Identification and characterization of LIM family genes in Tartary buckwheat: insights into functional divergence and abiotic stress responses

BACKGROUND: LIM domain proteins have been reported to participate in cytoskeleton dynamics, transcriptional regulation, and stress-related processes in plants. However, the LIM gene family has not been systematically characterized in Tartary buckwheat (Fagopyrum tataricum), and its potential roles in stress responses remain unclear. RESULTS: In the present study, 16 LIM genes were identified from the Tartary buckwheat genome and grouped into two subfamilies, CRP-like and DA1&DAR. Comparative analyses showed clear differences between the two subfamilies in gene structure, conserved motifs, and predicted protein architectures, implying functional diversification. Only one segmental duplication event (FtPLIM2a/FtPLIM2b) was detected, and the low Ka/Ks value indicated that this gene pair has undergone purifying selection. Synteny analysis showed that FtLIM genes displayed closer collinearity with dicot species, especially soybean, while no orthologous pairs were detected with the monocots included in this study. Most collinear gene pairs belonged to the CRP-like subfamily. Promoter analysis identified multiple cis-acting elements associated with growth and development, phytohormone responsiveness, and abiotic stress responses. Public transcriptome datasets revealed tissue-specificity expression patterns of FtLIM genes and distinct expression features between the two subfamilies. Several genes showed differential expression under salt, drought, and low-temperature conditions. Among them, FtLIM1a was consistently up-regulated across different stress treatments, while FtDAR4 was down-regulated under all three stress conditions. In the low-temperature dataset, FtWLIM2b showed altered expression under repeated cold treatment, indicating a potential association with cold adaptation. In addition, real-time fluorescence quantitative polymerase chain reaction analysis showed that most FtLIM genes responded to exogenous ABA and MeJA treatments. CONCLUSIONS: This study provided a genome-wide characterization of the LIM gene family in Tartary buckwheat and identified several candidate genes potentially involved in abiotic stress responses. These results laid a foundation for future functional studies of FtLIM genes.