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Plant Physiol. 2017 Oct;175(2):786-801. doi: 10.1104/pp.17.00715. Epub 2017 Aug 15.

Catastrophic Unbalanced Genome Rearrangements Cause Somatic Loss of Berry Color in Grapevine.

Author information

1
Instituto de Ciencias de la Vid y del Vino, Consejo Superior de Investigaciones Científicas-Universidad de La Rioja-Gobierno de La Rioja, 26007 Logroño, Spain pablo.carbonell@icvv.es.
2
Instituto de Ciencias de la Vid y del Vino, Consejo Superior de Investigaciones Científicas-Universidad de La Rioja-Gobierno de La Rioja, 26007 Logroño, Spain.
3
Unité Mixte de Recherche Biologie du Fruit et Pathologie, Institut National de la Recherche Agronomique, F-33140 Villenave d'Ornon, France.
4
Centro Nacional de Biotecnología, CNB-Consejo Superior de Investigaciones Científicas, 28049 Madrid, Spain.
5
Instituto de Biología Agrícola de Mendoza, Consejo Nacional de Investigaciones Científicas y Técnicas-UNCuyo-FCA, M5528AHB Chacras de Coria, Argentina.

Abstract

Grape (Vitis vinifera) color somatic variants that can be used to develop new grapevine cultivars occasionally appear associated with deletion events of uncertain origin. To understand the mutational mechanisms generating somatic structural variation in grapevine, we compared the Tempranillo Blanco (TB) white berry somatic variant with its black berry ancestor, Tempranillo Tinto. Whole-genome sequencing uncovered a catastrophic genome rearrangement in TB that caused the hemizygous deletion of 313 genes, including the loss of the functional copy for the MYB transcription factors required for anthocyanin pigmentation in the berry skin. Loss of heterozygosity and decreased copy number delimited interspersed monosomic and disomic regions in the right arm of linkage groups 2 and 5. At least 11 validated clustered breakpoints involving intrachromosomal and interchromosomal translocations between three linkage groups flanked the deleted fragments, which, according to segregation analyses, are phased in a single copy of each of the affected chromosomes. These hallmarks, along with the lack of homology between breakpoint joins and the randomness of the order and orientation of the rearranged fragments, are all consistent with a chromothripsis-like pattern generated after chromosome breakage and illegitimate rejoining. This unbalanced genome reshuffling has additional consequences in reproductive development. In TB, lack of sexual transmission of rearranged chromosomes associates with low gamete viability, which compromises fruit set and decreases fruit production. Our findings show that catastrophic genome rearrangements arise spontaneously and stabilize during plant somatic growth. These dramatic rearrangements generate new interesting phenotypes that can be selected for the improvement of vegetatively propagated plant species.

PMID:
28811336
PMCID:
PMC5619900
DOI:
10.1104/pp.17.00715
[Indexed for MEDLINE]
Free PMC Article

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