Improving Mapping Strategies to Discover Genes Involved in Tolerance to pH Stress in Blueberry

Blueberries are small fruits of high nutritional value produced by various species of plants in the genus Vaccinium. While most blueberries grow strictly on acidic soils, the wild V. arboreum (sparkleberry) tolerates a soil pH up to 6.5. Evolution of blueberries has produced plants with different levels of ploidy, ranging from diploid to hexaploid. One of the most commonly cultivated species is tetraploid V. corymbosum, which contains 4X=2n=48 chromosomes with an estimated size of 600 Mb/haploid genome. A reference genome with annotations was developed from diploid V. corymbosum. In the present study, RNA-Seq data was used for (i) comparison of multiple strategies to improve mapping of reads across Vaccinium species to the V. corymbosum reference and (ii) analysis of differential gene expression in plants from tetraploid V. corymbosum and diploid V. arboreum grown at control pH 4.5 and challenging pH 6.5. Our results using different mapping software revealed an impairment between mapping rate and conversion to gene counts. Estimation of differential expression using quasi-likelihood F test yielded 337 and 4,867 genes in V. corymbosum and V. arboreum, respectively, responding to pH treatment. Both species shared regulation of genes involved in nutrient homeostasis and lignin metabolism. V. arboreum exhibited regulation of signaling pathways related to abiotic/biotic stress, cellulose and lignin biosynthesis, and nutrient uptake, while V. corymbosum did not. These responses likely enable V. arboreum to tolerate higher soil pH. Lack of differential expression of these pathways in V. corymbosum might be related to this species’ strict soil adaptation.