Inter-simple-sequence-repeat (ISSR) polymorphisms are useful for finding markers associated with disease resistance gene clusters

Ratnaparkhe, Milind B.; Tekeoglu, M.; Muehlbauer, F. J.

doi:10.1007/s001220050925

Cited by 105 publications

(59 citation statements)

References 17 publications

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“…However, these sequence homologies may indicate duplications of genome segments of unknown size between potato chromosomes IX, XII and VIII. These findings are in agreement with other studies (Yu et al 1996;Ratnaparkhe et al 1998), suggesting that disease resistance loci in plants are often accompanied by microsatellite sequences.…”

Section: Discussionsupporting

confidence: 93%

Potato chromosomes IX and XI carry genes for resistance to potato virus M

et al. 2006

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Two new loci for resistance to potato virus M (PVM), Gm and Rm, have been mapped in potato. The gene Gm was derived from Solanum gourlayi, whereas, Solanum megistacrolobum is the source of the gene Rm. Gm confers resistance to PVM infection after mechanical inoculation. Rm induces a hypersensitive response in potato plants. Two diploid populations segregating for Gm and Rm, bulked segregant analysis (BSA) using random amplified polymorphic DNA (RAPD) and inter-simple sequence repeat (ISSR), and available potato molecular maps were instrumental for mapping the resistance loci. The novel locus Gm was mapped to a central region on potato chromosome IX. The locus Rm was placed on the short arm of chromosome XI, close to the marker loci GP250 and GP283, where a hotspot for monogenic and polygenic resistance to diverse pathogens is located in the potato and tomato genome.

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Section: Discussionsupporting

confidence: 93%

Potato chromosomes IX and XI carry genes for resistance to potato virus M

et al. 2006

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“…ISSR primers of repeat motifs (microsatellites) that are abundant and dispersed throughout genomes anchor at either the 5' or 3' end with one or a few specific nucleotides. Sequences are amplified between two microsatellite loci (Wang et al, 1994;Wang et al, 2008;Zietkiewicz et al, 1994;Ratnaparkhe et al, 1998). 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).…”

Section: Introductionmentioning

confidence: 99%

“…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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“…Because of these reasons, ISSR are being used for population authentication and population molecular ecology studies. [8][9][10][11][12][13][14][15][16] The present study was undertaken with the objective of establishing specific molecular markers using ISSR for authenticating eight wild D. officinale populations. …”

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confidence: 99%

Intersimple Sequence Repeats (ISSR) Molecular Fingerprinting Markers for Authenticating Populations of Dendrobium officinale KIMURA et MIGO

Shen

Ding

Liu

et al. 2006

Biological & Pharmaceutical Bulletin

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(previous name: Dendrobium candidum WALL. ex LINDL. 2)) is an endangered species in China and ranked "the first of the nine Chinese fairy herbs." The stems of D. officinale have been used as a traditional Chinese tonic medicine called Tiepi Fengdou 3) for hundreds of years. It can benefit human health in many aspects, such as nourishing yin and clearing away unhealthy heat, benefiting the stomach, promoting the production of body fluid, resisting cancer and prolonging life 1,3) This treasured herb is in severe shortage, making it expensive; the highest grade costs ¥12000-30000 per kg. 4)In our previous studies, rDNA ITS regions of D. officinale and other four adulterant species were sequenced. A pair of allele-specific diagnostic primers was designed to authenticate D. officinale from the other species based on rDNA ITS sequences of D. officinale and the other 37 species of Dendrobium.5,6) Recently, we have focused on the authentication of D. officinale populations using DNA molecular markers, which will lay the foundation for the selection of high-quality population resources.Intersimple sequence repeats (ISSR) have become a good DNA molecular marker for research on populations of the same species, a technique established based on PCR by Zietkiewicz et al. in 1994. 7) The main advantages of ISSR are: no need for DNA sequence information prior to amplification, low cost, simple operation, high stability, and abundance of genomic information. Because of these reasons, ISSR are being used for population authentication and population molecular ecology studies. [8][9][10][11][12][13][14][15][16] The present study was undertaken with the objective of establishing specific molecular markers using ISSR for authenticating eight wild D. officinale populations. MATERIALS AND METHODS Plant MaterialsAll materials used in this study were collected in China. Voucher samples were identified by Dr. Xiaoyu Ding and preserved by means of tissue culture in the College of Life Sciences, Nanjing Normal University. Wherever possible, three to five individuals were sampled from each population. The details are shown in Table 1.DNA Extraction Complete genomic DNA samples were extracted from fresh leaves using Dneasy Plant Mini Kits (QIAGEN), the concentrations of the DNA samples were measured spectrophotometrically, and each sample was diluted to 20 ng ml Ϫ1 with TE buffer for PCR amplification. Selection of Primers To select suitable primers for the study of populations of D. officinale, 76 ISSR primers, which were all purchased from Sangon Co., Ltd., China, were screened using two DNA samples. From the preliminary screening, 32 primers that could amplify visible bands were selected for further examination. Eventually, 10 ISSR primers that produced clear and reproducible bands were selected for the amplification of all DNA samples (Table 2).ISSR Profiling ISSR amplifications were carried out in a 25 ml volume containing Tris-HCl 10 mM, KCl 10 mM, (NH 4 ) 2 SO 4 8 mM (pH 9.0), MgCl 2 1.2-1.8 mM, Taq DNA polymerase1.5 U, dNTP 80 mM, pri...

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Inter-simple-sequence-repeat (ISSR) polymorphisms are useful for finding markers associated with disease resistance gene clusters

Cited by 105 publications

References 17 publications

Potato chromosomes IX and XI carry genes for resistance to potato virus M

Potato chromosomes IX and XI carry genes for resistance to potato virus M

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

Intersimple Sequence Repeats (ISSR) Molecular Fingerprinting Markers for Authenticating Populations of Dendrobium officinale KIMURA et MIGO

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