Genetic relationships and discrimination of ten influential Upland cotton varieties using RAPD markers

Influential Upland cotton ( Gossypium hirsutum L.) varieties are those that have the higher genetic contributions to modern Upland cultivars than other germplasms. Our previous research has shown significant differences in general combining ability (GCA) effects for yield, yield components, and fiber properties among ten influential cotton varieties. In this study, we used random amplified polymorphic DNA (RAPD) data to evaluate DNA variation of these ten varieties. Of 86 random decamer primers screened for their capability of amplifying DNA via the polymerase chain reaction (PCR), 63 generated a total of 312 DNA fragments. Forty two bands were polymorphic, which showed a low percentage (13.5%) of DNA variation among these influential varieties. Genetic similarities among the ten varieties based on RAPD data were from 92.7% to 97.6%. All of the varieties were individually identified by variety specific markers in genetic fingerprinting. One primer, UBC-149, amplified a 1,430-bp DNA fragment that was absent in five varieties and present in the other five varieties. This RAPD marker had significant negative relationships with GCA-effect estimates for seed cotton yield, lint yield, number of bolls per plant and micronaire, and significant positive relationships with GCA effects for boll size and seed index. This finding, for the first time, identifies a DNA fragment in cotton that is a potential DNA marker linked to a yield gene(s) or a yield-related gene(s).