Molecular Marker Development and Gene Cloning for Diverse Disease Resistance in Pepper (Capsicum annuum L.): Current Status and Prospects

The production of chili pepper (Capsicum annuum L.) is hindered by several biotic factors even though striding progresses were made in genetic improvement in the last two decades. Among the advancements were the fast-track genetic improvement of disease-resistant varieties by the use of marker-assisted selection (MAS) and the conventional breeding-based introgression of major resistance genes. Marker development, marker-based identification and fine mapping have revealed a large number of resistance genes, from which cloning of some candidate genes demonstrated the applicability and versatility of map-based cloning for disease resistance. In some of the recent fine mapping of disease resistance QTLs, closely linked DNA markers were identified, which in turn resulted in the rapid introgression of target gene(s) into breeding lines. Also, progresses were made on the characterization and map-based cloning of resistance genes conferring broad-spectrum resistance. As the number of identified and characterized resistance genes and the DNA markers linked to resistance genes are steadily generated, the development of multiple/durable resistance to major chili pepper diseases is accelerated by MAS. In the present review, the development of molecular markers, marker-based mapping of genes conferring resistance to ten major chili pepper diseases were discussed, focusing on the recent advancements in major and QTL-spanning resistance gene mapping. The review provides up-to-date insights into the development of DNA markers linked to disease resistance genes and the cloning of resistance genes, which are all so crucial in pepper breeding for disease resistance.