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Chloroplast simple sequence repeat (cpSSR) markers in  Citrus  were developed and used to analyze chloroplast diversity of  Citrus  and closely related genera. Fourteen cpSSR primer pairs from the chloroplast genomes of tobacco ( Nicotiana tabacum  L.) and  Arabidopsis  were found useful for analyzing the  Citrus  chloroplast genome (cpDNA) and recoded with the prefix SPCC (SSR Primers for  Citrus  Chloroplast). Eleven of the 14 primer pairs revealed some degree of polymorphism among 34 genotypes of  Citrus ,  Fortunella ,  Poncirus  and some of their hybrids, with polymorphism information content (PIC) values ranging from 0.057 to 0.732, and 18 haplotypes were identified. The cpSSR data were analyzed with NTSYS-pc software, and the genetic relationships suggested by the unweighted pair group method based on arithmetic means (UPGMA) dendrogram were congruent with previous taxonomic investigations: the results showed that all samples fell into seven major clusters, i.e.,  Citrus medica  L.,  Poncirus ,  Fortunella ,  C. ichangensis  Blanco,  C. reticulata  Swingle,  C. aurantifolia  (Christm.) Swingle and  C. grandis  (L.) Osbeck. The results of previous studies combined with our cpSSR analyses revealed that: (1) Calamondin ( C. madurensis  Swingle) is the result of hybridization between kumquat ( Fortunella ) and mandarin ( C. reticulata ), where kumquat acted as the female parent; (2) Ichang papeda ( C. ichangensis ) has a unique taxonomic status; and (3) although Bendiguangju mandarin ( C. reticulata ) and Satsuma mandarin ( C. reticulata ) are similar in fruit shape and leaf morphology, they have different maternal parents. Bendiguangju mandarin has the same cytoplasm as sweet orange ( C. sinensis ), whereas Satsuma mandarin has the cytoplasm of  C. reticulata . Seventeen PCR products from SPCC1 and 21 from SPCC11 were cloned and sequenced. The results revealed that mononucleotide repeats as well as insertions and deletions of small segments of DNA were associated with SPCC1 polymorphism, whereas polymorphism generated by SPCC11 was essentially due to the variation in length of the mononucleotide repeats.

A set of primers for analyzing chloroplast DNA diversity in Citrus and related genera