Genetic diversity analysis in Opal cotton hybrids based on SSR, ISSR, and RAPD markers

Department of Biology, School of Basic Sciences, Science and Research Branch, Islamic Azad University, Tehran, Iran .
Genetics and molecular research: GMR (Impact Factor: 0.78). 01/2013; 12(1):256-69. DOI: 10.4238/2013.January.30.12
Source: PubMed


Cotton is one of the most economically important crops in Iran; hybridization is a means to increase the genetic diversity and obtain new elite cultivars in this crop. We examined agronomic characteristics and molecular genetic diversity in the Opal cotton (Gossypium hirsutum) cultivar and in F(2) progenies. Ten homo-primers and seven hetero-primers of 26 RAPD primers produced 261 reproducible bands, with an average of 4.18 bands per primer and 22% polymorphism. The OPB12/OPH08 primer gave the highest effective number of alleles (N(E)), and the largest Shannon index (I), Nei's genetic diversity (H), and polymorphism information content (PIC) values. Some RAPD bands were present in the parental genotypes but were absent in their hybrids. Ten ISSR primers produced 206 reproducible bands, with 49.4% polymorphism. The UBC807 locus gave the highest N(E), I, H, and PIC values. Some ISSR bands occurred only in the parental genotype, while others were only present in the hybrid genotypes. Four microsatellite loci produced 12 alleles, ranging from 181 to 236 bp, with 54% polymorphism. The TMB1421 locus, with a monomorphic allele, was digested with three restriction enzymes (CAP-microsatellite) to evaluate sequence variations among samples. Association analysis between molecular markers and agronomic data revealed a significant correlation between ISSR-UBC807-1500 and yield. The Mantel test performed among the genetic distance matrices obtained from RAPD, ISSR and SSR showed a non-significant regression between RAPD versus ISSR and ISSR versus SSR, while RAPD versus SSR showed a significant regression; regression for ISSR and RAPD+ISSR+SSR combined data was also significant. Cluster analysis (UPGMA) based on these three types of molecular markers differentiated cotton genotypes and their progenies. Among the molecular markers, ISSR revealed more genetic variation among the genotypes. However, using all three types of molecular markers provided a better overall view of cotton genome polymorphism.

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    • "In the era of modern biotechnology, several molecular techniques have been developed for the genetic studies and characterizations of different organisms, among which random amplified polymorphic DNA (RAPD), inter-simple sequence repeat (ISSR), amplified fragment length polymorphism (AFLP), sequence-related amplified polymorphism (SRAP), and simple sequence repeat (SSR) analysis are well established and widely used [12] [13] [14] [15]. RAPD is a more reliable molecular technique for the genetic characterization of organisms, especially of plants. "
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    ABSTRACT: Background Angelica sinensis is a well-known traditional Chinese medicinal plant. We have aimed to assess the genetic diversity and relationships in A. sinensis cultivars collected from different locations of China, and also some other Angelica species. Results We have employed an improved random amplified polymorphic DNA (RAPD) technique for the amplification of DNA materials form ten Angelica cultivars, and the results were verified by inter-simple sequence repeat (ISSR) analysis. Twenty six RAPD primers were used for RAPD, and the amplified bands were found highly polymorphic (96%). Each primer amplified 8-14 bands with an average number of 10.25. The cluster dendrogram showed the index of similarity coefficients ranging from 0.41 to 0.92. The similarity coefficients were higher between different cultivars of A. sinensis, and lower between different species. Twenty ISSR primers were used for the amplification, and each primer had amplified 6-10 bands with an average number of 7.2 bands per primer. The cluster dendogram showed the index of similarity coefficients ranging from 0.35 to 0.89. Conclusions This study genetically characterized the Angelica species, which might have significant contribution in genetic and ecological conservation of this important medicinal plant. Also, this study indicates the improved RAPD and ISSR analysis are important and potent molecular tools for the study of genetic diversity and authentication of organisms.
    Full-text · Article · Mar 2015 · Electronic Journal of Biotechnology
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    • "Recent technological progresses made in single-locus markers reduced the importance of multi-locus markers. SSRs are the marker system of choice for genetic diversity evaluation in species with reduced polymorphism, otherwise, both SSRs and ISSRs could be used for the same (López-Aljorna et al. 2007; Gomes et al. 2008; Kumar and Sharma 2011; Jia et al. 2011; Noormohammadi et al. 2013). Many expressed sequence tags (EST) were developed for Fagaceae species such as Quercus petraea, Q. robur, C. sativa and F. sylvatica (NCBI dbEST, "

    Full-text · Article · Dec 2014 · Journal of Genetics
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    • "RAPD analysis can reveal high degrees of polymorphisms, does not require prior DNA sequence information of the species, and is easy to manipulate (Williams et al. 1990; Devaiah and Venkatasubramanian, 2008; Chen et al. 2010; Yazbeck et al. 2011; Bhat et al. 2012; Shakeel et al. 2013; Noormohammadi et al. 2013; Zhang et al. 2013). Therefore , researchers could explore its application for authentication of traditional Chinese medicines. "
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    ABSTRACT: As an edible fruit and source of traditional medicine, D. longan is grown in most areas of Southern China. Identification of D. longan cultivars by using molecular markers is important genetically. In this study, we cloned fragments from improved randomly amplified polymorphic DNA (RAPD), and developed stably diagnostic sequence-characterized amplified region (SCAR) markers. The specific RAPD bands of D. longan cultivars from Guangxi, with size ranging from 500 bp to 900 bp were gel-purified, cloned and sequenced. Four clones named LY2-1, LY4-7, LY4-8 and LY5-2 were identified. In order to investigate whether the fragments were specific for the species, four pairs of SCAR primers were then designed. PCR amplifications were conducted to analyze 18 samples including different D. longan cultivars and other species. The specific bands with expected sizes were amplified in five D. longan samples but not in others. To identify and characterize the difference between D. longan and D. confinis, PCR amplifications were performed again. The specific bands with expected sizes were found in D. longan but not in D. confinis by SCAR markers LY2-1, LY4-7 and LY5-2, respectively. These results showed that our developed SCAR markers could be very useful as a specific D. longan variety authentication. Therefore, our study provides an effective and precise PCR-based diagnostic method and markers to identify D. longan species.
    Full-text · Article · Oct 2013 · SpringerPlus
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