Genome-wide identification and expression pattern of the PIN gene family under abiotic stress in Nelumbo nucifera

Abstract

[Objective] To characterize NnPIN gene family in lotus (Nelumbo nucifera) and analyze their roles in abiotic stress, in order to provide genetic resources for the breeding of new lotus varieties with stress resistance. [Methods] This study used bioinformatics methods to conduct a genome-wide identification of the NnPIN gene family in lotus, and used qRT-PCR to analyze their response to low temperature, flooding, and exogenous application of abscisic acid (ABA). [Results] (1) A total of 12 NnPIN genes with transmembrane domains were identified in lotus genome, named NnPIN1-12 respectively, which were distributed on 6 chromosomes, and were mainly located in the plasma membrane and endoplasmic reticulum. (2) Phylogenetic analysis showed that NnPIN proteins can be divided into two types: Classical and non-classical based on the length of the central hydrophilic ring, and the same type had a similar structure. The classic type had complete motifs 1 to 12, while the non-classic type missed the central hydrophilic ring (motif 6, 8, 9, 12). (3) Cis-acting element analysis found that the NnPIN genes have a large number of light, abiotic stress and hormone responsive elements in the promoter region, specifically having anaerobic, ABA, low temperature, and other response elements. (4) The NnPIN genes family, except NnPIN8, responded positively to exogenous ABA and low temperature stress. In addition, NnPIN6 and NnPIN7 positively responded to flooding stress, while NnPIN1-5, NnPIN8, NnPIN9, and NnPIN12 responded negatively to flooding stress. [Conclusion] The NnPIN gene family members are specifically involved in response to abiotic stress in lotus.

Keywords

• lotus
• pin gene family
• bioinformatics
• abiotic stress
• expression pattern