Simple sequence repeat markers associated/linked with agronomic traits, as core primers, are eminently suitable for DNA fingerprinting in Upland cotton.

Analyzing the genetic differences among crop germplasm resources scientifically and accurately is very important for the selection of core accessions, the identification of new cultivars, and the determination of seed purity. However, phenotypic selection is not sufficient to identify genetically distinct accessions. In this study, 26 out of 83 simple sequence repeat markers associated/linked with cotton important agronomic traits derived from our previous and other published research, corresponding to the 26 chromosomes of Upland cotton ( L.), were selected as core primers for DNA fingerprinting construction. The 26 markers showed clear band patterns, good repeatability and high polymorphism. The average alleles, gene diversity index and polymorphism information content were 3.12, 0.4312 and 0.3830, respectively. Using TM-1, a genetic standard line for Upland cotton, as the control, DNA fingerprinting pattern and DNA barcodes were obtained based on the core primers. There was a significant positive correlation between genetic distance matrix determined using 26 core primers and that determined using more primers (335) derived from previous research, further suggesting that the core primers were eminently suitable for DNA fingerprinting in Upland cotton. This study provides a molecular basis for assessing identification, authenticity and seed purity of cotton cultivars.