| Summary: | <p>Abstract</p> <p>Background</p> <p>The EcoTILLING technique allows polymorphisms in target genes of natural populations to be quickly analysed or identified and facilitates the screening of genebank collections for desired traits. We have developed an EcoTILLING platform to exploit <it>Capsicum </it>genetic resources. A perfect example of the utility of this EcoTILLING platform is its application in searching for new virus-resistant alleles in <it>Capsicum </it>genus. Mutations in translation initiation factors (eIF4E, eIF(iso)4E, eIF4G and eIF(iso)4G) break the cycle of several RNA viruses without affecting the plant life cycle, which makes these genes potential targets to screen for resistant germplasm.</p> <p>Results</p> <p>We developed and assayed a cDNA-based EcoTILLING platform with 233 cultivated accessions of the genus <it>Capsicum</it>. High variability in the coding sequences of the <it>eIF4E </it>and <it>eIF(iso)4E </it>genes was detected using the cDNA platform. After sequencing, 36 nucleotide changes were detected in the CDS of <it>eIF4E </it>and 26 in <it>eIF(iso)4E</it>. A total of 21 <it>eIF4E </it>haplotypes and 15 <it>eIF(iso)4E </it>haplotypes were identified. To evaluate the functional relevance of this variability, 31 possible eIF4E/eIF(iso)4E combinations were tested against <it>Potato virus Y</it>. The results showed that five new <it>eIF4E </it>variants (<it>pvr2<sup>10</sup></it>, <it>pvr2<sup>11</sup></it>, <it>pvr2<sup>12</sup></it>, <it>pvr2<sup>13 </sup></it>and <it>pvr2<sup>14</sup></it>) were related to PVY-resistance responses.</p> <p>Conclusions</p> <p>EcoTILLING was optimised in different <it>Capsicum </it>species to detect allelic variants of target genes. This work is the first to use cDNA instead of genomic DNA in EcoTILLING. This approach avoids intronic sequence problems and reduces the number of reactions. A high level of polymorphism has been identified for initiation factors, showing the high genetic variability present in our collection and its potential use for other traits, such as genes related to biotic or abiotic stresses, quality or production. Moreover, the new <it>eIF4E </it>and <it>eIF(iso)4E </it>alleles are an excellent collection for searching for new resistance against other RNA viruses.</p>
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