Genetic Diversity in Cotton Assessed by Variation in Ribosomal RNA Genes and AFLP Markers

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Abstract
Variation in the ribosomal RNA genes (rDNA) and amplified fragment length polymorphism (AFLP) markers has been used to establish the extent of genetic diversity and relatedness in plants. The utility of these methods to detect inter‐ and intra‐specific variation in cotton (Gossypium spp.) has not been reported and could be useful in cultivar identification and in marker assisted selection. The objectives of this study were to: (i) determine the molecular organization of the rDNA genes by restriction enzyme mapping and (ii) assess the level of AFLPs in Old and New World species of cotton. A restriction site map of the rDNA gene structure of G. hirsutum L. cv. TM1 was constructed from DNA digested with 12 restriction enzymes and hybridized to heterologous probes. Four EcoRI‐MseI primer‐pair combinations were used for the AFLP analysis. The rDNA gene structure in cotton was found to be similar to that of most higher plants. The rDNA repeat size was 9.4 kbp in G. hirsutum and G. barbadense L., and 9.6 and 9.8 kbp in G. arboreum L. and G. herbaceum L., respectively. No intraspecific polymorphism was detected in the spacer. The presence of two SspI sites in G. arboreum and G. herbaceum and a single site in G. hirsutum and G. barbadense separated Old and New World cottons. The AFLP method produced a 10‐fold increase in the number of DNA bands per plant, compared with random amplified polymorphic DNA (RAPD) methods. The AFLP data assigned the species–genotypes into groups that corresponded with their origin and/or pedigree relationships.