Towards increasing genetic variability and improving fruit quality in peach using genomic and bioinformatic tools

• Autores: Octávio Manuel Ribeiro Serra
• Directores de la Tesis: Pere Arús Gorina (dir. tes.), Werner Howad (codir. tes.), Roser Tolrà Pérez (tut. tes.)
• Lectura: En la Universitat Autònoma de Barcelona ( España ) en 2017
• Idioma: español
• Tribunal Calificador de la Tesis: Antonio Barbadilla Prados (presid.), Yolanda Gogorcena Aoiz (secret.), Maria Margarida Moutinho Girao de Oliveira (voc.)
• Programa de doctorado: Programa de Doctorado en Biología y Biotecnología Vegetal por la Universidad Autónoma de Barcelona
• Materias:
  • Ciencias de la vida
    • Biología vegetal (botánica)
      • Genética vegetal
• Enlaces
  • Tesis en acceso abierto en:  TESEO  TDX 
• Resumen

  • Peach is a major fruit species, cultivated worldwide, with an outstanding adaptation to contrasting climate conditions, which world production has doubled in the last two decades. Increasing peach consumption requires enhancing fruit quality, a challenging objective for a fruit that has a short postharvest life. An important shortcoming for peach breeding is its low level of variability, narrowing the possibilities for its improvement. Other elements that may further condition peach production and breeding are climate change, the globalization of peach market and the changing eating habits of the population. Facing these challenges requires implementation of new strategies allowing a better exploitation of the variability that still exists inside the species and the introduction of new variability using other cultivated or wild relatives. In this work we aim to contribute in the development of such novel approaches. First we studied the genetic basis of the slow melting flesh (SMF) trait, characterized by the longer postharvest life of fruits, with higher firmness values after harvest than regular melting flesh (MF) peaches. SMF is present in some North American peach and nectarine cultivars, one of which (‘Big Top’), has become a reference for nectarine production in Spain. We studied two F1 populations using ‘Big Top’ as female parent, built linkage maps using the 9k peach SNP chip, and measured SMF. Quantitative trait loci (QTL) analysis allowed us to find two consistent QTLs for SMF co-localizing with maturity date QTLs in linkage group four (G4) and G5 that explained each >20% of phenotypic variability. The QTL on G5 was exclusive to ‘Big Top’, which can be the cause of its specific SMF behavior. In a second topic, we tested a new strategy, marker assisted introgression (MAI), to introduce new variability from exotic sources into cultivated perennial species in a short timeframe, using molecular markers to accelerate the process. As a side result we developed a set of introgression lines (ILs) of almond in the genetic background of peach, an optimal tool for genetic analysis of complex traits. In the final topic of this thesis we aimed to study the recombination process in wide crosses (almond × peach) in comparison with that of intraspecific crosses (peach), using resequence data of a cross between an almond × peach hybrid and its peach parent (‘Earlygold’). Understanding which factors control the occurrence of crossovers (COs) is critical to control the introgression process from an exotic donor to elite cultivated materials. We developed a bioinformatics pipeline to detect SNP and indel variants, in silico genotyped each individual, and determined the CO positions using the variants called. We found that the distribution of COs was heterogeneous in the genome, but similar in intra and interspecific meioses, and that a strong reduction of recombination occurred at the interspecific level, which we associated with DNA sequence divergence. We studied the CO regions, found some with high CO frequency (hotspots) and identified DNA motifs associated with these regions. Other recombination events such as noncrossovers (NCOs) were also detected for the hybrid meiosis about five times more frequently than COs. Finally, we associated low recombination in the hybrid with low pollen fertility, suggesting DNA sequence divergence as a possible cause for a gradual process of reproductive isolation in plants. Overall, our results supply new information on the inheritance of key commercial peach traits, tools for the fine analysis of complex characters, a breeding strategy for the enrichment of peach genome with valuable genes from other species, and data on how interspecific recombination proceeds. At the same time, we provide molecular tools to facilitate the translation of this knowledge into new and improved cultivars.