Genetic characterization of different demes in Prunus persica revealed by RAPD markers

Cheng, Zhongping

doi:10.1016/j.scienta.2006.10.020

Cited by 12 publications

(10 citation statements)

References 11 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The broad potential of persimmon retrotransposon primers for future analyses of classification and phylogenetic relationship was further made evident by the clearcut separation between persimmon and its several related species, the unambiguous clusters that were congruent with geographic origins within the persimmon species, and groupings of citrus, grape, and pear that were consistent with the genetic relationships or taxonomic classifications reported in these crops. In addition, we detected high similarity among peach and its variations, supporting the results of Cheng (2007). The IRAP molecular data generated by these persimmon retrotransposon primers revealed genotypes of high genetic similarity in peach, bud sports in persimmon, and different superior lines from 'Mandarin Oranges', which could all be distinguished well, suggesting that the transferable persimmon retrotransposon primers tested might offer a potential primer resource for variation identification, especially in bud sports.…”

Section: Discussionsupporting

confidence: 82%

“…DNA isolation of persimmon, apple, pear, and hawthorn followed the methods of Doyle and Doyle (1987); isolation of citrus, grape, loquat, kiwifruit, jujube, chestnut, and ginkgo DNA followed the methods of Cheng et al (2003); plum and peach DNA isolation followed the protocol of Cheng (2007). Quality and quantity of DNA preparations were checked by standard spectrophotometry and the samples were diluted to a concentration of 10 ng/μL before use.…”

Section: Genomic Dna Extractionmentioning

confidence: 99%

See 1 more Smart Citation

Transferability of retrotransposon primers derived from Persimmon (Diospyros kaki Thunb.) across other plant species

Hu²,

Zhang

et al. 2013

Genet. Mol. Res.

View full text Add to dashboard Cite

ABSTRACT.Retrotransposon-based molecular markers are powerful molecular tools. However, these markers are not readily available due to the difficulty in obtaining species-specific retrotransposon primers. Although recent techniques enabling the rapid isolation of retrotransposon sequences have facilitated primer development, this process nonetheless remains time-consuming and costly. Therefore, research into the transferability of retrotransposon primers developed from one plant species onto others would be of great value. The present study investigated the transferability of retrotransposon primers derived from 'Luotian-tianshi' persimmon (Diospyros kaki Thunb.) across other fruit crops, as well as within the genus using inter-retrotransposon amplified polymorphism molecular marker. Fourteen of the 26 retrotransposon primers tested (53.85%) produced robust and reproducible amplification products across all fruit crops tested, indicating their applicability across plant species. Four of the 13 fruit crops showed the best transferability performances: persimmon, grape, citrus, and peach. Furthermore, similarity coefficients and UPGMA clustering indicated that these primers could further offer a potential tool for germplasm differentiation, parentage identification, genetic diversity assessment, classification, and phylogenetic studies across a variety of plant species. Transferability was further confirmed by examining published primers derived from Rosaceae, Gramineae, and Solanaceae. This study is one of the few currently available studies concerning the transferability of retrotransposon primers across plant species in general, and is the first successful study of the transferability of retrotransposon primers derived from persimmon. The primers presented here will help reduce costs for future retrotransposon primer development and therefore contribute to the popularization of retrotransposon molecular markers.

show abstract

Section: Discussionsupporting

confidence: 82%

Section: Genomic Dna Extractionmentioning

confidence: 99%

Transferability of retrotransposon primers derived from Persimmon (Diospyros kaki Thunb.) across other plant species

Hu²,

Zhang

et al. 2013

Genet. Mol. Res.

View full text Add to dashboard Cite

show abstract

“…The markers provide a very reliable and convenient tool for analyzing genetic diversity of P. davidiana. Recent literatures from many studies reported genetic variations on peach and related species in the subgenus Amygdalus using molecular biological analyses Bouhadida et al, 2007;Cheng, 2007a;Cheng, 2007b;Cheng and Huang, 2009;Cipriani et al, 1999;Dirlewanger et al, 2002;Shiran, 2007;Sosinski et al, 2000;Testolin et al, 2000;Wang et al, 2002), however, the genetic diversity and genetic structure of natural populations of P. davidiana still remains unknown.…”

Section: Introductionmentioning

confidence: 99%

Genetic Diversity and Genetic Structure in Natural Populations of Prunus davidiana Germplasm by SSR Markers

Cheng

Gašić

Wang

et al. 2011

JAS

Self Cite

View full text Add to dashboard Cite

Prunus davidiana, which is a wild species, can be used as rootstocks for cultivation of fruit trees, breeding germplasm for improving resistance to diseases and insects, pioneer trees for recovering vegetation in arid areas, decoration trees for parks and gardens, and a potential medicinal plant for human health. Despite the valuable characteristics of P. davidiana, the genetic variations of resources of P. davidiana remain unclear. In this study, we used seven natural populations (GE; GH; ST; SF; SJ; SY; NX short for Heshui, Gansu; Huating Gansu; Taibai, Shaanxi; Fuxian, Shaanxi; Jiaocheng, Shanxi; Yangquan, Shanxi; Xiji, Ningxia, respectively) of P. davidiana collected at distribution center in China to generate a fingerprint using 15 SSR markers by multifluorophore fragment analysis to assess transportability of the markers, genetic diversity and genetic structure within and among populations. Our data show that a 92% transportability rate was found from closely related species of P. davidiana based on SSR markers developed, and DNA polymorphisms were also detected among accessions by the selected SSR markers. The SSR markers amplified 137 alleles in total for all accessions with an average value of 9.13 alleles, ranging from the highest value of 15 alleles for UDP96-013 to the lowest value of 3 alleles for CPPCT017. Rare alleles, present at less than or equal to 5% of all accessions by marker, showed the highest value in BPPCT 020. By analyzing all accessions, the majority of the 192 accessions from seven populations were found to cluster together according to the given populations, while the minority from the given populations was distributed within clusters. The SY population appeared to have the most diversity among populations, followed by the NX population according to comprehensive analysis of all indices. The seven populations analyzed by unweighted parsimony and principal coordinate analysis were divided into two groups: ST, SY and SF; NX, GE, SJ and GH. A stark difference was found in the genetic variation—with 16% among populations and 84% within populations. Our results from this study imply that most SSR markers developed from related species can be used for genetic analyses of P. davidiana; some markers have more relevant applications for genetic analyses such as UDP96-013 for diversity evaluation and BPPCT 020 for mining rare alleles in P. davidiana; SY and NX are preferred when considering conservation and agronomic utilization.

show abstract

“…For cluster analysis, in addition, bootstrapping is performed to obtain the strength of clusters, which can be thought as a confidence limit and can be included in the dendrogram as percentage values 11, 13, 14. Some studies, further, provide all pairwise similarities in matrix form 9, 15–17…”

Section: Introductionmentioning

confidence: 99%

Evaluation of confidence limit estimates of cluster analysis on molecular marker data

Kayış

2011

J Sci Food Agric

View full text Add to dashboard Cite

show abstract

Genetic characterization of different demes in Prunus persica revealed by RAPD markers

Cited by 12 publications

References 11 publications

Transferability of retrotransposon primers derived from Persimmon (Diospyros kaki Thunb.) across other plant species

Transferability of retrotransposon primers derived from Persimmon (Diospyros kaki Thunb.) across other plant species

Genetic Diversity and Genetic Structure in Natural Populations of Prunus davidiana Germplasm by SSR Markers

Evaluation of confidence limit estimates of cluster analysis on molecular marker data

Contact Info

Product

Resources

About