A Unique Mutation in a MYB Gene Cosegregates with the Nectarine Phenotype in Peach

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.

Genome-wide association study of 12 agronomic traits in peach

“…The fruit glabrous trait (nectarine) was recently associated with a recessive transposable element insertion in an MYB gene ( ppa026143m ) on scaffold_5, located in the 15,897,836 to 15,899,002 bp interval5. The present results revealed that the SNP that was mostly associated to fruit hairiness was located in the 17,576,893 bp of scaffold_5, with a −log 10 P value of 121.92 and a minor allele frequency of 0.22, corresponding to 1.7 Mb distance of ppa026143m (Table 1).…”

“…However, this may have only been possible in peach due to its low rate of polymorphism, resulting from self-pollination and grafting7. On the other hand, results for fruit hairiness and fruit flesh colour were not consistent with the results of gene identification obtained through reverse genetics45. This inconsistency might be due to fruit hairiness and fruit flesh colour being determined by the insertion of transposable elements45, a type of variation difficult to screen using next-generation sequencing with low sequence depth, and that cannot be identified by GWAS, using SNPs only.…”

“…Owing to its small genome and relatively short juvenile period, the peach is considered as a model species for comparative and functional genomic studies of the Rosaceae family2. So far, a number of linkage analyses to examine the genetic basis for peach fruit traits have been performed (www.rosaceae.org), but only a few genes were clearly identified as related to qualitative traits such as flesh adhesion3, texture3 and colour4 and fruit hairiness5.…”

SNP development for genetic diversity analysis in apricot

“…In addition, SNPs occur in both coding and non-coding regions of genes and may influence gene function by determining changes in the encoded amino acid (non-synonymous SNPs). These functional changes could be responsible for phenotypic changes in plants (Martínez-Gómez et al 2012;Adami et al 2013;Vendramin et al 2014). …”

“…Finally, SNP analysis via the Sequenom approach has been used in peach for the fine mapping of the genomic region controlling maturity date in scaffold 4 ) and of the G locus in scaffold 5 (Vendramin et al 2014). In both cases, this approach made it possible to identify a candidate gene responsible for these traits.…”