Rosaceae is one of the major families in the plant kingdom with important economic value. However, many of them are attacked by Valsa canker, resulting in serious loss of production and profits. Nucleotide-binding leucine-rich repeats (NLRs) play a key role in the plant immune response as the largest class of resistance genes. Currently, we performed a genome-wide identification of NLR genes in Rosaceae and revealed some NLR genes in response to Valsa canker using multispecies bioinformatics including co-expression network analysis and RNASeq data. A total of 3718 NLR genes were identified from genomes of 19 plant species (include 9 Rosaceae plants) and classified them into 15 clades. The NLRs display species- and group-specific expansions that are derived from both the whole genome duplication and the tandem duplication. Additionally, the expression of some NLR members was low under normal growth conditions in various plant tissues, while significantly enhanced after the infection of Valsa canker. Furthermore, co-expression network analysis shows that the 13 NLR members were distributed in key nodes of differentially expressed genes which could be considered as promosing key regulators for the resistance of Valsa canker. Therefore, our findings provide a reference for the evolution of NLR genes in Rosaceae and the key regulators of Valsa canker resistance.

The ATP-binding cassette (ABC) transporter family plays a critical role in plant growth, development, and disease resistance. However, the evolution and functional characteristics of the ABC gene family in Rosaceae species have not been fully studied. In this study, we performed the first whole-genome identification, as well as an evolutionary analysis and comparative analysis of ABC genes in Rosaceae plants. We identified 3037 ABC genes in 20 plant species, classifying them into eight subfamilies. Comparative analysis revealed significant variations in family size and expansion patterns among species, suggesting adaptive evolution. Tandem duplication (TD: where genes are duplicated in sequence) and whole-genome duplication (WGD: duplication of the entire genome) were identified as the primary drivers of ABC family expansion. In pears, gene pairs produced by WGD underwent purifying selection. Gene ontology (GO) enrichment analysis indicated the involvement of ABC proteins in transmembrane transport and signal transduction pathways. Under Valsa pyri infection, most ABC genes were upregulated in the early stages, highlighting the role of ABCG genes in pathogen response. A weighted gene co-expression network analysis (WGCNA) identified five key ABCG genes potentially involved in pathogen resistance regulation. Our findings provide insights into the evolutionary adaptability of the ABC gene family and their potential applications in plant disease defense.

Valsa canker, a destructive necrotrophic disease caused by Valsa species (V. mali and V. pyri), threatens global apple and pear production. Resistance breeding has gained much attention because of its environmental friendliness and effectiveness, making it extremely critical to obtain key disease resistance genes. In this study, we identified that the expression of PbeSTOP2, a C2H2-type transcription factor in ‘Duli-G03’ (Pyrus betulifolia, rootstock of pear), was induced in response to signals from Vp and Vp metabolites (VpM). Transient expression in fruits and stable overexpression in suspension cells demonstrated that PbeSTOP2 enhances resistance to Vp. In overexpressing cells, genes associated with jasmonic acid (JA) and pattern-triggered immunity (PTI) signaling were upregulated, and endogenous JA and auxin (IAA) levels increased. These results revealed that JA signaling was involved in the enhanced Valsa canker resistance conferred by PbeSTOP2 overexpression. This finding on host disease resistance should facilitate the breeding efforts for Valsa canker resistance.