Abstract:

Cotton is an important economic crop with complex genomes, yet the development of cotton molecular markers lags behind that of other diploid crops, posing challenges. This study utilized the highly polymorphic and accurate Multiple Dispersed Nucleotide Polymorphisms (MNP) marker approach to construct fingerprints for the main cotton varieties in China. This achievement provides a technical foundation for variety identification, genetic diversity analysis, and molecular breeding. Using public cotton genome information, a panel of 940 MNP markers was developed. Subsequently, 98 cotton samples underwent multiplex PCR amplification, library construction, sequencing, and genotyping. As a result, a fingerprint database for each cotton variety was established. Pairwise comparisons based on MNP genotypes were conducted to determine genetic differences, followed by a sequential phylogenetic analysis. Effective amplification products were obtained from all 940 MNP loci in the 98 cotton samples, with amplification product lengths ranging from 163 to 274 bp and an average of 270 bp. A total of 940 polymorphic loci were detected in the 98 samples, with an average discriminative power (DP) of 0.46. When comparing genetic differences between any two varieties, an average of 410.26 MNP loci showed differences, accounting for an average difference of 44.84%. The NJ phylogenetic tree revealed that the 98 cotton samples could be divided into three groups based on MNP markers, roughly corresponding to their distribution in the Yellow River basin, the Yangtze River basin, and the Xinjiang region. The 940 MNP markers developed in this study can accurately classify cotton varieties, and the DNA fingerprints of the 98 cotton varieties constructed using these markers provide technical support for variety identification, variety rights protection, and germplasm innovation.

Key words: cotton, marker, MNP, fingerprint, variety identification