Construction of DNA Fingerprinting with SSR Markers for Xinjiang Cotton Varieties

Background: Xinjiang is the largest cotton production base and cotton production reserve in China. However, due to repeated use of several breeding backbones parents, the genetic variation of Xinjiang cotton varieties decreased, and it was difficult to identify cotton varieties only based on field morphological characteristics. Therefore, rapid and accurate cotton variety identification and purity detection are of great significance to the protection of new varieties and identification of true and false seeds for the healthy development of cotton seed market in Xinjiang. Results In this study, the DNA fingerprints of 240 Xinjiang conventional cotton varieties approved in Xinjiang before 2018 were constructed using SSR (Simple sequence repeats) markers based on capillary electrophoresis. 73 pairs of core primers, which are highly polymorphic, stable and located on 26 cotton chromosomes (select two to three pairs on each chromosome), were screened out from 5152 pairs of SSR primers, and were used to construct the DNA fingerprints in 240 Xinjiang cotton materials. By using the 73 pairs core primers, 381 polymorphic sites were detected. The primer polymorphism information (PIC) ranged from 0.0916 to 0.8039, with an average value of 0.4956. Combined with the characteristic primers and primers of cotton varieties (52, 51, 47 and 47 pairs in Xinluzao, Xinluzhong, Xinhaimian and Xincaimian, respectively), the least primers to construct detailed molecular fingerprints of cotton varieties were selected. Conclusion The accurate molecular fingerprint database of 240 cotton varieties approved in Xinjiang up to 2018 was constructed in this study. Which provides an efficient and fast theoretical and technical system for the identification of the purity and authenticity of cotton varieties in Xinjiang, protects the rights and interests of breeders, and is of great significance for promoting the supervision of seed quality in the cotton seed market in Xinjiang.