title: Genetic diversity analysis in Opal cotton hybrids based on SSR, ISSR, and RAPD markers.
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 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.
authors: Department of Biology, School of Basic Sciences, Science and Research Branch, Islamic Azad University, Tehran, Iran. z-nouri@srbiau.ac.ir
authors: Z
authors: Z
authors: Noormohammadi
authors: Y
authors: Y
authors: Hasheminejad-Ahangarani Farahani
authors: M
authors: M
authors: Sheidai
authors: S
authors: S
authors: Ghasemzadeh-Baraki
authors: O
authors: O
authors: Alishah
mesh_terms: D000483:Alleles; D015415:Biomarkers; D017931:DNA Primers / Q000737:chemistry; D014644:Genetic Variation; D005838:Genotype; D003368:Gossypium / Q000235:genetics*; D006824:Hybridization, Genetic; D018895:Microsatellite Repeats; D011110:Polymorphism, Genetic; D019105:Random Amplified Polymorphic DNA Technique / Q000379:methods
chemical_list: D015415:Biomarkers; D017931:DNA Primers