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ARS Home » Pacific West Area » Riverside, California » National Clonal Germplasm Repository for Citrus » Research » Publications at this Location » Publication #308677
Title: Genetic analysis of citron (Citrus medica L.) using simple sequence repeats and single nucleotide polymorphisms

Author
item RAMADUGU, C. - University Of California
item Keremane, Manjunath
item HU, X. - University Of California
item KARP, D. - University Of California
item FEDERICI, C. - University Of California
item KAHN, T. - University Of California
item ROOSE, M. - University Of California
item Lee, Richard

Submitted to: Scientia Horticulturae
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/2/2015
Publication Date: 9/4/2015
Citation: Ramadugu, C., Keremane, M.L., Hu, X., Karp, D., Federici, C.T., Kahn, T., Roose, M.L., Lee, R.F. 2015. Genetic analysis of citron (Citrus medica L.) using simple sequence repeats and single nucleotide polymorphisms. Scientia Horticulturae. 195:124-137.

Interpretive Summary: Citron is thought to be one of the three ancestral species, along with pummelo and mandarins, that have been hybridized over the years to constitute most of the commercial cultivars of citrus that are familiar in the markets today. Most of the accessions of citron present in collections in the United States and in the collections in Riverside, California have been collected from the Mediterranean. In this study, citron DNA extracted from regions in China where citron is thought to have originated was compared to DNA extracted from representative citrons from the citrus collection in Riverside. Comparisons were done using three different methods: simple sequence repeat markers (SSR), single nucleotide polymorphisms (SNPs) of a nuclear gene region, malate dehydrogenase, and SNPs of a chloroplast gene, rps16. Population structure analyses clustered the 47 citrons being compared into three distinct groups: one group having wild non-fingered citrons generally having locules, juice sacs and seeds within the fruit; the second group having fingered citrons without locules, juice sacs or seeds and also some non-fingered citrons with reduced locules, juice and seeds; and the third group with non-fingered citrons with locules, juice sacs and seeds. Groups one and two originated from China while group three contained citrons thought to have been originally collected from the Mediterranean area. A citron specific SSR marker was identified from this study. The identification of study of new germplasm will factilitate citrus breeding programs.

Technical Abstract: Citron (Citrus medica L.) is one of the three basic species of the genus Citrus L. that has contributed to the development of many commercial cultivars. We analyzed the genetic diversity of a total of 54 varieties (47 citrons) to understand the relationships within the species. Thirty two varieties were from Yunnan province, China, presumably a major center of origin of citron. Many representative citrons originating from the Mediterranean region were also included in the study. Genetic analysis was conducted using a) 23 microsatellite markers, b) single nucleotide polymorphisms (SNPs) generated from sequences of a nuclear gene malate dehydrogenase and c) SNPs from a chloroplast gene, rps16. 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 of mostly fingered citrons that did not have any locules, juice sacs or seeds and some non-fingered types with reduced locules, juice sacs but with seeds. All accessions that clustered in groups I and II originated from China. The third cluster consisted of non-fingered citrons assumed to be from the Mediterranean region. Neighbor-joining and Maximum parsimony analyses were conducted with the SSR and SNP data. With a combination of the SSR and SNP approaches, we were able to differentiate between all citrons in the dataset. Net nucleotide distances between the clusters ranged from 0.1 to 0.17 indicating considerable diversity within the citron group. A citron-specific microsatellite marker was identified and characterized. We observed a high level of heterozygosity in certain citrons contrary to previous reports. Identification and study of new germplasm will facilitate breeding programs.