Genetic factors driving variation of stomatal density in apples

Abstract

Climate change will likely increase plant abiotic stress due to severe drought and extreme temperatures, leading to higher agricultural demand for fresh water. Irrigation alone is unlikely to solve these global challenges, but an alternative and sustainable solution is breeding for plant functional traits to enhance climate resilience. Stomata regulate plant-water relations and the known mechanisms underlying their function make them promising targets for crop improvement. Here, we investigate the variation in stomatal density among apples trees (Malus × domestica Borkh.), with apples being the third most valuable fruit crop worldwide. We surveyed the variation in stomatal density across a genetically diverse population of 269 accessions located in Waedenswil, Switzerland, in 2019, 2020, and 2021. Density curves for stomatal density resembled normal distribution with a median of 361, 340, and 339 mm-2 for 2019, 2020, and 2021, respectively. Stomatal density varied significantly across accessions but was not significantly different across years (p < 0.001). Extreme accessions ranged from a minimum of 181 mm-2 to a maximum of 528 mm-2, and stomatal density was negatively correlated with water-use efficiency (rs = -0.51, p < 0.001), as measured by leaf gas-exchange. Using genome-wide association studies, we identified SNPs associated with stomatal density on chromosomes 2, 9, and 10. On chromosome 9, a key genetic regulator of stomatal development was identified in a haploblock consisting of six biallelic SNPs within 102.3 kb. Depending on allelic combination in the haploblock, stomatal density varied by almost 100 mm-2. Furthermore, two additional candidate genes were identified near the haploblocks on chromosome 10, located approximately 530 and 1810 kb away from the associated SNPs. Our study identified the genomic regions driving the variation in stomatal density of apple leaves and provides the foundation for targeted breeding of stomatal traits to improve climate resilience.