Integrative genomics approaches validate PpYUC11-like as candidate gene for the stony hard trait in peach (P. persica L. Batsch) View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2018-05-18

AUTHORS

Marco Cirilli, Daniela Giovannini, Angelo Ciacciulli, Remo Chiozzotto, Stefano Gattolin, Laura Rossini, Alessandro Liverani, Daniele Bassi

ABSTRACT

BackgroundTexture is one of the most important fruit quality attributes. In peach, stony hard (SH) is a recessive monogenic trait (hd/hd) that confers exceptionally prolonged firm flesh to fully ripe fruit. Previous studies have shown that the SH mutation affects the fruit ability to synthesize appropriate amounts of indol-3-acetic acid (IAA), which orchestrates the ripening processes through the activation of system 2 ethylene pathway. Allelic variation in a TC microsatellite located within the first intron of PpYUC11-like (a YUCCA-like auxin-biosynthesis gene) has been recently proposed as the causal mutation of the SH phenotype.ResultsThe simple genetic determinism of the SH trait has been clarified through genome-wide association and LD analyses in a diverse set of accessions, restricting the hd locus to an interval of about 1.8 Mbp in chromosome 6. The comparison of fruit transcriptome data from non-SH (melting flesh) and SH accessions provided an expression patterns overview of the annotated transcripts within the hd locus, confirming the absence of PpYUC11-like expression in SH fruits. To explore further possible associations between genomic variants at the hd locus and the SH phenotype, re-sequencing data of the SH accession ‘D41–62’ were compared with several SH and non-SH accessions with different genetic backgrounds. A further step of validation was provided through the evaluation of variant-trait association in two bi-parental F2 populations issued from the SH accession ‘D41–62’ and a panel of advanced breeding selections, showing perfect co-segregation of the PpYUC11-like intron TC20 allele and the SH phenotype.ConclusionsIn this study, we provide a multi-level validation of the genetic control of the SH trait through the integration of genome-wide association mapping, transcriptome analysis and whole-genome resequencing data for SH and non-SH accessions, and marker-trait association in a panel of advanced breeding selections and segregating progenies. Collectively, our data confirm with high confidence the role of allelic variation at PpYUC11-like locus as the genetic determinant of the SH trait, opening interesting perspectives at both biological and applied research level. More... »

PAGES

88

Identifiers

URI

http://scigraph.springernature.com/pub.10.1186/s12870-018-1293-6

DOI

http://dx.doi.org/10.1186/s12870-018-1293-6

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1104089064

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/29776387


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121 selection
122 set
123 simple genetic determinism
124 step
125 stony
126 study
127 trait associations
128 traits
129 transcriptome analysis
130 transcriptome data
131 transcripts
132 validation
133 variants
134 variation
135 whole-genome resequencing data
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