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. 2014 Mar 3;9(3):e90574.
doi: 10.1371/journal.pone.0090574. eCollection 2014.

A unique mutation in a MYB gene cosegregates with the nectarine phenotype in peach

Elisa Vendramin  1 , Giorgio Pea  2 , Luca Dondini  3 , Igor Pacheco  4 , Maria Teresa Dettori  1 , Laura Gazza  1 , Simone Scalabrin  5 , Francesco Strozzi  2 , Stefano Tartarini  3 , Daniele Bassi  4 , Ignazio Verde  1 , Laura Rossini  6
Affiliations

A unique mutation in a MYB gene cosegregates with the nectarine phenotype in peach

Elisa Vendramin et al. PLoS One. .

Erratum in

  • PLoS One. 2014;9(10):e112032

Abstract

Nectarines play a key role in peach industry; the fuzzless skin has implications for consumer acceptance. The peach/nectarine (G/g) trait was described as monogenic and previously mapped on chromosome 5. Here, the position of the G locus was delimited within a 1.1 cM interval (635 kb) based on linkage analysis of an F2 progeny from the cross 'Contender' (C, peach) x 'Ambra' (A, nectarine). Careful inspection of the genes annotated in the corresponding genomic sequence (Peach v1.0), coupled with variant discovery, led to the identification of MYB gene PpeMYB25 as a candidate for trichome formation on fruit skin. Analysis of genomic re-sequencing data from five peach/nectarine accessions pointed to the insertion of a LTR retroelement in exon 3 of the PpeMYB25 gene as the cause of the recessive glabrous phenotype. A functional marker (indelG) developed on the LTR insertion cosegregated with the trait in the CxA F2 progeny and was validated on a broad panel of genotypes, including all known putative donors of the nectarine trait. This marker was shown to efficiently discriminate between peach and nectarine plants, indicating that a unique mutational event gave rise to the nectarine trait and providing a useful diagnostic tool for early seedling selection in peach breeding programs.

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Conflict of interest statement

Competing Interests: Dr. Simone Scalabrin, one of the authors of the manuscript, is currently affiliated with IGA Technology Services. This does not alter the authors' adherence to all PLOS ONE policies on sharing data and materials.

Figures

Figure 1
Figure 1. LG 5 CxA map around the G locus.
Linkage map obtained from analysis of the CxA F2 progeny. On the left side distances are indicated in cM; on the right the marker name, the physical position on Peach v1.0 and marker skewedness are reported. The peach/nectarine locus and the indelG marker are shown in bold.
Figure 2
Figure 2. Alignment of Quetta reads against a 635 kb interval of Peach v1.0 pseudomolecule 5.
Alignment results of reads, obtained by the resequencing of ‘Quetta’, against the peach genome region identified by the mapping interval in LG5 (from 15,853,006 bp to 16,488,104 bp). Top panel: intron-exon structure of ppa023143m. Central panel: plot of ‘Quetta’ paired-end distance (blue) and frequencies of single reads (yellow) at the ppa023143m locus. Bottom panel: blue lines are paired reads, green and red lines correspond to single reads with missing mate on the right and left side, respectively. The orange arrow points to the putative insertion inside exon 3 of ppa023143m.
Figure 3
Figure 3. Variant discovery in PpeMYB25 (annotation refinement of ppa023143m).
Five nectarine genotypes (‘Madonna di Agosto’, MdA; ‘Quetta’, Q; ‘Stark Red Gold’, SRG; ‘Goldmine’, G; ‘Ambra’, A) were analyzed to confirm the presence of the insertion within exon 3 of PpeMYB25. (A) Long-range amplification products reveal for all the accessions a fragment of about 7 kb (compared to 960 bp expected from the reference genome). (B) Double digestion results of the long-range PCR products show the same pattern for all the genotypes. (C) Position and structure of the Ty-copia retrotransposon deduced by the by the NGS analysis of ‘Quetta’ long-range amplicon. The insertion results in a truncated version of the R2R3-MYB protein.
Figure 4
Figure 4. Aminoacid alignment of the R2 and R3 MYB repeat sequences.
MYB domains (pfam00249) of peach PpeMYB25, cotton GhMYB25 (ACJ07153.1, [39]) and Antirrhinum AmMYBML1 (CAB433991.1, [54]) were aligned using the Muscle on line tool at EBI (http://www.ebi.ac.uk/Tools/msa/muscle/). Graphic display of the alignment was obtained using BoxShade (http://www.ch.embnet.org/software/BOX_form.html). Black shaded residues are identical, grey shaded residues are similar. Coordinates in the protein sequences are indicated.
Figure 5
Figure 5. Expression analysis of PpeMYB25 in peach and nectarine flower buds.
(A) The expression patterns of the R2R3-MYB gene were evaluated in ‘Contender’ [C] and ‘Ambra’ [A] buds at seven, five, four and one week before anthesis (WBA). Genomic DNA of the two cultivars was also tested as a control. The same samples were analyzed for expression of RPII as standard (B) and checked for DNA contamination (C).
Figure 6
Figure 6. Functional Marker indelG.
A marker assay was developed based on sequence information on the PpeMYB25 gene and the Ty1-copia insertion. Three primers were designed to discriminate peach and nectarine genotypes (A, B). A panel of nectarines including the putative donors of the trait, show a unique fragment of about 200 bp (C). A set of peaches, of diverse pedigree and origins (Table 1) (D), shows homozygous or heterozygous patterns.
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