Objective The study was carried out to understand the Phytophthora disease resistance and genetic diversity of pepper germplasm materials, and to provide references for the establishment of core pepper germplasm bank and improvement of pepper Phytophthora disease resistance breeding.

Method The Phytophthora disease resistance of 96 pepper germplasm materials was evaluated by using modified root irrigation inoculation method and the genetic diversity of them with 20 SSR molecular markers selected from the whole genome were analyzed.

Result The results show that there was only 1 immune material, 6 highly resistant, 24 resistant, 53 susceptible and 12 highly susceptible materials among the 96 materials, which were basically consistent with the field performance. The results of genetic diversity analysis showed that a total of 79 alleles were detected among 20 SSR markers, with 2-9 alleles per marker and an average of 3.95 alleles. Shannon's index ranged from 0.2992 to 1.9893, with an average of 0.9513, indicating that the genetic polymorphism of the 20 SSR molecular markers selected was high. Nei's genetic diversity index ranged from 0.1614 to 0.8440, with an average of 0.5259, indicating high genetic diversity among materials. Cluster analysis results showed that the tested materials could be divided into three groups at the genetic distance of 0.37, including 3, 14 and 79 materials, respectively. Additionally, the genetic distance among 8 groups of materials was close to 0.

Conclusion The improved root irrigation inoculation method is suitable for the identification of pepper Phytophthora disease, and the results are basically consistent with those of the field performance. Moreover, it is more convenient. The genetic polymorphisms of the 20 SSR molecular markers selected are high and suitable for genetic diversity analysis of pepper germplasms. The 96 pepper germplasm materials are rich in resources, but there are homogeneous materials, and some materials should be discarded properly during germplasm preservation.