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

Publication Overview
TitleA set of primers for analyzing chloroplast DNA diversity in Citrus and related genera
AuthorsCheng Y, Vicente Md, Meng H, Guo W, Tao N, Deng X
TypeJournal Article
Journal NameTree physiology
CitationCheng Y, Vicente Md, Meng H, Guo W, Tao N, Deng X. A set of primers for analyzing chloroplast DNA diversity in Citrus and related genera. Tree physiology. 2005; 25(6):661-672.


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.
This publication contains information about 14 features:
Feature NameUniquenameType
SPCC 1SPCC 1genetic_marker
SPCC 10SPCC 10genetic_marker
SPCC 11SPCC 11genetic_marker
SPCC 12SPCC 12genetic_marker
SPCC 13SPCC 13genetic_marker
SPCC 14SPCC 14genetic_marker
SPCC 2SPCC 2genetic_marker
SPCC 3SPCC 3genetic_marker
SPCC 4SPCC 4genetic_marker
SPCC 5SPCC 5genetic_marker
SPCC 6SPCC 6genetic_marker
SPCC 7SPCC 7genetic_marker
SPCC 8SPCC 8genetic_marker
SPCC 9SPCC 9genetic_marker
This publication contains information about 31 stocks:
Stock NameUniquenameType
Allen Eureka lemonAllen Eureka lemonaccession
Bendiguangju mandarinBendiguangju mandarinaccession
Bendizaoju tangerineBendizaoju tangerineaccession
Cleopatra mandarinCleopatra mandarinaccession
Duwei pummeloDuwei pummeloaccession
Fingered CitronFingered Citronaccession
Goutou sour orangeGoutou sour orangeaccession
Guoqin No. 4 satsumeGuoqin No. 4 satsumeaccession
Hongju tangerineHongju tangerineaccession
Ichang papedaIchang papedaaccession
Jincheng orangeJincheng orangeaccession
Kuikan mandarinKuikan mandarinaccession
Nanfeng mandarinNanfeng mandarinaccession
Nanju tangerineNanju tangerineaccession
Newhall orangeNewhall orangeaccession
Page tangeloPage tangeloaccession
Red marsh grapefruitRed marsh grapefruitaccession


Additional details for this publication include:
Property NameValue
Publication TypeJournal Article
Publication Date2005
Published Location|||
Language Abbreng
KeywordsCitrus, Fortunella, Poncirus, hybrids, genetic variation, chloroplast DNA, DNA fingerprinting, sequence homology, microsatellite repeats, nucleotide sequences, molecular sequence data