To comprehensively elucidate the regulatory mechanisms of late embryogenesis abundant (LEA) proteins in higher plant embryogenesis and abiotic stress responses.

Hidden Markov model and bioinformatics were used to screen and identify LEA genes family from the whole genome of Malus sieversii, and their sequence features, conserved motifs, gene structures, cis-acting elements, and expression patterns were analyzed.

The 119 LEA genes were identified in the whole genome of Malus sieversii. According to their conserved structural domains and phylogenetic relationships, they were categorized into eight different groups (LEA1-LEA6, DHN, SMP), among which the MsiLEA2 group was the most gene-rich. Analysis of the cis-acting elements showed that most of the MsiLEA genes were associated with light response elements, abiotic stress response. In addition, some genes were related to biosynthetic pathways, such as abscisic acid response, growth hormone response, methyl jasmonate response, and meristematic tissue expression. The analysis of the expression pattern of Malus sieversii LEA genes in different periods of seed low-temperature stratification and in different organs showed that the expression of MsiDHN3 decreased during seed low-temperature stratification and was higher in all organs, indicating that MsiDHN3 plays a role in the low-temperature stratification of Malus sieversii seeds.

This study provides new insights into the formation of the MsiLEA genes family in Malus sieversii, it also deepens the understanding of the potential roles of these genes during embryonic developmental stages and abiotic stress response in Malus sieversii seeds. These results are instructive for future functional studies of the MsiLEA genes family and provide a theoretical basis for exploring the role of MsiLEA genes in the embryonic developmental stages of Malus sieversii seeds.