Status of perennial tree germplasm resources in India and their utilization in the context of global genome sequencing efforts

Tree species are characterized by their perennial growth habit, woody morphology, long juvenile period phase, mostly outcrossing behaviour, highly heterozygosity genetic makeup, and relatively high genetic diversity. The economically important trees have been an integral part of the human life system due to their provision of timber, fruit, fodder, and medicinal and/or health benefits. Despite its widespread application in agriculture, industrial and medicinal values, the molecular aspects of key economic traits of many tree species remain largely unexplored. Over the past two decades, research on forest tree genomics has generally lagged behind that of other agronomic crops. Genomic research on trees is motivated by the need to support genetic improvement programmes mostly for food trees and timber, and develop diagnostic tools to assist in recommendation for optimum conservation, restoration and management of natural populations. Research on long-lived woody perennials is extending our molecular knowledge and understanding of complex life histories and adaptations to the environment, enriching a field that has traditionally drawn its biological inference from a few short-lived herbaceous species. These concerns have fostered research aimed at deciphering the genomic basis of complex traits that are related to the adaptive value of trees. This review summarizes the highlights of tree genomics and offers some priorities for accelerating progress in the next decade.

Progress in physiological and genetic research concerning forest tree response to low temperature

Forest trees are a great model for physiological and genetic studies of plant resistance to unfavourable environmental conditions, since the same species can successfully acclimate at different latitudes. Modern biology, such as genomics, transcriptomics, proteomics, etc., significantly facilitates these studies and accelerates the acquisition of new knowledge. This allows for a more effective implementation of conservation measures and the renewal of forest ecosystems.This review contains information on the latest scientific achievements in the field of acclimatization and tolerance to abiotic stresses, such as cold and frost, of forest trees. There is no doubt that in the course of evolution forest trees developed a complex and dynamic mechanism for controlling the entry into the winter dormancy stage, which allows woody plants to successfully survive in cold and freezing conditions and is initiated long before the beginning of winter. Studying the function of individual genes in forest tree species, however, remains an incredibly difficult task due to large genomes, specific development as well as the lack of standard techniques and routine procedures. In recent years, similarities between the well-studied genetic response to low temperatures of the model plant Arabidopsis thaliana and forest trees have been identified, which produced meaningful analogies and allows for issues of functional genetics to be addressed more effectively.The main goal of this work was to show that findings from forest tree genomics can be effectively used as a tool for the reproduction and protection of important tree species through the identification of the predisposition of specific populations to climate change and their adaptive capacity.

The genomics of local adaptation in trees: Are we out of the woods yet?

There is substantial interest in uncovering the genetic basis of the traits underlying adaptive responses in tree species, as this information will ultimately aid conservation and industrial endeavors across populations, generations, and environments. Fundamentally, the characterization of such genetic bases is within the context of a genetic architecture, which describes the mutlidimensional relationship between genotype and phenotype through the identification of causative variants, their relative location within a genome, expression, pleiotropic effect, environmental influence, and degree of dominance, epistasis, and additivity. Here, we review theory related to polygenic local adaptation and contextualize these expectations with methods often used to uncover the genetic basis of traits important to tree conservation and industry. A broad literature survey suggests that most tree traits generally exhibit considerable heritability, that underlying quantitative genetic variation (QST) is structured more so across populations than neutral expectations (FST) in 69% of comparisons across the literature, and that single-locus associations often exhibit small estimated per-locus effects. Together, these results suggest differential selection across populations often acts on tree phenotypes underlain by polygenic architectures consisting of numerous small to moderate effect loci. Using this synthesis, we highlight the limits of using solely single-locus approaches to describe underlying genetic architectures and close by addressing hurdles and promising alternatives towards such goals, remark upon the current state of tree genomics, and identify future directions for this field. Importantly, we argue, the success of future endeavors should not be predicated on the shortcomings of past studies and will instead be dependent upon the application of theory to empiricism, standardized reporting, centralized open-access databases, and continual input and review of the community’s research.