Using genome wide association to assist new apple cultivar development in mitigating climate change

There is increasing evidence of the impacts of climate change on apple production globally. One consequence of rising temperatures is an increase in fire blight (Erwinia amylovora) incidence, resulting in a loss of fruiting canopy, hence a reduction in yield. Another is changing patterns of winter chilling negatively affecting budbreak, which can reduce flower quantity and quality. Most current commercial cultivars are susceptible to fire blight and require substantive winter chill for budbreak. A preliminary genome wide association study showed that single nucleotide polymorphisms (SNPs) significantly associated with these traits were located in multiple genomic regions. Several SNPs associated with fire blight resistance were located on chromosomes (Chr) 4, Chr9 and Chr15, based on a glasshouse shoot test. These SNPs were close to, or within genes associated with responses to plant stress reactions or disease defence. Eleven SNPs significantly associated with budbreak were consistently found in 2020 and 2021. Several of these SNPs were found adjacent to candidate genes known as being involved in dormancy regulation in apple, such as the FLOWERING LOCUS C-LIKE, INDUCER OF C-REPEAT BINDING FACTOR EXPRESSION 1, and MITOCHONDRIAL PHOSPHATE TRANSPORTER genes. These SNPs also mapped to the same QTL region identified in an F₁ apple mapping population in Germany. SNPs located in these regions are candidate markers for selecting breeding lines with various patterns of winter chilling, which can contribute to development of new apple cultivars adapted to global warming effects.