Cynara cardunculus L. (2n=2x=34), a member of the Asteraceae family, is native to the Mediterranean Basin and includes three taxa: globe artichoke (var. scolymus), cultivated cardoon (var. altilis) and their progenitor wild cardoon (var. sylvestris). The cultivated cardoon stands out for its high biomass production with limited agricultural inputs, making it an ideal candidate for sustainable agriculture. The availability of a high-quality genome sequence is crucial for QTL analysis, as it provides a reference framework for accurately mapping genetic markers and identifying genomic regions associated with traits of interest. We obtained a chromosome-scale genome assembly of the cultivated cardoon (Altilis 41 - ‘A41’) by Nanopore sequencing. A total of 63GB (58X coverage) of reads were generated, assembled with NextDenovo, and polished with Medaka. Overall, 332 contigs (N50=12.5 Mb) were scaffolded into 17 chromosomes using Hi-C, for a total genome size of 973.85 Mb. The genome annotation, obtained by applying Helixer and Braker-3 pipelines, revealed 31,581 protein-coding genes, with a BUSCO score of 97.9%. Based on our reference genome, QTL mapping for biomass related traits was perfomed in an F1 population derived from a cross between an highly heterozygous genotype of globe artichoke (Romanesco ‘C3’) and a cultivated cardoon (‘A41’). Low pass genotyping and genotype imputation were used to identify molecular markers for mapping QTLs onto the A41 genome. Overall, 23 genomic regions associated with biomass yield and distributed across 12 of the 17 chromosomes were spotted, spanning ~50 Mb (5% of the genome size). To improve candidate genes discovery, syntenic analyses among ~360 plant species were also performed, allowing the identification of syntenic QTLs (sQTLs). This study represents a significant advancement in understanding the genetic control of biomass production in C. cardunculus. Acknowledgments: This work was supported by project Prin 2022 20225HAJE7.
Exploiting the First High Chromosome Scale Genome of Cultivated Cardoon for Breeding Purposes
Gaccione L.;Martina M.;Lanteri S.;Vergnano E.;Portis E.;Barchi L.
2025-01-01
Abstract
Cynara cardunculus L. (2n=2x=34), a member of the Asteraceae family, is native to the Mediterranean Basin and includes three taxa: globe artichoke (var. scolymus), cultivated cardoon (var. altilis) and their progenitor wild cardoon (var. sylvestris). The cultivated cardoon stands out for its high biomass production with limited agricultural inputs, making it an ideal candidate for sustainable agriculture. The availability of a high-quality genome sequence is crucial for QTL analysis, as it provides a reference framework for accurately mapping genetic markers and identifying genomic regions associated with traits of interest. We obtained a chromosome-scale genome assembly of the cultivated cardoon (Altilis 41 - ‘A41’) by Nanopore sequencing. A total of 63GB (58X coverage) of reads were generated, assembled with NextDenovo, and polished with Medaka. Overall, 332 contigs (N50=12.5 Mb) were scaffolded into 17 chromosomes using Hi-C, for a total genome size of 973.85 Mb. The genome annotation, obtained by applying Helixer and Braker-3 pipelines, revealed 31,581 protein-coding genes, with a BUSCO score of 97.9%. Based on our reference genome, QTL mapping for biomass related traits was perfomed in an F1 population derived from a cross between an highly heterozygous genotype of globe artichoke (Romanesco ‘C3’) and a cultivated cardoon (‘A41’). Low pass genotyping and genotype imputation were used to identify molecular markers for mapping QTLs onto the A41 genome. Overall, 23 genomic regions associated with biomass yield and distributed across 12 of the 17 chromosomes were spotted, spanning ~50 Mb (5% of the genome size). To improve candidate genes discovery, syntenic analyses among ~360 plant species were also performed, allowing the identification of syntenic QTLs (sQTLs). This study represents a significant advancement in understanding the genetic control of biomass production in C. cardunculus. Acknowledgments: This work was supported by project Prin 2022 20225HAJE7.
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