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Acta Agron Sin ›› 2017, Vol. 43 ›› Issue (05): 718-729.doi: 10.3724/SP.J.1006.2017.00718

• CROP GENETICS & BREEDING·GERMPLASM RESOURCES·MOLECULAR GENETICS • Previous Articles     Next Articles

Genetic Diversity Analysis of Potato varieties

DUAN Shao-Guang,JIN Li-Ping*,LI Guang-Cun,BIAN Chun-Song,XU Jian-Fei,HU Jun,QU Dong-Yu   

  1. Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences / Key Laboratory of Biology and Genetic Improvement of Tuber and Root Crop, Ministry of Agriculture, Beijing 100081, China
  • Received:2016-10-18 Revised:2017-01-21 Online:2017-05-12 Published:2017-02-20
  • Contact: Jin Liping, E-mail: jinliping@caas.cn E-mail:duanshaoguang@caas.cn
  • Supported by:

    The work was supported by the National Key Technology Support Program of China during the Twelfth Five-year Plan Period (2012BAD02B05) and the China Agriculture Research System (CARS10).

Abstract:

Based on the 16 phenotype traits, we performed UPGMA cluster analysis for 454 potato accessions. All the accessions were grouped into two clusters A1 and A at the Euclidean distance of 14.66. The cluster A1 was further grouped into two subclusters A11 and A12 at the Euclidean distance of 12.74. All the accessions were grouped into nine clusters (A, B, C, H, D, E, F, G, and I) at the Euclidean distance of 11.73, and the cluster I was the biggest group, accounting for 57.5% of all the accessions. The cluster analysis more accurately revealed the morphological difference among potato materials, and distinguished the parental materials with different ecological types and genetic differences. Meanwhile, the genetic diversity of 559 potato accessions from worldwide was analyzed with 36 pairs of SSR primers. A total of 134 polymorphic alleles were amplified. Polymorphic alleles were amplified by each pair of primer ranging from one to seven, with a mean of 3.72. The fragment size amplified varied from 106 to 308 bp. The polymorphic information content values (PIC) were from 0.1545 to 0.7743 with a mean of 0.5783, which indicated SSR markers can reflect more abundant genetic diversity information in potato varieties. The further phylogenetic tree analysis showed that all 559 accessions were clustered into three groups. Group I was a mixed one, containing 133 (23.8%) materials from almost all regions. Group II was one mostly gathered by accessions from Europe, North America, Northeast and Northwest regions in China. There were 187 materials in this group, accounting for 33.5% of all. Group III consisted of 239 accessions (42.8%), mainly distributing in North America, South America, Northeast and Southwest regions in China. The clustering results based on phenotypic traits were similar to those based on SSR markers, both highly relating to geographic location, indicating that both method should be combined to use in potato genetic polymorphism evaluation.

Key words: Potato, Germplasm, Agronomic trait, SSR maker, Genetic diversity

[1]Hawkes J G, Hjerting J P. The potatoes of Bolivia: Their breeding value and evolutionary relationships. Oxford: Oxford University Press, 1989 [2]Bamberg J, del Rio A. Accumulation of Genetic Diversity in the US Potato Genebank. Am J Potato Res, 2016. 93: 430–435 [3]Spooner D M. Species delimitations in plants: lessons learned from potato taxonomy by a practicing taxonomist. View Issue TOC, 2016, 54: 191–203 [4]Machida-Hirano R. Diversity of potato genetic resources. Breed Sci, 2015, 65: 26–40 [5]孙慧生, 陈伊里, 叶超龄. 种质资源与品种选育. 见: 黑龙江省农业科学院马铃薯研究所主编. 中国马铃薯栽培学(第4章). 北京: 中国农业出版社, 1990. pp 78–127 Sun H S, Chen Y L, Ye C L. Germplasm resources and breeding. In: Potato Research Institute of Heilongjiang Academy of Agricultural Sciences, eds. Chinese Potato Cultivation (Chapter IV). Beijing: China Agriculture Press, 1990. pp 78–127 (In Chinese) [6]Ullstrup A J. Evolution and dynamics of corn diseases and insect problems since the advent of hybrid corn. In: Walden D B, eds. Maize Breeding and Genetics. New York: Wiley-Interscience, 1978. pp 283–297 [7]Petra O, Catherine C B, Ralf S P. A genetic analysis of quantitative resistance to late blight in potato: Towards marker-assisted selection. Mol Breed, 1999, 5: 399–415 [8]Hamilton J P, Hansey C N, Whitty B R, Stoffel K, Massa1 A N, van Deynze A, De Jong W S, Douches D S, Buell C R. Single nucleotide polymorphism discovery in elite north american potato germplasm. BMC Genom, 2011, 12: 302 [9]段艳凤. 中国马铃薯主要育成品种SSR指纹图谱构建与遗传关系分析. 中国农业科学院硕士学位论文, 北京, 2009 Duan Y F. Construction of Fingerprinting and Analysis of Genetic Relationship with SSR Markers for Main Potato Cultivars (Solanum tuberosum L.) in China. MS Thesis of Chinese Academy of Agricultural Sciences, Beijing, China, 2009 (in Chinese with English abstract) [10]Haan S, Nú?ez J, Bonierbale M, Ghislain M, van der Maesen J. A simple sequence repeat (SSR)marker comparison of a large In- and Ex-situ potato landrace cultivar collection from Peru reaffirms the complementary nature of both conservation strategies. Diversity, 2013, 5: 505-521. [11]Sharmab V, Nandineni M R. Assessment of genetic diversity among Indian potato (Solanum tuberosum L.) collection using microsatellite and retrotransposon based marker systems. Mol Phylogenet Evol, 2014, 73: 10–17 [12]Herrera M R, Nú?ez J, Guzman F, Ghislain M, Spooner D M. A new potato genetic identity kit of 24 SSR markers for high throughput fingerprinting of large collections. In: VI International Solanaceae Conference, Madison, 2006 [13]徐 敏. 中国马铃薯审定品种系谱分析及遗传多样性研究. 中国农业科学院硕士学位论文, 北京, 2007 Xu M. Pedigree and Diversity of Approved Potato Cultivars (Solanum tuberosum L.) in China. MS Thesis of Chinese Academy of Agricultural Sciences, Beijing, 2007 (in Chinese with English abstract) [14]王胜军, 陆作嵋, 万建民. 采用表型和分子标记聚类研究杂交釉稻亲本的遗传多样性. 中国水稻科学, 2006, 20: 475–480 Wang S J, Lu Z M, Wan J M. Genetic diversity of parental lines in indica hybrid rice based on phenotypic characters and SSR cluster analysis. Chin J Rice Sci, 2006, 20: 475–480 (in Chinese with English abstract) [15]Jansky S H, Dawson J, Spooner D M. How do we address the disconnect between genetic and morphological diversity in germplasm collections? Am J Bot, 2015, 102: 1213–1215 [16]Ghislain M, Spooner D M, Rodriguez F, Villamon F, Nunez J, Vasquez C, Waugh R, Bonierbale M. Selection of highly informative and user-friendly microsatellites (SSRs) for genotyping of cultivated potato. Theor Appl Genet, 2004, 108: 881–890 [17]Ghislain M, Rodríguez F, Villamón F, Nú?ez J, Waugh R, Bonierbale M. Establishment of microsatellite assays for potato genetic identification/International Potato Center (CIP) . In: Scientist and Farmer: Partners in Research for the 21st Century Program Report, Lima : International Potato Center, 2001. pp 98–129 [18]Pavek J, Corsini D. Utilization of potato genetic resources in variety development. Am J Potato Res, 2001, 78: 433–441 [19]Loiselle F, Tai G C C, Christie B R, Tarn T R. Relationship between inbreeding coefficient and clonal selection in a potato cultivar development program. Am J Potato Res, 1989, 66: 747–753 [20]Kim J H, Joung H, Kim H Y, Lim Y P. Estimation of genetic variation and relationship in potato (Solanum tuberosum L.) cultivars using AFLP markers. Am J Potato Res, 1998, 75: 107–112 [21]Love S L. Founding clones, major contributing ancestors, and exotic progenitors of prominent North American potato cultivars. Am J Potato Res, 1999, 76: 263–272 [22]Loiselle F, Tai G C C, Tarn T R, Christie B R. The use of multivariate analyses to elimiate redunant variables when evaluating potatoes for chip quality. Plant Breed, 1989, 103: 153–162 [23]Fu Y B, Peterson G W, Richards K W, Tarn T R, Percy J E. Genetic diversity of Canadian and exotic potato germplasm revealed by simple sequence repeat markers. Am J Potato Res, 2009, 86: 38–48 [24]Kumar R, Kang G S, Pandey S K, Gopal J. Genetic base and relatedness of Indian early maturing potato (Solanum tuberosum) selections. J Agric Sci, 2011, 149: 217–225

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