The State of the Art: Molecular Genomics and Marker-Assisted Breeding

Abstract

Focus on tree biotechnology reflects the challenges posed by the genetic attributes of trees. The genetic attributes of trees stand in stark contrast to those of domesticated annual crops. Trees typically have long generation times and are wind pollinated with out-crossing mating systems. Traditional tree breeding is a lengthy process that cannot efficiently capture nonadditive genetic variation, primarily because inbred lines would suffer from inbreeding depression. Clonal propagation of elite genotypes allows for the capture of both additive and nonadditive genetic variation, and the addition of transgenes can confer new or enhanced traits. The molecular analysis of plants often focused on the single gene level. But the recent technological advances have changed this paradigm. The way the genes and genetic information are organized within the genome and the methods of collecting and analyzing this information and the determination of their biological functionality are referred to as genomics. Genomic approaches are permeating every aspect of plant biology, and since they rely on DNA-coded information, they expand molecular analyses from a single to a multispecies level. Plant genomics is reversing the previous paradigm of identifying genes behind biological functions and instead focuses on finding biological functions behind genes. It also reduces the gap between phenotype and genotype. This introductory chapter overviews two main sections: first, the current understanding of genomes, their genetic structure at the inter- and intra-species level, and how whole genomes are sequenced; and second, on finding the biological and functional significance of DNA sequence. It is also worthwhile to note that these technologies, though extensively used in agricultural species, are only used in forest tree species research. Except for some tropical (avocado, mango, and papaya) and temperate (apple, Prunus, and Pyurus) fruit species, these ­techniques are not extensively used in other tree crops.