Abstract
The breeding of forest trees is only a few decades old, and is a much more complicated, longer, and expensive endeavor than the breeding of agricultural crops. One breeding cycle for forest trees can take 20–30 years. Recent advances in genomics and molecular biology have revolutionized traditional plant breeding based on visual phenotype assessment: the development of different types of molecular markers has made genotype selection possible. Marker-assisted breeding can significantly accelerate the breeding process, but this method has not been shown to be effective for selection of complex traits on forest trees. This new method of genomic selection is based on the analysis of all effects of quantitative trait loci (QTLs) using a large number of molecular markers distributed throughout the genome, which makes it possible to assess the genomic estimated breeding value (GEBV) of an individual. This approach is expected to be much more efficient for forest tree improvement than traditional breeding. Here, we review the current state of the art in the application of genomic selection in forest tree breeding and discuss different methods of genotyping and phenotyping. We also compare the accuracies of genomic prediction models and highlight the importance of a prior cost-benefit analysis before implementing genomic selection. Perspectives for the further development of this approach in forest breeding are also discussed: expanding the range of species and the list of valuable traits, the application of high-throughput phenotyping methods, and the possibility of using epigenetic variance to improve of forest trees.
Highlights
The breeding of forest trees is only a few decades old, and is a much more complicated, longer, and expensive endeavor than the breeding of agricultural crops
Picea glauca was done using two iSelect Infinium (Illumina) single-nucleotide polymorphic marker (SNP) arrays: PgAS1 [59] and PgLM3 [57]. Both had a similar number of assayed SNPs (13,162 and 14,139, respectively), but the first array was mainly designed for population genetics and genetic association studies, whereas the second one was constructed for population genetics, genomic prediction, and linkage mapping purposes [77]
SNPs and Diversity Arrays Technology (DArT) markers were not compared on forest trees, but DArT was used on Eucalyptus grandis [41,43] and various eucalyptus species and hybrids [22], whereas DArTSeq was used on E. robusta [49] and E. urophylla × E. grandis [50]
Summary
In contrast to agricultural crops with their breeding history of centuries or even millennia, the history of forest tree breeding is relatively recent It was only in the late 1950s in the USA and Europe that the increasing demand for wood for construction, fuel, and paper production, and the reduction in natural forests generated the need for forest tree domestication using modern breeding methods [1]. Unlike annual crops and fruit trees, forest trees were practically not subject to domestication, which would have reduced their genetic diversity, and they represent wild populations. Their nearly absent pedigree makes it difficult to estimate their breeding values. Breeders are looking for new ways to improve the efficiency of forest breeding, i.e., to accelerate the selection of valuable genotypes
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