Recombination determinants and consequences

Recombination determinants and consequences


Chromosome recombinant

To meet the challenge of transitioning viticulture to practices with low environmental impact, the creation of resistant grapevine varieties by crossbreeding has been a success. To combine even more traits of resistance, quality and adaptation to climate change, it is now necessary to optimize breeding programs and, in particular, the efficiency of genome mixing via meiotic recombination. Since very little has been studied in grapevines, the genomic factors influencing the location of crossovers remain to be explored. As resistance phenotypes are introgressed from wild species of the Vitis genus, recombination in an interspecific context is particularly interesting to study.


Approaches and resources

Recombination profiles are established in different interspecific contexts following the construction of high-density genetic maps obtained from Genotyping-by-Sequencing data.  A strategy based on bioinformatics and bioanalysis methods is being developed to better understand the location of cross-overs, and structural, transcriptional and haplotypic divergence maps are being produced.  In particular, structural genomics tools for locating centromeres, telomeres and chromosome repeat regions and gene annotation pipelines are being implemented. Comparative genomics tools are used to identify structural variations, as well as statistical and modeling tools. In the future, a tool for predicting the location of cross-overs will be created as a decision aid for future grapevine breeding programs.


Vine Genetics and Metabolism Team

Vine Genetics and Improvement Team


Département BAP

Preliminary results

A study based on interspecific hybrids shows that the composition of haplotypes present during recombination directly impacts its distribution along chromosomes (Delame et al., 2018). Recombination frequency is similar between exclusively homologous haplotypes (V. vinifera - V. vinifera) and exclusively non-homologous haplotypes (V. rotundifolia - V. vinifera), as illustrated on chromosome 10 in Figure. On the other hand, when a homologous and a non-homologous zone are present on the same chromosome, recombination is completely suppressed in the non-homologous zone and its frequency is increased in the homologous zone (cf. chromosome 2 in the figure).

Chromosome 10
Chromosome 2

Figure after Delame et al. 2018: Recombination rate analysis in homologous versus non-homologous regions. Variation in genetic distance is plotted against physical distance for hybrid (red dots) and V. vinifera (green triangles) genetic maps. The rate of recombination is represented by the slope of the curves. The bars below the graphs show the haplotypic context of the hybrid parent (to be associated with the hybrid map in red dots) with homologous regions in dark grey and non-homologous regions in red.

Modification date: 07 May 2024 | Publication date: 24 January 2024 | By: INRAE Grand Est-Colmar