Abstract
The recent introduction of next generation sequencing (NGS) technologies represents a major revolution in providing new tools for identifying the genes and/or genomic intervals controlling important traits for selection in breeding programs. In perennial fruit trees with long generation times and large sizes of adult plants, the impact of these techniques is even more important. High-throughput DNA sequencing technologies have provided complete annotated sequences in many important tree species. Most of the high-throughput genotyping platforms described are being used for studies of genetic diversity and population structure. Dissection of complex traits became possible through the availability of genome sequences along with phenotypic variation data, which allow to elucidate the causative genetic differences that give rise to observed phenotypic variation. Association mapping facilitates the association between genetic markers and phenotype in unstructured and complex populations, identifying molecular markers for assisted selection and breeding. Also, genomic data provide in silico identification and characterization of genes and gene families related to important traits, enabling new tools for molecular marker assisted selection in tree breeding. Deep sequencing of transcriptomes is also a powerful tool for the analysis of precise expression levels of each gene in a sample. It consists in quantifying short cDNA reads, obtained by NGS technologies, in order to compare the entire transcriptomes between genotypes and environmental conditions. The miRNAs are non-coding short RNAs involved in the regulation of different physiological processes, which can be identified by high-throughput sequencing of RNA libraries obtained by reverse transcription of purified short RNAs, and by in silico comparison with known miRNAs from other species. All together, NGS techniques and their applications have increased the resources for plant breeding in tree species, closing the former gap of genetic tools between trees and annual species.
Highlights
Breeding of tree species is a longer and time consuming process compared to annual species
The profusion of recent next generation sequencing (NGS)-based studies performed in trees, briefly outlined in this review, firstly indicates that the old promise of genomics to make gene approaches affordable to many non-model species is already a matter of fact, driven by technological and important economic improvements
DNA sequencing cost based on calculations performed by the National Human Genome Research Institute has decreased from about $5,000 per raw megabase in 2001 to $0.015 in 20159
Summary
Breeding of tree species is a longer and time consuming process compared to annual species. The long generation time impairs the development of crosses until the species overcome the juvenile period, being between 3 and 10 years depending on the species. The large size of trees makes it difficult to obtain large numbers of individuals for segregation families, and NGS Applied to Breeding Tree Species precludes the management of plants under greenhousecontrolled conditions. Some otherwise useful techniques aimed at identifying gene variants such as ‘tilling’ and ‘ecotilling’ can hardly be applied to trees. The identification and functional analysis of gene orthologs from model plants presents a bottleneck for efficient transformation and regeneration protocols in many of these species
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