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Genetic diversity and population structure of core watermelon (Citrullus lanatus) genotypes using DArTseq-based SNPs

Published online by Cambridge University Press:  21 January 2016

Xingping Yang ,
Runsheng Ren ,
Rumiana Ray ,
Jinhua Xu ,
Pingfang Li ,
Man Zhang ,
Guang Liu ,
Xiefeng Yao  and
Andrzej Kilian
Xingping Yang*
Affiliation:
Institute of Vegetable Crops, Jiangsu Academy of Agricultural Sciences, 50 Zhongling Street, Nanjing210014, People's Republic of China Efficient Horticulture Crop Genetic Improvement Laboratory, National Agricultural Science and Technology Innovation Center in East China, Nanjing210014, People's Republic of China
Runsheng Ren
Affiliation:
Institute of Vegetable Crops, Jiangsu Academy of Agricultural Sciences, 50 Zhongling Street, Nanjing210014, People's Republic of China Efficient Horticulture Crop Genetic Improvement Laboratory, National Agricultural Science and Technology Innovation Center in East China, Nanjing210014, People's Republic of China Division of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Sutton Bonington Campus, LoughboroughLE12 5RD, UK
Rumiana Ray
Affiliation:
Division of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Sutton Bonington Campus, LoughboroughLE12 5RD, UK
Jinhua Xu
Affiliation:
Institute of Vegetable Crops, Jiangsu Academy of Agricultural Sciences, 50 Zhongling Street, Nanjing210014, People's Republic of China Efficient Horticulture Crop Genetic Improvement Laboratory, National Agricultural Science and Technology Innovation Center in East China, Nanjing210014, People's Republic of China
Pingfang Li
Affiliation:
Institute of Vegetable Crops, Jiangsu Academy of Agricultural Sciences, 50 Zhongling Street, Nanjing210014, People's Republic of China Efficient Horticulture Crop Genetic Improvement Laboratory, National Agricultural Science and Technology Innovation Center in East China, Nanjing210014, People's Republic of China
Man Zhang
Affiliation:
Institute of Vegetable Crops, Jiangsu Academy of Agricultural Sciences, 50 Zhongling Street, Nanjing210014, People's Republic of China Efficient Horticulture Crop Genetic Improvement Laboratory, National Agricultural Science and Technology Innovation Center in East China, Nanjing210014, People's Republic of China
Guang Liu
Affiliation:
Institute of Vegetable Crops, Jiangsu Academy of Agricultural Sciences, 50 Zhongling Street, Nanjing210014, People's Republic of China Efficient Horticulture Crop Genetic Improvement Laboratory, National Agricultural Science and Technology Innovation Center in East China, Nanjing210014, People's Republic of China
Xiefeng Yao
Affiliation:
Institute of Vegetable Crops, Jiangsu Academy of Agricultural Sciences, 50 Zhongling Street, Nanjing210014, People's Republic of China Efficient Horticulture Crop Genetic Improvement Laboratory, National Agricultural Science and Technology Innovation Center in East China, Nanjing210014, People's Republic of China
Andrzej Kilian
Affiliation:
Diversity Arrays Technology, University of Canberra, Kirinari Street, Bruce, ACT2600, Australia
*
*Corresponding author. E-mail: xingping@jaas.ac.cn
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Abstract

Watermelon [Citrullus lanatus (Thunb.) Matsum. & Nakai var. lanatus] is an economically important vegetable belonging to the Cucurbitaceae family. Genotypes that exhibit agronomically important traits are selected for the development of elite cultivars. Understanding the genetic diversity and the genotype population structure based on molecular markers at the genome level can speed up the utilization of diverse genetic resources for varietal improvement. In the present study, we carried out an analysis of genetic diversity based on 3882 SNP markers across 37 core watermelon genotypes, including the most widely used watermelon varieties and wild watermelon. Based on the SNP genotyping data of the 37 watermelon genotypes screened, gene diversity and polymorphism information content values across chromosomes varied between 0.03–0.5 and 0.02–0.38, with averages of 0.14 and 0.13, respectively. The two wild watermelon genotypes were distinct from cultivated varieties and the remaining 35 cultivated genotypes were differentiated into three major clusters: 20 genotypes were grouped in cluster I; 11 genotypes were grouped in cluster II; three advanced breeding lines of yellow fruit flesh and genotype SW043 were grouped in cluster III. The results from neighbour-joining dendrogram, principal coordinate analysis and STRUCTURE analysis approaches were consistent, and the grouping of genotypes was generally in agreement with their origins. Here we reveal the genetic relationships among the core watermelon genotypes maintained at the Jiangsu Academy of Agricultural Sciences, China. The molecular and phenotypic characterization of the existing core watermelon genotypes, together with specific agronomic characteristics, can be utilized by researchers and breeders for future watermelon improvement.

Keywords

core genotypesgenetic diversitymolecular markersSNPswatermelon
Type
Research Article
Information
Plant Genetic Resources , Volume 14 , Issue 3 , September 2016 , pp. 226 - 233
Copyright
Copyright © NIAB 2016 

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References

Boyhan, G, Norton, J, Abrahams, B and Wen, H (1994) A new source of resistance to anthracnose (Race 2) in watermelon. HortScience 29: 111–112.Google Scholar
Che, KP, Liang, CY, Wang, YG, Jin, DM, Wang, B, Xu, Y, Kang, GB and Zhang, HY (2003) Genetic assessment of watermelon genotype using the AFLP technique. HortScience 38: 81–84.Google Scholar
Crall, JM, Elmstrom, GW and McCuistion, FT (1994) SSDL: a high-quality icebox watermelon breeding line resistant to fusarium wilt and anthracnose. HortScience 29: 707–708.Google Scholar
Elshire, RJ, Glaubitz, JC, Sun, Q, Poland, JA, Kawamoto, K, Buckler, ES and Mitchell, SE (2011) A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species. PLoS ONE 6: e19379.Google Scholar
Esteras, C, Formisano, G, Roig, C, Díaz, A, Blanca, J, Garcia-Mas, J, Gómez-Guillamón, ML, López-Sesé, AI, Lázaro, A and Monforte, AJ (2013) SNP genotyping in melons: genetic variation, population structure, and linkage disequilibrium. Theoretical and Applied Genetics 126: 1285–1303.Google Scholar
Evanno, G, Regnaut, S and Goudet, J (2005) Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Molecular Ecology 14: 2611–2620.Google Scholar
Gichimu, BM, Owuor, BO, Mwai, GN and Dida, MM (2009) Morphological characterization of some wild and cultivated watermelon (Citrullus sp.) accessions in Kenya. Journal of Agricultural and Biological Science 4: 10–18.Google Scholar
Guo, S, Zhang, J, Sun, H, Salse, J, Lucas, WJ, Zhang, H, Zheng, Y, Mao, L, Ren, Y, Wang, Z, Min, J, Guo, X, Murat, F, Ham, BK, Zhang, Z, Gao, S, Huang, M, Xu, Y, Zhong, S, Bombarely, A, Mueller, LA, Zhao, H, He, H, Zhang, Y, Zhang, Z, Huang, S, Tan, T, Pang, E, Lin, K, Hu, Q, Kuang, H, Ni, P, Wang, B, Liu, J, Kou, Q, Hou, W, Zou, X, Jiang, J, Gong, G, Klee, K, Schoof, H, Huang, Y, Hu, X, Dong, S, Liang, D, Wang, J, Wu, K, Xia, Y, Zhao, X, Zheng, Z, Xing, M, Liang, X, Huang, B, Lv, T, Wang, J, Yin, Y, Yi, H, Li, R, Wu, M, Levi, A, Zhang, X, Giovannoni, JJ, Wang, J, Li, Y, Fei, Z and Xu, Y (2013) The draft genome of watermelon (Citrullus lanatus) and resequencing of 20 diverse accessions. Nature Genetics 45: 51–58.Google Scholar
Gupta, P, Rustgi, S and Mir, R (2008) Array-based high-throughput DNA markers for crop improvement. Heredity 101: 5–18.Google Scholar
Gusmini, G, Song, R and Wehner, TC (2005) New sources of resistance to gummy stem blight in watermelon. Crop Science 45: 582–588.Google Scholar
Hopkins, DL and Thompson, CM (2002) Evaluation of Citrullus sp. germplasm for resistance to Acidovorax avenae subsp. citrulli . Plant Disease 86: 61–64.Google Scholar
Hwang, J, Jumsoon, K, Byeonggu, S, Kwanghwan, K and Younghoon, P (2011) Genetic diversity in watermelon cultivars and related species based on AFLPs and EST-SSRs. Notulae Botanicae Horti Agrobotanici Cluj-Napoca 39: 285–292.Google Scholar
Kilian, A, Wenzl, P, Huttner, E, Carling, J, Xia, L, Blois, H, Caig, V, Heller-Uszynska, K, Jaccoud, D, Hopper, C, Aschenbrenner-Kilian, M, Evers, M, Peng, K, Cayla, C, Hok, P and Uszynski, G (2012) Diversity Arrays Technology: a generic genome profiling technology on open platforms. Data Production and Analysis in Population Genomics 888: 67–89.Google Scholar
Kwon, YS, Oh, YH, Yi, SI, Kim, HY, An, JM, Yang, SG, Ok, SH and Shin, JS (2010) Informative SSR markers for commercial variety discrimination in watermelon (Citrullus lanatus). Genes & Genomics 32: 115–122.Google Scholar
Levi, A, Thomas, CE, Keinath, AP and Wehner, TC (2001a) Genetic diversity among watermelon (Citrullus lanatus and Citrullus colocynthis) accessions. Genetic Resources and Crop Evolution 48: 559–566.Google Scholar
Levi, A, Thomas, CE, Wehner, TC and Zhang, X (2001b) Low genetic diversity indicates the need to broaden the genetic base of cultivated watermelon. HortScience 36: 1096–1101.Google Scholar
Levi, A, Wechter, WP, Harris, KR, Davis, AR and Fei, Z (2010) High-frequency oligonucleotides in watermelon expressed sequenced tag-unigenes are useful in producing polymorphic polymerase chain reaction markers among watermelon genotypes. Journal of the American Society for Horticultural Science 135: 369–378.Google Scholar
Liu, K and Muse, SV (2005) PowerMarker: an integrated analysis environment for genetic marker analysis. Bioinformatics 21: 2128–2129.Google Scholar
Mujaju, C, Werlemark, G, Garkava-Gustavsson, L and Nybom, H (2010) High Levels of RAPD and SSR marker diversity in landraces of watermelon (Citrullus lanatus) in Southern Africa. Acta Horticulturae 918: 291–296.Google Scholar
Mujaju, C, Sehic, J and Nybom, H (2013) Assessment of EST-SSR markers for evaluating genetic diversity in watermelon accessions from Zimbabwe. American Journal of Plant Sciences 4: 1448.Google Scholar
Nielsen, NH, Backes, G, Stougaard, J, Andersen, SU and Jahoor, A (2014) Genetic diversity and population structure analysis of European hexaploid bread wheat (Triticum aestivum L.) varieties. PLOS ONE 9: e94000.Google Scholar
Perrier, X, Flori, A and Bonnot, F (2003) Methods of data analysis. In: Hamon, P, Seguin, M, Perrier, X and Glassman, JC (eds) Genetic Diversity of Cultivated Tropical Plants. Science Publishers, Inc. and CIRAD, Montpellier, pp. 31–63.Google Scholar
Powell, W, Morgante, M, Andre, C, Hanafey, M, Vogel, J, Tingey, S and Rafalski, A (1996) The comparison of RFLP, RAPD, AFLP and SSR (microsatellite) markers for genotype analysis. Molecular Breeding 2: 225–238.Google Scholar
Pritchard, JK, Stephens, M and Donnelly, P (2000) Inference of population structure using multilocus genotype data. Genetics 155: 945–959.Google Scholar
Ren, R, Wang, M, Chen, X and Zhang, Z (2012) Characterization and molecular mapping of Yr52 for high-temperature adult-plant resistance to stripe rust in spring wheat germplasm PI 183527. Theor Appl Genet 125: 847–857.Google Scholar
Sansaloni, C, Petroli, C, Jaccoud, D, Carling, J, Detering, F, Grattapaglia, D and Kilian, A (2011) Diversity Arrays Technology (DArT) and next-generation sequencing combined: genome-wide, high throughput, highly informative genotyping for molecular breeding of Eucalyptus . BMC Proceedings 5: P54.Google Scholar
Singh, N, Choudhury, DR, Singh, AK, Kumar, S, Srinivasan, K, Tyagi, R, Singh, N and Singh, R (2013) Comparison of SSR and SNP markers in estimation of genetic diversity and population structure of Indian rice varieties. PLOS ONE 8: e84136.Google Scholar
Tetteh, AY, Wehner, TC and Davis, AR (2010) Identifying resistance to powdery mildew race 2W in the USDA-ARS watermelon genotype collection. Crop Science 50: 933–939.Google Scholar
Tetteh, AY, Wehner, TC and Davis, AR (2013) Inheritance of resistance to powdery mildew Race 2 in Citrullus lanatus var. lanatus . HortScience 48: 1227–1230.Google Scholar
Thies, JA and Levi, A (2007) Characterization of watermelon (Citrullus lanatus var. citroides) genotype for resistance to root-knot nematodes. HortScience 42: 1530–1533.Google Scholar
Van Inghelandt, D, Melchinger, AE, Lebreton, C and Stich, B (2010) Population structure and genetic diversity in a commercial maize breeding program assessed with SSR and SNP markers. Theoretical and Applied Genetics 120: 1289–1299.Google Scholar
Wang, YH, Behera, TK and Kole, C (2011) Genetics, Genomics and Breeding of Cucurbits. New York: CRC Press.Google Scholar
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