Based on 22 qualitative traits, 13 quantitative traits, and 27 molecular markers (26 SSR and 1 InDel), in the current study we compared the diversity and population structure of 94 local landraces and 85 current breeding lines of pepper in China. The results showed that the Shannon Diversity indices of 9 qualitative traits and 8 quantitative traits in current breeding lines were greater than those of landraces, of which 11 were fruit organ-related traits. Compared with current breeding lines, the mean values of Gene Diversity index and Polymorphism Information content of local landraces were higher by 0.08 and 0.09, respectively. Population structure and phylogenetic tree analysis showed that the 179 germplasm resources could be divided into two taxa, dominated by local landraces and current breeding lines, respectively. The above results indicated that the diversity of quantitative traits of current breeding lines were higher than that of local landraces, especially traits related to fruit organs, but the genetic diversity based on molecular markers was lower than that of local landraces. Therefore, in the future breeding process, we should not only focus on the selection of target traits, but also strengthen the background selection based on molecular markers. Moreover, the genetic information of other domesticated species and wild species will be transferred to the breeding lines through interspecific crosses to expand the genetic background of the breeding material.

The Cucumber mosaic virus (CMV) presents a significant threat to pepper cultivation worldwide, leading to substantial yield losses. We conducted a transcriptional comparative study between CMV-resistant (PBC688) and -susceptible (G29) pepper accessions to understand the mechanisms of CMV resistance. PBC688 effectively suppressed CMV proliferation and spread, while G29 exhibited higher viral accumulation. A transcriptome analysis revealed substantial differences in gene expressions between the two genotypes, particularly in pathways related to plant–pathogen interactions, MAP kinase, ribosomes, and photosynthesis. In G29, the resistance to CMV involved key genes associated with calcium-binding proteins, pathogenesis-related proteins, and disease resistance. However, in PBC688, the crucial genes contributing to CMV resistance were ribosomal and chlorophyll a–b binding proteins. Hormone signal transduction pathways, such as ethylene (ET) and abscisic acid (ABA), displayed distinct expression patterns, suggesting that CMV resistance in peppers is associated with ET and ABA. These findings deepen our understanding of CMV resistance in peppers, facilitating future research and variety improvement.

Based on 22 qualitative traits, 13 quantitative traits, and 27 molecular markers (26 SSR and 1 InDel), in the current study we systematically compared the diversity and population structure of 94 local landraces and 85 current breeding lines of pepper in China. The results showed that the Shannon Diversity indices of 9 qualitative traits and 8 quantitative traits in current breeding lines were greater than those of landraces, of which 11 were fruit organ-related traits. Compared with current breeding lines, the mean values of Gene Diversity index and Polymorphism Information content of local landraces were higher by 0.08 and 0.09, respectively. Population structure and phylogenetic tree analysis showed that the 179 germplasm resources could be divided into two taxa, dominated by local landraces and current breeding lines, respectively. The above results indicated that the diversity of quantitative traits of current breeding lines were higher than that of local landraces, especially traits related to fruit organs, but the genetic diversity based on molecular markers was lower than that of local landraces. Therefore, in the future breeding process, we should not only focus on the selection of target traits, but also strengthen the background selection based on molecular markers. Moreover, the genetic information of other domesticated species and wild species will be transferred to the breeding lines through interspecific crosses to expand the genetic background of the breeding material.