Fingerprinting trifoliate orange germ plasm accessions with isozymes, RFLPs, and inter-simple sequence repeat markers

Fang, David D.; Roose, Mikeal L.; Krueger, Robert R.; Federici, Claire T.

doi:10.1007/s001220050550

Cited by 155 publications

(102 citation statements)

References 33 publications

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“…This transition was genus/ species specific, occurring only in P. trifoliata. As a group, the trifoliate oranges all tend to be similar to one another (Fang et al 1997) and are divergent from the genus Citrus (Nicolosi et al 2000;Barkley et al 2006;Pang et al 2007). This may explain why these alleles of different sizes share the same point mutation in the flanking sequence.…”

Section: Locus Gt03mentioning

confidence: 99%

What phylogeny and gene genealogy analyses reveal about homoplasy in citrus microsatellite alleles

et al. 2009

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Sixty-five microsatellite alleles amplified from ancestral citrus accessions classified in three separate genera were evaluated for sequence polymorphism to establish the basis of inter-and intra-allelic genetic variation, evaluate the extent of size homoplasy, and determine an appropriate model (stepwise or infinite allele) for analysis of citrus microsatellite alleles. Sequences for each locus were aligned and subsequently used to determine relationships between alleles of different taxa via parsimony. Interallelic size variation at each SSR locus examined was due to changes in repeat copy number with one exception. Sequencing these alleles uncovered new distinct point mutations in the microsatellite region and the region flanking the microsatellite. Several of the point mutations were found to be genus, species, or allele specific, and some mutations were informative about the inferred evolutionary relationships among alleles. Overall, homoplasy was observed in alleles from all three loci, where the core microsatellite repeat was changed causing alleles of the same size class to be identical in state but not identical by descent. Because nearly all changes in allele size (with one exception) were due to expansion or contraction of the repeat motif, this suggests that a stepwise mutation model, which assumes homoplasy may occur, would be the most appropriate for analyzing Citrus SSR data. The collected data indicate that microsatellites can be a useful tool for evaluating Citrus species and two related genera since repeat motifs were reasonably well retained. However, this work also demonstrated that the number of microsatellite alleles is clearly an underestimate of the number of sequence variants present.

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Section: Locus Gt03mentioning

confidence: 99%

What phylogeny and gene genealogy analyses reveal about homoplasy in citrus microsatellite alleles

et al. 2009

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“…Methods such as restriction fragment length polymorphism (Fang et al, 1997;Fu et al, 2004), randomly amplified polymorphic DNA (AkaKacar et al, 2005;Rodriguez et al, 2005), amplified fragment length polymorphism (Fu et al, 2004;Campos et al, 2005), simple sequence repeats (SSR) (Barkley et al, 2006(Barkley et al, , 2009, inter-simple sequence repeats Capparelli et al, 2004), and sequence-related amplified polymorphism (SRAP) (Uzun et al, 2009) have been used.…”

Section: Introductionmentioning

confidence: 99%

Molecular characterization of sour orange (Citrus aurantium) accessions and their relatives using SSR and SRAP markers

Polat¹,

Kaçar

Yeşiloğlu³

et al. 2012

Genet. Mol. Res.

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ABSTRACT. Citrus production with its many varieties is of importance since it provides economically important products for Turkish exports. Sour orange is a rootstock commonly used for propagating the different scion varieties. Knowledge of the genetic diversity of the rootstock accessions would be useful in order to improve citrus breeding programs. We studied genetic relationships and diversity of 51 accessions of sour orange (Citrus aurantium) and their relatives using SSR (simple sequence repeat) and SRAP (sequence-related amplified polymorphism) molecular markers. Twenty-one SRAP primer combinations were tested on these accessions and relatives, producing 167 polymorphic fragments, with a mean of 8.0 and a mean polymorphism information content value of 0.47. Seventeen SSR primers also produced 30 polymorphic fragments, with a mean of 1.4 per primer and a mean polymorphism information content value of 0.39. The unweighted pair-group method with arithmetic average analysis using combined SSR and SRAP data showed a similarity range from 0.71 to 1.00 among the accessions. In the cluster analysis, sour orange relatives were indicated as a separate group from sour orange. 'Macrophylla' and 'Mexican lime' were the accessions most distinct (0.71) from the others. We conclude that genetic diversity in these sour orange accessions is lower and some of them were identical.

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“…Molecular markers such as isozymes, RFLP and RAPD have been applied to study genetic diversity (1,6,7,10,14,29) and relationships within the genus Citrus (15,27) in order to complement morphological data and thus shed more light on the classification of Citrus.…”

Section: Introductionmentioning

confidence: 99%

Characterization of Citrus Cultivars and Clones in Cyprus Through Microsatellite and RAPD Analysis

Hvarleva

Kapari-Isaia

Papayiannis

et al. 2008

Biotechnology & Biotechnological Equipment

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Fingerprinting trifoliate orange germ plasm accessions with isozymes, RFLPs, and inter-simple sequence repeat markers

Cited by 155 publications

References 33 publications

What phylogeny and gene genealogy analyses reveal about homoplasy in citrus microsatellite alleles

What phylogeny and gene genealogy analyses reveal about homoplasy in citrus microsatellite alleles

Molecular characterization of sour orange (Citrus aurantium) accessions and their relatives using SSR and SRAP markers

Characterization of Citrus Cultivars and Clones in Cyprus Through Microsatellite and RAPD Analysis

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