Genetical genomics identifies the genetic architecture for growth and weevil resistance in spruce

Building resiliency in conifer forests: Interior spruce crosses among weevil resistant and susceptible parents produce hybrids appropriate for multi-trait selection

Tree planting programs now need to consider climate change increasingly, therefore, the resistance to pests plays an essential role in enabling tree adaptation to new ranges through tree population movement. The weevil Pissodes strobi (Peck) is a major pest of spruces and substantially reduces lumber quality. We revisited a large Interior spruce provenance/progeny trial (2,964 genotypes, 42 families) of varying susceptibility, established in British Columbia. We employed multivariate mixed linear models to estimate covariances between, and genetic control of, juvenile height growth and resistance traits. We performed linear regressions and ordinal logistic regressions to test for impact of parental origin on growth and susceptibility to the pest, respectively. A significant environmental component affected the correlations between resistance and height, with outcomes dependent on families. Parents sourced from above 950 m a.s.l. elevation negatively influenced host resistance to attacks, probably due to higher P. engelmannii proportion. For the genetic contribution of parents sourced from above 1,200 m a.s.l., however, we found less attack severity, probably due to a marked mismatch in phenologies. This clearly highlights that interspecific hybrid status might be a good predictor for weevil attacks and delineates the boundaries of successful spruce population movement. Families resulting from crossing susceptible parents generally showed fast-growing trees were the most affected by weevil attacks. Such results indicate that interspecific 'hybrids' with a higher P. glauca ancestry might be genetically better equipped with an optimized resource allocation between defence and growth and might provide the solution for concurrent improvement in resistance against weevil attacks, whilst maintaining tree productivity.

UV-B-induced molecular mechanisms of stress physiology responses in the major northern Chinese conifer Pinus tabuliformis Carr

During their lifetimes, plants are exposed to different abiotic stress factors eliciting various physiological responses and triggering important defense processes. For UV-B radiation responses in forest trees, the genetics and molecular regulation remain to be elucidated. Here, we exposed Pinus tabuliformis Carr., a major conifer from northern China, to short-term high-intensity UV-B and employed a systems biology approach to characterize the early physiological processes and the hierarchical gene regulation, which revealed a temporal transition from primary to secondary metabolism, the buildup of enhanced antioxidant capacity and stress-signaling activation. Our findings showed that photosynthesis and biosynthesis of photosynthetic pigments were inhibited, while flavonoids and their related derivates biosynthesis, as well as glutathione and glutathione S-transferase mediated antioxidant processes, were enhanced. Likewise, stress-related phytohormones (jasmonic acid, salicylic acid and ethylene), kinase and reactive oxygen species signal transduction pathways were activated. Biological processes regulated by auxin and karrikin were, for the first time, found to be involved in plant defense against UV-B by promoting the biosynthesis of flavonoids and the improvement of antioxidant capacity in our research system. Our work evaluated the physiological and transcriptome perturbations in a conifer's response to UV-B, and generally, highlighted the necessity of a systems biology approach in addressing plant stress biology.

Combining QTL Mapping and Transcriptomics to Decipher the Genetic Architecture of Phenolic Compounds Metabolism in the Conifer White Spruce

Conifer forests worldwide are becoming increasingly vulnerable to the effects of climate change. Although the production of phenolic compounds (PCs) has been shown to be modulated by biotic and abiotic stresses, the genetic basis underlying the variation in their constitutive production level remains poorly documented in conifers. We used QTL mapping and RNA-Seq to explore the complex polygenic network underlying the constitutive production of PCs in a white spruce (Picea glauca) full-sib family for 2 years. QTL detection was performed for nine PCs and differentially expressed genes (DEGs) were identified between individuals with high and low PC contents for five PCs exhibiting stable QTLs across time. A total of 17 QTLs were detected for eight metabolites, including one major QTL explaining up to 91.3% of the neolignan-2 variance. The RNA-Seq analysis highlighted 50 DEGs associated with phenylpropanoid biosynthesis, several key transcription factors, and a subset of 137 genes showing opposite expression patterns in individuals with high levels of the flavonoids gallocatechin and taxifolin glucoside. A total of 19 DEGs co-localized with QTLs. Our findings represent a significant step toward resolving the genomic architecture of PC production in spruce and facilitate the functional characterization of genes and transcriptional networks responsible for differences in constitutive production of PCs in conifers.

Functional and morphological evolution in gymnosperms: A portrait of implicated gene families

Gymnosperms diverged from their sister plant clade of flowering plants 300 Mya. Morphological and functional divergence between the two major seed plant clades involved significant changes in their reproductive biology, water-conducting systems, secondary metabolism, stress defense mechanisms, and small RNA-mediated epigenetic silencing. The relatively recent sequencing of several gymnosperm genomes and the development of new genomic resources have enabled whole-genome comparisons within gymnosperms, and between angiosperms and gymnosperms. In this paper, we aim to understand how genes and gene families have contributed to the major functional and morphological differences in gymnosperms, and how this information can be used for applied breeding and biotechnology. In addition, we have analyzed the angiosperm versus gymnosperm evolution of the pleiotropic drug resistance (PDR) gene family with a wide range of functionalities in plants' interaction with their environment including defense mechanisms. Some of the genes reviewed here are newly studied members of gene families that hold potential for biotechnological applications related to commercial and pharmacological value. Some members of conifer gene families can also be exploited for their potential in phytoremediation applications.

Multi-trait genomic selection for weevil resistance, growth, and wood quality in Norway spruce

Plantation-grown trees have to cope with an increasing pressure of pest and disease in the context of climate change, and breeding approaches using genomics may offer efficient and flexible tools to face this pressure. In the present study, we targeted genetic improvement of resistance of an introduced conifer species in Canada, Norway spruce (Picea abies (L.) Karst.), to the native white pine weevil (Pissodes strobi Peck). We developed single- and multi-trait genomic selection (GS) models and selection indices considering the relationships between weevil resistance, intrinsic wood quality, and growth traits. Weevil resistance, acoustic velocity as a proxy for mechanical wood stiffness, and average wood density showed moderate-to-high heritability and low genotype-by-environment interactions. Weevil resistance was genetically positively correlated with tree height, height-to-diameter at breast height (DBH) ratio, and acoustic velocity. The accuracy of the different GS models tested (GBLUP, threshold GBLUP, Bayesian ridge regression, BayesCπ) was high and did not differ among each other. Multi-trait models performed similarly as single-trait models when all trees were phenotyped. However, when weevil attack data were not available for all trees, weevil resistance was more accurately predicted by integrating genetically correlated growth traits into multi-trait GS models. A GS index that corresponded to the breeders' priorities achieved near maximum gains for weevil resistance, acoustic velocity, and height growth, but a small decrease for DBH. The results of this study indicate that it is possible to breed for high-quality, weevil-resistant Norway spruce reforestation stock with high accuracy achieved from single-trait or multi-trait GS.

A molecular and genomic reference system for conifer defence against insects

Insect pests are part of natural forest ecosystems contributing to forest rejuvenation but can also cause ecological disturbance and economic losses that are expected to increase with climate change. The white pine or spruce weevil (Pissodes strobi) is a pest of conifer forests in North America. Weevil-host interactions with various spruce (Picea) species have been explored as a genomic and molecular reference system for conifer defence against insects. Interactions occur in two major phases of the insect life cycle. In the exophase, adult weevils are free-moving and display behaviour of host selection for oviposition that is affected by host traits. In the endophase, insects live within the host where mobility and development from eggs to young adults are affected by a complex system of host defences. Genetic resistance exists in several spruce species and involves synergism of constitutive and induced chemical and physical defences that comprise the conifer defence syndrome. Here, we review conifer defences that disrupt the weevil life cycle and mechanisms by which trees resist weevil attack. We highlight molecular and genomic aspects and a possible role for the weevil microbiome. Knowledge of this conifer defence system is supporting forest health strategies and tree breeding for insect resistance.

Partial correlation analysis of transcriptomes helps detangle the growth and defense network in spruce

In plants, there can be a trade-off between resource allocations to growth vs defense. Here, we use partial correlation analysis of gene expression to make inferences about the nature of this interaction. We studied segregating progenies of Interior spruce subject to weevil attack. In a controlled experiment, we measured pre-attack plant growth and post-attack damage with several morphological measures, and profiled transcriptomes of 188 progeny. We used partial correlations of individual transcripts (expressed sequence tags, ESTs) with pairs of growth/defense traits to identify important nodes and edges in the inferred underlying gene network, for example, those pairs of growth/defense traits with high mutual correlation with a single EST transcript. We give a method to identify such ESTs. A terpenoid ABC transporter gene showed strongest correlations (P = 0.019); its transcript represented a hub within the compact 166-member gene-gene interaction network (P = 0.004) of the negative genetic correlations between growth and subsequent pest attack. A small 21-member interaction network (P = 0.004) represented the uncovered positive correlations. Our study demonstrates partial correlation analysis identifies important gene networks underlying growth and susceptibility to the weevil in spruce. In particular, we found transcripts that strongly modify the trade-off between growth and defense, and allow identification of networks more central to the trade-off.

Genotypes, Networks, Phenotypes: Moving Toward Plant Systems Genetics

One of the central goals in biology is to understand how and how much of the phenotype of an organism is encoded in its genome. Although many genes that are crucial for organismal processes have been identified, much less is known about the genetic bases underlying quantitative phenotypic differences in natural populations. We discuss the fundamental gap between the large body of knowledge generated over the past decades by experimental genetics in the laboratory and what is needed to understand the genotype-to-phenotype problem on a broader scale. We argue that systems genetics, a combination of systems biology and the study of natural variation using quantitative genetics, will help to address this problem. We present major advances in these two mostly disconnected areas that have increased our understanding of the developmental processes of flowering time control and root growth. We conclude by illustrating and discussing the efforts that have been made toward systems genetics specifically in plants.

Different Alleles of a Gene Encoding Leucoanthocyanidin Reductase (PaLAR3) Influence Resistance against the Fungus Heterobasidion parviporum in Picea abies

Despite the fact that fungal diseases are a growing menace for conifers in modern silviculture, only a very limited number of molecular markers for pathogen resistance have been validated in conifer species. A previous genetic study indicated that the resistance of Norway spruce (Picea abies) to Heterobasidion annosum s.l., a pathogenic basidiomycete species complex, is linked to a quantitative trait loci that associates with differences in fungal growth in sapwood (FGS) that includes a gene, PaLAR3, which encodes a leucoanthocyanidin reductase. In this study, gene sequences showed the presence of two PaLAR3 allelic lineages in P. abies. Higher resistance was associated with the novel allele, which was found in low frequency in the four P. abies populations that we studied. Norway spruce plants carrying at least one copy of the novel allele showed a significant reduction in FGS after inoculation with Heterobasidion parviporum compared to their half-siblings carrying no copies, indicating dominance of this allele. The amount of (+) catechin, the enzymatic product of PaLAR3, was significantly higher in bark of trees homozygous for the novel allele. Although we observed that the in vitro activities of the enzymes encoded by the two alleles were similar, we could show that allele-specific transcript levels were significantly higher for the novel allele, indicating that regulation of gene expression is responsible for the observed effects in resistance, possibly caused by differences in cis-acting elements that we observe in the promoter region of the two alleles.

Genetical genomics of Populus leaf shape variation

BACKGROUND

Leaf morphology varies extensively among plant species and is under strong genetic control. Mutagenic screens in model systems have identified genes and established molecular mechanisms regulating leaf initiation, development, and shape. However, it is not known whether this diversity across plant species is related to naturally occurring variation at these genes. Quantitative trait locus (QTL) analysis has revealed a polygenic control for leaf shape variation in different species suggesting that loci discovered by mutagenesis may only explain part of the naturally occurring variation in leaf shape. Here we undertook a genetical genomics study in a poplar intersectional pseudo-backcross pedigree to identify genetic factors controlling leaf shape. The approach combined QTL discovery in a genetic linkage map anchored to the Populus trichocarpa reference genome sequence and transcriptome analysis.

RESULTS

A major QTL for leaf lamina width and length:width ratio was identified in multiple experiments that confirmed its stability. A transcriptome analysis of expanding leaf tissue contrasted gene expression between individuals with alternative QTL alleles, and identified an ADP-ribosylation factor (ARF) GTPase (PtARF1) as a candidate gene for regulating leaf morphology in this pedigree. ARF GTPases are critical elements in the vesicular trafficking machinery. Disruption of the vesicular trafficking function of ARF by the pharmacological agent Brefeldin A (BFA) altered leaf lateral growth in the narrow-leaf P. trichocarpa suggesting a molecular mechanism of leaf shape determination. Inhibition of the vesicular trafficking processes by BFA interferes with cycling of PIN proteins and causes their accumulation in intercellular compartments abolishing polar localization and disrupting normal auxin flux with potential effects on leaf expansion.

CONCLUSIONS

In other model systems, ARF proteins have been shown to control the localization of auxin efflux carriers, which function to establish auxin gradients and apical-basal cell polarity in developing plant organs. Our results support a model where PtARF1 transcript abundance changes the dynamics of endocytosis-mediated PIN localization in leaf cells, thus affecting lateral auxin flux and subsequently lamina leaf expansion. This suggests that evolution of differential cellular polarity plays a significant role in leaf morphological variation observed in subgenera of genus Populus.

Prediction accuracies for growth and wood attributes of interior spruce in space using genotyping-by-sequencing

Background

Genomic selection (GS) in forestry can substantially reduce the length of breeding cycle and increase gain per unit time through early selection and greater selection intensity, particularly for traits of low heritability and late expression. Affordable next-generation sequencing technologies made it possible to genotype large numbers of trees at a reasonable cost.

Results

Genotyping-by-sequencing was used to genotype 1,126 Interior spruce trees representing 25 open-pollinated families planted over three sites in British Columbia, Canada. Four imputation algorithms were compared (mean value (MI), singular value decomposition (SVD), expectation maximization (EM), and a newly derived, family-based k-nearest neighbor (kNN-Fam)). Trees were phenotyped for several yield and wood attributes. Single- and multi-site GS prediction models were developed using the Ridge Regression Best Linear Unbiased Predictor (RR-BLUP) and the Generalized Ridge Regression (GRR) to test different assumption about trait architecture. Finally, using PCA, multi-trait GS prediction models were developed. The EM and kNN-Fam imputation methods were superior for 30 and 60% missing data, respectively. The RR-BLUP GS prediction model produced better accuracies than the GRR indicating that the genetic architecture for these traits is complex. GS prediction accuracies for multi-site were high and better than those of single-sites while multi-site predictability produced the lowest accuracies reflecting type-b genetic correlations and deemed unreliable. The incorporation of genomic information in quantitative genetics analyses produced more realistic heritability estimates as half-sib pedigree tended to inflate the additive genetic variance and subsequently both heritability and gain estimates. Principle component scores as representatives of multi-trait GS prediction models produced surprising results where negatively correlated traits could be concurrently selected for using PCA2 and PCA3.

Conclusions

The application of GS to open-pollinated family testing, the simplest form of tree improvement evaluation methods, was proven to be effective. Prediction accuracies obtained for all traits greatly support the integration of GS in tree breeding. While the within-site GS prediction accuracies were high, the results clearly indicate that single-site GS models ability to predict other sites are unreliable supporting the utilization of multi-site approach. Principle component scores provided an opportunity for the concurrent selection of traits with different phenotypic optima.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1597-y) contains supplementary material, which is available to authorized users.

Conservation and divergence of gene expression plasticity following c. 140 million years of evolution in lodgepole pine (Pinus contorta) and interior spruce (Picea glauca×Picea engelmannii)

Species respond to environmental stress through a combination of genetic adaptation and phenotypic plasticity, both of which may be important for survival in the face of climatic change. By characterizing the molecular basis of plastic responses and comparing patterns among species, it is possible to identify how such traits evolve. Here, we used de novo transcriptome assembly and RNAseq to explore how patterns of gene expression differ in response to temperature, moisture, and light regime treatments in lodgepole pine (Pinus contorta) and interior spruce (a natural hybrid population of Picea glauca and Picea engelmannii). We found wide evidence for an effect of treatment on expression within each species, with 6413 and 11,658 differentially expressed genes identified in spruce and pine, respectively. Comparing patterns of expression among these species, we found that 74% of all orthologs with differential expression had a pattern that was conserved in both species, despite 140 million yr of evolution. We also found that the specific treatments driving expression patterns differed between genes with conserved versus diverged patterns of expression. We conclude that natural selection has probably played a role in shaping plastic responses to environment in these species.

Extensive functional pleiotropy of REVOLUTA substantiated through forward genetics

In plants, genes may sustain extensive pleiotropic functional properties by individually affecting multiple, distinct traits. We discuss results from three genome-wide association studies of approximately 400 natural poplar (Populus trichocarpa) accessions phenotyped for 60 ecological/biomass, wood quality, and rust fungus resistance traits. Single-nucleotide polymorphisms (SNPs) in the poplar ortholog of the class III homeodomain-leucine zipper transcription factor gene REVOLUTA (PtREV) were significantly associated with three specific traits. Based on SNP associations with fungal resistance, leaf drop, and cellulose content, the PtREV gene contains three potential regulatory sites within noncoding regions at the gene's 3' end, where alternative splicing and messenger RNA processing actively occur. The polymorphisms in this region associated with leaf abscission and cellulose content are suggested to represent more recent variants, whereas the SNP associated with leaf rust resistance may be more ancient, consistent with REV's primary role in auxin signaling and its functional evolution in supporting fundamental processes of vascular plant development.

Network analysis reveals the relationship among wood properties, gene expression levels and genotypes of natural Populus trichocarpa accessions

High-throughput approaches have been widely applied to elucidate the genetic underpinnings of industrially important wood properties. Wood traits are polygenic in nature, but gene hierarchies can be assessed to identify the most important gene variants controlling specific traits within complex networks defining the overall wood phenotype. We tested a large set of genetic, genomic, and phenotypic information in an integrative approach to predict wood properties in Populus trichocarpa. Nine-yr-old natural P. trichocarpa trees including accessions with high contrasts in six traits related to wood chemistry and ultrastructure were profiled for gene expression on 49k Nimblegen (Roche NimbleGen Inc., Madison, WI, USA) array elements and for 28,831 polymorphic single nucleotide polymorphisms (SNPs). Pre-selected transcripts and SNPs with high statistical dependence on phenotypic traits were used in Bayesian network learning procedures with a stepwise K2 algorithm to infer phenotype-centric networks. Transcripts were pre-selected at a much lower logarithm of Bayes factor (logBF) threshold than SNPs and were not accommodated in the networks. Using persistent variables, we constructed cross-validated networks for variability in wood attributes, which contained four to six variables with 94-100% predictive accuracy. Accommodated gene variants revealed the hierarchy in the genetic architecture that underpins substantial phenotypic variability, and represent new tools to support the maximization of response to selection.

Populus trichocarpa cell wall chemistry and ultrastructure trait variation, genetic control and genetic correlations

The increasing ecological and economical importance of Populus species and hybrids has stimulated research into the investigation of the natural variation of the species and the estimation of the extent of genetic control over its wood quality traits for traditional forestry activities as well as the emerging bioenergy sector. A realized kinship matrix based on informative, high-density, biallelic single nucleotide polymorphism (SNP) genetic markers was constructed to estimate trait variance components, heritabilities, and genetic and phenotypic correlations. Seventeen traits related to wood chemistry and ultrastructure were examined in 334 9-yr-old Populus trichocarpa grown in a common-garden plot representing populations spanning the latitudinal range 44° to 58.6°. In these individuals, 9342 SNPs that conformed to Hardy-Weinberg expectations were employed to assess the genomic pair-wise kinship to estimate narrow-sense heritabilities and genetic correlations among traits. The range-wide phenotypic variation in all traits was substantial and several trait heritabilities were > 0.6. In total, 61 significant genetic and phenotypic correlations and a network of highly interrelated traits were identified. The high trait variation, the evidence for moderate to high heritabilities and the identification of advantageous trait combinations of industrially important characteristics should aid in providing the foundation for the enhancement of poplar tree breeding strategies for modern industrial use.