Developing a linkage map of C. cardunculus L. based on SRAP, SSR, SNP markers and localization of phenotypic traits

MARTIN, E.; ACQUAVIVA, E.J.; CRAVERO, V.; PORTIS, E.; SCAGLIONE, D; LANTERI, S.; COINTRY, E.

Viterbo

Congreso; 8th International Symposium on Artichoke, Cardoon and their wild relatives; 2012

In order to develop a linkage map for C. cardunculus L. and to compare this map to another one previously developed for the specie, a F1 mapping population of 81 individuals was generated from an intraspecific cross between a local genotype of wild cardoon (var. sylvestris) as female parent and the globe artichoke “Estrella del Sur FCA” (var. scolymus) as male parent,  using a two-way pseudo test cross strategy.  The population was genotyped using a combination of SRAP (Sequence Related Amplified Polymorphism), SSR (Simple Sequence Repeats), SNPs (Single Nucleotide Polymorphism)  and three phenotypic markers (“Color Head”, “Spine Leaf” and “Spine Head”).  A total of 421 segregating loci were identified (336 SRAP, 77 SSR, 5 SNPs and 3 phenotypic traits).  The female parent map consisted in 127 loci, spread over 15 linkage groups  (988.09 cM) with a mean inter-marker distance of  7.78 cM, while the male parent map resulted in 112 loci, distributed in 10 linkage groups (578.2 cM) with a mean inter-marker distance of 5.16 cM. The alignment between the female and male maps was made possible by intercross markers and determined  17 major linkage groups, corresponding to the haploid number of the specie (2n=34). The phenotypic traits “Color Head” and “Spine Leaf” were included in the cardoon map. “Color Head” was located in the 14 LG between C_Me5Em3.01 and C_CyEM_86 markers, whereas “Spine Leaf” was included in the 7 LG between C_Me1Em5.03 and C_M21Em5.01 markers. The trait “Spine Head” was included between  Acyltrans_1snp and Celms-07 markers in the 7 LG of the globe artichoke map. The presence of 48 loci (14 Celms, 30 CyEM and four SNPs targeting genes involved in the synthesis of caffeoylquinic acid) in common between both and the integrated SSR-based linkage map, previously developed for the specie, allowed the map alignment of the linkage groups. Moreover, a set of 17 new SSR markers was positioned in these maps (11 CyEM and six Celms). The map generated represents an important tool for the localization of interesting agronomic traits as well as, for molecular assisted selection breeding strategy and could be used to map integration and comparative assay.