Scariolo, F.; Palumbo, F.; Farinati, S.; Barcaccia, G. Pipeline to Design Inbred Lines and F1 Hybrids of Leaf Chicory (Radicchio) Using Male Sterility and Genotyping-by-Sequencing. Plants2023, 12, 1242.
Scariolo, F.; Palumbo, F.; Farinati, S.; Barcaccia, G. Pipeline to Design Inbred Lines and F1 Hybrids of Leaf Chicory (Radicchio) Using Male Sterility and Genotyping-by-Sequencing. Plants 2023, 12, 1242.
Scariolo, F.; Palumbo, F.; Farinati, S.; Barcaccia, G. Pipeline to Design Inbred Lines and F1 Hybrids of Leaf Chicory (Radicchio) Using Male Sterility and Genotyping-by-Sequencing. Plants2023, 12, 1242.
Scariolo, F.; Palumbo, F.; Farinati, S.; Barcaccia, G. Pipeline to Design Inbred Lines and F1 Hybrids of Leaf Chicory (Radicchio) Using Male Sterility and Genotyping-by-Sequencing. Plants 2023, 12, 1242.
Abstract
Chicory, a horticultural crop cultivated worldwide, presents many botanical varieties and local biotypes. Among these, Italian radicchio group cultivars of pure Cichorium intybus L. and interspecific hybrids with Cichorium endivia L., as the “Red of Chioggia” biotype which in turn includes several phenotypes. This study deals with a pipeline for 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 radicchio of Chioggia. Two thousand nine hundred fifty-three 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 1,131 and 1,071 coding sequences in chicory and endive, respectively. In parallel, 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, combining the genotype information of the core collection, the best ten 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 for understanding the potential application of RADseq in improving molecular breeding strategies aimed at the development of inbred lines and F1 hybrids in leaf chicory.
Keywords
chicory; endive; RADseq; male-sterility; molecular breeding; SNPs; inbred lines; F1 hybrids; predicted breeding value
Subject
Biology and Life Sciences, Biochemistry and Molecular Biology
Copyright:
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
