Objective Biological information and expressions under saline-alkali stress of the family members of response regulator gene (RR) in apple were investigated.

Method Using the conserved sequence of PF00643 in genome of Malus hupehensis Rehd, members of the MdRR family were identified. Physiochemical properties, motifs, gene structure, chromosomal localization, cis-acting elements, and phylogenetic tree of the members were analyzed by MEGA-X, TBtools, and MEME. RNA-seq was employed to examine their expressions under saline-alkali stress.

Result The 38 identified MdRRs were named as MdRR1-38 that contained 138-774 amino acids with molecular weights ranging 15,874.61-85,191.72 Da, isoelectric points 4.62-9.14, instability coefficients 34.77-80.77, fat coefficients 59.88-109.42, and average hydrophilicity coefficients −0.934-0.312. There were α-helices, extended chains, disordered coils, and amorphous regions in the structure which was dominant by α-helices and disordered coils in each member. As indicated by the cis-acting elements and GO analysis, MdRRs played crucial roles in the stimulus response and signal transduction of plant hormones, stress response, and growth and development regulations. They might interact with multiple proteins, such as AHP, SnRK2, TFIIA, ETR2, HSD, and others to regulate the plant resistance. Under saline-alkali stress, the expressions of 13 MdRRs in the leaves and 7 in the roots exhibited a pattern of initial rise followed by a decline, while those of 11 MdRRs in the leaves and 17 in the roots showed an opposite trend.

Conclusion There were 38 MdRR family genes identified in apple. The expressions of most of them were affected by a saline-alkali treatment, indicating their close association with the stress response of the plant.