerance in Ammopiptanthus mongolicus. BMCGenomics. 2012; 13: 266. doi: 10.1186/1471-2164-13-266 PMID: 22721448 - Zhou, Gao, et al.
16	Ersoz ES, Wright MH, Rashbrook VK, Nicolet CM, Neale DB:Highthroughput genotyping andmapping of single nucleotide polymorphisms in loblolly pine (Pinus taeda L.). Tree Genet Genomes 2009 - AJ, Pande (Show Context) Citation Context ...osome number of the species. The aforementioned highly saturated maps, with less than 2 cM mean distance between markers, are in the range of recently published linkage maps for other conifer species =-=[20,22,24,27,51]-=-. Estimated map length was higher in the female than in the male parent. Differences in genome length between parental maps are usually found in conifer species [90-93] and it may be a consequence of ...
15	Association genetics of complex traits in conifers. Trends Plant Sci - Neale, Savolainen - 2004 (Show Context) Citation Context ...al. BMC Genomics 2014, 15:464 http://www.biomedcentral.com/1471-2164/15/464 power of association studies is higher than QTL mapping [9]. However, the rapid decay in linkage disequilibrium of conifers =-=[10]-=- makes the development of genome wide association studies in these species laborious and advocates in favor of candidate gene approaches [11]. In the past, identification of candidate genes underlying...
13	Thiec D, Scotti-Saintagne C, Bodénès C, Kremer A, Guehl J-M. 2008. Quantitative trait loci controlling water use efficiency and related traits in Quercus robur L. Tree Genetics & Genomes 4 - Brendel, Le (Show Context) Citation Context ...station or breeding programs. QTL and association studies of drought tolerance traits have been developed in several tree species, such as P. taeda [23,63,64], Populus sp. [19,65,66] or Quercus robur =-=[43,67]-=-. Several QTL and association studies in P. pinaster have analyzed the molecular basis of different processes related to growth or wood quality traits [68-73], terpenes [74] and serotiny [75]. However...
13	A consensus map for loblolly pine (Pinus taeda L.). I. Construction and integration of individual linkage maps from two outbred three-generation pedigrees. Genetics 151: 321–330 - MM, BK, et al. - 1999 (Show Context) Citation Context ...ale parent. Differences in genome length between parental maps are usually found in conifer species [90-93] and it may be a consequence of differences in the recombination rate between parental trees =-=[94,95]-=-. The accuracy of the SNP genotyping assays previously proved [20,82] has been confirmed in this study by genes with more than one SNP that mapped in almost all cases within a distance lower than 1 cM...
12	Mapping QTLs associated with drought resistance in rice: Progress, problems and prospects. Plant Growth Regulation 29 - Price, Courtois - 1999
12	Genetic analysis of the fungus, Bremia lactucae, using restriction fragment length polymorphisms, Genetics 120 - Hulbert - 1988 (Show Context) Citation Context ...f circa 10 cM were kept. Total genome length was calculated as the sum of all mapped marker intervals. Estimated genome length was determined from the partial linkage data according to Hulbert et al. =-=[86]-=- modified by Chakravarti et al. [87] (Method 3). To estimate genome length using framework maps, a minimum LOD score of three was chosen. Observed map coverage was calculated as the ratio of total gen...
12	Quantitative genetic analysis of biomass and wood chemistry of Populus under different nitrogen levels. New Phytol - Novaes, Osorio, et al. - 2009 (Show Context) Citation Context ...their drought response were selected to maximize the variability of the F1 obtained progeny, at molecular and functional levels. Although some recent QTL studies in trees worked with larger progenies =-=[51,100,101]-=-, the 162 obtained siblings in this study are in the range or higher than other QTL analysis in trees [31,46,69,70,102]. On the other side, gas exchange parameters are extremely sensible to variations...
10	Causse M: The candidate gene approach in plant genetics: a review - Pflieger, Lefebvre (Show Context) Citation Context ... within QTL confidence intervals, some of them with known function in other species, could be considered as a preliminary step that contributes to the detection of genes underlying traits of interest =-=[30]-=-. Additionally, QTL mapping allows the evaluation of the genetic basis for potential adaptation in natural populations [31,32] and to extend the understanding of relationships between different morpho...
9	A spruce gene map infers ancient plant genome reshuffling and subsequent slow evolution in the gymnosperm lineage leading to extant conifers - Pavy (Show Context) Citation Context ...osome number of the species. The aforementioned highly saturated maps, with less than 2 cM mean distance between markers, are in the range of recently published linkage maps for other conifer species =-=[20,22,24,27,51]-=-. Estimated map length was higher in the female than in the male parent. Differences in genome length between parental maps are usually found in conifer species [90-93] and it may be a consequence of ...
9	Association genetics in Pinus taeda L. II. Carbon isotope discrimination. Heredity 101, - Gonzalez-Martinez, Huber, et al. - 2008 (Show Context) Citation Context ...tic resources of P. pinaster in conservation, afforestation or breeding programs. QTL and association studies of drought tolerance traits have been developed in several tree species, such as P. taeda =-=[23,63,64]-=-, Populus sp. [19,65,66] or Quercus robur [43,67]. Several QTL and association studies in P. pinaster have analyzed the molecular basis of different processes related to growth or wood quality traits ...
8	Krutovsky KV, Neale DB: Forest-tree population genomics and adaptive evolution - SC (Show Context) Citation Context ...t less information is available about its genetic regulation. Complex functional trait dissection can be achieved through two approaches: association studies and QTL (Quantitative Trait Loci) mapping =-=[8]-=-. The resolution * Correspondence: cervera@inia.es 1Departamento de Ecología y Genética Forestal, INIA-CIFOR. Ctra, de La Coruña Km 7.5, 28040 Madrid, Spain 2Unidad Mixta de Genómica y Ecofisiología F...
8	Pot D, Plomion C, Monteverdi MC, Barreneche T, Lauteri M, Villani F. 2004. Identification of QTLs affecting adaptative traits in Castanea sativa Mill - Casasoli (Show Context) Citation Context ...tep that contributes to the detection of genes underlying traits of interest [30]. Additionally, QTL mapping allows the evaluation of the genetic basis for potential adaptation in natural populations =-=[31,32]-=- and to extend the understanding of relationships between different morpho-functional traits [33]. The identification of the main QTL involved in drought response could be a first step to develop mark...
8	Recombination rate differences for pollen parents and seed parents in pine. Heredity 77 - PLOMION, O’MALLEY - 1996 (Show Context) Citation Context ...ale parent. Differences in genome length between parental maps are usually found in conifer species [90-93] and it may be a consequence of differences in the recombination rate between parental trees =-=[94,95]-=-. The accuracy of the SNP genotyping assays previously proved [20,82] has been confirmed in this study by genes with more than one SNP that mapped in almost all cases within a distance lower than 1 cM...
7	Scotti-Saintagne C, Kremer A, Jolivet Y, Dreyer E, Brendel O: Quantitative trait loci of tolerance to waterlogging in a European oak (Quercus robur L.): physiological relevance and temporal effect patterns. Plant, Cell and Environment - Parelle, Zapater - 2007 (Show Context) Citation Context ...station or breeding programs. QTL and association studies of drought tolerance traits have been developed in several tree species, such as P. taeda [23,63,64], Populus sp. [19,65,66] or Quercus robur =-=[43,67]-=-. Several QTL and association studies in P. pinaster have analyzed the molecular basis of different processes related to growth or wood quality traits [68-73], terpenes [74] and serotiny [75]. However...
6	NC, Neale DB: DNA sequence variation and selection of tag single-nucleotide polymorphisms at candidate genes for drought-stress response in Pinus taeda L - SC, Ersoz, et al. (Show Context) Citation Context ...tic resources of P. pinaster in conservation, afforestation or breeding programs. QTL and association studies of drought tolerance traits have been developed in several tree species, such as P. taeda =-=[23,63,64]-=-, Populus sp. [19,65,66] or Quercus robur [43,67]. Several QTL and association studies in P. pinaster have analyzed the molecular basis of different processes related to growth or wood quality traits ...
6	Gonzalez-Martınez SC, Le Provost G, Plomion C, Ribeiro MM, Sebstiani F, Alia R, Vendramin GG. 2007. Range-wide phylogeography and gene zones in Pinus pinaster Ait. revealed by chloroplast microsatellite markers - Bucci (Show Context) Citation Context ...ous genes for these sequences. The high level of synteny and colinearity observed between the genetic maps developed for individuals that belong to populations with very different genetic backgrounds =-=[98]-=- points out the high reliability in the marker order obtained. Thus, it is possible the development of a composite genetic map for the species by integrating the genetic maps developed by de Miguel et...
5	Leipner J: Genetic analysis of cold-tolerance of photosynthesis in maize - Fracheboud, Jompuk, et al. (Show Context) Citation Context ...oint of measurements respectively. de Miguel et al. BMC Genomics 2014, 15:464 Page 12 of 19 http://www.biomedcentral.com/1471-2164/15/464 the development of inbred line populations for annual species =-=[103,104]-=-. In this study, four vegetative copies of each genotype were established in a completely randomized block design in a greenhouse. All these efforts allowed the identification of significant and sugge...
4	Shinohara K, Tsumura Y: The construction of a high-density linkage map for identifying SNP markers that are tighly linked to a nuclear-recessive major gene for male sterility in Cryptomeria japonica D.Don - Moriguchi, Ujino-Ihara, et al. - 2012
4	Meirmans P, Ritland K, Isabel N: QTL mapping in white spruce: gene maps and genomic regions underlying adaptive traits across pedigrees, years and environments - Pelgas, Bousquet (Show Context) Citation Context ...r hand, replication of each genotype is needed for a reliable phenotypic evaluation [49], especially when working with physiological parameters that are extremely sensible to environmental conditions =-=[41,50,51]-=-. Mediterranean species are particularly threatened by drought [52-54], especially in the context of climatic change predictions [55]. Pinus pinaster Ait. is an important conifer in Mediterranean regi...
4	Christodoulakis D: Long-term increase in climatic dryness in the East-Mediterranean as evidenced for the island of Samos. Regional Environ Change 2005 - Körner, Sarris
4	Alıa R, Bataillon T, Torre S, Zabal-Aguirre M, Vendramin GG, Gonzalez-Martınez SC. 2011.Molecular footprints of local adaptation in two Mediterranean conifers.Molecular Biology & Evolution 28 - Grivet, Sebastiani (Show Context) Citation Context ...dictions [55]. Pinus pinaster Ait. is an important conifer in Mediterranean region with a high ecological and socio-economical value [56-58]. Although P. pinaster shows evidence of drought adaptation =-=[59,60]-=-, recurrent or severe drought periods can limit its growth [61,62]. Understanding the molecular basis of drought tolerance is of high importance for a suitable management of the available genetic reso...
4	Cahalan C, Pichavant F, Plomion C: QTLs and candidate genes for wood properties in maritime pine (Pinus pinaster Ait - Pot, Rodrigues, et al. (Show Context) Citation Context ...tional levels. Although some recent QTL studies in trees worked with larger progenies [51,100,101], the 162 obtained siblings in this study are in the range or higher than other QTL analysis in trees =-=[31,46,69,70,102]-=-. On the other side, gas exchange parameters are extremely sensible to variations in the environmental conditions. To cope with the problem of environmental noise in phenotypic evaluation, different s...
4	Madur D, Pot D, Neale D, Plomion C: Comparative genome and QTL mapping between maritime and loblolly pines - Chagné, GR, et al.
3	Drought effects and water use efficiency: improving crop production in dry environments. Functional Plant Biology 37: iii–vi - MM, Davies (Show Context) Citation Context ...e annotation, Photochemistry, Photosynthesis, Pinus pinaster, QTL, Water use efficiency Background Drought resistance is crucial for growth and survival of species living in water scarce environments =-=[1]-=-. Unraveling the molecular mechanisms that control functional traits, such as photosynthesis and water use efficiency in response to drought, is especially relevant in view of its implication in survi...
3	Queval G, Noctor G, Harbinson J: Photosynthetic control of electron transport and the regulation of gene expression - CH, Neukermans
3	SK, Southerton SG: Generation and analysis of expressed sequence tags from six developing xylem libraries in Pinus radiata D Don - Li, HX, et al.
3	Sillanpaa MJ, Arjas E, Repo T, Savolainen O: Genetic basis of climatic adaptation in scots pine by bayesian quantitative trait locus analysis - Hurme (Show Context) Citation Context ...tep that contributes to the detection of genes underlying traits of interest [30]. Additionally, QTL mapping allows the evaluation of the genetic basis for potential adaptation in natural populations =-=[31,32]-=- and to extend the understanding of relationships between different morpho-functional traits [33]. The identification of the main QTL involved in drought response could be a first step to develop mark...
3	DF, Bahnisch LM, Liu C: Identification of causal relationships among traits related to drought resistance in Stylosanthes scabra using QTL analysis - BR, BP, et al. (Show Context) Citation Context ...ot distinguish whether the traits could be causally related or simply varying in association. However, the coincidence of QTL for two traits is strong evidence that they could be functionally related =-=[36]-=-. QTL co-localization of SLA with WUEi and Fv’Fm’ was found in LG 5 and LG 7 pointing towards a strong interrelationship between SLA, WUEi and Fv’Fm’. The aforementioned co-localization could indicate...
3	Richards JH: Identification and characterization of QTL underlying whole plant physiology in Arabidopsis thaliana: δ13C, stomatal conductance and transpiration efficiency. Plant Cell Environ 2005 - TE, JK, et al.
3	Pot D, Plomion C, Rozenberg P, Guehl JM: Genetic parameters and QTL analysis of δ13C and ring width in maritime pine. Plant Cell Environ 2002 - Brendel (Show Context) Citation Context ...] and serotiny [75]. However, to date only association studies based on a few potential candidate genes [59,60] and one QTL study have analyzed the molecular basis of drought tolerance in P. pinaster =-=[44]-=-. The main objective of this work was to unravel the genetic basis of different functional parameters related to carbon uptake and water use efficiency in response to drought for P. pinaster. For this...
3	Christodoulakis D, Körner C. Recent decline in precipitation and tree growth in the eastern Mediterranean. Glob Change Biol 2007; 13(6 - Sarris
3	Achere V, Favre JM, FaivreRampant P, Aragones A, Da Silva Perez, Havengt L, Ritter E (2003) Identification of QTL controlling growth, chemical and physical wood property traits in Pinus pinaster (Ait). Silvae Genet 52:8–15 - Markussen, Fladung (Show Context) Citation Context ...tional levels. Although some recent QTL studies in trees worked with larger progenies [51,100,101], the 162 obtained siblings in this study are in the range or higher than other QTL analysis in trees =-=[31,46,69,70,102]-=-. On the other side, gas exchange parameters are extremely sensible to variations in the environmental conditions. To cope with the problem of environmental noise in phenotypic evaluation, different s...
3	Nagasaka K, Tsumura Y: AFLP and CAPS linkage maps of Cryptomeria japonica - Nikaido, Ujino, et al.
3	Madur D, Neale D, Plomion C, Powell W, Troggio M, Morgante M: Analysis of the distribution of marker classes in a genetic linkage map: a case study in Norway spruce (Picea abies Karst - Scotti, Burelli, et al.
3	Mikkonen M, Karhu A, Garcia-Gil MR, O'Malley D, Lee B, Neale DB, Savolainen O: Comparing EST-based genetic maps between Pinus sylvestris and Pinus taeda. Theor Appl Genet 2003 - Komulainen, GR
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2	J: The genomic architecture and association genetics of adaptive characters using a candidate SNP approach in boreal black spruce - Prunier, Pelgas, et al. (Show Context) Citation Context ...th functional annotation allows to identify positional candidate genes for these QTL [19,28]. Suggested candidate genes are suitable for association studies that can validate markertrait associations =-=[29]-=-. Therefore, identification of positional candidate genes within QTL confidence intervals, some of them with known function in other species, could be considered as a preliminary step that contributes...
2	Pekić S, Quarrie S: Identification of QTL for drought responses in maize and their use in testing causal relationships between traits - Lebreton, Lazić-Jančić, et al. - 1995 (Show Context) Citation Context ... mapping allows the evaluation of the genetic basis for potential adaptation in natural populations [31,32] and to extend the understanding of relationships between different morpho-functional traits =-=[33]-=-. The identification of the main QTL involved in drought response could be a first step to develop marker assisted selection (MAS) strategies for these traits [11]. Consequently, the detection of QTL ...
2	A quantitative genetics approach to nitrogen use efficiency in sugarcane - Whan, Robinson, et al. - 2010
2	D: Mapping quantitative trait loci associated with chlorophyll a fluorescence parameters in soybean (Glycine max (L.) Merr - Yin, Meng, et al. (Show Context) Citation Context ...onse have been largely implemented for non-forest model species [34-39]. Some of these QTL studies in crop species have recently identified genomic regions controlling photochemistry of carbon uptake =-=[40,41]-=-. Breeding programs implemented in crops have reported yield improvement associated with increased photosynthesis [42]. However, fewer QTL analyses on functional drought response of forest tree specie...
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2	Intensity and timing of warming and drought differentially affect growth patterns of cooccuring Mediterranean tree species - Granda, Camarero, et al. - 2013
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2	Harvengt L, Plomion C, Garnier-Géré P: Association mapping for growth, straightness and wood chemistry traits in the Pinus pinaster Aquitaine breeding population - Lepoittevin
2	Yani A, Marpeau A: Genetic determinism of delta 3-carene in maritime pine using RAPD markers. Genome - Plomion - 1996 (Show Context) Citation Context ...65,66] or Quercus robur [43,67]. Several QTL and association studies in P. pinaster have analyzed the molecular basis of different processes related to growth or wood quality traits [68-73], terpenes =-=[74]-=- and serotiny [75]. However, to date only association studies based on a few potential candidate genes [59,60] and one QTL study have analyzed the molecular basis of drought tolerance in P. pinaster [...
2	Aranda I: Functional and genetic characterization of gas exchange and intrinsic water use efficiency in a full-sib family of Pinus pinaster Ait. in response to drought. Tree Physiol 2012 - Miguel, Sánchez-Gómez, et al. (Show Context) Citation Context ...y in response to drought. Methods Plant material, experimental setup and phenotypic evaluation Plant material, experimental setup and phenotypic evaluation are explained in detail in de Miguel et al. =-=[76]-=-. Briefly, 162 seedlings from a F1 full-sib family of P. pinaster obtained from a controlled cross between a male parent (Oria6) from Oria, a natural population from South-East Spain (37° 31 ’N 2° 21 ...
2	Collada C, Favre JM, Harvengt L - MA, Chagné, et al. (Show Context) Citation Context ...rcial kit DNeasy Plant mini kit (Qiagen, Düsseldorf, Germany) for SNP array B (detailed below). A total of twenty nine primer pairs designed for amplification of nSSR loci in P. pinaster and P. taeda =-=[79,80]-=- were tested for their segregations in the mapping population and both progenitors and six progeny individuals were genotyped. The whole mapping progeny was then genotyped only for polymorphic microsa...
2	Frigerio J-M, Chaumeil P, Garnier-Gere P - Chancerel, Lepoittevin, et al.
2	Goto Y: Detection of quantitative trait loci for wood strength in Cryptomeria japonica. Can J Forest Res-Revue Canadienne De Recherche Forestiere 2000 - Kuramoto, Kondo, et al.
2	S: Identification of quantitative trait loci for wood quality and growth across eight full-sib coastal Douglas-fir families - Ukrainetz, Ritland, et al. (Show Context) Citation Context ...their drought response were selected to maximize the variability of the F1 obtained progeny, at molecular and functional levels. Although some recent QTL studies in trees worked with larger progenies =-=[51,100,101]-=-, the 162 obtained siblings in this study are in the range or higher than other QTL analysis in trees [31,46,69,70,102]. On the other side, gas exchange parameters are extremely sensible to variations...
2	Vigneron P, Bouvet J-M, Plomion C, Gion J-M: Plasticity of primary and secondary growth dynamics in Eucalyptus hybrids: a quantitative genetics and QTL mapping perspective - Bartholomé, Salmon (Show Context) Citation Context ...tional levels. Although some recent QTL studies in trees worked with larger progenies [51,100,101], the 162 obtained siblings in this study are in the range or higher than other QTL analysis in trees =-=[31,46,69,70,102]-=-. On the other side, gas exchange parameters are extremely sensible to variations in the environmental conditions. To cope with the problem of environmental noise in phenotypic evaluation, different s...
1	Aranda I: Effects of drought on mesophyll conductance and photosynthetic limitations at different tree canopy layers. Plant Cell Environ 2013 - FJ, Sánchez-Gómez, et al.
1	Southerton SG, Bossinger G, Thumma BR: Dissection of complex traits in forest trees: opportunities for marker-assisted selection - Thavamanikumar (Show Context) Citation Context ...ver, the rapid decay in linkage disequilibrium of conifers [10] makes the development of genome wide association studies in these species laborious and advocates in favor of candidate gene approaches =-=[11]-=-. In the past, identification of candidate genes underlying QTL was difficult due to the use of anonymous markers and limited sequences with functional information, and thus restricted the approach to...
1	Brignolas F, Jorge V, Orléans F, Champenoux F: Integrating genome annotation and QTL position to identify candidate genes for productivity, architecture and water-use efficiency in Populus spp - Monclus, JC, et al. (Show Context) Citation Context ...Nowadays, gene-based markers are easily developed and much more functional information is available for a wide range of organisms [13-18], allowing to integrate functional annotation with QTL studies =-=[19]-=-. Moreover, the development and application of high throughput genotyping technologies have allowed the construction of dense genetic maps [[20-27], http://dendrome.ucdavis. edu/cmap/]. The use of hig...
1	Noirot C, Klopp C, Ehrenmann F, Boury C, Le Provost G, Label P, Lalanne C: High-density linkage mapping in a pine tree reveals a genomic region associated with inbreeding depression and de Miguel et al. BMC Genomics 2014, 15:464 Page 15 of 19 http://www.b - Chancerel, Lamy, et al. (Show Context) Citation Context ...zLaguna et al., unpublished). The genotyping of SNP array C was developed at CNIO, Madrid, Spain. Finally, SNP array D contained 10,593 SNPs identified from unigene set “PineContig_v2” of P. pinaster =-=[20]-=-. The four genotyping assays were carried out according to the manufacturer’s instructions (Illumina Inc., San Diego, CA, USA) and SNPs clusters revised manually with Illumina Genome Studio v.1.9.4 so...
1	Gonzalez-Martinez SC, Neale D: Patterns of population structure and environmental associations to aridity across the range of loblolly pine (Pinus taeda - AJ, Heerwaarden, et al. (Show Context) Citation Context ...tic resources of P. pinaster in conservation, afforestation or breeding programs. QTL and association studies of drought tolerance traits have been developed in several tree species, such as P. taeda =-=[23,63,64]-=-, Populus sp. [19,65,66] or Quercus robur [43,67]. Several QTL and association studies in P. pinaster have analyzed the molecular basis of different processes related to growth or wood quality traits ...
1	Langley CH, Neale DB: Combination of multipoint maximum likelihood (MML) and regression mapping algorithms to construct a high-density genetic linkage map for loblolly pine (Pinus taeda L - PJ, KA, et al. (Show Context) Citation Context ...osome number of the species. The aforementioned highly saturated maps, with less than 2 cM mean distance between markers, are in the range of recently published linkage maps for other conifer species =-=[20,22,24,27,51]-=-. Estimated map length was higher in the female than in the male parent. Differences in genome length between parental maps are usually found in conifer species [90-93] and it may be a consequence of ...
1	Vadez V, Yadav YP, Hash CT, Yadav RS: Integration of gene-based markers in a pearl millet genetic map for identification of candidate genes underlying drought tolerance quantitative trait loci - Sehgal, Rajaram, et al. (Show Context) Citation Context ...f loci involved in the genetic control of the targeted trait and the combination of high density gene based maps with functional annotation allows to identify positional candidate genes for these QTL =-=[19,28]-=-. Suggested candidate genes are suitable for association studies that can validate markertrait associations [29]. Therefore, identification of positional candidate genes within QTL confidence interval...
1	Fatokun C, Muranaka S, Visser R: Breeding drought tolerant cowpea: constraints, accomplishments, and future prospects. Euphytica 2009 - Agbicodo
1	Struik PC, Stomph TJ, Wang H: Using chromosome introgression lines to map quantitative trait loci for photosynthesis parameters in rice (Oryza sativa L.) leaves under drought and well-watered field conditions - Gu, Yin (Show Context) Citation Context ...onse have been largely implemented for non-forest model species [34-39]. Some of these QTL studies in crop species have recently identified genomic regions controlling photochemistry of carbon uptake =-=[40,41]-=-. Breeding programs implemented in crops have reported yield improvement associated with increased photosynthesis [42]. However, fewer QTL analyses on functional drought response of forest tree specie...
1	Edmeades GO: Breeding and cereal yield progress - Fischer (Show Context) Citation Context ...ecently identified genomic regions controlling photochemistry of carbon uptake [40,41]. Breeding programs implemented in crops have reported yield improvement associated with increased photosynthesis =-=[42]-=-. However, fewer QTL analyses on functional drought response of forest tree species have been performed [11,43-46] and to our knowledge none of them has focused on the photochemical machinery. QTL stu...
1	Tschaplinski TJ, Yin T, Tuskan GA: Genome anchored QTLs for biomass productivity in hybrid Populus grown under contrasting environments. PLoS One 2013 - Muchero, MM, et al.
1	Kolli RK, Kwon W, Laprise R: Regional climate projections. Contribution of Working group I to the Fourth Assessment Report of the Intergovernmental Panel on Climate Change - JH, Hewitson, et al. (Show Context) Citation Context ...ters that are extremely sensible to environmental conditions [41,50,51]. Mediterranean species are particularly threatened by drought [52-54], especially in the context of climatic change predictions =-=[55]-=-. Pinus pinaster Ait. is an important conifer in Mediterranean region with a high ecological and socio-economical value [56-58]. Although P. pinaster shows evidence of drought adaptation [59,60], recu...
1	Piñol J: Drought-induced mortality and hydraulic architecture in pine populations of the NE Iberian Peninsula. For Ecol Manag 2002, 161:247–256. de Miguel et al - Martínez-Vilalata (Show Context) Citation Context ...terranean region with a high ecological and socio-economical value [56-58]. Although P. pinaster shows evidence of drought adaptation [59,60], recurrent or severe drought periods can limit its growth =-=[61,62]-=-. Understanding the molecular basis of drought tolerance is of high importance for a suitable management of the available genetic resources of P. pinaster in conservation, afforestation or breeding pr...
1	Tuskan GA, Sewell MM, Gebre GM, Todd DE, Pendley CD: Phenotypic variation and quantitative trait locus identification for osmotic potential in an interspecific hybrid inbred F2 poplar pedigree grown in contrasting environments. Tree Physiol 2006 - TJ (Show Context) Citation Context ...ster in conservation, afforestation or breeding programs. QTL and association studies of drought tolerance traits have been developed in several tree species, such as P. taeda [23,63,64], Populus sp. =-=[19,65,66]-=- or Quercus robur [43,67]. Several QTL and association studies in P. pinaster have analyzed the molecular basis of different processes related to growth or wood quality traits [68-73], terpenes [74] a...
1	Durel CE, O'Malley DM: Genetic dissection of height in maritime pine seedlings raised under accelerated growth conditions. Theor Appl Genet - Plomion - 1996
1	Heuertz M, Hernández-Serrano A, Pausas JG, Vendramin GG, Verdú M, González-Martínez SC: In situ genetic association for serotiny, a fire-related trait, in Mediterranean maritime pine (Pinus pinaster - KB (Show Context) Citation Context ...robur [43,67]. Several QTL and association studies in P. pinaster have analyzed the molecular basis of different processes related to growth or wood quality traits [68-73], terpenes [74] and serotiny =-=[75]-=-. However, to date only association studies based on a few potential candidate genes [59,60] and one QTL study have analyzed the molecular basis of drought tolerance in P. pinaster [44]. The main obje...
1	Díaz L, Sáez-Laguna E, SánchezGómez D - Miguel, María, et al. (Show Context) Citation Context ...a and 1 x TBE and visualized in a 4300 DNA Analyzer (LI-COR Biosciences, Lincoln, NE, USA). Fragments were scored visually as codominant markers. SAMPL genotyping was performed as in de Miguel et al. =-=[81]-=- with several modifications. Preamplification was carried out using EcoRI + A / MseI + C primer combination. In order to identify the most informative selective primer combinations (those with a highe...
1	Ooijen JW: MapQTL 6.0, software for the mapping of quantitative trait loci in experimental populations of diploid species. Edited by Kiazma BV - Van - 2009 (Show Context) Citation Context ...sion and accuracy of QTL placement, QTL analyses were performed using the framework linkage maps. QTL detection was carried out using the regression algorithm implemented in the software MapQTL® v6.0 =-=[88]-=-. Interval mapping was applied followed by multiple QTL mapping (MQM) when more than one QTL was found for a trait. Analyses were performed using a mapping step size of one. The thresholds (95% and 99...
1	decoding the conifer giga-genome - Mackay, JFD (Show Context) Citation Context ...nization and evolution at a finer scale [27]. In addition, high density linkage maps can be used to position scaffolds along linkage groups contributing to the assembly of a reference genome sequence =-=[24,96]-=-. P. pinaster genome sequencing is currently in progress, and it should be noted that Oria6, the male progenitor of the mapping family, is the genotype from which the haploid line was selected and its...
1	Lázaro-Gimeno D, Sáez-Laguna E, Díaz L, Torralba L, Mendoza-Poudereux I, Segura J, Cervera M: Selection of haploid cell lines from megagametophyte cultures of maritime pine as a DNA source for massive sequencing of the species. Plant Cell Tiss Org Cult 20 - Arrillaga, Guevara, et al. (Show Context) Citation Context ...equencing is currently in progress, and it should be noted that Oria6, the male progenitor of the mapping family, is the genotype from which the haploid line was selected and its DNA used as template =-=[97]-=-. Table 4 Identified QTL in Gal1056, Oria6 and GxO maps (Continued) 3 Oria6 6 2.1 ch 9 - 34.3 0-43.3 0-68.7 Fv’Fm’S3LG6m GxO 29.1 6 3.7 ch 13.3 54.8 0-80 0-124.8 Fv’Fm’S3LG6i 7 4.5 gw 15.6 63.7 55...