Genetic diversity and population structure of the mandarin germplasm revealed by nuclear and mitocho

Mandarins (C. reticulata) are considered as one of the four main species involved in the origin of cultivated citrus. However, the classification of the mandarin germplasm is still controversial and numerous cases of introgressionfrom other species are known or suspected in this germplasm. The main objective of this work was to analyzethe genetic diversity structure of mandarin germplasm and its relationship with the other citrus species. Fifty microsatellite (SSR) markers, 25 Insertion-Deletion (InDel) nuclear markers and four mitochondrial InDel markerswere genotyped for 223 accessions. 'Structure' software was applied on nuclear data to check and quantifypotential interspecific introgressions in the mandarin germplasm, mainly the pummelo and papeda genomes. Within the mandarin germplasm without identified introgression, seven clusters were revealed by 'Structure' analysis. Five of them should be true basic mandarin groups and the other two include genotypes of known orsupposed hybrid origin. The contributions of these seven groups to the mandarin genotypes were estimated. The mitochondrial InDel analysis revealed eight mitotypes, in which the mandarin germplasm was representedin four of them. In this work, new insights in the organization of mandarin germplasm and its structure havebeen found, and different mandarin core collections were determined. This will allow a better management anduse of citrus germplasm collections and to perform genetic association studies.