Rosario Paolo Mauro

Genetic mapping and identification of QTL for earliness in the globe artichoke/cultivated cardoon complex

BackgroundThe Asteraceae species Cynara cardunculus (2n = 2x = 34) includes the two fully cross-compatible domesticated taxa globe artichoke (var. scolymus L.) and cultivated cardoon (var. altilis DC). As both are out-pollinators and suffer from marked inbreeding depression, linkage analysis has focussed on the use of a two way pseudo-test cross approach.ResultsA set of 172 microsatellite (SSR) loci derived from expressed sequence tag DNA sequence were integrated into the reference C. cardunculus genetic maps, based on segregation among the F1 progeny of a cross between a globe artichoke and a cultivated cardoon. The resulting maps each detected 17 major linkage groups, corresponding to the species’ haploid chromosome number. A consensus map based on 66 co-dominant shared loci (64 SSRs and two SNPs) assembled 694 loci, with a mean inter-marker spacing of 2.5 cM. When the maps were used to elucidate the pattern of inheritance of head production earliness, a key commercial trait, seven regions were shown to harbour relevant quantitative trait loci (QTL). Together, these QTL accounted for up to 74% of the overall phenotypic variance.ConclusionThe newly developed consensus as well as the parental genetic maps can accelerate the process of tagging and eventually isolating the genes underlying earliness in both the domesticated C. cardunculus forms. The largest single effect mapped to the same linkage group in each parental maps, and explained about one half of the phenotypic variance, thus representing a good candidate for marker assisted selection.

The genome sequence of the outbreeding globe artichoke constructed de novo incorporating a phase-aware low-pass sequencing strategy of F1 progeny.

Globe artichoke (Cynara cardunculus var. scolymus) is an out-crossing, perennial, multi-use crop species that is grown worldwide and belongs to the Compositae, one of the most successful Angiosperm families. We describe the first genome sequence of globe artichoke. The assembly, comprising of 13,588 scaffolds covering 725 of the 1,084 Mb genome, was generated using ~133-fold Illumina sequencing data and encodes 26,889 predicted genes. Re-sequencing (30×) of globe artichoke and cultivated cardoon (C. cardunculus var. altilis) parental genotypes and low-coverage (0.5 to 1×) genotyping-by-sequencing of 163 F1 individuals resulted in 73% of the assembled genome being anchored in 2,178 genetic bins ordered along 17 chromosomal pseudomolecules. This was achieved using a novel pipeline, SOILoCo (Scaffold Ordering by Imputation with Low Coverage), to detect heterozygous regions and assign parental haplotypes with low sequencing read depth and of unknown phase. SOILoCo provides a powerful tool for de novo genome analysis of outcrossing species. Our data will enable genome-scale analyses of evolutionary processes among crops, weeds, and wild species within and beyond the Compositae, and will facilitate the identification of economically important genes from related species.

Selection of shade-adapted subterranean clover species for cover cropping in orchards.

The environmental side effects of intensive agriculture have underlined the need to develop sustainable farming systems. In particular, the use of cover cropping in orchards is a means of improving cash crop yield and of reducing the quantity of applied fertilisers. In the Mediterranean environment, subterranean clover species could be the best choice for cover cropping, but they are only poorly adapted to the heavily shaded conditions characteristic of modern high-density orchards. The plant traits needed to improve adaptation of subterranean clover are not well understood. Therefore, in a two-year experiment we studied the effects of four shading levels, of 0%, 40%, 60% and 90% reduction of photosynthetic active radiation, on phenology, growth and development of two subterranean clover species: Trifolium brachycalycinum cv. ‘Clare’ and T. Subterraneum ecotype ‘Ragalna’. Our results show that shading progressively delayed seedling emergence by up to 21 days, the initiation of flowering by up to 27 days, and the end of flowering by up to 25 days. Shading also lengthened the life cycle from 237 to 267 days. Shading reduced both soil cover by up to 38.2% and cover crop density by up to 39.7%. Shading lowered both the quantity of above-ground dry biomass by up to 820 g m−2 and photosynthetically active surface area by up to 213 cm2 plant−1. Trifolium brachycalycinum ‘Clare’ was more productive in terms of above-ground dry biomass yield, but T. Subterraneum ‘Ragalna’ was better adapted to shading in terms of rapid emergence, earliness and the time taken to achieve soil cover. These species differences suggest that the breeding targets for improving the adaptation of subterranean clover to heavy shading are the ability to maintain earliness and the capacity to quickly break down hard-seededness under conditions of partial shade. A rapid initial increase in photosynthetically active surface area is particularly needed for maximising light harvesting during the early growth period.

Clonal selection in a globe artichoke landrace: characterization of superior germplasm to improve cultivation in Mediterranean environments

R. P. MAURO, E. PORTIS*, S. LANTERI, A. LO MONACO AND G. MAUROMICALE Dipartimento di Scienze delle Produzioni Agrarie e Alimentari (DISPA) – Agronomical Sciences, University of Catania, via Valdisavoia 5, I-95123 Catania, Italy Dipartimento di Scienze Agrarie, Forestali ed Alimentari (DISAFA) – Plant Genetics and Breeding, University of Torino, via L. da Vinci 44, I-10095 Grugliasco, Torino, Italy