The potential of markers to target resilience traits in Prunus : preliminary works on comparing GWAS and genomic prediction approaches

Abstract:

As perennial plants, stone fruit trees must cope, individually, with the fluctuating threat of multiple pests and diseases over their entire lifetime. To date, we lack varieties that combine a low level of susceptibility against several of these pests and diseases and pesticides remain the most effective means of control. In a context of urgent demand for the reduction of phytosanitary products, alternative and durable solutions must be found. To address these challenges, the selection of disease resilient trees, i.e. trees that are minimally affected by perturbations or which rapidly return to the state pertained before exposure to these disturbances, seems to be a promising but still misunderstood and under-exploited solution.

Our objective is thus to better characterize the genetic architecture of disease resilience components of two major stone fruit tree species: apricot and peach. To do so, two core collections composed by 150 apricot and 206 peach replicated accessions are maintained under low phytosanitary conditions respectively in two and three contrasted environments in South-East of France. These accessions have been densely genotyped with the Illumina HiSeq 2000 NGS technique for apricot and the IRSC 16K SNP array for peach.

We monitored the multiple symptoms of respectively eight and three pests and diseases over the years since 2020 for apricot and 2021 for peach. Thanks to this integrative phenotyping on several sites and years, we were able to study the different strategies and phenotypic manifestations of disease resilience. In a second step, we performed different models of genome wide association studies (GWAS) which allowed us to identify genetic markers linked to resilience components (i.e. resistance, tolerance or recovery capacity) to these diverse pests and diseases. These GWAS analyses were conducted jointly on diseases affecting both apricot and peach, such as rust, in order to compare the genetic architecture of disease resilience for these two closely related species. Finally, different genomic prediction models accounting for non-additive, inbreeding and GxE effects were performed on a selected disease subset in order to compare these two approaches.

After showing these preliminary results, we will discuss the perspectives of marker assisted selection or genomic selection for resilience components, and how it could become a more concrete goal for breeders.

Key words:

multi-disease challenge; disease resilience; plant immunity; genome-wide association studies (GWAS); Genomic prediction (GP); stone fruit tree; core collections; low phytosanitary inputs