Genetic analysis of citron (Citrus medica L.) using simple sequence repeats and single nucleotide polymorphisms

•Studied 47 citrons; many from Yunnan, an area of origin; many novel taxa.•Conducted analysis using microsatellites and single nucleotide polymorphisms.•Heterozygosity observed in some. Structure analysis revealed three populations.•Clusters 1 and 2 from China (non-fingered, fingered); cluster 3 from Mediterranean.•A citron-specific microsatellite marker identified.

Citron (Citrus medica L.) is one of the three basic species of the genus Citrus L. that have contributed to the development of cultivated citrus. We analyzed the genetic diversity of 47 citrons (32 from Yunnan Province, China; and 15 of Mediterranean origin) to understand their diversity and relationships within the species. Genetic analysis was conducted using data from microsatellite markers, single nucleotide polymorphisms generated from sequences of a nuclear malate dehydrogenase gene and a chloroplast gene, rps16. Neighbor joining and maximum parsimony analyses were conducted. All three approaches found citron to be monophyletic. Population structure analysis clustered the 47 citrons into three distinct groups. The first group consisted of wild, non-fingered citrons generally having locules, juice sacs and seeds within the fruit. The second cluster consisted mostly of fingered citrons that lacked locules, juice sacs or seeds, and some non-fingered types with smaller locules and vestigial juice sacs, but with seeds. All accessions that clustered in groups I and II originated in China. The third cluster consisted of citrons cultivated in the Mediterranean region. Genetic distance between the clusters from population structure analysis indicated considerable diversity within the species. A citron-specific microsatellite marker was identified and characterized. We observed considerable heterozygosity in certain citrons, contrary to previous reports.

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