Association genetics and expression patterns of a CBF4 homolog in Populus under abiotic stress

New strategies for prevention and treatment of abiotic stress require an improved understanding of stress responses. Here, we examined response differences of a C-repeat binding factor gene (PsCBF4) between five species in the genus Populus. We also used a candidate gene-based approach to identify single nucleotide polymorphisms (SNPs) within PsCBF4 that were associated with physiological and biochemical traits in a natural population (528 unrelated individuals) of Populus simonii. We first isolated a 1,044-bp PsCBF4 cDNA encoding a polypeptide of 256 amino acids. Expression profiling revealed that CBF4 is differentially expressed under cold, heat, drought, and salt conditions among five Populus species. Cold stress is the most significant interspecific difference, and PsCBF4 transcript levels ranged from 6.5 to 379.5 times higher than in unstressed controls. A natural population of P. simonii showed high nucleotide diversity (π T = 0.00880, θ w = 0.01192) and low linkage disequilibrium (r (2) ≥ 0.1, within 700 bp) across PsCBF4. Association analysis showed that nine SNPs (false discovery rate Q < 0.10) and two haplotypes (Q < 0.10) were significantly associated with six physiological and biochemical traits, with each marker explaining 3.36-6.12 % of the phenotypic variance in the corresponding trait. Transcript analysis further detected significant differences among genotypic classes for all significant SNPs. Identification of these significant associations will help reveal the molecular bases of physiological and biochemical differences and provide a starting point for marker-assisted selection for traits involved in stress tolerance in P. simonii.