Genome-Wide Identification and Expression Analysis of the Nucleotide-Binding Leucine-Rich Repeat Gene Families in Rubber Tree

Anthracnose, caused by Colletotrichum spp., significantly threats rubber trees globally. The nucleotide-binding and leucine-rich repeat (NLR) protein family constitutes one of the largest and most widespread classes of plant immune receptors. However, the specific relationship between NLR genes and anthracnose resistance in rubber trees remains poorly understood. This study comprehensively identified all NLR family members in the reference genome of the wild rubber tree germplasm MT/VB/25A 57/8. From 39,340 annotated proteins, 253 were classified as NLR family members, including 155 coiled-coil NLR (CNL) and 35 Toll/interleukin-1 receptor NLR (TNL) proteins. Conserved motifs were identified in both CNL and TNL proteins, Notably, TNL proteins showed higher occurrence of conserved motif 8 in C-terminal LRR domains than CNL proteins. Chromosomal mapping indicated that CNL and TNL protein-coding genes predominantly localized on chromosomes 1, 3, 8, 12, and 14. The observed NLR distribution and diversity likely resulted from tandem, ectopic, and segmental gene duplications, with tandem duplications being the most prevalent. Comparative transcriptome and quantitative RT-PCR analyses revealed two specific CNL genes (LOC110667987 and LOC110668014) preferentially expressed in resistant germplasm and significantly upregulated upon infection by Colletotrichum siamense. Identification of these genes provides insight into molecular mechanisms underlying anthracnose resistance and will facilitate development of novel markers associated with resistance in rubber trees.