Diversity of Chloroplast DNA in Various Mandarins (Citrus spp.) and Other Citrus Demonstrated by CAPS Analysis

Yamamoto, Masashi; Tsuchimochi, Yui; Ninomiya, Takanori; Koga, T.; Kitajima, Akira; Yamasaki, Akira; Inafuku-Teramoto, Sayuri; Yang, Xuehu; Yang, Xiao; Zhong, Guoqiang; Nasir, Nasril; Kubo, Tatsuya; Tominaga, Shigeto

doi:10.2503/jjshs1.82.106

Cited by 16 publications

(10 citation statements)

References 25 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…sinensis ) and pummelo ( C . maxima ) into the same category [33,47,50,53,54,57], but this study separated them into different categories. Curk and colleagues classified citrus varieties into six categories with three chloroplast DNA markers and three mitochondrial DNA markers [47].…”

Section: Resultsmentioning

confidence: 99%

Hybrid Origins of Citrus Varieties Inferred from DNA Marker Analysis of Nuclear and Organelle Genomes

et al. 2016

Self Cite

View full text Add to dashboard Cite

Most indigenous citrus varieties are assumed to be natural hybrids, but their parentage has so far been determined in only a few cases because of their wide genetic diversity and the low transferability of DNA markers. Here we infer the parentage of indigenous citrus varieties using simple sequence repeat and indel markers developed from various citrus genome sequence resources. Parentage tests with 122 known hybrids using the selected DNA markers certify their transferability among those hybrids. Identity tests confirm that most variant strains are selected mutants, but we find four types of kunenbo (Citrus nobilis) and three types of tachibana (Citrus tachibana) for which we suggest different origins. Structure analysis with DNA markers that are in Hardy–Weinberg equilibrium deduce three basic taxa coinciding with the current understanding of citrus ancestors. Genotyping analysis of 101 indigenous citrus varieties with 123 selected DNA markers infers the parentages of 22 indigenous citrus varieties including Satsuma, Temple, and iyo, and single parents of 45 indigenous citrus varieties, including kunenbo, C. ichangensis, and Ichang lemon by allele-sharing and parentage tests. Genotyping analysis of chloroplast and mitochondrial genomes using 11 DNA markers classifies their cytoplasmic genotypes into 18 categories and deduces the combination of seed and pollen parents. Likelihood ratio analysis verifies the inferred parentages with significant scores. The reconstructed genealogy identifies 12 types of varieties consisting of Kishu, kunenbo, yuzu, koji, sour orange, dancy, kobeni mikan, sweet orange, tachibana, Cleopatra, willowleaf mandarin, and pummelo, which have played pivotal roles in the occurrence of these indigenous varieties. The inferred parentage of the indigenous varieties confirms their hybrid origins, as found by recent studies.

show abstract

Section: Resultsmentioning

confidence: 99%

Hybrid Origins of Citrus Varieties Inferred from DNA Marker Analysis of Nuclear and Organelle Genomes

et al. 2016

Self Cite

View full text Add to dashboard Cite

show abstract

“…Ninomiya et al (2015) and Nonaka et al (2017) reported the cultivar identification and parental analysis of new citrus cultivars in Japan using these markers. In addition, for chloroplast (cp) DNA analysis, CAPS uses universal primers and has proven to be a simple and reliable method for many genera (Cipriani and Morgante, 1993;Taberlet et al, 1991), including citrus (Asadi Abkenar et al, 2004;Fujii et al, 2016;Nicolosi et al, 2000;Yamamoto et al, 2013Yamamoto et al, , 2017. These results indicate the usefulness of CAPS analysis in terms of both the nuclear genome and cpDNA for phylogenetic studies of citrus.…”

Section: Introductionmentioning

confidence: 96%

Investigation and DNA Analysis of Local <i>Citrus</i> Genetic Resources Grown on the Chuuk Islands of Micronesia

2018

Self Cite

View full text Add to dashboard Cite

An investigation of local citrus genetic resources grown on the Chuuk Islands of the Federated States ofMicronesia was conducted in August 2013. A total of 21 accessions were examined. According to the morphological traits, ten, four, four, two, and one accession resembled lime (local name "Nayimis"), sour orange ("Kurukur"), calamondin ("Tangerin" and "Gunkan"), sweet orange ("Kurukur" and "American Kurukur"), and pummelo ("Kurukur"), respectively. Next, cleaved amplified polymorphic sequence (CAPS) analysis was conducted. Then, precise accession identification was made based on the results of CAPS analysis in conjunction with morphological traits. "Nayimis" accessions were classified into at least two types. Genotypes of "Nayimis" type 1 were identical to those of Mexican lime. A genetic influence from mandarin was detected in "Nayimis" type 2. Although the morphological traits of all "Kurukur" sour orange types were similar, their diversity was revealed by CAPS analysis. The genotype of one "Kurukur" accession was identical to that of sour orange. Genotypes of the sweet orange-type "Kurukur" and "American Kurukur" were different. The types of "American Kurukur" and sweet orange were the same. Pummelo-type "Kurukur" was considered to be true pummelo based on the results of morphological and molecular markers. Morphologically, the calamondin-like accessions "Tangerin" and "Gunkan" showed the same genotype combinations on CAPS analysis. These genotypes were identical to those of calamondin used as a control. The combined results of morphological and molecular markers offer valuable information for the identification of citrus genetic resources on the Chuuk Islands.

show abstract

“…(Palmer et al, 1988;Bayer et al, 2009;Lu et al, 2011). More recently, different molecular markers such as cleaved amplified polymorphic sequence (CAPS) of cpDNA (Yamamoto et al, 2013;Ninomiya et al, 2015;Fujii et al, 2016) (Nonaka et al, 2017;Dorji and Yapwattanaphun, 2015;Froelicher et al, 2011), have been used for identification, parentage analysis and phylogeny of citrus species or cultivars.…”

Section: Introduction Smentioning

confidence: 99%

Molecular genetic diversity assessment of Citrus species grown in Iran revealed by SSR, ISSR and CAPS molecular markers

Sharafi

Abkenar

Sharafi

2017

JSR

View full text Add to dashboard Cite

En este estudio, se analizó la diversidad genética en 19 cultivares de cítricos mediante la repetición de secuencia simple (SSR), la repetición de secuencia inter-simple (ISSR) y los marcadores de secuencia polimórfica amplificada segmentada (CAPS). Se utilizaron nueve cebadores para SSR, nueve cebadores ISSR y dos cebadores para CAPS para la puntuación del alelo. Se analizaron una región de ADN de cloroplasto (rbcL-ORF106) y una región de ADN mitocondrial (18S-5S) usando marcador de secuencia polimórfica amplificada escindida (CAPS) en 19 accesiones de cítricos cultivadas en Irán. En total, se detectaron 45 genes SSR y 131 ISSR polimórficos alelos y organelos del genoma del árbol. El análisis de conglomerados de los datos SSR y ISSR se realizó utilizando el método UPGMA y se basó en el coeficiente de Jaccard. El resultado de esta investigación mostró que los cebadores SSR e ISSR eran altamente informativos y eficientes para detectar la variabilidad genética y las relaciones de las accesiones de los cítricos. Y el análisis de marcadores de CAPS Los resultados mostraron que Bakraee y uno de tipo off cal mexicana tenían un patrón de bandas similar al Clementine Mandarin, mientras que Pummelo se consideraba como padre materno de otros genotipos estudiados Citron considerado como padre padre mostró un patrón de bandas definido entre 19 genotipos estudiados que confirmó Citoplasma herencia de orgánulos celulares de la madre.

show abstract

Diversity of Chloroplast DNA in Various Mandarins (Citrus spp.) and Other Citrus Demonstrated by CAPS Analysis

Cited by 16 publications

References 25 publications

Hybrid Origins of Citrus Varieties Inferred from DNA Marker Analysis of Nuclear and Organelle Genomes

Hybrid Origins of Citrus Varieties Inferred from DNA Marker Analysis of Nuclear and Organelle Genomes

Investigation and DNA Analysis of Local <i>Citrus</i> Genetic Resources Grown on the Chuuk Islands of Micronesia

Molecular genetic diversity assessment of Citrus species grown in Iran revealed by SSR, ISSR and CAPS molecular markers

Contact Info

Product

Resources

About