Hybrid vigour - poplars play it cool

Non-Additive Gene Expression in Carbon and Nitrogen Metabolism Drives Growth Heterosis in Populus deltoides

Growth heterosis is crucial for Populus deltoides breeding, a key industrial-timber and ecological-construction tree species in temperate regions. However, the molecular mechanisms underlying carbon (C)-nitrogen (N) metabolism coordination in regulating growth heterosis remain unclear. Herein high-hybrids of P. deltoides exhibited high-parent heterosis and mid-parent heterosis in growth traits and key enzymes of C-N metabolism. In hybrids, gene expression patterns were mainly biased toward female parent. Parental contribution to growth heterosis in P. deltoides is differentiation, rather than absolute maternal or paternal dominance contributions. Parental genes were predominantly and dynamically inherited in a non-additive manner, mainly with dominant expression patterns. A total of 44 non-additive genes associated with photosynthetic C fixation, starch and sucrose metabolism, sucrose transport, photorespiration, and nitrogen metabolism coregulated growth heterosis by coordinating C-N metabolism. Growth-regulating factors 4 interacted with DELLA genes to promote growth by enhancing this coordination. Additionally, five critical genes were identified. Briefly, the above genes in high-hybrids improved photosynthesis and N utilisation by regulating carbohydrate accumulation and enzyme activity, while reducing respiratory energy consumption, thereby providing more energy for growth and promoting growth heterosis. Our findings offer new insights and theoretical basis for deep understanding genetic and molecular regulation mechanisms of tree heterosis and its application in precision hybrid breeding.

Comprehensive transcriptome and metabolome analysis deciphers the mechanism underlying rapid xylem growth in the dominant hybrid poplar QB3

MAIN CONCLUSION

Compared with its parents, the heterosis in growth of QB3 is primarily attributed to the upregulation of auxin and brassinosteroid-related genes, as well as the induced expression of numerous xylem and phloem synthesis genes, particularly the accumulation of lignin. Interestingly, QB3 significantly increased resistance to gray mold, which may be related to anthocyanin accumulation. Our findings illuminate the complex interplay of biological mechanisms that govern the regulation of wood growth and resistance. Poplar, as a fast-growing energy species widely distributed in the northern hemisphere, has important ecological and economic value. The hybridization of poplars is very common and often can bring to the progeny superior growth and resilience traits, but the molecular mechanism of heterosis remains to be studied. Through decades of crossbreeding work, a high-growth rate hybrid offspring named QinBai3 (QB3) was selected from P. alba × (P. alba × P. glandulosa), which provided an ideal model for investigating the molecular mechanism of heterosis. We found that the plant height, ground diameter, and xylem thickness of QB3 were much higher than those of I101 and 84 K. Through transcriptome and qRT-PCR analyses, we found that the expression levels of poplar regulatory genes associated with vegetative growth, brassinosteroid (BR), and auxin hormone signaling were significantly elevated in July compared to February. Meanwhile, compared to its parents, QB3 exhibited more specifically up-regulated genes in the processes of xylem and phloem synthesis, notably PalOPS and PalPRX52. However, in response to certain abiotic stresses, such as water deprivation and UV-B exposure, more down-regulated genes were identified. Metabolome analyses indicated that QB3 significantly increased the levels of lignin and anthocyanin, a result that aligns with the transcriptome data. Additionally, chemical assays confirmed the substantial accumulation of lignin and anthocyanin in QB3, suggesting that increased lignin accumulation may enhance the stem growth rate of QB3. Surprisingly, QB3 significantly increased resistance to Botrytis cinerea B05.10, which was accompanied by anthocyanin accumulation. In addition, our study offers detailed insights into the molecular mechanisms underlying rapid growth and stress resistance in hybrid poplar, thereby providing a new theoretical foundation and practical guidance for forest genetic breeding.

High-quality genome assembly enables prediction of allele-specific gene expression in hybrid poplar

Poplar (Populus) is a well-established model system for tree genomics and molecular breeding, and hybrid poplar is widely used in forest plantations. However, distinguishing its diploid homologous chromosomes is difficult, complicating advanced functional studies on specific alleles. In this study, we applied a trio-binning design and PacBio high-fidelity long-read sequencing to obtain haplotype-phased telomere-to-telomere genome assemblies for the 2 parents of the well-studied F1 hybrid "84K" (Populus alba × Populus tremula var. glandulosa). Almost all chromosomes, including the telomeres and centromeres, were completely assembled for each haplotype subgenome apart from 2 small gaps on one chromosome. By incorporating information from these haplotype assemblies and extensive RNA-seq data, we analyzed gene expression patterns between the 2 subgenomes and alleles. Transcription bias at the subgenome level was not uncovered, but extensive-expression differences were detected between alleles. We developed machine-learning (ML) models to predict allele-specific expression (ASE) with high accuracy and identified underlying genome features most highly influencing ASE. One of our models with 15 predictor variables achieved 77% accuracy on the training set and 74% accuracy on the testing set. ML models identified gene body CHG methylation, sequence divergence, and transposon occupancy both upstream and downstream of alleles as important factors for ASE. Our haplotype-phased genome assemblies and ML strategy highlight an avenue for functional studies in Populus and provide additional tools for studying ASE and heterosis in hybrids.

Morphological and Physiological Responses of Hybrid Aspen (Populus tremuloides Michx. × Populus tremula L.) Clones to Light In Vitro

Micropropagation of fast-growing tree genotypes such as the hybrid aspen (Populus tremuloides Michx. × Populus tremula L.) is increasing. The efficiency of micropropagation depends on the luminaires, hence luminescent electric diodes (LED), which emit light of a narrow spectrum, are gaining popularity. Mostly, different LEDs are combined to increase the photosynthetic efficiency. However, light also acts as an environmental signal, which triggers specific responses in plants, which are genotype specific, and regarding hybrid aspen, are likely affected by heterosis. In this study, morphological and physiological responses of clones of hybrid aspen with contrasting field performance to the spectral composition of illumination were studied in vitro. Among the 15 variables measured, area of leaves and concentration and ratio of chlorophyll a and b explained most of the variance (58.6%), thereby linking a specific combination of traits to productivity. These traits and their responses to light were affected by heterosis, as indicated by the clone-treatment interaction, particularly for the clone's moderate productivity. The top-performing clones were little sensitive to illumination due to efficient photosystems. Nevertheless, illumination with wider spectral composition had generally positive effects on plantlet performance. Accordingly, clone-specific illumination protocols and luminaries capable of it are advantageous for the efficiency of micropropagation of hybrid aspen.

Genetic Identification of Hybrid Walnuts (Juglans × intermedia Carr.) in Hungary, the Hidden Potential for Future Breeding

The question of the hybrid walnut (Juglans × intermedia Carr.) is still under debate in the Central European region. There is not simply just an underutilization, rather, even the existence of these hybrid forms is not broadly accepted. On the contrary, there is an intensive cross-breeding activity in the western part of Europe resulting in commercially available hybrid clones. In Hungary, several individuals have been reported with intermediate morphology from different old black walnut plantations. Due to the lacking information, a preliminary study was conducted in order to prove the difference of these selected trees and to test the hybrid state. For this purpose, DNA fingerprinting was used by applying 13 simple sequence repeat (SSR) markers for the identification of 22 hybrid genotypes selected from one study plot. A comparative analysis with a reference sample set of the ‘parental’ species and other known hybrids was performed as well. The genetic analysis resulted distinct, unique genotypes for all of the samples. Based on the genetic pattern, the analyzed hybrid group was clearly distinguishable from the other two walnut groups. The result of this study also highlights the hidden potential in walnut breeding in the Central European region. Future concepts concerning hybrid walnut utilization in plantation forestry, agroforestry or as breeding material are also discussed.

Distinctive Gene Expression Profiles and Effectors Consistent With Host Specificity in Two Formae Speciales of Marssonina brunnea

The knowledge on the host specificity of a pathogen underlying an interaction is becoming an urgent necessity for global warming. In this study, the gene expression profiles and the roles of effectors in host specificity were integrally characterized with two formae speciales, multigermtubi and monogermtubi, of a hemibiotrophic pathogen Marssonina brunnea when they were infecting respective susceptible poplar hosts. With a functional genome comparison referring to a de novo transcriptome of M. brunnea and Pathogen-Host Interaction database functional annotations, the multigermtubi strain showed abundant and significant differentially expressed unigenes (DEGs) (more than 40%) in colonizing the initial invasion stage and in the necrotrophic stage. The monogermtubi strain induced less than 10% of DEGs in the initial invasion stage but which abruptly increased to more than 80% DEGs in the necrotrophic stage. Both strains induced the least DEGs in the biotrophic stage compared to the initial invasion and necrotrophic stages. The orthologs of the effector genes Ecp6, PemG1, XEG1, ACE1, and Mg3LysM were exclusively induced by one of the two formae speciales depending on the infection stages. Some unigenes homologous to carbohydrate lytic enzyme genes, especially pectate lyases, were notably induced with multigermtubi forma specialis infection but not expressed in the monogermtubi forma specialis at an earlier infection stage. The extraordinary differences in the functional genome level between the two formae speciales of M. brunnea could be fundamental to exploring their host specificity determinant and evolution. This study also firstly provided the fungal transcriptome of the monogermtubi forma specialis for M. brunnea.