title: Application of Genomic Technologies to the Breeding of Trees.
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 providein silicoidentification 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 byin silicocomparison 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.
authors.affiliation: Instituto Valenciano de Investigaciones Agrarias Valencia, Spain.
authors.forename: Maria L
authors.initials: ML
authors.lastname: Badenes
authors.affiliation: Hortofruticulture Department, Agrifood Research and Technology Centre of AragonZaragoza, Spain; Genome Center, University of California, Davis, Davis, CAUSA.
authors.forename: Angel
authors.initials: A
authors.lastname: Fernández I Martí
authors.affiliation: Instituto Valenciano de Investigaciones Agrarias Valencia, Spain.
authors.forename: Gabino
authors.initials: G
authors.lastname: Ríos
authors.affiliation: Hortofruticulture Department, Agrifood Research and Technology Centre of Aragon Zaragoza, Spain.
authors.forename: María J
authors.initials: MJ
authors.lastname: Rubio-Cabetas
keywords: RNA-seq; association mapping; genome sequences; insertional mutant populations; next generation sequencing