Integrating evolutionary genomics of forest trees to inform future tree breeding amid rapid climate change.

Global climate change is leading to rapid and drastic shifts in environmental conditions, posing threats to biodiversity and nearly all life forms worldwide. Forest trees serve as foundational components of terrestrial ecosystems and play a crucial and leading role in combating and mitigating the adverse effects of extreme climate events, despite their own vulnerability to these threats. Therefore, understanding and monitoring how natural forests respond to rapid climate change is a key priority for biodiversity conservation. Recent progress in evolutionary genomics, driven primarily by cutting-edge multi-omics technologies, offers powerful new tools to address several key issues. These include precise delineation of species and evolutionary units, inference of past evolutionary histories and demographic fluctuations, identification of environmentally adaptive variants, and measurement of genetic load levels. As the urgency to deal with more extreme environmental stresses grows, understanding the genomics of evolutionary history, local adaptation, future responses to climate change, and conservation and restoration of natural forest trees will be critical for research at the nexus of global change, population genomics, and conservation biology. In this review, we explore the application of evolutionary genomics to assess the effects of global climate change using multi-omics approaches and discuss the outlook for breeding of climate-adapted trees.

The super-pangenome of Populus unveils genomic facets for its adaptation and diversification in widespread forest trees.

Understanding the underlying mechanisms and links between genome evolution and adaptive innovations stands as a key goal in evolutionary studies. Poplars, among the world's most widely distributed and cultivated trees, exhibit extensive phenotypic diversity and environmental adaptability. In this study, we present a genus-level super-pangenome comprising 19 Populus genomes, revealing the likely pivotal role of private genes in facilitating local environmental and climate adaptation. Through the integration of pangenomes with transcriptomes, methylomes, and chromatin accessibility mapping, we unveil that the evolutionary trajectories of pangenes and duplicated genes are closely linked to local genomic landscapes of regulatory and epigenetic architectures, notably CG methylation in gene-body regions. Further comparative genomic analyses have enabled the identification of 142 202 structural variants across species that intersect with a significant number of genes and contribute substantially to both phenotypic and adaptive divergence. We have experimentally validated a ∼180-bp presence/absence variant affecting the expression of the CUC2 gene, crucial for leaf serration formation. Finally, we developed a user-friendly web-based tool encompassing the multi-omics resources associated with the Populus super-pangenome (http://www.populus-superpangenome.com). Together, the present pioneering super-pangenome resource in forest trees not only aids in the advancement of breeding efforts of this globally important tree genus but also offers valuable insights into potential avenues for comprehending tree biology.

Intergrative metabolomic and transcriptomic analyses reveal the potential regulatory mechanism of unique dihydroxy fatty acid biosynthesis in the seeds of an industrial oilseed crop Orychophragmus violaceus.

BACKGROUND: Orychophragmus violaceus is a potentially important industrial oilseed crop due to the two 24-carbon dihydroxy fatty acids (diOH-FA) that was newly identified from its seed oil via a 'discontinuous elongation' process. Although many research efforts have focused on the diOH-FA biosynthesis mechanism and identified the potential co-expressed diacylglycerol acyltranferase (DGAT) gene associated with triacylglycerol (TAG)-polyestolides biosynthesis, the dynamics of metabolic changes during seed development of O. violaceus as well as its associated regulatory network changes are poorly understood. RESULTS: In this study, by combining metabolome and transcriptome analysis, we identified that 1,003 metabolites and 22,479 genes were active across four stages of seed development, which were further divided into three main clusters based on the patterns of metabolite accumulation and/or gene expression. Among which, cluster2 was mostly related to diOH-FA biosynthesis pathway. We thus further constructed transcription factor (TF)-structural genes regulatory map for the genes associated with the flavonoids, fatty acids and diOH-FA biosynthesis pathway in this cluster. In particular, several TF families such as bHLH, B3, HD-ZIP, MYB were found to potentially regulate the metabolism associated with the diOH-FA pathway. Among which, multiple candidate TFs with promising potential for increasing the diOH-FA content were identified, and we further traced the evolutionary history of these key genes among species of Brassicaceae. CONCLUSION: Taken together, our study provides new insight into the gene resources and potential relevant regulatory mechanisms of diOH-FA biosynthesis uniquely in seeds of O. violaceus, which will help to promote the downstream breeding efforts of this potential oilseed crop and advance the bio-lubricant industry.

Genomic survey of MYB gene family in six pearl millet (Pennisetum glaucum) varieties and their response to abiotic stresses.

In addition to their roles in developmental and metabolic processes, MYB transcription factors play crucial roles in plant defense mechanisms and stress responses. A comprehensive analysis of six pearl millet genomes revealed the presence of 1133 MYB genes, which can be classified into four phylogenetically distinct subgroups. The duplication pattern of MYB genes across the pearl millet genomes demonstrates their conserved and similar evolutionary history. Overall, MYB genes were observed to be involved in drought and heat stress responses, with stronger differential expressed observed in root tissues. Multiple analyses indicated that MYB genes mediate abiotic stress responses by modulating abscisic acid-related pathways, circadian rhythms, and histone modification processes. A substantial number of duplicated genes were determined to exhibit differential expression under abiotic stress. The consistent positive expression trend observed in duplicated gene pairs, such as PMA5G04432.1 and PMA2G00728.1, across various abiotic stresses suggests that duplicated MYB genes plays a key role in the evolution of adaptive responses of pearl millet to abiotic stresses.

Genomic insights into local adaptation and future climate-induced vulnerability of a keystone forest tree in East Asia.

Rapid global climate change is posing a substantial threat to biodiversity. The assessment of population vulnerability and adaptive capacity under climate change is crucial for informing conservation and mitigation strategies. Here we generate a chromosome-scale genome assembly and re-sequence genomes of 230 individuals collected from 24 populations for Populus koreana, a pioneer and keystone tree species in temperate forests of East Asia. We integrate population genomics and environmental variables to reveal a set of climate-associated single-nucleotide polymorphisms, insertion/deletions and structural variations, especially numerous adaptive non-coding variants distributed across the genome. We incorporate these variants into an environmental modeling scheme to predict a highly spatiotemporal shift of this species in response to future climate change. We further identify the most vulnerable populations that need conservation priority and many candidate genes and variants that may be useful for forest tree breeding with special aims. Our findings highlight the importance of integrating genomic and environmental data to predict adaptive capacity of a key forest to rapid climate change in the future.

Evaluation of genetic integrity of pearl millet seeds during aging by genomic-SSR markers.

Seed is an important way to store germplasm resources but its genetic integrity will decrease during long-term preservation. So, it's essential to update seeds according to the aging level of different species. Pearl millet [Cenchrus americanus (L.) Morrone syn., Pennisetum glaucum (L.) R. Br.] is a crucial forage grass, biofuel plant and important crops in the world bringing huge economic and ecological benefits. However, there is no report about the impact of aging on genetic integrity of its seeds. In this study, four genetic diversity indexes (the percentage of polymorphic bands, PPB; the effective number of alleles, Ne; the Nei's gene diversity index, H; the Shannon's information index, I) and 20 pairs of genomic-SSR primers were used to certify the optimal sample volume of pearl millet for molecular study and found that the best sample volume was 60. After the artificial aging test, the germination rate and four genetic diversity parameters (the number of alleles, Na; Ne; H; I) were used to evaluate the change of genetic integrity at different aging levels. The results showed that the germination rate and these four genetic diversity parameters declined with the increase of aging levels. Furthermore, when the germination rate of pearl millet seeds went down to 68.23%, a significant difference in genetic integrity was observed with unaged seeds. In conclusion, the optimal sample size of pearl millet was 60 and the critical point of germination rate to renew germplasm resources was 68.23% and these finds might contribute to the scientific study and the safe conservation of pearl millet.