Clarifying Omics Concepts, Challenges, and Opportunities forPrunusBreeding in the Postgenomic Era

Abstract

The recent sequencing of the complete genome of the peach, together with the availability of new high-throughput genome, transcriptome, proteome, and metabolome analysis technologies, offers new possibilities for Prunus breeders in what has been described as the postgenomic era. In this context, new biological challenges and opportunities for the application of these technologies in the development of efficient marker-assisted selection strategies in Prunus breeding include genome resequencing using DNA-Seq, the study of RNA regulation at transcriptional and posttranscriptional levels using tilling microarray and RNA-Seq, protein and metabolite identification and annotation, and standardization of phenotype evaluation. Additional biological opportunities include the high level of synteny among Prunus genomes. Finally, the existence of biases presents another important biological challenge in attaining knowledge from these new high-throughput omics disciplines. On the other hand, from the philosophical point of view, we are facing a revolution in the use of new high-throughput analysis techniques that may mean a scientific paradigm shift in Prunus genetics and genomics theories. The evaluation of scientific progress is another important question in this postgenomic context. Finally, the incommensurability of omics theories in the new high-throughput analysis context presents an additional philosophical challenge.

Recent advancements to study flowering time in almond and other Prunus species

“…In addition, Silva et al (2005) described several Quantitative Trait Loci (QTLs) linked to flowering time in an interspecific F1 almond × peach progeny using a Candidate Gene approach (CG) in G1, G2, G3, G5, G6, and G7. More recently, different works using SSR (Simple Sequence Repeat) markers in a F1 population between a seedling of “Tardy Nonpareil” (“R1000”) × “Desmayo Largueta” (R×D), also confirmed the location of Lb in G4 and identified other QTLs to flowering time in G1, G6, and G7 (Sánchez-Pérez et al, 2007b; Martínez-Gómez et al, 2012) (Figure 1). In the first study (2007), carried out in this R×D population, the SSR UDP-96003 was located very close to the Lb gene in G4 of the map.…”

“…The recent release of the complete peach genome sequence (Verde et al, 2013) together with four almond genome sequences (Koepke et al, 2013) and the sweet cherry genome publicly available since 2013 (Carrasco et al, 2013), offer new possibilities for integrating genetic and genomic approaches to find new CGs for flowering time in perennial plants (Martínez-Gómez et al, 2012). …”

Metabolic profiling of a range of peach fruit varieties reveals high metabolic diversity and commonalities and differences during ripening

“…Thus, in order to realign breeding programs to satisfy these demands, it is essential to assess the metabolic diversity of peaches from different varieties. In this sense, all the available high-throughput technologies based on genome, transcriptome, proteome, and metabolome analysis offer new possibilities for Prunus breeders in the post-genomic era (Martínez-Gómez, Sánchez-Pérez, & Rubio, 2012).…”

SNP development for genetic diversity analysis in apricot

“…In addition, SNPs occur in both coding and non-coding regions of genes and may influence gene function by determining changes in the encoded amino acid (non-synonymous SNPs). These functional changes could be responsible for phenotypic changes in plants (Martínez-Gómez et al 2012;Adami et al 2013;Vendramin et al 2014). …”