Bridging the genotype–phenotype gap for a Mediterranean pine by semi‐automatic crown identification and multispectral imagery

Santini, Filippo; Kefauver, Shawn C.; Araus, J. L.; Dios, Víctor Resco de; Martín-García, Saray; Grivet, Delphine; Voltas, Jordi

doi:10.1111/nph.16862

Cited by 17 publications

(20 citation statements)

References 85 publications

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“…Emerging phenotyping technologies might facilitate the assessment of the large number of traits and individuals required to improve our understanding of the adaptive patterns of populations (Alía & Majada, 2013). For example, using multispectral imagery, different traits related to transpiration and leaf water content have been recently assessed in P. halepensis (Santini et al., 2020). Spectral reflectance has been provided to be a useful tool to evaluate predawn water potential in oaks from dry ecosystems (Cotrozzi et al., 2017) and such information can be used to characterize provenances (Cavender‐Bares et al., 2016).…”

Section: Perspectives and Future Directionsmentioning

confidence: 99%

Adaptation of Mediterranean forest species to climate: Lessons from common garden experiments

et al. 2021

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1. Mediterranean ecosystems are biodiversity hotspots located between temperate mesic climates and semi-deserts and deserts. Mediterranean climates are characterized by a drought season but its length and severity can be highly variable across regions. In this review, we explored population genetic variation in functional traits and fitness in Mediterranean oak and pine species. We tested the hypothesis that increased drought tolerance has evolved as an adaptation to xeric and warm areas of the Mediterranean climate while increased competitive abilities have been favoured in more mesic regions, following a productivity-persistence trade-off within species.2. We first reviewed the literature and performed a meta-analysis of studies on Pinus sp. and Quercus sp. from Mediterranean climates, and then analysed a set of unpublished data from Spanish common garden experiments of species from the Mediterranean Basin, searching for evidence of trait genetic variation among populations, local adaptation and trait-environment associations.3. The meta-analysis showed that 82.9% (95% CI 75.7-89.4) of traits per study showed significant population genetic differentiation and that 52. 5% (35.6-69.2) of traits in studies with two or more Mediterranean environments exhibited population-by-environment interaction. Population differences in traits related to drought tolerance, cold hardiness and fitness were usually correlated with provenance precipitation and temperature gradients, suggesting that adaptation to different climatic regimes is an important process driving intraspecific genetic divergence. Within the Spanish trial network, however, predicted fitness functions based on climatic transfer distance failed to reveal significantly higher fitness of populations at experimental sites with climates closer to their provenances' ones.Neither the literature review nor the new analyses of the Spanish trial network provided evidence of a negative association between growth-and persistencerelated traits at the intraspecific level. 4. Synthesis. Population genetic differentiation in functional traits and fitness is common in Mediterranean species, driven, at least in part, by the adaptation to contrasting temperature and precipitation regimes. Because of experimental constraints or biological reality, our study failed to detect a trade-off between | 1023

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Section: Perspectives and Future Directionsmentioning

confidence: 99%

Adaptation of Mediterranean forest species to climate: Lessons from common garden experiments

et al. 2021

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“…Despite studies employing GWAS in some pine populations (Brown et al, 2003; De La Torre et al, 2019; Santini et al, 2021 Ding et al 2022), several challenges still remain that are related to the many SNPs associated with complex quantitative traits and the limited understanding of the molecular mechanisms by which these genetic variants are associated (Khatiwada et al, 2022). The identification of a gene affected by a QTL represents an enormous task, even more so in a species with a genome as large as LP.…”

Section: Discussionmentioning

confidence: 99%

Genome-wide association reveals novel insights into the molecular mechanisms regulating stem volume inPinus taeda

Bajay¹,

Aono²,

Francisco³

et al. 2022

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Pinus taeda(loblolly pine [LP]), a long-lived tree species, is one of the world's most economically important forest trees. Genetic improvement programs for loblolly and otherPinusspecies have focused on survival, biomass growth, resistance to diseases and pests, and stem shape. Among the growth traits, volume is the most widely considered in tree improvement programs. Despite the great interest in increasing volume growth, there are significant challenges to unraveling the molecular mechanisms behind this quantitative trait since it is presumably influenced by the action of large numbers of genes that may interact epistatically through unknown molecular mechanisms. The challenge of uncovering the genetic variants involved in variation for growth traits and their interaction is even greater in conifers such as LP because of the extremely large size and high complexity ofPinusgenomes. Here we present a comprehensive genetic analysis of LP involving genetic markers in association with volume (via genome-wide association studies [GWAS] and machine learning [ML]) to uncover pathways involved with good phenotypes for volume. The objective of this data integration was to provide a functional characterization of the genetic marker regions selected by GWAS and ML. We used a population of LP in the 2nd cycle of breeding and testing composed of full-sib progenies established at seven sites by the Cooperative Forest Genetics Research Program at the University of Florida. A total of 1,692 individuals were phenotyped and genotyped using sequence capture probes targeting putative genes. Probes were developed based on an elite germplasm transcriptome from LP. A total of 31,589 SNPs were identified and used to perform a GWAS through a multilocus mixed model. A precision core marker set with 7,864 SNPs selected through ML, i.e., feature selection (FS), was used for genomic selection (GS), providing a predictive accuracy (R Pearson coefficient) of approximately 0.79. For genome annotation and the construction of gene coexpression networks, three transcriptomes were assembled based on data from different pine species (Pinus taeda,Pinus elliottiiandPinus radiata). We selected genes associated with the target trait and assessed the cascade of related molecular mechanisms within coexpression networks. These results advance our understanding of the genetics influencing wood traits and reveal candidate genes for future functional studies as well as increase our understanding of quantitative genetics and the genomics of complex phenotypic variations in LP.

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“…(1) ln(VP) = 6.34 + 0.47T m + 0.96(P m ∕1000) − 0.22(Z∕1000) Santini et al (2020). We assumed constancy of phenotypic ranking in tree growth from age 15 onwards, as previously reported for P. halepensis (Sbay and Zas, 2018).…”

Section: Climate Variablesmentioning

confidence: 99%

Ground-Penetrating Radar as phenotyping tool for characterizing intraspecific variability in root traits of a widespread conifer

et al. 2021

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Background and Aim Drought is the main abiotic stress affecting Mediterranean forests. Root systems are responsible for water uptake, but intraspecific variability in tree root morphology is poorly understood mainly owing to sampling difficulties. The aim of this study was to gain knowledge on the adaptive relevance of rooting traits for a widespread pine using a non-invasive, high-throughput phenotyping technique. Methods Ground-Penetrating Radar (GPR) was used to characterize variability in coarse root features (depth, diameter and frequency) among populations of the Mediterranean conifer Pinus halepensis evaluated in a common garden. GPR records were examined in relation to aboveground growth and climate variables at origin of populations. Results Variability was detected for root traits among 56 range-wide populations categorized into 16 ecotypes. Root diameter decreased eastward within the Mediterranean basin. In turn, root frequency, but not depth and diameter, decreased following a northward gradient. Root traits also varied with climatic variables at origin such as the ratio of summer to annual precipitation, summer temperature or solar radiation. Particularly, root frequency increased with aridity, whereas root depth and diameter were maximum for ecotypes occupying the thermal midpoint of the species distribution range. Conclusion GPR is a high-throughput phenotyping tool that allows detection of intraspecific variation in root traits of P. halepensis and its dependencies on eco-geographic characteristics at origin, thereby informing on the adaptive relevance of root systems for the species. It is also potentially suited for inferring population divergence in resource allocation above- and belowground in forest genetic trials.

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Bridging the genotype–phenotype gap for a Mediterranean pine by semi‐automatic crown identification and multispectral imagery

Cited by 17 publications

References 85 publications

Adaptation of Mediterranean forest species to climate: Lessons from common garden experiments

Adaptation of Mediterranean forest species to climate: Lessons from common garden experiments

Genome-wide association reveals novel insights into the molecular mechanisms regulating stem volume inPinus taeda

Ground-Penetrating Radar as phenotyping tool for characterizing intraspecific variability in root traits of a widespread conifer

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