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Phenotypic and fine genetic characterization of the D locus controlling fruit acidity in peach.

Boudehri K, Bendahmane A, Cardinet G, Troadec C, Moing A, Dirlewanger E - BMC Plant Biol. (2009)

Bottom Line: We also constructed a peach BAC library of 52,000 clones with a mean insert size of 90 kb.The screening of the BAC library with markers tightly linked to D locus indicated that 1 cM corresponds to 250 kb at the vicinity of the D locus.We also constructed a peach BAC library of approximately 15x genome equivalent.

View Article: PubMed Central - HTML - PubMed

Affiliation: Institut National de la Recherche Agronomique/UR0419, Unité de Recherches sur les Espèces Fruitières, Centre de Bordeaux, Villenave d'Ornon, France. kboudehr@bordeaux.inra.fr

ABSTRACT

Background: Acidity is an essential component of the organoleptic quality of fleshy fruits. However, in these fruits, the physiological and molecular mechanisms that control fruit acidity remain unclear. In peach the D locus controls fruit acidity; low-acidity is determined by the dominant allele. Using a peach progeny of 208 F2 trees, the D locus was mapped to the proximal end of linkage group 5 and co-localized with major QTLs involved in the control of fruit pH, titratable acidity and organic acid concentration and small QTLs for sugar concentration. To investigate the molecular basis of fruit acidity in peach we initiated the map-based cloning of the D locus.

Results: In order to generate a high-resolution linkage map in the vicinity of the D locus, 1,024 AFLP primer combinations were screened using DNA of bulked acid and low-acid segregants. We also screened a segregating population of 1,718 individuals for chromosomal recombination events linked to the D locus and identified 308 individuals with recombination events close to D. Using these recombinant individuals we delimited the D locus to a genetic interval of 0.4 cM. We also constructed a peach BAC library of 52,000 clones with a mean insert size of 90 kb. The screening of the BAC library with markers tightly linked to D locus indicated that 1 cM corresponds to 250 kb at the vicinity of the D locus.

Conclusion: In the present work we presented the first high-resolution genetic map of D locus in peach. We also constructed a peach BAC library of approximately 15x genome equivalent. This fine genetic and physical characterization of the D locus is the first step towards the isolation of the gene(s) underlying fruit acidity in peach.

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Related in: MedlinePlus

F2 individuals screened with SCAR markers on agarose gel. (a) D-Scar0 on 3% agarose gel (b) D-Scar1 on 2% agarose (c) D-Scar3 digested with AccI, on 2% agarose gel (d) D-Scar6 on 3% agarose gel (e) D-Scar7 digested with MseI, on 3% agarose gel. Specific band for each allele is indicated (d for normally-acid and D for low-acid).
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Figure 3: F2 individuals screened with SCAR markers on agarose gel. (a) D-Scar0 on 3% agarose gel (b) D-Scar1 on 2% agarose (c) D-Scar3 digested with AccI, on 2% agarose gel (d) D-Scar6 on 3% agarose gel (e) D-Scar7 digested with MseI, on 3% agarose gel. Specific band for each allele is indicated (d for normally-acid and D for low-acid).

Mentions: Nine AFLP markers linked to the D locus were converted into simple codominant PCR-based markers. Four of them were codominant markers and five were dominant markers (Table 1). The codominant AFLP markers (pGC-AGG 430J-450F, pAC-AAC402J-412F and pGG-TAC215J-221F) were successfully converted into SCAR markers (D-Scar0, D-Scar1 and D-Scar2) and were confirmed as codominant markers (Table 2, Fig. 3). The codominant AFLP markers pTC-GTA218F-219J revealed a deletion of one nucleotide in 'Fantasia' compared to 'Ferjalou Jalousia®'. After sequencing the two alleles, three single nucleotide polymorphisms (SNPs) were detected; one of them was revealed after digestion with the restriction enzyme AccI and directly observed on agarose gel. This codominant Cleaved Amplified Polymorphism Sequence (CAPS) marker was named D-Scar3 (Fig. 3).


Phenotypic and fine genetic characterization of the D locus controlling fruit acidity in peach.

Boudehri K, Bendahmane A, Cardinet G, Troadec C, Moing A, Dirlewanger E - BMC Plant Biol. (2009)

F2 individuals screened with SCAR markers on agarose gel. (a) D-Scar0 on 3% agarose gel (b) D-Scar1 on 2% agarose (c) D-Scar3 digested with AccI, on 2% agarose gel (d) D-Scar6 on 3% agarose gel (e) D-Scar7 digested with MseI, on 3% agarose gel. Specific band for each allele is indicated (d for normally-acid and D for low-acid).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2698847&req=5

Figure 3: F2 individuals screened with SCAR markers on agarose gel. (a) D-Scar0 on 3% agarose gel (b) D-Scar1 on 2% agarose (c) D-Scar3 digested with AccI, on 2% agarose gel (d) D-Scar6 on 3% agarose gel (e) D-Scar7 digested with MseI, on 3% agarose gel. Specific band for each allele is indicated (d for normally-acid and D for low-acid).
Mentions: Nine AFLP markers linked to the D locus were converted into simple codominant PCR-based markers. Four of them were codominant markers and five were dominant markers (Table 1). The codominant AFLP markers (pGC-AGG 430J-450F, pAC-AAC402J-412F and pGG-TAC215J-221F) were successfully converted into SCAR markers (D-Scar0, D-Scar1 and D-Scar2) and were confirmed as codominant markers (Table 2, Fig. 3). The codominant AFLP markers pTC-GTA218F-219J revealed a deletion of one nucleotide in 'Fantasia' compared to 'Ferjalou Jalousia®'. After sequencing the two alleles, three single nucleotide polymorphisms (SNPs) were detected; one of them was revealed after digestion with the restriction enzyme AccI and directly observed on agarose gel. This codominant Cleaved Amplified Polymorphism Sequence (CAPS) marker was named D-Scar3 (Fig. 3).

Bottom Line: We also constructed a peach BAC library of 52,000 clones with a mean insert size of 90 kb.The screening of the BAC library with markers tightly linked to D locus indicated that 1 cM corresponds to 250 kb at the vicinity of the D locus.We also constructed a peach BAC library of approximately 15x genome equivalent.

View Article: PubMed Central - HTML - PubMed

Affiliation: Institut National de la Recherche Agronomique/UR0419, Unité de Recherches sur les Espèces Fruitières, Centre de Bordeaux, Villenave d'Ornon, France. kboudehr@bordeaux.inra.fr

ABSTRACT

Background: Acidity is an essential component of the organoleptic quality of fleshy fruits. However, in these fruits, the physiological and molecular mechanisms that control fruit acidity remain unclear. In peach the D locus controls fruit acidity; low-acidity is determined by the dominant allele. Using a peach progeny of 208 F2 trees, the D locus was mapped to the proximal end of linkage group 5 and co-localized with major QTLs involved in the control of fruit pH, titratable acidity and organic acid concentration and small QTLs for sugar concentration. To investigate the molecular basis of fruit acidity in peach we initiated the map-based cloning of the D locus.

Results: In order to generate a high-resolution linkage map in the vicinity of the D locus, 1,024 AFLP primer combinations were screened using DNA of bulked acid and low-acid segregants. We also screened a segregating population of 1,718 individuals for chromosomal recombination events linked to the D locus and identified 308 individuals with recombination events close to D. Using these recombinant individuals we delimited the D locus to a genetic interval of 0.4 cM. We also constructed a peach BAC library of 52,000 clones with a mean insert size of 90 kb. The screening of the BAC library with markers tightly linked to D locus indicated that 1 cM corresponds to 250 kb at the vicinity of the D locus.

Conclusion: In the present work we presented the first high-resolution genetic map of D locus in peach. We also constructed a peach BAC library of approximately 15x genome equivalent. This fine genetic and physical characterization of the D locus is the first step towards the isolation of the gene(s) underlying fruit acidity in peach.

Show MeSH
Related in: MedlinePlus