Fingerprint Construction and Genetic Diversity Analysis for 65 Potato (Solanum tuberosum) Varieties (Lines)
GAO Yu-Kun1,*, CUI Jiang-Hui1,*, XIANG Xiao-Dong2, XUE Wei3, YIN Cong-Pei1, REN Gen-Zeng1, LI Feng4, WANG Wei-Dong4, WANG Zhi-Gang4, WEI Shi-Lin1, LIANG Hong-Kai1, CHANG Jing-Hua1,**
1 College of Agronomy, Hebei Agricultural University, Baoding 071000, China;
2 Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China;
3 Baoding Vocational and Technical College, Baoding 071000, China;
4 Zhangjiakou Academy of Agricultural Sciences, Zhangjiakou 075000, China
Abstract Potato (Solanum tuberosum) is one of the most important crops in the world. Effective identification of potato varieties (lines) and evaluation of genetic diversity will help to obtain high yield and nice quality potato varieties with high tolerance to natural environments. In this study, 65 potato varieties were provided by Zhangjiakou Academy of Agricultural Sciences. The genetic diversity of 65 potato germplasm and the construction of DNA fingerprinting were accomplished by SSR molecular markers and phenotypic traits. 29 pairs of SSR primers with high polymorphism and clear bands were selected. These primers were used for amplification of all varieties (lines), and a total of 145 bands were amplified, including 100 polymorphism bands. Each pair of SSR primers amplified bands of 3~11, and the average percentage of polymorphic bands (PPB) of primers was 65.77%. According to the results of electrophoresis, SSR fingerprints of 65 germplasm resources were constructed with 5 pairs of primers, which were M03, M10, M12, S182 and STI039. Through polymorphism analysis based on SSR analysis of 65 potato varieties (lines), Nei's genetic diversity index (H)(0.35) and Shannon index (I) (0.52) indicated that the varieties (lines) had medium genetic diversity. The result of the population structure analysis showed that the corresponding Delta K value was maximum at K=3. Therefore, 65 potato varieties (lines) could be divided into 3 populations (Pop). Clustering analysis found that the genetic similarity coefficient of 65 varieties (lines) was between 0.62 and 0.91, and the varieties (lines) could be divided into 3 groups at the genetic similarity coefficient of 0.67. The results of the two clustering methods were basically consistent by SSR. The analysis of 32 phenotypic traits showed that the coefficient of variation (CV) of 23 phenotypic traits was higher above 36%. The average I and H of the population were 0.94 and 0.55, respectively. Significant correlation was found among phenotypic traits, including the color-related traits. It was significantly positive correlated between tuber skin color and stem color (r=0.48), between tuber skin color and flesh color (r=0.35) and between flesh color and eye depth (r=0.38). Using principal component analysis (PCA) to analyze phenotypic traits, 12 principal components (PC1~PC12) explained the total variation of 74.55% in 65 varieties (lines), and PC1~PC3 accounted for 30.08%. The two-dimensional figure showed the genetic distance among the phenotypes of 65 varieties (lines) reflected by PC1 and PC2 could be divided into 4 groups. Based on the clustering analysis of 32 phenotypic traits, the genetic similarity coefficient of 65 varieties (lines) was between 0.29 and 0.75, and all of the varieties (lines) could be divided into 3 groups at the similarity coefficient of 0.38. In summary, 5 SSR primers were used to construct the 65 potato varieties (lines) fingerprint. SSR markers clearly identified the population genetic structure among germplasm materials. In addition, the results of the investigation of molecular markers and phenotypic traits were encoded with QR codes, which could efficiently and conveniently view and identify the genetic diversity of 65 varieties (lines). This study will provide a theoretical basis for potato evaluation and breeding in the future. And the construction of fingerprints of 65 varieties (lines) will provide a basis for variety identification and intellectual property protection.
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