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Identification of QTLs linked to fruit quality traits in apricot (Prunus armeniaca L.) and biological validation through gene expression analysis using qPCR

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Abstract

Nine important fruit quality traits—including fruit weight, stone weight, fruit diameter, skin ground colour, flesh colour, blush colour, firmness, soluble solids content and acidity content—were studied for two consecutive years in two F1 apricot progeny derived from the crosses ‘Bergeron’ × ‘Currot’ (B×C) and ‘Goldrich’ × ‘Currot’ (G×C). Results showed great segregation variability between populations, which was expected because of the polygenic nature and quantitative inheritance of all the studied traits. In addition, some correlations were observed among the fruit quality traits studied. QTL (quantitative trait loci) analysis was carried out using the phenotypic data and genetic linkages maps of ‘B×C’ and ‘G×C’ obtained with SSR and SNP markers. The most significant QTLs were localised in LG4 for soluble solids content and in LG3 for skin and flesh colour. In LG4, we can highlight the presence of candidate genes involved in D-glucose and D-mannose binding, while in LG3, we identified MYB genes previously linked to skin colour by other authors. In order to clearly identify the candidate genes responsible for the analysed traits, we converted the QTLs into expression QTLs and analysed the abundance of transcripts in the segregating genotypes ‘GC 2–11’ and ‘GC 3–7’ from the G×C population. Using qPCR, we analysed the gene expression of nine candidate genes associated with the QTLs identified, including transcription factors (MYB 10), carotenoid biosynthesis genes (LOX 2, CCD1 and CCD4), anthocyanin biosynthesis genes (ANS, UFGT and F3’5’H), organic acid biosynthesis genes (NAD ME) and ripening date genes (NAC). Results showed variable expression patterns throughout fruit development and between contrasted genotypes, with a correlation between validated genes and linked QTLs. The MYB10 gene was the best candidate gene for skin colour. In addition, we found that monitoring NAC expression is a good RNA marker for evaluating ripening progression.

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Funding

This study was financially assisted by the Seneca Foundation of the Region of Murcia (Saavedra Fajardo Postdoctoral fellow 20397/SF/17) during the stay of Juan A. Salazar in Murcia. This study was also supported by the “Apricot breeding” project of the Spanish Ministry of Economy and Competiveness (AGL2013-41452-R) and the project “Breeding stone fruit species assisted by molecular tools” of the Seneca Foundation of the Region of Murcia (19879/GERM/15).

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Author notes

  1. Beatriz Ester García-Gómez and Juan Alfonso Salazar contributed equally to this work.

Authors and Affiliations

  1. Departamento de Mejora Vegetal, CEBAS-CSIC, PO Box 164, E-30100 Espinardo, Murcia, Spain

    Beatriz Ester García-Gómez, Juan Alfonso Salazar, Pedro Martínez-Gómez & David Ruiz

  2. Dipartimento di Scienze Agrarie, Università degli Studi di Bologna, Via Fanin 46, 40127, Bologna, Italy

    Luca Dondini

Authors
  1. Beatriz Ester García-Gómez
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  2. Juan Alfonso Salazar
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  3. Luca Dondini
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  4. Pedro Martínez-Gómez
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  5. David Ruiz
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Contributions

LD, PM-G and D.R. participated in the design and coordination of the study. D.R. and J.A.S. performed the phenotypic evaluation. B.E.G-G and J.A.S. Salazar carried out the SSR and SNP analyses, and B.E.G-G carried out the qPCR analysis. B.E.G-G, J.A.S., LD, PM-G and D.R. participated in the manuscript elaboration and discussion.

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Correspondence to Luca Dondini or Pedro Martínez-Gómez.

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Supplementary Figure 1

Genetic maps of F1 apricot progeny ‘Bergeron’ (B) × ‘Currot’ (C) and QTL identification by interval mapping analysis for two years of phenotyping: ripening time (RT), fruit weight (FW), stone weight (SW) and fruit diameter (CAL) are in blue; skin colour (SKC), flesh colour (FLSC) and blush colour (BLSC) are in orange; firmness (FIRM) is in violet; and malic acid (MALIC) and soluble solids (SS) are in red. The LOD threshold for QTL intervals: *α < 0.05, **α < 0.01. The assayed candidate genes are indicated with arrows in bold and italics. (PNG 2180 kb)

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Supplementary Figure 2

Genetic maps of F1 apricot progeny ‘Goldrich’ (G) × ‘Currot’ (C) and QTL identification by interval mapping analysis for two years of phenotyping: ripening time (RT), fruit weight (FW), stone weight (SW) and fruit diameter (CAL) are in blue; skin colour (SKC), flesh colour (FLSC) and blush colour (BLSC) are in orange; firmness (FIRM) is in violet; malic acid (MALIC) and soluble solids (SS) are in red. The LOD threshold for QTL intervals: *α < 0.05, **α < 0.01. The assayed candidate genes are indicated with arrows in bold and italics. (PNG 1504 kb)

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Supplementary Table 1

Description of assayed candidate genes through qPCR. (XLSX 17 kb)

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García-Gómez, B.E., Salazar, J.A., Dondini, L. et al. Identification of QTLs linked to fruit quality traits in apricot (Prunus armeniaca L.) and biological validation through gene expression analysis using qPCR. Mol Breeding 39, 28 (2019). https://doi.org/10.1007/s11032-018-0926-7

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  • DOI: https://doi.org/10.1007/s11032-018-0926-7

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