Fine-mapping and transcriptome analysis of the photosensitive leaf -yellowing gene CaLY1 in pepper (Capsicum annuum L.)

Leaf color is directly related to altered photosynthesis. Hence, leaf yellowing mutants can be widely used for the researching plant physiology and functional genomes, for cultivating new varieties of popular horticultural plants, and for identifying hybrid purity (as markers). Here, we constructed a 60Co-γ F2 population from the leaf -yellowing mutant R24 via radiation mutation with the inbred line WT21 of pepper. Genetic analysis showed that the leaf-yellowing of the mutant was controlled by a single recessive gene. By applying the Bulk Segregation Analysis and Kompetitive Allele Specific PCR markers, the leaf-yellowing gene CaLY1 (Capsicum annuum Leaf yellow 1) was mapped on chromosome 9, SNP5791587–SNP6011215, with a size of 214.5 kb. One non-synonymous mutated gene Capana09g000166 was found in the interval. The gene encoded a PsbX, which is the core complex of PSII. Transcriptome analysis further showed that 2301 differentially expressed genes were identified under shading treatment for 24 h in R24. The Gene Ontology enrichment pathways were related to photosynthesis light harvesting, cell wall, activity of quercetin 3-O-glucosyltransferase and flavonoid metabolic process, which likely regulate the response of pepper leaves to different light levels. Functional enrichment analysis indicated that the most abundant pathways were photosynthesis antenna proteins and metabolic.