R-ISSR as a new tool for genomic fingerprinting, mapping, and gene tagging

Ye, Chunjiang; Yu, Zhanwang; Kong, Fanna; Shu, Wu; Wang, Bin

doi:10.1007/bf02772707

Cited by 33 publications

(26 citation statements)

References 18 publications

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“…Bulk segregant analysis conducted for pooled groups of segregants selected from such populations allows quick and effective identification of markers linked to QTL(s) controlled by major genes (Michelmore et al 1991). The possibility of rapid screening of many loci (Michelmore et al 1991;Soller, 1992, Darvasi andSoller, 1994;Angaji, 2009;Semagn et al 2010), combined with the possibility of the application of markers exploring thus far unexamined chromosome regions, provides the possibility of the identification of a new range of variability as well as markers linked to the identified QTL(s) (Ye et al 2005;Saleh, 2011;Smolik et al 2012;Smolik, 2013b).…”

Section: With Various Concentrations Of No3mentioning

confidence: 99%

Chromosomal localization of selected SCARs converted from new RAPD, ISSR and R-ISSR markers linked to rye (Secale cereale L.) tolerance to nutrient deprivation stress identified using bulk segregant analysis

Smolik¹

2013

Electron. J. Biotechnol.

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Background: An adaptive mechanism in plant roots is initiated in the event of nitrogen and potassium deficiency, and it facilitates the active uptake of these elements in order to ensure plant growth and survival in stress conditions. Signaling and transduction of signals in response to changing nitrogen and potassium concentrations is a complex process, affected by interactions between various gene expression products, and often subjected to modifications. Results: In order to identify genotypic differences between phenotypes of two populations of recombinant inbred rye lines (153/79-1 x Ot1-3 and Ot0-6 x Ot1-3) in response to nutrition stress caused by nitrogen and potassium deficiency at the seedling stage, bulk segregant analysis was utilized. Identification of genotypic differences between and within pooled DNA samples involved 424 RAPD, 120 ISSR primers and 50 combinations of R-ISSR. Identified markers were sequenced and converted to SCAR, attributing to them unique ESTs annotations, and chromosomal ones to selected localizations. Significant relationships with the examined trait were described for nine and eight RAPD markers, four and five ISSR, one and three R-ISSR markers for population 153/79-1 x Ot1-3 and Ot0-6 x Ot1-3, respectively. Sequences identified for the rye genome were characterized by a uniqueness and a similarity to the sequence of aquaporin PIP1, a gene encoding protein related to the function of the transcription factor in plant response to iron deficiency and the putative ethylene-responsive transcription factor, cytosolic acetyl-CoA carboxylase, HvHKT1 transporter, as well as HCBT proteins. Conclusion: Identified molecular markers differentiating rye genotypes of extreme response of root system on nitrogen and potassium deficiency play a significant role in systemic plant response to stress, including stress caused by nitrogen and potassium deficiency. They may constitute a system facilitating selection, and together with the material they are described in, they may be a starting point for research on mechanisms of sensing and transduction of signal across the plant.

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Section: With Various Concentrations Of No3mentioning

confidence: 99%

Chromosomal localization of selected SCARs converted from new RAPD, ISSR and R-ISSR markers linked to rye (Secale cereale L.) tolerance to nutrient deprivation stress identified using bulk segregant analysis

Smolik¹

2013

Electron. J. Biotechnol.

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“…Because of the higher annealing temperature and longer sequence of ISSR primers, they can yield more reliable and reproducible bands than random amplification of polymorphic DNA (RAPD; Nagaoka and Ogihara, 1997;Wolfe et al, 1998;Goulao et al, 2001;Qian et al, 2001), and the cost of these analyses is lower than that of some other markers such as restriction fragment length polymorphisms (RFLPs), simple sequence repeats (SSRs), and amplified fragment length polymorphisms (AFLPs; Yang et al, 1996;Wang et al, 2008). In addition to freedom from the necessity of obtaining genomic sequence information, ISSR markers are technically simpler than many other marker systems in the genetic diversity studies of plants (Ratnaparkhe et al, 1998;Bornet and Branchard, 2001;Ye et al, 2005). To date, no report is available on applications of molecular markers in studies on the genetic diversity of A. rugosa.…”

Section: Introductionmentioning

confidence: 99%

Genetic Diversity and Population Structure of Korean Mint Agastache rugosa (Fisch & Meyer) Kuntze (Lamiaceae) Using ISSR Markers

Kang¹,

Suresh²,

Lee³

et al. 2013

Korean Journal of Plant Resources

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-Agastache rugosa, a member of the mint family (Labiatae), is a perennial herb widely distributed in East Asian countries. It is used in traditional medicine for the treatment of cholera, vomiting, and miasma. This study assessed the genetic diversity and population structures on 65 accessions of Korean mint A. rugosa germplasm based on inter simple sequence repeat (ISSR) markers. The selected nine ISSR primers produced reproducible polymorphic banding patterns. In total, 126 bands were scored; 119 (94.4%) were polymorphic. The number of bands generated per primer varied from 7 to 18. A minimum of seven bands was generated by primer 874, while a maximum of 18 bands was generated by the primer 844. Six primers (815, 826, 835, 844, 868, and 874) generated 100% polymorphic bands. This was supported by other parameters such as total gene diversity (HT) values, which ranged from 0.112 to 0.330 with a mean of 0.218. The effective number of alleles (NE) ranged from 1.174 to 1.486 with a mean value of 1.351. Nei's genetic diversity (H) mean value was 0.218, and Shannon's information index (I) mean value was 0.343. The high values for total gene diversity, effective number of alleles, Nei's genetic diversity, and Shannon's information index indicated substantial variations within the population. Cluster analysis showed characteristic grouping, which is not in accordance with their geographical affiliation. The implications of the results of this study in developing a strategy for the conservation and breeding of A. rugosa and other medicinal plant germplasm are discussed.

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“…21,[27][28][29][30] Moreover, ISSR analysis offers other advantages in wide applications for all organisms without requiring prior sequence information. 31) Therefore, for this study, we utilized ISSR markers to assess genetic fidelity of A. formosanus plantlets propagated in vitro for a period of more than 5 years. To our knowledge, this is the first report on the analysis of DNA sequence variation in micropropagated plantlets of A. formosanus.…”

mentioning

confidence: 99%

Analysis of Genetic Stability through Intersimple Sequence Repeats Molecular Markers in Micropropagated Plantlets of Anoectochilus formosanus HAYATA, a Medicinal Plant

Zhang

Dong

et al. 2010

Biological & Pharmaceutical Bulletin

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Anoectochilus formosanus HAYATA, commonly known as "Jewel Orchids," which has been used as Chinese folk medicines, is being subjected to a huge crisis, whose wild resources have gradually become more and more scarce. Hence, micropropagation protocol by axillary branching established for A. formosanus was employed for large-scale commercial production. In this study, due to the somaclonal variation and on the basis of some virtue of intersimple sequence repeats (ISSR) analysis, we firstly utilized the ISSR primers to investigate the genetic stability of A. formosanus propagated in vitro for a period of more than 5 years. Among the total 100 bands amplified by 17 ISSR markers, 77 bands were distributed in size from 500 bp to 1.5 kbp, while only 5 bands were beyond 1.8 kbp in size. Meanwhile, according to the cluster analysis, genetic similarity was more than 94% and the polymorphism rate was only 2.76% among the total 1810 scorable bands. All results demonstrate A. formosanus, multiplied by axillary branching, maintained high genetic fidelity even after a period of more than 5 years under in vitro propagation with only a low risk of genetic instability. The results from this study provide an important basis for giving evidence of genetic stability of A. formosanus before micropropagation for large-scale commercial production.

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R-ISSR as a new tool for genomic fingerprinting, mapping, and gene tagging

Cited by 33 publications

References 18 publications

Chromosomal localization of selected SCARs converted from new RAPD, ISSR and R-ISSR markers linked to rye (Secale cereale L.) tolerance to nutrient deprivation stress identified using bulk segregant analysis

Chromosomal localization of selected SCARs converted from new RAPD, ISSR and R-ISSR markers linked to rye (Secale cereale L.) tolerance to nutrient deprivation stress identified using bulk segregant analysis

Genetic Diversity and Population Structure of Korean Mint Agastache rugosa (Fisch & Meyer) Kuntze (Lamiaceae) Using ISSR Markers

Analysis of Genetic Stability through Intersimple Sequence Repeats Molecular Markers in Micropropagated Plantlets of Anoectochilus formosanus HAYATA, a Medicinal Plant

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