Origin of hemizygosity in grape: the case study of cv. Merlot

Abstract

Hemizygous genes, are genes present on only one copy of the genome (only one allele) and should not be confused with homozygous genes. Grapevine genome display a relatively high rate of hemizygous genes, varying between 13,5% and 15% (Peng et al., 2025). What is the origin of these hemizygous genes? Are they inherited, due to the cross between two highly heterozygous and structurally diverging parents or acquired along the clonal life, through segment loss?

To answer this question, we analyzed the cultivar ‘Merlot’ which is the result of a cross between ‘Cabernet franc’ and ‘Magdeleine noire des Charentes’ (Boursiquot et al., 2009). First mention of this cultivar dates back to the late XVIIIth century in France (Viala and Vermorel 1902–1910). Since that time ‘Merlot’, being one of the most planted cultivars worldwide, have been extensively propagated and many clones exist today in public or private collections.

We sequenced three clones of Merlot and both its parents using PacBio Hifi technology. We then assembled each genome, using trio-binning for the Merlot, resulting in haplotype resolved chromosome scale genomes. Merlot assemblies present many homozygous regions, the longest being on chromosome 4 with a length of 23Mb. We annotated genes for each genome and identified the hemizygous genes in Merlot (Sichel et al., 2023).

We characterized the transmitted genome regions from each parent and compared it to the corresponding ‘Merlot’ haplotype and we show that since its obtention, around 250 years ago, Merlot has accumulated few structural variants. Historical parental relationships within the grape gene pool may generate homozygous regions in current varieties and these regions may be confounded with hemizygous regions. We will present and discuss the origin of the hemizygous genes in ‘Merlot’.

References

Boursiquot, J.-M., Lacombe, T., Laucou, V., Julliard, S., Perrin, F.-X., Lanier, N., Legrand, D., Meredith, C., This, P., 2009. Parentage of Merlot and related winegrape cultivars of southwestern France: discovery of the missing link. Australian Journal of Grape and Wine Research, 15, 144–155. https://doi.org/10.1111/j.1755-0238.2008.00041.x

Peng, Y., Wang, Y., Liu, Y., Fang, X., Cheng, L., Long, Q., Su, D., Zhang, T., Shi, X., Xu, X., Xu, Q., Wang, N., Zhang, F., Liu, Z., Xiao, H., Yao, J., Tian, L., Hu, W., Chen, S., Wang, H., Huang, S., Gaut, B.S., Zhou, Y., 2025. The genomic and epigenomic landscapes of hemizygous genes across crops with contrasting reproductive systems. Proceedings of the National Academy of Sciences, 122, e2422487122. https://doi.org/10.1073/pnas.2422487122

Sichel, V., Sarah, G., Girollet, N., Laucou, V., Roux, C., Roques, M., Mournet, P., Cunff, L.L., Bert, P.F., This, P., Lacombe, T., 2023. Chimeras in Merlot grapevine revealed by phased assembly. BMC Genomics, 24, 396. https://doi.org/10.1186/s12864-023-09453-8

Viala, P. and Vermorel, V. (19021910) Ampélographie (Masson: Paris).