Association genetics identifies a specifically regulated Norway spruce laccase gene, PaLAC5, linked to Heterobasidion parviporum resistance

Preselection of QTL markers enhances accuracy of genomic selection in Norway spruce

Genomic prediction (GP) or genomic selection is a method to predict the accumulative effect of all quantitative trait loci (QTLs) in a population by estimating the realized genomic relationships between the individuals and by capturing the linkage disequilibrium between markers and QTLs. Thus, marker preselection is considered a promising method to capture Mendelian segregation effects. Using QTLs detected in a genome-wide association study (GWAS) may improve GP. Here, we performed GWAS and GP in a population with 904 clones from 32 full-sib families using a newly developed 50 k SNP Norway spruce array. Through GWAS we identified 41 SNPs associated with budburst stage (BB) and the largest effect association explained 5.1% of the phenotypic variation (PVE). For the other five traits such as growth and wood quality traits, only 2 - 13 associations were observed and the PVE of the strongest effects ranged from 1.2% to 2.0%. GP using approximately 100 preselected SNPs, based on the smallest p-values from GWAS showed the greatest predictive ability (PA) for the trait BB. For the other traits, a preselection of 2000-4000 SNPs, was found to offer the best model fit according to the Akaike information criterion being minimized. But PA-magnitudes from GP using such selections were still similar to that of GP using all markers. Analyses on both real-life and simulated data also showed that the inclusion of a large QTL SNP in the model as a fixed effect could improve PA and accuracy of GP provided that the PVE of the QTL was ≥ 2.5%.

Genetic variation of Picea abies in response to the artificial inoculation of Heterobasidion parviporum

Norway spruce Picea abies is one of Europe's most economically important tree species. However, it is highly susceptible to the root rot fungus Heterobasidion parviporum. Climate change will benefit the pathogen as the tree host is weakened by, e.g., extended drought. Breeding can improve forest health, and several root rot genetic markers are suggested to improve the resistance of Norway spruce. This study aimed to compare the resistance (here defined as necrosis length) of Norway spruce families and genotypes against two strains of H. parviporum under different water availabilities. Our results show that the family and the genotype within the family have an impact on the necrosis length that is related to the aggressiveness of the fungal strains. Under low water conditions, the necrosis increased only in horizontal directions in phloem and sapwood. Similarly, the growth (seedling height) was not disturbed by abiotic stress (less water), indicating that the stress level (drought) was too low in this setting. The knowledge gained in this study could improve forest health in the changing climate by understanding the response of Norway spruce to pathogenic attacks under additional stress at the family level. This knowledge could be strategically used in forest breeding to improve the resistance of Norway spruce trees against root rot.

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The online version contains supplementary material available at 10.1007/s10342-023-01534-3.

The long road to bloom in conifers

More than 600 species of conifers (phylum Pinophyta) serve as the backbone of the Earth's terrestrial plant community and play key roles in global carbon and water cycles. Although coniferous forests account for a large fraction of global wood production, their productivity relies largely on the use of genetically improved seeds. However, acquisition of such seeds requires recurrent selection and testing of genetically superior parent trees, eventually followed by the establishment of a seed orchard to produce the improved seeds. The breeding cycle for obtaining the next generation of genetically improved seeds can be significantly lengthened when a target species has a long juvenile period. Therefore, development of methods for diminishing the juvenile phase is a cost-effective strategy for shortening breeding cycle in conifers. The molecular regulatory programs associated with the reproductive transition and annual reproductive cycle of conifers are modulated by environmental cues and endogenous developmental signals. Mounting evidence indicates that an increase in global average temperature seriously threatens plant productivity, but how conifers respond to the ever-changing natural environment has yet to be fully characterized. With the breakthrough of assembling and annotating the giant genome of conifers, identification of key components in the regulatory cascades that control the vegetative to reproductive transition is imminent. However, comparison of the signaling pathways that control the reproductive transition in conifers and the floral transition in Arabidopsis has revealed many differences. Therefore, a more complete understanding of the underlying regulatory mechanisms that control the conifer reproductive transition is of paramount importance. Here, we review our current understanding of the molecular basis for reproductive regulation, highlight recent discoveries, and review new approaches for molecular research on conifers.

Genome-Wide SNP Markers Accelerate Perennial Forest Tree Breeding Rate for Disease Resistance through Marker-Assisted and Genome-Wide Selection

The ecological and economic importance of forest trees is evident and their survival is necessary to provide the raw materials needed for wood and paper industries, to preserve the diversity of associated animal and plant species, to protect water and soil, and to regulate climate. Forest trees are threatened by anthropogenic factors and biotic and abiotic stresses. Various diseases, including those caused by fungal pathogens, are one of the main threats to forest trees that lead to their dieback. Genomics and transcriptomics studies using next-generation sequencing (NGS) methods can help reveal the architecture of resistance to various diseases and exploit natural genetic diversity to select elite genotypes with high resistance to diseases. In the last two decades, QTL mapping studies led to the identification of QTLs related to disease resistance traits and gene families and transcription factors involved in them, including NB-LRR, WRKY, bZIP and MYB. On the other hand, due to the limitation of recombination events in traditional QTL mapping in families derived from bi-parental crosses, genome-wide association studies (GWAS) that are based on linkage disequilibrium (LD) in unstructured populations overcame these limitations and were able to narrow down QTLs to single genes through genotyping of many individuals using high-throughput markers. Association and QTL mapping studies, by identifying markers closely linked to the target trait, are the prerequisite for marker-assisted selection (MAS) and reduce the breeding period in perennial forest trees. The genomic selection (GS) method uses the information on all markers across the whole genome, regardless of their significance for development of a predictive model for the performance of individuals in relation to a specific trait. GS studies also increase gain per unit of time and dramatically increase the speed of breeding programs. This review article is focused on the progress achieved in the field of dissecting forest tree disease resistance architecture through GWAS and QTL mapping studies. Finally, the merit of methods such as GS in accelerating forest tree breeding programs is also discussed.

Enhanced lignin synthesis and ecotypic variation in defense-related gene expression in response to shade in Norway spruce

During the growth season, northern forests in Sweden daily receive more hours of far-red (FR)-enriched light or twilight (shade) as compared to southern forests. Norway spruce (shade-tolerant) are adapted to latitudinal variation in twilight characterized by a northward increase in FR requirement to maintain growth. Shade is a stressful condition that affects plant growth and increases plant's susceptibility to pathogen attack. Lignin plays a central role in plant defense and its metabolism is regulated by light wavelength composition (light quality). In the current work, we studied regulation of lignin synthesis and defense-related genes (growth-defense trade-offs) in response to shade in Norway spruce. In most angiosperms, light promotes lignin synthesis, whereas shade decreases lignin production leading to weaker stem, which may make plants more disease susceptible. In contrast, enhanced lignin synthesis was detected in response to shade in Norway spruce. We detected a higher number of immunity/defense-related genes up-regulated in northern populations as compared to south ones in response to shade. Enhanced lignin synthesis coupled with higher defense-related gene expression can be interpreted as an adaptive strategy for better survival in northern populations. Findings will contribute to ensuring deployment of well-adapted genetic material and identifying tree families with enhanced disease resistance.

Genetic architecture behind developmental and seasonal control of tree growth and wood properties in Norway spruce

Genetic control of tree growth and wood formation varies depending on the age of the tree and the time of the year. Single-locus, multi-locus, and multi-trait genome-wide association studies (GWAS) were conducted on 34 growth and wood property traits in 1,303 Norway spruce individuals using exome capture to cover ~130K single-nucleotide polymorphisms (SNPs). GWAS identified associations to the different wood traits in a total of 85 gene models, and several of these were validated in a progenitor population. A multi-locus GWAS model identified more SNPs associated with the studied traits than single-locus or multivariate models. Changes in tree age and annual season influenced the genetic architecture of growth and wood properties in unique ways, manifested by non-overlapping SNP loci. In addition to completely novel candidate genes, SNPs were located in genes previously associated with wood formation, such as cellulose synthases and a NAC transcription factor, but that have not been earlier linked to seasonal or age-dependent regulation of wood properties. Interestingly, SNPs associated with the width of the year rings were identified in homologs of Arabidopsis thaliana BARELY ANY MERISTEM 1 and rice BIG GRAIN 1, which have been previously shown to control cell division and biomass production. The results provide tools for future Norway spruce breeding and functional studies.

Transcriptomic Reprogramming and Genetic Variations Contribute to Western Hemlock Defense and Resistance Against Annosus Root and Butt Rot Disease

Western hemlock (Tsuga heterophylla) is highly susceptible to Annosus root and butt rot disease, caused by Heterobasidion occidentale across its native range in western North America. Understanding molecular mechanisms of tree defense and dissecting genetic components underlying disease resistance will facilitate forest breeding and disease control management. The aim of this study was to profile host transcriptome reprogramming in response to pathogen infection using RNA-seq analysis. Inoculated seedlings were clearly grouped into three types: quantitative resistant (QR), susceptible (Sus), and un-infected (Uif), based on profiles of H. occidentale genes expressed in host tissues. Following de novo assembly of a western hemlock reference transcriptome with more than 33,000 expressed genes, the defensive transcriptome reprogramming was characterized and a set of differentially expressed genes (DEGs) were identified with gene ontology (GO) annotation. The QR seedlings showed controlled and coordinated molecular defenses against biotic stressors with enhanced biosynthesis of terpenoids, cinnamic acids, and other secondary metabolites. The Sus seedlings showed defense responses to abiotic stimuli with a few biological processes enhanced (such as DNA replication and cell wall organization), while others were suppressed (such as killing of cells of other organism). Furthermore, non-synonymous single nucleotide polymorphisms (ns-SNPs) of the defense- and resistance-related genes were characterized with high genetic variability. Both phylogenetic analysis and principal coordinate analysis (PCoA) revealed distinct evolutionary distances among the samples. The QR and Sus seedlings were well separated and grouped into different phylogenetic clades. This study provides initial insight into molecular defense and genetic components of western hemlock resistance against the Annosus root and butt rot disease. Identification of a large number of genes and their DNA variations with annotated functions in plant resistance and defense promotes the development of genomics-based breeding strategies for improved western hemlock resistance to H. occidentale.

Genome-wide association identifies candidate genes for drought tolerance in coast redwood and giant sequoia

Drought is a major limitation for survival and growth in plants. With more frequent and severe drought episodes occurring due to climate change, it is imperative to understand the genomic and physiological basis of drought tolerance to be able to predict how species will respond in the future. In this study, univariate and multitrait multivariate genome-wide association study methods were used to identify candidate genes in two iconic and ecosystem-dominating species of the western USA, coast redwood and giant sequoia, using 10 drought-related physiological and anatomical traits and genome-wide sequence-capture single nucleotide polymorphisms. Population-level phenotypic variation was found in carbon isotope discrimination, osmotic pressure at full turgor, xylem hydraulic diameter, and total area of transporting fibers in both species. Our study identified new 78 new marker × trait associations in coast redwood and six in giant sequoia, with genes involved in a range of metabolic, stress, and signaling pathways, among other functions. This study contributes to a better understanding of the genomic basis of drought tolerance in long-generation conifers and helps guide current and future conservation efforts in the species.

Achievements and Challenges of Genomics-Assisted Breeding in Forest Trees: From Marker-Assisted Selection to Genome Editing

Forest tree breeding efforts have focused mainly on improving traits of economic importance, selecting trees suited to new environments or generating trees that are more resilient to biotic and abiotic stressors. This review describes various methods of forest tree selection assisted by genomics and the main technological challenges and achievements in research at the genomic level. Due to the long rotation time of a forest plantation and the resulting long generation times necessary to complete a breeding cycle, the use of advanced techniques with traditional breeding have been necessary, allowing the use of more precise methods for determining the genetic architecture of traits of interest, such as genome-wide association studies (GWASs) and genomic selection (GS). In this sense, main factors that determine the accuracy of genomic prediction models are also addressed. In turn, the introduction of genome editing opens the door to new possibilities in forest trees and especially clustered regularly interspaced short palindromic repeats and CRISPR-associated protein 9 (CRISPR/Cas9). It is a highly efficient and effective genome editing technique that has been used to effectively implement targetable changes at specific places in the genome of a forest tree. In this sense, forest trees still lack a transformation method and an inefficient number of genotypes for CRISPR/Cas9. This challenge could be addressed with the use of the newly developing technique GRF-GIF with speed breeding.

Genomic basis of white pine blister rust quantitative disease resistance and its relationship with qualitative resistance

The genomic architecture and molecular mechanisms controlling variation in quantitative disease resistance loci are not well understood in plant species and have been barely studied in long-generation trees. Quantitative trait loci mapping and genome-wide association studies were combined to test a large single nucleotide polymorphism (SNP) set for association with quantitative and qualitative white pine blister rust resistance in sugar pine. In the absence of a chromosome-scale reference genome, a high-density consensus linkage map was generated to obtain locations for associated SNPs. Newly discovered associations for white pine blister rust quantitative disease resistance included 453 SNPs involved in wide biological functions, including genes associated with disease resistance and others involved in morphological and developmental processes. In addition, NBS-LRR pathogen recognition genes were found to be involved in quantitative disease resistance, suggesting these newly reported genes are qualitative genes with partial resistance, they are the result of defeated qualitative resistance due to avirulent races, or they have epistatic effects on qualitative disease resistance genes. This study is a step forward in our understanding of the complex genomic architecture of quantitative disease resistance in long-generation trees, and constitutes the first step towards marker-assisted disease resistance breeding in white pine species.

Combining transcriptomics and genetic linkage based information to identify candidate genes associated with Heterobasidion-resistance in Norway spruce

The Heterobasidion annosum s.l species complex comprises the most damaging forest pathogens to Norway spruce. We revisited previously identified Quantitative Trait Loci (QTLs) related to Heterobasidion-resistance in Norway spruce to identify candidate genes associated with these QTLs. We identified 329 candidate genes associated with the resistance QTLs using a gene-based composite map for Pinaceae. To evaluate the transcriptional responses of these candidate genes to H. parviporum, we inoculated Norway spruce plants and sequenced the transcriptome of the interaction at 3 and 7 days post inoculation. Out of 298 expressed candidate genes 124 were differentially expressed between inoculation and wounding control treatment. Interestingly, PaNAC04 and two of its paralogs in the subgroup III-3 of the NAC family transcription factors were found to be associated with one of the QTLs and was also highly induced in response to H. parviporum. These genes are possibly involved in the regulation of biosynthesis of flavonoid compounds. Furthermore, several of the differentially expressed candidate genes were associated with the phenylpropanoid pathway including a phenylalanine ammonia-lyase, a cinnamoyl-CoA reductase, a caffeoyl-CoA O-methyltransferase and a PgMYB11-like transcription factor gene. Combining transcriptome and genetic linkage analyses can help identifying candidate genes for functional studies and molecular breeding in non-model species.