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

Abstract

ABSTRACT. 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 Genetic variation of intraspecific cotton hybrids 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 nonsignificant 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.

Development of RAPD-SCAR markers for different Ganoderma species authentication by improved RAPD amplification and molecular cloning

“…A combination of SCAR and RAPD has significantly improved the stability and authenticity of the technique (Dnyaneshwar et al, 2006;Su et al, 2007;Li et al, 2010;Kumla et al, 2012;Rajesh et al, 2013;Fu et al, 2013;Noormohammadi et al, 2013;Mei et al, 2014a,b). Previous studies successfully developed RAPD markers for different species of animals, plants, and microbes (Lee et al, 2013;Yang et al, 2013Yang et al, , 2014Dutta et al, 2014).…”

“…Random amplified polymorphic DNA (RAPD), inter-simple sequence repeat, simple sequence repeat, and amplified fragment length polymorphism analyses are the major molecular marker technologies currently used for the genetic characterization and identification of an organism (Williams et al, 1990;Agarwal et al, 2008;Fu et al, 2013;Noormohammadi et al, 2013;Mei et al, 2014a,b). The sequence characterized amplified region (SCAR) marker is another molecular marker, which is more stable and is generally derived from RAPD or intersimple sequence repeat (Dnyaneshwar et al, 2006;Su et al, 2007;Li et al, 2010;Kumla et al, 2012;Rajesh et al, 2013).…”

Genetic characterization and authentication of Dimocarpus longan Lour. using an improved RAPD technique

“…In addition, its secondary metabolic products have been shown to have antioxidative (Okuyama et al, 1999;Rangkadilok et al, 2005Rangkadilok et al, , 2007Sun et al, 2007;Jiang et al, 2009), antiobesity , anticancer (Chung et al, 2010), antityrosinase (Prasad et al, 2010), and immunomodulatory activities (Su et al, 2010;Zhong et al, 2010;Yi et al, 2011). Several molecular markers have been developed and applied since 1980, including random amplified polymorphic DNA (RAPD) (Williams et al, 1990;Devaiah and Venkatasubramanian, 2008;Ruzicka et al, 2009;Yazbeck et al, 2011;Noormohammadi et al, 2013), inter-simple sequence repeats (Feofilov et al, 2011;Ganopoulos et al, 2011;Noormohammadi et al, 2013), and amplified fragment length polymorphism (Vos et al, 1995). These molecular markers have been extensively utilized across various fields for assessments of genetic diversity, genotype fingerprinting, and molecular-assisted breeding.…”

An improved DNA marker technique for genetic characterization using RAMP-PCR with high-GC primers

“…These include random amplified polymorphic DNA (RAPD) (Williams et al, 1990;Hess et al, 2000;Lima et al, 2011;Kumla et al, 2012;Fu et al, 2000Fu et al, , 2013Shakeel et al, 2013;Lamine and Mliki, 2015), internal transcribed spacer (Hess et al, 2000;Varela et al, 2004;Pachuau et al, 2014), simple sequence repeat (Noormohammadi et al, 2013;Lamine and Mliki, 2015), inter-simple sequence repeat (ISSR) (Noormohammadi et al, 2013;Khadivi-Khub and Soorni, 2014), inter-retrotransposon amplified polymorphism (Noormohammadi et al, 2013), single primer amplification reaction (Satish et al, 2016), amplified fragment length polymorphism (Vos et al, 1995;Han et al, 2007;Khadivi-Khub and Soorni, 2014), and restriction fragment length polymorphism (Jeffreys et al, 1985;Tanksley et al, 1989) techniques. These techniques have been applied widely to various unicellular and multicellular organisms across different research areas.…”