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.
[1] 毕方铖,谭晓风,乌云塔娜.2006.改良CTAB法对白梨品种DNA提取效果的研究[J].茂名学院学报,16(4):22-26.
(Bi F C,Tan X F,Wuyun T N.2006.Research on DNA extracting effect of white pear using modified method of CTAB[J].Journal of Maoming College,16(4):22-26.)
[2] 陈俊愉.2000.中国花卉品种分类学[M].中国林业出版社,北京.pp.13-14.
(Chen J Y.2000.China Floriculture Taxology[M].China Forestry Publishing House,Beijing,China,pp.13-14.)
[3] 陈其福,李艳美,李佳荫,等.2019.基于SSR标记的食荚菜豆指纹图谱构建[J].北方园艺,(09):1-7.
(Chen Q F,Li Y M,Li J Y,et al.2019.Construction of fingerprint of Viburnum# bean based on SSR marker[J].Northern Horticulture,(9):1-7.)
[4] 段绍光,金黎平,李广存,等.2017.马铃薯品种遗传多样性分析[J].作物学报,43(5):718-729.
(Duan S G,Jing L P,Li G C,et al.2017.Genetic diversity analysis of potato varieties[J].Acta Agronomica Sinica,43(5):718-729.)
[5] 韩志强,任勇谕,夏宇飞,等.2019.毛白杨多态SSR引物库和种质资源指纹图谱库构建[J].北京林业大学学报,41(7):10-18.
(Han Z Q,Ren Y Y,Xia Y F,et al.2019.Construction of polymorphic SSR primer library and germplasm resource fingerprint database of Populus tomentosa[J].Journal of Beijing Forestry University,41(7):10-18.)
[6] 何婷婷.2018.3个马铃薯新品系的主要性状及细胞学和SSR指纹分析[D].硕士学位论文,内蒙古农业大学,导师:于卓,pp.13-19.
(He T T.2018.Analysis of main characters and cytology and SSR fingerprint of three new potato strains[D].Thesis for M.S.,Inner Mongolia Agricultural University,Supervisor:Yu Z,pp.13-19.)
[7] 贺丹,唐婉,刘阳,等.2012.尾叶紫薇与紫薇F1代群体主要表型性状与SSR标记的连锁分析[J].北京林业大学学报,34(6):121-125.
(He D,Tang W,Liu Y,et al.2012.Linkage analysis of phonotypic traits of Lagerstroemia caudata and L.indica F1 population using SSR markers[J].Journal of Beijing Forestry University,34(6):121-125.)
[8] 李为民,李思锋,黎斌.2012.利用SSR分子标记分析秦岭冷杉自然居群的遗传多样性[J].植物学报,47(4):413-421.
(Li W M,Li S F,Li B.2012.Genetic diversity in natural populations of Abies chensiensis based on nuclear simple sequence repeat markers[J].Chinese Bulletin of Botany,47(4):413-421.)
[9] 李晓曼,段蒙蒙,王鹏,等.2018.栽培萝卜植株地上部表型多样性分析[J].植物遗传资源学报,19(4):668-675.
(Li X M,Duan M M,Wang P,et al.2018.Phenotypic diversity analysis of cultivated radish (Raphanus sativus L.)[J].Journal of Plant Genetic Resources,19(4):668-675.)
[10] 刘清文,宋跃,李甲明,等.2015.利用核心简单重复序列(SSR)标记分析西洋梨品种资源遗传多样性[J].农业生物技术学报,23(5):579-587.
(Liu Q W,Song Y,Li J M,et al.2015.Analysis of genetic diversity of European Pear (Pyrus communis L.) cultivars using core Simple Sequence Repeat (SSR) Markers[J].Journal of Agricultural Biotechnology,23(5):579-587.)
[11] 刘喜才,张丽娟.2006.马铃薯种质资源描述规范和数据标准[M].北京:中国农业出版社,pp.13-24.
(Liu X C,Zhang L J.2006.Descriptors and Data Standard for Potato (Solanum tuberosum L.)[M].China Agriculture Press,Beijing,China,pp.13-24.)
[12] 罗兵,徐港明,孙海燕,等.2014.利用简单重复序列(SSR)标记分析太湖稻区现代粳稻品种的遗传多样性[J].农业生物技术学报,22(12):1502~1513.
(Luo B,Xu G M,Sun H Y,et al.2010.2014.Genetic diversity analysis of modern Japonica rice (Oryza satiua L.) from Taihu area based on simple sequence repeat (SSR) markers[J].Journal of Agricultural Biotechnology,22(12):1502-1513.)
[13] 潘根,张义,赵立宁,等.2019.利用SSR标记构建我国亚麻品种DNA指纹图谱及遗传多样性分析[J].中国麻业科学,41(4):145-150.
(Pan G,Zhang Y,Zhao L N,et al.2019.Establishment of DNA fingerprinting and genetic diversity analysis of flax varieties in China using SSR markers[J].Plant Fiber Sciences in China,41(4):145-150.)
[14] 吴承来,张倩倩,董炳雪,等.2010.我国部分玉米自交系遗传关系和遗传结构解析[J].作物学报,36(11):1820-1831.
(Wu C L,Zhang Q Q,Dong B X,et al.2010.Analysis of genetic structure and genetic relationships of partial maize in breed lines in China[J].Acta Agronomica Sinica,36(11):1820-1831.)
[15] 夏腾飞,王蕾,徐金青,等.2018.267份青藏高原青稞种质材料的表型多样性分析[J].西北农业学报,27(02):182-193.
(Xia T F,Wang L,Xu J P,et al.2018.The genotypic diversity analysis of 267 six-rowed hulless barley accessions from the Qinghai-tibetan plateau[J].Acta Agriculturae Boreali-occidentalis Sinica,27(2):182-193.)
[16] 项晓冬,高玉坤,崔江慧,等.2019.葡萄同源四倍体F2群体的遗传变异分析[J].植物遗传资源学报,20(04):960-974.
(Xiang X D,Gao Y K,Cui J H,et al.2019.Genetic variation analysis in F2 population from autotetraploid grape hybrid[J].Journal of Plant Genetic Resources,20(4):960-974.)
[17] 袁娟.2013.基于马铃薯全基因组序列SSR标记的开发及验证[D].硕士学位论文,四川农业大学,导师:杨先泉,pp.23.
(Yuan J.2013.Genome-wide development and identification of SSRs in potato[D].Thesis for M.S.,Sichuan Agricultural University,Supervisor:Yang X Q,pp.23.)
[18] 张萌.2012.基于SSR分子标记的葡萄种质资源遗传多样性分析及品种鉴定[D].硕士学位论文,南京农业大学,导师:陶建敏,pp.51-56.
(Zhang M.2012.Analysis of genetic diversity and cultivar identification of grapevine germplasm resources based on SSR molecular markers[D].Thesis for M.S.,Nanjing Agriclutural University,Supervisor:Tao J M,pp.51-56.)
[19] 张锐剑,常志远,叶胜海,等.2019.常规粳稻品种遗传多样性分析及DNA指纹图谱构建[J/OL].分子植物育种,1-12.
(Zhang R J,Chang Z Y,Ye S H,et al.2019.Analysis of genetic diversity and construction of DNA fingerprint for conventional Japonica rice[J/OL].Molecular Plant Breeding,1-12.)
[20] Bae K M,Sim S C,Hong J H,et al.2015.Development of genomic SSR markers and genetic diversity analysis in cultivated radish (Raphanus sativus L.)[J].Horticulture,Environment,and Biotechnology,56(2):216-224.
[21] Duan Y F,Liu J,Xu J F,et al.2019.DNA fingerprinting and genetic diversity analysis with simple sequence repeat markers of 217 potato cultivars (Solanum tuberosum L.) in China[J].American Journal of Potato Research,96:21-32.
[22] Emanuelli F,Lorenzi S,Grzeskowiak L,et al.2013.Genetic diversity and population structure assessed by SSR and SNP markers in a large germplasm collection of grape[J].BMC Plant Biology,13(1):39-56.
[23] Evanno G,Regnaut S,Goudet J.2005.Detecting the number of clusters of individuals using the software STRUCTURE:A simulation study[J].Molecular Ecology,14(8):2611-2620.
[24] Ghislain M,Spooner D M,Rodríguez F,et al.2004.Selection of highly informative and user-friendly microsatellites (SSRs) for genotyping of cultivated potato[J].Theoretical and Applied Genetics,108(5):881-890.
[25] Khadivi-Khub A,Karimi E,Hadian J.2014.Population genetic structure and trait associations in forest savory using molecular,morphological and phytochemical markers[J].Gene,546(2):297-308.
[26] Labate,Joanne A.2000.Software for population genetic Analyses of molecular marker data[J].Crop Science,40(6):1521.
[27] Lee O N,Park H Y.2017.Assessment of genetic diversity in cultivated radishes (Raphanus sativus) by agronomic traits and SSR markers[J].Scientia Horticulturae,223:19-30.
[28] Lian Q,Tang D,Bai Z Y,et al.2019.Acquisition of deleterious mutations during potato polyploidization[J].Journal of Integrative Plant Biology,61(1):7-11.
[29] Milbourne D,Meyer R C,Collins A J,et al.1998.Isolation,Characterisation and mapping of simple sequence repeat loci in potato[J].Molecular and General Genetics,259(3):233-245.
[30] Rivera A,Monteagudo A B,Igartua E,et al.2016.Assessing genetic and phenotypic diversity in pepper (Capsicum annuum L.) landraces from North-West Spain[J].Scientia Horticulturae,203:1-11.
[31] Rutuja S P,Krishnan S.2019.Genetic diversity between and within the natural populations of Garcinia indica (Thouars) Choisy:A high value medicinal plant from Northern Western Ghats of India using ISSR markers[J].Journal of Applied Research on Medicinal and Aromatic Plants,15(2019):1-8.
[32] Song X Y,Zhang C Z,Li Y,et al.2016.SSR analysis of genetic diversity among 192 diploid potato cultivars[J].Horticultural Plant Journal,2(3):163-171.
[33] Wang J,Hou L,W R Y,et al.2017.Genetic diversity and population structure of 288 potato (Solanum tuberosum L.) germplasms revealed by SSR and AFLP markers[J].Journal of Integrative Agriculture,16(11):2434-2443.
