X-ray computed tomography to decipher the genetic architecture of tree branching traits: oak as a case study

Song, Jialin; Brendel, Oliver; Bodénès, Catherine; Plomion, Christophe; Kremer, Antoine; Colin, Frédéric

doi:10.1007/s11295-016-1083-y

Cited by 7 publications

(5 citation statements)

References 44 publications

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“…Ballesta et al [43] reported that the pedigree-based heritability estimate of BQ in E. globulus at 4 years of age was less than 0.1. In other tree species, traits related to branch quality have been described to be moderately heritable [66,67]. In the present study, among the models based on SNP and HAP markers, BC had the highest predictive ability of branch quality.…”

Section: Discussionsupporting

confidence: 50%

SNP and Haplotype-Based Genomic Selection of Quantitative Traits in Eucalyptus globulus

Ballesta

Maldonado

Pérez‐Rodríguez

et al. 2019

Plants

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Eucalyptus globulus (Labill.) is one of the most important cultivated eucalypts in temperate and subtropical regions and has been successfully subjected to intensive breeding. In this study, Bayesian genomic models that include the effects of haplotype and single nucleotide polymorphisms (SNP) were assessed to predict quantitative traits related to wood quality and tree growth in a 6-year-old breeding population. To this end, the following markers were considered: (a) ~14 K SNP markers (SNP), (b) ~3 K haplotypes (HAP), and (c) haplotypes and SNPs that were not assigned to a haplotype (HAP-SNP). Predictive ability values (PA) were dependent on the genomic prediction models and markers. On average, Bayesian ridge regression (BRR) and Bayes C had the highest PA for the majority of traits. Notably, genomic models that included the haplotype effect (either HAP or HAP-SNP) significantly increased the PA of low-heritability traits. For instance, BRR based on HAP had the highest PA (0.58) for stem straightness. Consistently, the heritability estimates from genomic models were higher than the pedigree-based estimates for these traits. The results provide additional perspectives for the implementation of genomic selection in Eucalyptus breeding programs, which could be especially beneficial for improving traits with low heritability.

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Section: Discussionsupporting

confidence: 50%

SNP and Haplotype-Based Genomic Selection of Quantitative Traits in Eucalyptus globulus

Ballesta

Maldonado

Pérez‐Rodríguez

et al. 2019

Plants

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“…It had already been characterized at the genetic34,35 and genomic36,37 levels. This tree (used as a female parent) has also been crossed with accession A4 (used as a male parent) to generate a full-sib progeny for studies of the genetic architecture of quantitative traits38–47. A graft copy of “3P” was placed in darkness in July 2009, to trigger the release of as much starch as possible from second-flush leaves, in an in-house procedure that has been shown to improve the quality of DNA extraction from oak leaves.…”

Section: Methodsmentioning

confidence: 99%

Oak genome reveals facets of long lifespan

et al. 2018

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Oaks are an important part of our natural and cultural heritage. Not only are they ubiquitous in our most common landscapes but they have also supplied human societies with invaluable services, including food and shelter, since prehistoric times. With 450 species spread throughout Asia, Europe and America, oaks constitute a critical global renewable resource. The longevity of oaks (several hundred years) probably underlies their emblematic cultural and historical importance. Such long-lived sessile organisms must persist in the face of a wide range of abiotic and biotic threats over their lifespans. We investigated the genomic features associated with such a long lifespan by sequencing, assembling and annotating the oak genome. We then used the growing number of whole-genome sequences for plants (including tree and herbaceous species) to investigate the parallel evolution of genomic characteristics potentially underpinning tree longevity. A further consequence of the long lifespan of trees is their accumulation of somatic mutations during mitotic divisions of stem cells present in the shoot apical meristems. Empirical and modelling approaches have shown that intra-organismal genetic heterogeneity can be selected for and provides direct fitness benefits in the arms race with short-lived pests and pathogens through a patchwork of intra-organismal phenotypes. However, there is no clear proof that large-statured trees consist of a genetic mosaic of clonally distinct cell lineages within and between branches. Through this case study of oak, we demonstrate the accumulation and transmission of somatic mutations and the expansion of disease-resistance gene families in trees.

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“…Clones were obtained by grafting and established in a common garden in 1998 following a randomized block design (INRA experimental station of Bourran, latitude 44.332492°N, longitude 0.413993°E). For this study, we randomly selected 30 genotypes among 207 full-sibs that have been intensively used to study the genetic architecture of plants traits (Brendel et al 2008, Song et al 2017. In early May 2017, we collected one branch per tree with pole pruners.…”

Section: Oak Common Garden and Leaf Samplesmentioning

confidence: 99%

Oak genotype and phenolic compounds differently affect the performance of two insect herbivores with contrasting diet breadth

et al. 2019

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Research on plant-herbivore interactions has long recognized that plant genetic variation plays a central role in driving insect abundance and herbivory, as well as in determining plant defense. However, how plant genes influence herbivore feeding performances, and which plant defensive traits mediate these effects, remain poorly understood. Here we investigated the feeding performances of two insect leaf chewers with contrasting diet breadth (the generalist Lymantria dispar L. and the specialist Thaumetopoea processionea L.) on different genotypes of pedunculate oak (Quercus robur L.) and tested the role of leaf phenolics. We used leaves from four clones of 30 Q. robur full-sibs grown in a common garden to estimate the performance of both herbivores in laboratory feeding trials and to quantify the concentration of constitutive chemical defences (phenolic compounds). We found that tree genetics influenced leaf consumption by T. processionea but not by L. dispar. However genetic variation among trees did not explain growth rate variation in either herbivore nor in leaf phenolics. Interestingly, all phenolic compounds displayed a positive relationship with L. dispar growth rate, and leaf consumption by both herbivores displayed a positive relationship with the concentrations of condensed tannins, suggesting that highly defended leaves could induce a compensatory feeding response. While genetic variation in oaks did not explain herbivore growth rate, we found positive genetic correlations between the two herbivores for leaf consumption and digestion. Overall, we found that oak genotype and phenolic compounds partly and independently contribute to variability in herbivore performance. We challenged the current view of plant-insect interaction and provided little support to the idea that the effect of plant genotype on associated organisms is driven by plant defences. Together, our results point to the existence of genetically determined resistance traits in oaks whose effects differ between herbivores and motivate further research on mechanisms governing oak-herbivore interactions.

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X-ray computed tomography to decipher the genetic architecture of tree branching traits: oak as a case study

Cited by 7 publications

References 44 publications

SNP and Haplotype-Based Genomic Selection of Quantitative Traits in Eucalyptus globulus

SNP and Haplotype-Based Genomic Selection of Quantitative Traits in Eucalyptus globulus

Oak genome reveals facets of long lifespan

Oak genotype and phenolic compounds differently affect the performance of two insect herbivores with contrasting diet breadth

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