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Development of diagnostic markers for selection of the subacid trait in peach

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Abstract

Peaches with low acidity are preferred in the market and this trait is usually selected in commercial breeding programs. A major gene (D/d) has been described for this character located on linkage group 5 of peach, where the low acid character is determined by the dominant D allele. In this paper, we analyze a collection of 231 varieties and 542 offspring to identify diagnostic markers for this character. The CPPCT040 single sequence repeat (SSR) is known to be tightly linked to D. We found that one of its alleles (193) is diagnostic for the subacid character and identified with high probability individuals with low acidity (titratable acidity <5.5 mg/l). The region around CPPCT040 was explored using 13 DNA fragments for a total of 5,297 bp, covering a length of 70.4 kbp of the peach genome. The sequenced fragments detected 19 single nucleotide polymorphisms (SNPs) and five indels. All subacid individuals shared a large haplotype (>24 kb) around CPPCT040, a region with higher than average SNPs between acid and subacid varieties. The CPPCT040 marker plus one of the SNPs identified (DH875) were used to genotype a collection of 542 seedlings, from different crosses expected to segregate for this character, which were phenotyped by tasting the fruit in the field. Data provided by both markers were always consistent and only 24 plants (4 %) did not fit the expectations. These markers and others that can be obtained from the haplotype identified can be readily used for marker-assisted selection in peach breeding.

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Acknowledgments

Funding for this research was partly provided from project AGL2012-40228-C02-01 from the Spanish Ministry of Economy and Knowledge. We thank Christian Fontich for providing data and plant material from the peach progenies of ASF-IRTA breeding program supported by Fruit Futur.

Data archiving statement

FASTA sequences of the subacid variety “Honey Glo” and the acid variety “Glenna” have been submitted to the NCBI GeneBank using the BankIt tool, with accession numbers KJ023869–KJ023894. Both varieties are homozygous at all loci. A table with the full list of accession numbers is presented in SM2.

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Authors and Affiliations

  1. IRTA. Centre for Research in Agricultural Genomics CSIC-IRTA-UAB-UB, Campus UAB, Cerdanyola del Vallès (Bellaterra), 08193, Barcelona, Spain

    I. Eduardo, E. López-Girona, W. Howad, P. Arús & M. J. Aranzana

  2. IRTA. Centre de Mas de Bover. Crta, De Reus - El Morell Km 4,5, 43120, Constantí, Tarragona, Spain

    I. BatlIe

  3. IRTA. Estació Experimental de Lleida, Parc de Gardeny, Edifici Fruitcentre, 25003, Lleida, Spain

    G. Reig & I. Iglesias

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  1. I. Eduardo
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  2. E. López-Girona
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  3. I. BatlIe
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  4. G. Reig
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  6. W. Howad
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  7. P. Arús
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  8. M. J. Aranzana
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Corresponding author

Correspondence to M. J. Aranzana.

Additional information

Communicated by A. G. Abbott

I. Eduardo and E. López-Girona contributed equally to this work.

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Fig. S1

Probability of finding CPPCT040193 (▲) and CPPCT040199 (□) alleles at different TA (g/l) values. (PDF 30 kb)

Fig. S2

Graphical summary of a 117.5 kbp region flanking the marker CPPCT040 (in black). Green arrows represent the transcripts annotated in the peach genome (http://www.rosaceae.org/ species/prunus_persica/genome_v1.0). The amplicons sequenced in 38 peach acid and subacid varieties are highlighted in red (monomorphic), blue (polymorphic) and pink (amplicon containing the SNP DS875 genotyped by HRM). (PDF 165 kb)

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Eduardo, I., López-Girona, E., BatlIe, I. et al. Development of diagnostic markers for selection of the subacid trait in peach. Tree Genetics & Genomes 10, 1695–1709 (2014). https://doi.org/10.1007/s11295-014-0789-y

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  • DOI: https://doi.org/10.1007/s11295-014-0789-y

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