ABSTRACT
     Vegetables, including peppers, are continuously exposed to pathogen attack. 
However, viral diseases stand out as the main limiting factor for these crops. The best 
strategy to control these diseases is the identification of resistance genes and their 
employment to develop resistant varieties. To that end, it is important to exploit the 
variability present in these species that in the Capsicum genus is maintained at gene banks. 
However, to efficiently handle and exploit the resources is necessary to quantify and 
analyze inter- and intraspecific variability. In addition, any strategy to reduce the costs of 
the phenotyping process will be really advantageous.
     The main objective of this thesis is focused on the characterization and utilization of 
the genetic variability present in the cultivated species of the Capsicum genus (C. annuum, 
C. chinense, C. frutescens, C. baccatum and C. pubescens). Thus, this work expects to 
analyze and describe the distribution of the variability in these species, and to develop 
tools that allow efficient exploration and utilization of the variability maintained in gene 
banks. To that end, an EcoTILLING platform has been developed to allow efficient 
screening of the Capsicum accession collection from the COMAV gene bank. As a pilot 
experiment, this platform was explored to search for allelic variants of genes eIF4E and 
eIF(iso)4E, involved in resistance to viruses in pepper crops and other crops.
     This work is an example where EcoTILLING based on cDNA is both cost- and time-
effective: it involves different species of the genus Capsicum and only mutations in the 
coding sequences, the most interesting, are detected. The use of cDNA as starting material 
instead of genomic DNA had not been previously described. cDNA makes the 
amplification of candidate genes in a group of closely related species easier and reduces 
number of amplification cycles and enzymatic reactions per sample. 36 SNPs were 
detected in the 21 coding sequences of the eIF4E gene as well as 26 changes in the 17 
eIF(iso)4E sequences. This result shows that the pepper accession collection used is highly 
variable. Finally, 19 different eIF4E proteins and 10 eIF(iso)4E were identified. Of these, 
five eIF4E proteins and one eIF(iso)4E have been previously published, confirming that 
our EcoTILLING platform contains a good representation of Capsicum variability.
     A collection of 31 accessions that represents eIF4E/eIF(iso)4E allele combinations 
was mechanically inoculated against Potato virus Y (PVY) and Tobacco etch virus (TEV). 
Five new eIF4E alleles (pvr210, pvr211, pvr212, pvr213, pvr214) are related to resistance 
responses to PVY and TEV. The plants carrying any of these alleles do not show PVY-
F14K systemic infection. On the other hand, these alleles do not block TEV-7DA isolate 
replication, like the accessions with resistance alleles previously published (pvr1 or pvr22). 
However, the accessions with PVY-F14K resistance alleles showed a highly promising 
tolerant response against TEV-7DA.
     The new resistance alleles have non-conservative amino acid changes localized in 
regions I (exon 1) and II (exon 2) of the eIF4E protein. These changes seem to be 
responsible for the resistance against PVY-F14K and TEV-7DA. The eIF4E proteins coded 
for C. baccatum alleles pvr212, pvr213, pvr214 and C. chinense allele pvr211 have the same 
amino acid substitution, N65D. On the other hand, the combination of several amino acid 
changes in the eIF4E protein from C. chinense allele pvr210, could explain the responses 
caused by this allele.
     The study of the phylogenetic relationships between the species of the Capsicum 
genus is of great agronomic relevance. These species are potential variability sources to be 
used for C. annuum breeding. Ten microsatellites and four AFLP combinations were used 
to characterize 260 Capsicum accessions. The molecular analysis clearly verified the close 
relationships between C. chinense and C. frutescens. The results also showed that wild 
species C. cardenasii and C. eximium are molecularly indistinguishable, whereas C. 
baccatum and C. praetermissum are distinct species that form a very compact group. In 
this work, in contrast to other studies, C. chacoense is placed in the C. baccatum complex 
and C. tovarii is not clearly member of any Capsicum complex.
     In addition to the taxonomy analysis intraspecific differentiations were identified. C. 
baccatum and C. pubescens show a pair of genetic groups that correspond to Bolivian 
accessions and to the Peruvian-Ecuadorian accessions. Besides, the C. chinense accessions 
from Peru could be differentiated from the rest of the accessions. Different factors may 
have enhanced this genetic differentiation. In Bolivia, Ecuador and Peru, the use of these 
species fruits for self-consumption is related to cultural aspects. On the other hand, C. 
pubescens and C. baccatum are cultivated in mountainous regions of these countries, 
where access is complicated, making seed exchange more difficult. Thus, continuous 
selection and genetic isolation, may have caused the genetic differentiation observed. 
     In this study, accessions from Ecuador and Peru have shown high and similar 
diversity to Bolivian accessions. Being Bolivia an important center of diversity for the 
Capsicum genus, accessions from these countries may be a natural genetic heritage, which 
could be employed for the pepper breeding programs. The data on the distribution of 
genetic variability will increase management effectiveness of accessions, and will allow to 
redesign the Capsicum platform for analysis by EcoTILLING or new mutations isolation 
techniques.