THE GENOME SEQUENCE OF SOLANUM COMMERSONII DUN., A VALUABLE SOURCE OF RESISTANT GENES FOR POTATO BREEDING
Creators: name: Contaldi, Felice
Publisher: name: Università degli Studi di Napoli Federico II
Year: 2015

description: The tetraploid cultivated potato (Solanum tuberosum, 2n=4x=48) is the fourth most important crop for humans. Since the cultivated varieties are derived from a small number of genotypes, potato is characterized by a low genetic variability. Fortunately, it has about 200 wild tuber-bearing relatives that represent an incredible source of genetic variation and a reservoir of useful genes for the development of new varieties with improved resistance, nutrient content and productivity. However, several constrains hamper wild germplasm utilization. Among them, sexual incompatibility between wild and cultivated species and linkage drag make classical breeding methods time-consuming and laborious. In addition, few genomic resources ara available that can help breeders in their work of producing genetic variability and select superior clones. For all these reasons there has been an under-utilization of the potato genetic resources. The objective of this research was to develop new genomic tools that enable the expansion of the existing breeding strategies for an efficient exploitation of potato genetic resources.
Nowadays, sequencing technology combined with the availability of the S. tuberosum reference genome allows the characterization of the genetic variations affecting the cultivated potato. However, no genome sequence is available for a wild potato species. Therefore our study was addressed to sequence the genome of one of the most important tuber-bearing species, S. commersonii (2n=2x=24), that possesses several resistances to biotic and abiotic stresses. We de novo sequenced the genome of S. commersonii to 103x coverage using Illumina technology producing a 862 Mb genome. On the basis of sequence homology, 39,290 protein-coding genes were predicted and supported by transcript data and further annotation. We used the orthology and paralogy proteins relationships for the reconstruction of the complete collection of evolutionary histories of all S. commersonii protein-coding genes across a phylogeny of 12 sequenced plants. Interestingly, we discovered 8,578 S. commersonii-specific gene families lacking in S. tuberosum. HMM models and manual curation were used to annotate 2,523 non-redundant NBS-encoding R gene candidates, and comparison analysis with potato R-genes supported the idea that a locus rearrangement occurred during evolution. In order to find out the genetic determinants of S. commersonii resistance to low temperatures and capacity to cold harden, we focused on genes involved in abiotic stress response. Out of roughly 2,800 cold resistance genes, we found that 126 were unique in S. commersonii. To investigate further, a transcriptome analysis by using a custom microarray chip was carried out in two different experimental conditions. This allowed us to detect all the expressed genes involved in cold acclimation and to hypothesize the molecular dinamics at the basis of the different response to low temperature in S. commersonii vs. S. tuberosum. The experimental work carried out in this PhD reports the first genome sequence for a wild relative of the cultivated potato The genome sequence of S. commersonii has substantially increased our understanding on wild potatoes and these information might be used to overcome the limitations due to the low variability of domesticated germplasm. It will also offer the potential of better using wild relatives for potato breeding and evolutionary studies.