Pipeline to Design Inbred Lines and F1 Hybrids of Leaf Chicory (Radicchio) Using Male Sterility and Genotyping-by-Sequencing

Francesco Scariolo; Fabio Palumbo; Silvia Farinati; Gianni Barcaccia

doi:10.3390/plants12061242

Pipeline to Design Inbred Lines and F1 Hybrids of Leaf Chicory (Radicchio) Using Male Sterility and Genotyping-by-Sequencing

Plants (Basel). 2023 Mar 9;12(6):1242. doi: 10.3390/plants12061242.

Authors

Francesco Scariolo¹, Fabio Palumbo¹, Silvia Farinati¹, Gianni Barcaccia¹

Affiliation

¹ Department of Agronomy Food Natural resources Animals Environment, Campus of Agripolis, University of Padova, 35020 Legnaro, PD, Italy.

Abstract

Chicory, a horticultural crop cultivated worldwide, presents many botanical varieties and local biotypes. Among these, cultivars of the Italian radicchio group of the pure species Cichorium intybus L. and its interspecific hybrids with Cichorium endivia L.-as the "Red of Chioggia" biotype-includes several phenotypes. This study uses a pipeline to address the marker-assisted breeding of F1 hybrids: it presents the genotyping-by-sequencing results of four elite inbred lines using a RADseq approach and an original molecular assay based on CAPS markers for screening mutants with nuclear male sterility in the radicchio of Chioggia. A total of 2953 SNP-carrying RADtags were identified and used to compute the actual estimates of homozygosity and overall genetic similarity and uniformity of the populations, as well as to determine their genetic distinctiveness and differentiation. Molecular data were further used to investigate the genomic distribution of the RADtags among the two Cichorium species, allowing their mapping in 1131 and 1071 coding sequences in chicory and endive, respectively. Paralleling this, an assay to screen the genotype at the male sterility locus Cims-1 was developed to discriminate wild-type and mutant alleles of the causative gene myb80-like. Moreover, a RADtag mapped close to this genomic region proved the potential application of this method for future marker-assisted selection tools. Finally, after combining the genotype information of the core collection, the best 10 individuals from each inbred line were selected to compute the observed genetic similarity as a measure of uniformity as well as the expected homozygosity and heterozygosity estimates scorable by the putative progenies derived from selfing (pollen parent) and full-sibling (seed parent) or pair-wise crossing (F1 hybrids). This predictive approach was conducted as a pilot study to understand the potential application of RADseq in the fine tuning of molecular marker-assisted breeding strategies aimed at the development of inbred lines and F1 hybrids in leaf chicory.

Keywords: F1 hybrids; RADseq; SNPs; chicory; endive; inbred lines; male sterility; molecular breeding; predicted breeding value.

Grants and funding

This study was performed within the Agritech National Research Center and received funding from the European Union Next-Generation EU (Piano Nazionale di Ripresa e Resilienza (PNRR)—Missione 4 Componente 2, Investimento 1.4—D.D. 1032 17/06/2022, CN00000022. Our study represents an original paper related to both Spoke 1 “Plant, animal and microbial genetic resources and adaptation to climate changes” and Spoke 4 “Multifunctional and resilient agriculture and forestry systems for the mitigation of climate change risks”. In particular, it is a baseline for the fulfilment of milestones within Task 1.3.5 titled “Genome-wide strategies for fast-forward molecular breeding aimed at the assessment of genetic distinctiveness, uniformity and stability (DUS) and identity of pre-commercial varieties” and Task 4.1.1 titled “Next-generation genotyping and -omics technologies for the molecular prediction of multiple resilient traits in crop plants”. This manuscript reflects only the authors’ views and opinions, and neither the European Union nor the European Commission can be considered responsible for them.