Biodiv Sci ›› 2008, Vol. 16 ›› Issue (6): 555-561.DOI: 10.3724/SP.J.1003.2008.08132

• Original Papers • Previous Articles     Next Articles

Screening of SSR core primers with polymorphism on a cotton panel

Zhao-E Pan, Junling Sun, Yinhua Jia, Zhongli Zhou, Baoyin Pang, Xiongming Du()   

  1. Cotton Research Institute, Chinese Academy of Agricultural Sciences; Key Laboratory of Cotton Genetic Improvement of Agricultural Ministry, Anyang, Henan 455000


A large number of polymorphic Simple Sequence Repeat (SSR) primers are needed to assess genetic diversity and construct genetic maps for cotton varieties. Our objective was to screen the cotton core primers with polymorphism based on a standard cotton panel. In the experiment, 12 accessions with significantly different phenotypes and genetic background were used as panel germplasm for screening 5,914 pairs of SSR primers obtained from the Cotton Microsatellite Database ( A total of 4,800 pairs of SSR primers accounting for 90. 6% of the 5,300 effectively amplified primers were polymorphic among different species. Of these, about 500 pairs of primers, 9.4% of effectively amplified primers, could distinguish among cotton varieties. We suggest the use of 319 pairs of polymorphic primers with suitable amplification and clear bands as core primers for evaluating cotton germplasm and depicting fingerprints. We found 277 pairs of polymorphic primers that can identify upland cotton varieties. Moreover, we recommend 13 SSR primer pairs with polymorphism in all three species of upland cotton, sea island cotton and Asiatic cotton as the first-choice markers for molecular fingerprint and germplasm identification. Here we publish 319 core primer pairs and their polymorphic information, which will be helpful to regulate the procedure and promote the efficiency for screening SSR primers, and will play an important role in cotton genetic diversity evaluation, fingerprint construction, seed genuineness and purity identification of the cotton varieties.

Key words: cotton, SSR, primer, polymorphism