Self-incompatibility (SI) is a complex mechanism that prevents plants from self-fertilizing to preserve and promote genetic variability. The angiosperm species have developed two different SI systems, the sporophytic (SSI) and the gametophytic (GSI) systems. SI is a significant impediment to steady fruit production in fruit tree species of the Rosaceae. In Rosaceae, GSI is genetically regulated via a single locus, named the ‘S-locus’, which includes a minimum of two polymorphic and relatively intercorrelated S genes: a pistil-expressed S-RNase gene and several pollen-expressed SFBB (S-locus F-Box Brothers) or SFB (S haplotype-specific F-box protein). This necessitates the interaction of S-RNases with the male determinants. Although genetic and molecular analyses of S genes have shown that mutations in both pistils and pollen-specific components induce self-compatibility in many species and cultivars, other genes or molecules outside the S-locus can co-participate in the male gamete rejection in GSI. However, we highlight and synthesize the most recent knowledge on different mechanisms of GSI in Rosaceae in this current review.

Prunus zhengheensis, an extremely rare population of apricots, originated in warm South-East China and is an excellent material for genetic breeding. However, most apricots and two related species (P. sibirica, P. mandshurica) are found in the cold northern regions in China and the mechanism of their distribution is still unclear. In addition, the classification status of P. zhengheensis is controversial. Thus, we generated a high-quality haplotype-resolved genome for P. zhengheensis, exploring key genetic variations in its adaptation and the causes of phylogenetic incongruence. We found extensive phylogenetic discordances between the nuclear and organelle phylogenies of P. zhengheensis, which could be explained by incomplete lineage sorting. A 242.22-Mb pan-genome of the Armeniaca section was developed with 13 chromosomal genomes. Importantly, we identified a 566-bp insertion in the promoter of the HSFA1d gene in apricot and showed that the activity of the HSFA1d promoter increased under low temperatures. In addition, HSFA1d overexpression in Arabidopsis thaliana indicated that HSFA1d positively regulated plant growth under chilling. Therefore, we hypothesized that the insertion in the promoter of HSFA1d in apricot improved its low-temperature adaptation, allowing it to thrive in relatively cold locations. The findings help explain the weather adaptability of Armeniaca plants.

The formation of multi-pistil flowers reduces the yield and quality in Japanese apricot (Prunus mume). However, the molecular mechanism underlying the formation of multi-pistil flowers remains unknown. In the current study, overexpression of PmKNAT2/6-a, a class I KNOTTED1-like homeobox (KNOX) member, in Arabidopsis (Arabidopsis thaliana) resulted in a multi-pistil phenotype. Analysis of the upstream regulators of PmKNAT2/6-a showed that AGAMOUS-like 24 (PmAGL24) could directly bind to the PmKNAT2/6-a promoter and regulate its expression. PmAGL24 also interacted with Like Heterochromatin Protein 1 (PmLHP1) to recruit lysine trimethylation at position 27 on histone H3 (H3K27me3) to regulate PmKNAT2/6-a expression, which is indirectly involved in multiple pistils formation in Japanese apricot flowers. Our study reveals that the PmAGL24 transcription factor, an upstream regulator of PmKNAT2/6-a, regulates PmKNAT2/6-a expression via direct and indirect pathways and is involved in the formation of multiple pistils in Japanese apricot.

ALMT (aluminum-activated malate transporter) proteins play crucial roles in the transport of organic acids and have significant implications for plant stress responses and development. While extensively studied in some plants, the characteristics and functional divergence of the ALMT gene family have not yet been thoroughly explored in Prunus mume and some other Rosaceae species. In this study, we systematically analyzed the ALMT gene family across nine Rosaceae species to explore their evolutionary relationships, structural characteristics, and functional roles. A total of 138 ALMT genes were identified and categorized into four groups based on a phylogenetic analysis. The motif analysis confirmed the accuracy of the phylogenetic grouping. The collinearity analysis indicated that whole-genome duplication events were the primary drivers of ALMT gene expansion in these species. Furthermore, the cis-acting element analysis revealed diverse regulatory elements associated with environmental responses, including abscisic acid, light, and jasmonic acid. The gene expression correlation analysis showed that PmALMT1 is primarily associated with malic acid accumulation, whereas PmALMT8 is related to citric acid accumulation. Further transient expression in Nicotiana benthamiana validated the above conclusion. This comprehensive analysis provides valuable insights into the evolution, function, and regulation of the ALMT gene family in Rosaceae species.

The Knotted1-like Homeobox gene is crucial for plant morphological development and growth. Physicochemical characteristics, phylogenetic relationships, chromosomal localization, cis-acting elements, and tissue-specific expression patterns of the 11 PmKNOX genes found in the Japanese apricot genome in this study were examined. Proteins of 11 PmKNOX were soluble proteins with isoelectric points between 4.29 and 6.53, molecular masses between 15.732 and 44.011 kDa, and amino acid counts between 140 and 430. The identified PmKNOX gene family was split into three subfamilies by jointly constructing the phylogenetic tree of KNOX proteins in Japanese apricot and Arabidopsis thaliana. Combined outcomes of the analyzed conserved motifs and gene structures of the 11 PmKNOX genes from the same subfamily displayed comparable gene structure and motif patterns. The 11 PmKNOX members were distributed across six chromosomes, while two sets of PmKNOX genes were found to be collinear. Analysis of the 2000 bp promoter upstream of the coding region of the PmKNOX gene revealed that most PmKNOX genes might be involved in the physiological metabolism, growth and development processes of plants. The PmKNOX gene expression profile revealed that these genes were expressed at varying levels in different tissues, and most of them were linked to the meristems of leaf and flower buds, suggesting that PmKNOX may be involved in plants’ apical meristems. In Arabidopsis thaliana, functional validation of PmKNAT2a and PmKNAT2b revealed that these two genes might be involved in regulating leaf and stem development. In addition to laying the groundwork for future research on the function of these genes, understanding the evolutionary relationships between members of the PmKNOX gene family provides opportunities for future breeding in Japanese apricots.