Contrasting relations between diversity of candidate genes and variation of bud burst in natural and segregating populations of European oaks

Derory, Jérémy; Scotti‐Saintagne, Caroline; Bertocchi, Evangelista; Dantec, Loı̈ck Le; Graignic, Noémie; Jauffres, A.; Casasoli, M.; Chancerel, Émilie; Bodénès, Catherine; Alberto, Florian J.; Kremer, Antoine

doi:10.1038/hdy.2009.170

Cited by 29 publications

(27 citation statements)

References 65 publications

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“…The highest differentiations were found investigating the genes ALDH, ERD (Part1), and IDH (Part 2) with values above 0.05 (Table 5). Derory et al (2010) found comparable results for SNPs analyzed in candidate genes and microsatellites for Q. petraea.…”

Section: Single Nucleotide Polymorphismssupporting

confidence: 61%

DNA sequence variation and development of SNP markers in beech (Fagus sylvatica L.)

Seifert¹,

Vornam²,

Finkeldey³

2012

Eur J Forest Res

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European beech (Fagus sylvatica L.) is one of the most important deciduous tree species in Central Europe. The potential of beech to adapt to climate change, higher temperatures, and less precipitation in the summer months is still unknown. Most studies in beech used microsatellite, AFLP (amplified fragment length polymorphism), or isozyme markers, which have only a restricted potential to analyze adaptation. Only few studies investigated genes probably involved in the adaptation to drought stress and bud phenology in beech. In this study, SNP (single nucleotide polymorphisms) markers were developed in order to analyze adaptation and their technical advantages compared to microsatellites and AFLPs were discussed. Partial sequences of ten candidate genes probably involved in drought stress and/or bud phenology were identified at the genomic level, and SNPs and indels (insertions/deletions) in coding and non-coding regions were analyzed. Plant material was sampled along a precipitation gradient in Germany. In total, 8,145 bp were sequenced and analyzed, 4,038 bp were located in exon and 4,107 bp in intron regions. 63 SNPs and 11 indels were detected, which are differently distributed over the studied gene regions. The nucleotide diversity ranged from 0 to 6.62 (p 9 10 -3 ) and is comparable to other tree species, whereas the mean nucleotide diversity (2.64) for F. sylvatica is comparatively low. These results will help to investigate the genetic basis of drought stress and bud burst and to conduct association mapping in natural populations. Furthermore, the detected SNPs can also be used for population genetic studies.

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Section: Single Nucleotide Polymorphismssupporting

confidence: 61%

DNA sequence variation and development of SNP markers in beech (Fagus sylvatica L.)

Seifert¹,

Vornam²,

Finkeldey³

2012

Eur J Forest Res

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“…Furthermore, this discrepancy increases as the number of loci involved in the trait increases. (Eveno et al, 2008), bud set in P. sylvestris (Pyhäjärvi et al, 2008) and Picea abies (Heuertz et al, 2006), phenological traits (bud burst, length of growing season and leaf abscission) and growth traits (height growth and diameter) in Populus tremula Luquez et al, 2007), bud burst in Quercus petraea (Derory et al, 2010) and growth, phenology and wood characters in Picea glauca (Namroud et al, 2008). In each case, the level of differentiation of the candidate genes was similar to that of neutral markers, whereas Q ST values were much higher.…”

Section: Discussionmentioning

confidence: 98%

Decoupling of differentiation between traits and their underlying genes in response to divergent selection

Kremer

Corre²

2011

Heredity

Self Cite

108

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We dissected the relationship between genetic differentiation (Q ST ) for a trait and its underlying genes (G STq , differentiation for a quantitative locus) in an evolutionary context, with the aim of identifying the conditions in which these two measurements are decoupled. We used two parameters (y B and y W ) scaling the contributions of inter-and intrapopulation allelic covariation between genes controlling the trait of interest. We monitored the changes in y B and y W , Q ST and G STq over successive generations of divergent and stabilizing selection, in simulations for an outcrossing species with extensive gene flow. The dynamics of these parameters are characterized by two phases. Initially, during the earliest generations, differentiation of the trait increases very rapidly and the principal and immediate driver of Q ST is y B . During subsequent generations, G STq increases steadily and makes an equal contribution to Q ST . These results show that selection first captures beneficial allelic associations at different loci at different populations, and then targets changes in allelic frequencies. The same patterns are observed when environmental change modifies divergent selection, as shown by the very rapid response of y B to the changes of selection regimes. We compare our results with previous experimental findings and consider their relevance to the detection of molecular signatures of natural selection.

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“…A strong expression QTL for ASI was also identified in the same region (Le Provost, unpublished), suggesting that transcript abundance is controlled in cis by polymorphism(s) within or in proximity of the gene, reinforcing its functional, expressional, and positional attributes. The meta-QTL analysis of Derory et al (2010) also showed how repeated phenotypic assessments either among clonal replicates or across years contribute to reduce substantially the confidence intervals of QTLs.…”

Section: Update On Qtl Detectionmentioning

confidence: 99%

“…In Europe, five mapping populations for oak (three Q. robur, one Q. petraea, and one Q. robur × Q. petraea) were produced (https://w3.pierroton.inra.fr/QuercusPortal/index.php). One (Q. robur) has been used to identify genomic regions involved in species differentiation (Scotti-Saintagne et al 2004a), to study the genetic architecture of quantitative traits (Saintagne et al 2004;Scotti-Saintagne et al 2004b;Scotti-Saintagne et al 2005;Gailing et al 2005;Casasoli et al 2006;Parelle et al 2007;Brendel et al 2008;Derory et al 2010), to map genes of interest (Porth et al 2005a) and to examine the level of macrosynteny with European chestnut Casasoli et al 2006) for which one FS mapping population and linkage map was produced.…”

Section: Available Mapping Populations In the Fagaceaementioning

confidence: 99%

“…Regarding stomatal density, Gailing et al (2008) detected 18 genomic regions on 10 linkage groups with a range of QTL effects varying from 3.6 to 15.9 % on male and female maps. Derory et al (2010) performed a meta-QTL analysis for bud burst assessed over 13 "year × site" observations. Initiation of the growing season, defined by bud flush date, has profound implications for adaptation of forest trees to their environment, with early flushing genotypes being susceptible to spring frost damage.…”

Section: Update On Qtl Detectionmentioning

confidence: 99%

See 1 more Smart Citation

Genomics of Fagaceae

Kremer

Abbott

Carlson

et al. 2012

Tree Genetics & Genomes

116

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An overview of recent achievements and development of genomic resources in the Fagaceae is provided, with major emphasis on the genera Castanea and Quercus. The Fagaceae is a large plant family comprising more than 900 species belonging to 8-10 genera. Using a wide range of molecular markers, population genetics and gene diversity surveys were the focus of many studies during the past 20 years. This work set the stage for investigations in genomics beginning in the early 1990s and facilitated the application of genetic and quantitative trait loci mapping approaches. Transferability of markers across species and comparative mapping have indicated tight macrosynteny between Quercus and Castanea. Omic technologies were more recently developed and the corresponding resources are accessible via electronic and physical repositories (expressed sequence tag sequences, single-nucleotide polymorphisms, candidate genes, cDNA clones, bacterial artificial chromosome (BAC) libraries) that have been installed in North America and Europe. BAC libraries and physical maps were also constructed in Castanea and Quercus and provide the necessary resources for full nuclear genome sequencing projects that are currently under way in Castanea mollissima (Chinese chestnut) and Quercus robur (pedunculate oak). Communicated by T. DrudgeA contribution to the Special Issue "The genomes of the giants: a walk through the forest of tree genomes" A. Kremer :

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Contrasting relations between diversity of candidate genes and variation of bud burst in natural and segregating populations of European oaks

Cited by 29 publications

References 65 publications

DNA sequence variation and development of SNP markers in beech (Fagus sylvatica L.)

DNA sequence variation and development of SNP markers in beech (Fagus sylvatica L.)

Decoupling of differentiation between traits and their underlying genes in response to divergent selection

Genomics of Fagaceae

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