Genome-wide association study of water-use efficiency and shoot biomass conferred by V. berlandieri rootstocks in grapevine

Deciphering the genetic basis of above and below ground organs communication is essential for plant adaptation. In grafted perennial crops, such as grapevine, identifying genes from the roots system controlling the expression of shoot traits is essential to improve plant adaptation to environmental conditions through rootstock breeding. However, the grapevine rootstocks genetic control on conferred scion traits has rarely been explored and even less considering genetic diversity at the intra-species level through GWAS. In this study we used a Vitis berlandieri natural population comprising 211 genotypes, grafted with a single scion genotype, to identify genetic regions associated with water use efficiency and shoot biomass conferred to the scion using GWAS in field conditions. Water use efficiency was evaluated by δ13C over three years and the shoot biomass produced every year during the first two years of growth after plantation. δ13C and shoot biomass were not correlated. δ13C indicated a moderate broad sense heritability from 0.34 to 0.46 in the absence or under moderate water deficit. Heritability falls to zero under strong water deficit indicating a major contribution of environmental conditions. The shoot biomass heritability was moderate to strong from 0.34 to 0.70. One QTL for δ13C explained 54% of the genetic variance. The QTL was associated with a gene homolog to AT4G22790, coding for a mate family protein involved in stomatal aperture regulation in response to carbon dioxide concentration. Four QTL for shoot biomass were linked with genes homologous to AT5G19350, AT4G37130, AT1G22020, and AT1G15780 known to be involved in vegetative growth and root development, hormonal signalling, photorespiration, and response to light, respectively. This study represents the first GWAS carried out for scion traits conferred by a natural Vitis berlandieri rootstock population in a field experiment. It contributes to the understanding of the genetic basis of shoot plant performance regulated by roots. Ultimately, these outcomes provide valuable targets for breeding programs suggesting that rootstocks selection based on genetic information and morphological traits could improve crop adaptation to future environments, contributing to sustainable agriculture.