Molecular Markers: Principles and Methodology

Gupta, P. K.; Varshney, Rajeev K.; Prasad, Manoj

doi:10.1007/978-94-017-2356-5_2

Cited by 38 publications

(34 citation statements)

References 126 publications

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“…The higher expected heterozygosity (also referred to as diversity index) value for a marker system means a higher capacity to detect genetic variation. Selection of a particular type of molecular marker is critical and depends on the intended use (Gupta et al 2002). In the present study, ISSRs produced 133 polymorphic bands, with the highest mean values of PIC and expected heterozygosity.…”

Section: Discussionmentioning

confidence: 62%

EST-PCR, EST-SSR and ISSR markers to identify a set of wild cranberries and evaluate their relationships

Bykova

Debnath

2015

Can. J. Plant Sci.

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An, D., Bykova, N. V. and Debnath, S. C. 2015. EST-PCR, EST-SSR and ISSR markers to identify a set of wild cranberries and evaluate their relationships. Can. J. Plant Sci. 95: 1155Á1165. The cranberry (Vaccinium marcrocarpon Ait.) is a woody, evergreen, perennial vine with great potential for economic and health benefits. Selection and use of genetically diverse genotypes are key factors in any crop breeding program to develop cultivars with a broad genetic base. Molecular markers play a major role in selecting diverse genotypes. One hundred and two wild cranberry clones collected from four Canadian provinces and five cultivars were screened with inter simple sequence repeat (ISSR), expressed sequence tagÁ simple sequence repeat (EST-SSR) and ESTÁpolymerase chain reaction (PCR) markers to validate the genetic diversity and relationships among them. EST-PCRs (0.54) and EST-SSRs (0.35) generated higher frequency of major alleles than ISSRs (0.08), but ISSRs presented a higher level of polymorphism and greater polymorphic information content and expected heterozygosity than EST-SSRs and EST-PCRs. Combined cluster analysis by the unweighted pair-group method with arithmetic averages (UPGMA) separated the wild clones and cultivars into four main clusters, which was in agreement with the principal coordinate (PCo) analysis. Analysis of molecular variation detected sufficient variations among genotypes within communities and among communities within provinces with ISSR (66 and 36%, respectively), EST-PCR (72 and 34%, respectively) and EST-SSR (72 and 34%, respectively) markers. These values were 71 and 35%, respectively, for combined analysis. Combined use of three types of molecular markers, for the first time in Vaccinium species, detected a sufficient degree of variation among cranberry genotypes, allowing for differentiation and rendering these technologies valuable for genotype identification in a diverse cranberry germplasm and for more efficient parental choice in the current cranberry breeding program. Abbreviations: AFLP, amplified fragment length polymorphism; AMOVA, analysis of molecular variance; CCC, cophenetic correlation coefficient; EST, expressed sequence tag; ISSR, inter simple sequence repeat; PCo, principal coordinate; PCR, polymerase chain reaction; PIC, polymorphism information content; RAPD, randomly amplified polymorphic DNA; SSR, simple (short) sequence repeat; UPGMA, unweighted pair group method with arithmetic means Can.

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Section: Discussionmentioning

confidence: 62%

EST-PCR, EST-SSR and ISSR markers to identify a set of wild cranberries and evaluate their relationships

Bykova

Debnath

2015

Can. J. Plant Sci.

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“…Menurut Gupta et al (2002), STS merupakan marka berbasis PCR yang terdiri atas sekuen pendek dan khas, yang mampu mengidentifikasi satu atau lebih lokus spesifik. Marka ini diperoleh melalui proses sekuensing fragmen hasil RAPD, RFLP, AFLP, atau gen yang ukurannya telah diketahui (Bahagiawati, 2011).…”

Section: Pendahuluanunclassified

Keragaman Genetika Empat Belas Aksesi Kentang (Solanum tuberosum L.) Berdasarkan Marka SSR dan STS (Genetic Diversity of Fourteen Potato Accessions Based on SSR and STS Markers)

Nugroho¹,

Reflinur²,

Lestari³

et al. 2016

J. AgroBiogen

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Potato is one of high economically horticultural plant. The increasing of national consumption of potato becomes a challenge for potato breeders. The success of breeding programs is depending on availability of genetic diversity. The aim of this research was to analyze the genetic diversity of fourteen accessions of potato by using SSR and STS markers. PCR analysis was scored as biner data and the collected data was analyzed using NTSYS and PowerMarker. The result showed that there were 63% polymorphic (12 markers) of total markers. As many as 60 alleles with the size of 200-500 bp were identified by a range of 2-9 alleles per locus. The polymorphism level was 0.59 (0.36-0.74). Result also showed the average of major allele frequency was 49.42% (35.71-63.64%). Nine markers which have polymorphism level more than 0.5 could be used to detect genetic diversity of potato. The average of genetic diversity index was 0.65. Cluster analysis showed that 14 accessions of potato were split in two groups (coefficient 0.70). The first groups consisted of Atlantik, GM 05, Granola Kembang Merbabu 17, and the second groups consist of Repita, Maglia, Medians, CIP397078.7, CIP392781.1, Margahayu, Granola, CIP394613.139, Amabile, and Tenggo. The information of genetic diversity of this germplasm could be used as a preliminary basis for choosing crossing parents in potato breeding in Indonesia.Keywords: Potato (Solanum tuberosum L.), SSR, STS, genetic diversity. ABSTRAKKentang (Solanum tuberosum L.) merupakan salah satu tanaman hortikultura yang memiliki nilai ekonomis tinggi. Meningkatnya kebutuhan konsumsi kentang nasional menjadi tantangan bagi pemulia kentang. Tersedianya sumber keragaman genetika merupakan prasyarat keberhasilan program pemuliaan suatu varietas. Penelitian ini bertujuan menganalisis keragaman genetika empat belas aksesi kentang menggunakan marka simple sequence repeats (SSR) dan sequence-tagged sites (STS). Hasil analisis polymerase chain reaction (PCR) diberi skor sebagai data biner. Analisis data dilakukan menggunakan perangkat lunak NTSYS dan PowerMarker. Hasil penelitian menunjukkan dari 19 marka yang digunakan terdapat 12 marka (63%) yang bersifat polimorfik. Sebanyak 60 alel berukuran antara 200-500 bp dengan kisaran 2-9 alel per lokus berhasil dideteksi. Nilai polymorphic information content (PIC) menunjukkan rerata sebesar 0,59 dengan nilai tertinggi 0,74 (RGH-SSR 21) dan nilai terendah 0,36 (RGH-SSR 30). Rerata frekuensi alel utama adalah 49,42% dengan nilai terendah 35,71% (STG-0016) dan nilai tertinggi 63,64% (RGH-SSR 40). Terdapat 9 marka dengan nilai PIC >0,5 yang dapat digunakan untuk mendeteksi keragaman genetika aksesi kentang. Keragaman aksesi kentang tersebut cukup tinggi, seperti yang direfleksikan oleh nilai rerata diversitas gen, yaitu 0,65. Hasil analisis klaster menunjukkan bahwa keempat belas aksesi kentang tersebut mengelompok menjadi dua kelompok utama pada koefisien 0,70. Kelompok pertama terdiri atas varietas Atlantik, GM 05, Granola Kembang, dan Merbabu 17, sedangkan kelomp...

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“…ISSR markers are also suitable for the identification and DNA fingerprinting (Gupta et al, 2002;Gupta & Varshney, 2000). This method has several benefits over other techniques: first, it is known to be able to discriminate between closely related genotypes (Fang & Roose, 1997;Hodkinson et al, 2002) and second, it can detect polymorphisms without any previous knowledge of the crop's DNA sequence.…”

Section: Wwwintechopencommentioning

confidence: 99%

DNA Based Techniques for Studying Genetic Diversity

Abdel-Mawgood¹

2012

Genetic Diversity in Microorganisms

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Molecular Markers: Principles and Methodology

Cited by 38 publications

References 126 publications

EST-PCR, EST-SSR and ISSR markers to identify a set of wild cranberries and evaluate their relationships

EST-PCR, EST-SSR and ISSR markers to identify a set of wild cranberries and evaluate their relationships

Keragaman Genetika Empat Belas Aksesi Kentang (Solanum tuberosum L.) Berdasarkan Marka SSR dan STS (Genetic Diversity of Fourteen Potato Accessions Based on SSR and STS Markers)

DNA Based Techniques for Studying Genetic Diversity

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