Genomics unlocks the potential of genetic resources for citrus breeding

The genus Citrus includes 162 species, but sweet oranges, grapefruits, lemons, and mandarins dominate global trade. For over 100 years, many native citrus cultivars have seen limited production. With the growing demand for new hybrid scions with higher sugar content, easy peeling, and good aroma, minor genetic resources offer potential for breeding, although low selection rates have limited their use. Recent genome sequencing of major citrus cultivars has advanced DNA marker and marker-assisted selection techniques. Additionally, Genome-wide Association Studies have identified key quantitative trait loci, and genomic prediction studies show higher prediction scores for various fruit traits. Genomic studies have clarified the origin and evolution of the genus Citrus, revealing that current species are hybrids of four ancient taxa (C. maxima, C. medica, C. reticulata, and C. micrantha) with several minor taxa, prompting a revision of the classification. Pedigree analysis of 67 native cultivars highlights the potential of some, like Kishu, Tachibana, Kaikoukan, and Kunenbo, as breeding parents. These advances have deepened our understanding of citrus origins, as well as the processes of domestication and diversification, revolutionizing breeding practices and enhancing the use of genetic resources in the citrus breeding program at the National Agriculture and Food Research Organization.