Mapping yield-associated QTL in globe artichoke

Portis, Ezio; Mauro, Rosario Paolo; Barchi, Lorenzo; Acquadro, Alberto; Mauromicale, Giovanni; Lanteri, Sergio

doi:10.1007/s11032-014-0061-z

Cited by 21 publications

(15 citation statements)

References 39 publications

(41 reference statements)

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“…The few genomics data currently available for this crop include a restriction site associated DNA sequencing (RADseq) genome analysis 10 and RNAseq data, which provided a reference transcriptome of 38 K unigenes 11 . In addition, several C. cardunculus genetic maps have been developed based on a two-way pseudo-testcross approach and QTL analyses for key breeding traits have been conducted 12 13 14 15 . The sequence of the chloroplast genome has recently been reported 16 .…”

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confidence: 99%

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

Scaglione

Reyes-Chin-Wo

Acquadro

et al. 2016

Sci Rep

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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.

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confidence: 99%

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

Scaglione

Reyes-Chin-Wo

Acquadro

et al. 2016

Sci Rep

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111

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“…DNA was extracted from young leaves of “Romanesco C3” and “Altilis 41” and the eight selected F 1 progeny following the Lanteri et al ( 2004 ) protocol, then used as template for amplification with a set of 217 SSR primer pairs (Acquadro et al, 2005 , 2009 ; Scaglione et al, 2009 ) which recognize loci distributed over all 17 C. cardunculus chromosomes (Portis et al, 2012 , 2014 ). Each 10 μL PCR was based on 7 ng template combined with 1x PCR buffer, 1 mM MgCl 2 , 0.5 U Taq DNA polymerase (Qiagen Inc., Venlo, Netherlands), 40 nM 5′-labeled (FAM, HEX, or TAMRA) forward primer, 40 nM unlabeled reverse primer and 0.2 mM dNTP.…”

Section: Methodsmentioning

confidence: 99%

Leaf polyphenol profile and SSR-based fingerprinting of new segregant Cynara cardunculus genotypes

et al. 2015

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The dietary value of many plant polyphenols lies in the protection given against degenerative pathologies. Their in planta role is associated with the host's defense response against biotic and abiotic stress. The polyphenol content of a given plant tissue is strongly influenced by the growing environment, but is also genetically determined. Plants belonging to the Cynara cardunculus species (globe artichoke and the cultivated and wild cardoon) accumulate substantial quantities of polyphenols mainly mono and di-caffeoylquinic acid (CQA) in their foliage. Transgressive segregation for CQA content in an F1 population bred from a cross between a globe artichoke and a cultivated cardoon led to the selection of eight segregants which accumulated more CQA in their leaves than did those of either of their parental genotypes. The selections were grown over two seasons to assess their polyphenol profile (CQAs, apigenin and luteolin derivatives and narirutin), and were also fingerprinted using a set of 217 microsatellite markers. The growing environment exerted a strong effect on polyphenol content, but two of the selections were able to accumulate up to an order of magnitude more CQA than either parent in both growing seasons. Since the species is readily vegetatively propagable, such genotypes can be straightforwardly exploited as a source of pharmaceutically valuable compounds, while their SSR-based fingerprinting will allow the genetic identity of clonally propagated material to be easily verified.

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“…Herbaceous 7-15 Genetic maps; marker arrays; QTLs for yield, biomass production, earliness Acquadro et al, 2005;Lanteri et al, 2006Lanteri et al, , 2012Angelini et al, 2009;Portis et al, 2009Portis et al, , 2012Portis et al, , 2014Sonnante et al, 2011;Scaglione et al, 2012;Mauromicale et al, 2014;Martin et al, 2015;Francaviglia et al, 2016 Agave (Agave spp.) Herbaceous 1-34 RAPD marker array; transcriptomic sequences Vega et al, 2001;Davis et al, 2011;Gross et al, 2013 Tall wheatgrass (Thino pyrum ponticum) Wang et al, 2010Wang et al, , 2014Pearson et al, 2015 Bamboo (Bambusa balcooa)…”

Section: Efficiency Of Light Interceptionmentioning

confidence: 99%

Marginal Lands to Grow Novel Bio-Based Crops: A Plant Breeding Perspective

Pancaldi

Trindade

2020

Front. Plant Sci.

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The biomass demand to fuel a growing global bio-based economy is expected to tremendously increase over the next decades, and projections indicate that dedicated biomass crops will satisfy a large portion of it. The establishment of dedicated biomass crops raises huge concerns, as they can subtract land that is required for food production, undermining food security. In this context, perennial biomass crops suitable for cultivation on marginal lands (MALs) raise attraction, as they could supply biomass without competing for land with food supply. While these crops withstand marginal conditions well, their biomass yield and quality do not ensure acceptable economic returns to farmers and cost-effective biomass conversion into bio-based products, claiming genetic improvement. However, this is constrained by the lack of genetic resources for most of these crops. Here we first review the advantages of cultivating novel perennial biomass crops on MALs, highlighting management practices to enhance the environmental and economic sustainability of these agro-systems. Subsequently, we discuss the preeminent breeding targets to improve the yield and quality of the biomass obtainable from these crops, as well as the stability of biomass production under MALs conditions. These targets include crop architecture and phenology, efficiency in the use of resources, lignocellulose composition in relation to bio-based applications, and tolerance to abiotic stresses. For each target trait, we outline optimal ideotypes, discuss the available breeding resources in the context of (orphan) biomass crops, and provide meaningful examples of genetic improvement. Finally, we discuss the available tools to breed novel perennial biomass crops. These comprise conventional breeding methods (recurrent selection and hybridization), molecular techniques to dissect the genetics of complex traits, speed up selection, and perform transgenic modification (genetic mapping, QTL and GWAS analysis, marker-assisted selection, genomic selection, transformation protocols), and novel high-throughput phenotyping platforms. Furthermore, novel tools to transfer genetic knowledge from model to orphan crops (i.e., universal markers) are also conceptualized, with the belief that their development will enhance the efficiency of plant breeding in orphan biomass crops, enabling a sustainable use of MALs for biomass provision.

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Mapping yield-associated QTL in globe artichoke

Cited by 21 publications

References 39 publications

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

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

Leaf polyphenol profile and SSR-based fingerprinting of new segregant Cynara cardunculus genotypes

Marginal Lands to Grow Novel Bio-Based Crops: A Plant Breeding Perspective

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