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An LTR retrotransposon in the promoter of a PsMYB10.2 gene associated with the regulation of fruit flesh color in Japanese plum

View ORCID ProfileArnau Fiol, Sergio García, View ORCID ProfileChristian Dujak, View ORCID ProfileIgor Pacheco, View ORCID ProfileRodrigo Infante, View ORCID ProfileMaria José Aranzana
doi: https://doi.org/10.1101/2022.01.26.477575
Arnau Fiol
1Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB, 08193, Bellaterra, Barcelona, Spain
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Sergio García
1Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB, 08193, Bellaterra, Barcelona, Spain
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Christian Dujak
1Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB, 08193, Bellaterra, Barcelona, Spain
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Igor Pacheco
2Instituto de Nutrición y Tecnología de Alimentos (INTA), Universidad de Chile, El Líbano 5524, Santiago, Chile
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Rodrigo Infante
3Departamento de Producción Agrícola, Facultad de Ciencias Agronómicas, Universidad de Chile, Santa Rosa 11315, Santiago, Chile
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Maria José Aranzana
1Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB, 08193, Bellaterra, Barcelona, Spain
4IRTA (Institut de Recerca i Tecnologia Agroalimentàries), Barcelona, Spain
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  • For correspondence: mariajose.aranzana@irta.cat
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ABSTRACT

Japanese plums exhibit wide diversity of fruit coloration. The red to black hues are caused by the accumulation of anthocyanins, while their absence results in yellow, orange or green fruits. In Prunus, MYB10 genes are determinants for anthocyanin accumulation. In peach, QTLs for red plant organ traits map in an LG3 region with three MYB10 copies (PpMYB10.1, PpMYB10.2 and PpMYB10.3). In Japanese plum the gene copy number in this region differs with respect to peach, with at least three copies of PsMYB10.1. Polymorphisms in one of these copies correlate with fruit skin color. The objective of this study was to determine a possible role of LG3-PsMYB10 genes in the natural variability of the flesh color trait and to develop a molecular marker for marker-assisted selection (MAS). We explored LG3-PsMYB10 variability, including the analysis of long-range sequences obtained in previous studies through CRISPR-Cas9 enrichment sequencing. We found that the PsMYB10.2 gene was only expressed in red flesh fruits. Its role in promoting anthocyanin biosynthesis was validated by transient overexpression in Japanese plum fruits. The analysis of long-range sequences identified an LTR retrotransposon in the promoter of the expressed PsMYB10.2 gene that explained the trait in 93.1% of the 145 individuals analyzed. We hypothesize that the LTR retrotransposon may promote the PsMYB10.2 expression and activate the anthocyanin biosynthesis pathway. We provide a molecular marker for the red flesh trait which, together with that for skin color, will serve for the early selection of fruit color in breeding programs.

Competing Interest Statement

The authors have declared no competing interest.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted January 26, 2022.
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An LTR retrotransposon in the promoter of a PsMYB10.2 gene associated with the regulation of fruit flesh color in Japanese plum
Arnau Fiol, Sergio García, Christian Dujak, Igor Pacheco, Rodrigo Infante, Maria José Aranzana
bioRxiv 2022.01.26.477575; doi: https://doi.org/10.1101/2022.01.26.477575
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An LTR retrotransposon in the promoter of a PsMYB10.2 gene associated with the regulation of fruit flesh color in Japanese plum
Arnau Fiol, Sergio García, Christian Dujak, Igor Pacheco, Rodrigo Infante, Maria José Aranzana
bioRxiv 2022.01.26.477575; doi: https://doi.org/10.1101/2022.01.26.477575

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