The tender stems (turions) of chicory (Cichorium intybus L. Catalogna group) are widely consumed as fresh or processed food in central and southern Italy. They are also known as 'puntarelle' and considered as elite groceries, cultivated as local varieties in Apulia and Lazio. The project CISIA has developed markers based on metabolic, transcriptional and allelic variations aimed to identity, traceability and valorisation of the Galatina and Molfettese Apulian landraces propagated by local enterprises. A de novo reference transcriptome was assembled using RNA of several organs (borne on young and adult plants of Galatina) and Illumina HiSeq2000 technology. Ca. 170M reads were generated (100bp paired-end) and assembled into 96,514 contigs of 1,168bp average length (N50 = 1,435bp). Among them, 68,260 (70.7%) showed significant similarity (Evalue <1e-5) to proteins in public databases (NCBI, TAIR, SwissProt, TrEMBL); 61,343 (63.6%) were classified based on gene ontology criteria and 13,536 (14.0%) were mapped onto 130 KEGG pathways. RNA-seq experiments (50bp single-end reads) were performed to collect gene transcriptional variation and polymorphism data using stems of Galatina and Molfettese grown in the two regions. Ca. 1,700 genes were found to maintain the differential expression patterns, suggesting that they may be putative markers as being feebly dependent on the environment. Polymorphic SSR (ca. 100) and high-quality SNPs (ca. 71,000) were effective to discriminate the two varieties, representing potential tools for fingerprinting and map enrichment in assisted breeding.
VALORISATION AND TRACEABILITY OF MADE IN ITALY PRODUCTS: TRANSCRIPTOME ASSEMBLY AND MARKER DEVELOPMENT OF 'PUNTARELLE' - CHICORY STEMS.
TESTONE G;MELE G;NICOLODI C;GONNELLA M;SERIO F;RENNA M;SOBOLEV A;CAPITANI D;MANNINA L;DI GIACOMO E;FRUGIS G;IANNELLI A;GIANNINO D
2014
Abstract
The tender stems (turions) of chicory (Cichorium intybus L. Catalogna group) are widely consumed as fresh or processed food in central and southern Italy. They are also known as 'puntarelle' and considered as elite groceries, cultivated as local varieties in Apulia and Lazio. The project CISIA has developed markers based on metabolic, transcriptional and allelic variations aimed to identity, traceability and valorisation of the Galatina and Molfettese Apulian landraces propagated by local enterprises. A de novo reference transcriptome was assembled using RNA of several organs (borne on young and adult plants of Galatina) and Illumina HiSeq2000 technology. Ca. 170M reads were generated (100bp paired-end) and assembled into 96,514 contigs of 1,168bp average length (N50 = 1,435bp). Among them, 68,260 (70.7%) showed significant similarity (Evalue <1e-5) to proteins in public databases (NCBI, TAIR, SwissProt, TrEMBL); 61,343 (63.6%) were classified based on gene ontology criteria and 13,536 (14.0%) were mapped onto 130 KEGG pathways. RNA-seq experiments (50bp single-end reads) were performed to collect gene transcriptional variation and polymorphism data using stems of Galatina and Molfettese grown in the two regions. Ca. 1,700 genes were found to maintain the differential expression patterns, suggesting that they may be putative markers as being feebly dependent on the environment. Polymorphic SSR (ca. 100) and high-quality SNPs (ca. 71,000) were effective to discriminate the two varieties, representing potential tools for fingerprinting and map enrichment in assisted breeding.I documenti in IRIS sono protetti da copyright e tutti i diritti sono riservati, salvo diversa indicazione.
