Resequencing Piedmontese Pepper Ecotypes (RisEPP)

Pepper in Piedmont

The vegetable sector in Piedmont (North-West Italy) represents about 6% of the agricultural sector. Most of the farmers implement the agro-environmental measures of the Rural Development Program of the Piedmont Region, whch ensures the quality and safety of their productions. Among the vegetables grown in Piedmont, pepper (Capsicum annuum L.) play a key role and is grown over about 500 ha. Valuable local varieties, which are the result of secular selections for adaptation to specific ecological niches, are grown. They are morphologically recognizable and provide a product with organoleptic and sensorial qualities particularly appreciated by consumers. Although the berries of local pepper ecotypes gain high prices on the market, the local environmental stresses as well as biotic factors can consistently reduce their yields, thus they loss competitiveness in respect to commercial varieties and F 1 hybrids, which are spreading in cultivation.

Genomics and Trancriptomics

The recent availability of the C. annuum genome sequence makes it possible the re-sequencing of genotypes of the species and the identification, at high precision, of allelic and structural variants. On the other hand, RNA sequencing allows to directly estimate the level of gene expression in different tissues and cell types in response to biotic and abiotic stresses, as well as to trace genes involved in the response to such stresses.

Within the RisEPP Project, funded by the CRC (Cassa di Risparmio di Cuneo) Foundation, the following activities have been carried out:

Genome re-sequencing of four piedmontese pepper breeding lines of the local varieties 'Cuneo', 'Quadrato di Carmagnola', 'Corno di Carmagnola' and 'Tumaticot'. Each line is the results of selection programs carried out by the DISAFA (Plant Genetics and Breeding) in collaboration with the AGRION Foundation. Side by side the re-sequencing of targeted genomic regions in pepper genotypes showing resistance/tolerance to pathogens, causing a drastic reduction in production, has been carried out.

Transcriptomic analysis of changes induced by drought stress and recovery in the pepper breeding line 'Cuneo'. Plants of the breeding line were subjected in a controlled environment (green house) to water stress at three developmental stages (5th true leaf, flowering and fruit setting). Drought-stress was followed by 24 h of recovery. RNA-sequencing profiles of stressed/recovered and controls plants highlighted Differentially Expressed Genes (DE s), among which Trancription factors (TF) up and down regulated in both stressed and recovered plants at the different plant developmental stages.

Effect of drought stress on the quantity/quality of the production of the breeding line 'Cuneo'. The breding line was subjected to water stressed, in tunnel, at the experimental fields of the AGRION. The effect of the drought stress on morphological/productive trait as well as on the organoleptic quality of the berries was assessed.

Effect of the environment on the quantity/quality of the production and characterization of the Cuneo germplasm in cultivation. The breeding line of 'Cuneo' was grown in three farms in the province of Cuneo, located in areas characterized by different pedo-climatic conditions. This has made it possible to evaluate the interaction genotype x environment on the quantity and quality of the production. The latter was also compared with the one of the 'Cuneo' ecotype grown in each farm, with the goal to assess the correspondence of the material locally grown with the ideotype of the pepper 'Cuneo'. This activity has been carried out in collaboration with technical staff of the Confagricoltura di Cuneo and AGRION

First data on the four re-sequenced pepper genomes and RNAseq following drought stress induction have been presented in:

* mirror repository, data for the genome reconstruction were derived from http://peppergenome.snu.ac.kr/download.php

** the genome version is v1.6; the annotation version is v2.0