SNP identification in two local C. cardunculus genotypes by GBS

CACCHIARELLI, PAOLO; ZAYAS, ALDANA; LESKOVAR, DANIEL; MARTIN EUGENIA

Rosario

Congreso; XIII Argentine Congress of Bioinformatics and Computational Biology (XIII CAB2C); 2023

A2B2C - SOIBIO - RIABIO

The genetic diversity analysis coupled with new generation sequencing technologies such as Genotypingby Sequences (GBS) provides a valuable tool for breeding programs of crops. The species Cynaracardunculus (2n=2X=34) includes three taxa: the globe artichoke, the domesticated cardoon, and the wildcardoon. The globe artichoke is traditionally cultivated for its immature flower heads worldwide,especially in Mediterranean countries, USA, Peru, and Argentina, whereas the wild cardoon, consideredthe ancestor of both domesticated forms, is cultivated for its biomass as energy crop.The objective of this study was to identify polymorphisms in two C. cardunculus genotypes by applyingGBS technology. The plant material was one genotype of Estrella del Sur FCA (ES) globe artichoke cultivarand a local genotype of wild cardoon (WC), both previously used as parental in local genetic maps of thespecies. Genomic DNA was isolated from young leaves of each genotype using DNeasy Plant mini Kit(QIAGEN) and quantified with Qubit 2.0 fluorometer (Thermo Fisher). DNA libraries were preparedaccording to a double restriction system and were sequenced using a Hiseq2500 (Illumina) at the TexasA&M Genomics and Bioinformatics Service. A total of 5.292.112 raw data was obtained for the ESgenotype and 6.581.974 raw data for WC. The raw reads obtained from both genotypes were cleanedand mapped on the globe artichoke reference genome V2 using fastp and BWA, respectively. Afterfiltering with fastp we obtained 3.033.318 reads from ES genotype and 3.749.488 reads from WC. Variantcalling was performed using lofreq tool and 25.128 SNP variants were detected in the ES genotype and25.352 SNPs in WC. The distribution of each type of SNP was analyzed and classified as transitions ortransversions.In conclusion, the GBS technology successfully revealed thousands of polymorphisms in C. cardunculusand can be used in the development of high-density genetic maps to assist breeding programs of thespecies