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Understanding genetic diversity, population structure and development of a core collection of Indian accessions of watermelon (Citrullus lanatus (Thunb.) Matsum. and Nakai)

Published online by Cambridge University Press:  04 November 2020

Saheb Pal ,
Muttanna Revadi ,
RN Thontadarya ,
DC Lakshmana Reddy ,
B. Varalakshmi ,
Chithra Devi Pandey  and
Eguru Sreenivasa Rao Open the ORCID record for Eguru Sreenivasa Rao [Opens in a new window]
Saheb Pal
Affiliation:
Division of Vegetable Crops
Muttanna Revadi
Affiliation:
Division of Vegetable Crops
RN Thontadarya
Affiliation:
Division of Vegetable Crops
DC Lakshmana Reddy
Affiliation:
Division of Biotechnology, ICAR-Indian Institute of Horticultural Research, Bangalore, India
B. Varalakshmi
Affiliation:
Division of Vegetable Crops
Chithra Devi Pandey
Affiliation:
Division of Germplasm Conservation, ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
Eguru Sreenivasa Rao*
Affiliation:
Division of Vegetable Crops
*
*Corresponding author. E-mail: esrao1973@gmail.com
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Abstract

Most of the modern-day improved watermelon varieties succumb to various biotic and abiotic stresses mainly because of their narrow genetic base. Insights into the genetic diversity and population structure are crucial for broadening the genetic base and improving the adaptive value. The present experiment was conducted to study the genetic diversity and population structure of a germplasm panel comprising 336 Citrullus sp. accessions. Another objective was to formulate a core collection of Indian Citrullus sp. accessions. Data from 23 highly polymorphic microsatellite markers were used for genetic diversity and population structure analysis while both molecular and phenotypic data from 17 traits were used to formulate the core set. The markers yielded a total of 69 alleles with an average of three alleles per locus. Initially, the accessions clustered into two populations and an admixture group. Intra-population analysis revealed three and two statistically distinct subpopulations in Pop I and Pop II, respectively. The exotic collections were predominant in Pop I-A, Pop II-A and Pop II-B while the Indian accessions were preponderant in Pop I-B and Pop I-C. Pop I-B recorded the maximum magnitude of gene diversity and the highest number of alleles. The well-adapted Indian landraces could be deployed in future watermelon improvement programmes. The formulated core collection (n = 46; 23.71% of the entire collection studied) would ease in maintenance of the diversity present among indigenous Citrullus sp. accessions; would ease trait search while exploring Indian diversity and can be pooled with other collection(s) to form a global core of watermelon.

Keywords

Genetic diversityIndian core setPopulation structureWatermelon
Type
Research Article
Information
Plant Genetic Resources , Volume 18 , Issue 5 , October 2020 , pp. 359 - 368
Copyright
Copyright © NIAB 2020

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References

Agrama, HA, Yan, WG, Lee, F, Fjellstrom, R, Chen, MH, Jia, M and McClung, A (2009) Genetic assessment of a mini-core subset developed from the USDA Rice Gene bank. Crop Science 49: 1336–1346.10.2135/cropsci2008.06.0551CrossRefGoogle Scholar
Black, CA (1965) Methods of Soil Analysis: Part I- Physical and Mineralogical Properties. American Society of Agronomy. Madison, Wisconsin, USA. 1572 p.Google Scholar
Chomicki, G and Renner, SS (2015) Watermelon origin solved with molecular phylogenetics including linnaean material: another example of museomics. New Phytologist 205: 526–532.CrossRefGoogle ScholarPubMed
Dane, F and Liu, J (2007) Diversity and origin of cultivated and citron type watermelon (Citrullus lanatus). Genetic Resources and Crop Evolution 54: 1255–1265.10.1007/s10722-006-9107-3CrossRefGoogle Scholar
Dane, F, Liu, J and Zhang, C (2007) Phylogeography of the bitter apple Citrullus colocynthis. Genetic Resources and Crop Evolution 54: 327–336.CrossRefGoogle Scholar
Doyle, JJ and Doyle, JJ (1987) A rapid isolation procedure for small quantities of fresh leaf tissue. Phytochemical Bulletin 19: 11–15.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.CrossRefGoogle ScholarPubMed
Frankel, OH and Brown, AHD (1984) Plant genetic resources today: a critical appraisal. In: Holden, JHW and Williams, JT (eds.) Crop Genetic Resources: Conservation and Evaluation. London: Allen and Unwin Ltd. pp. 249–257.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.CrossRefGoogle ScholarPubMed
Hwang, J, Kang, J, Son, B, Kim, K and Park, Y (2011) Genetic diversity in watermelon cultivars and related species based on AFLP and EST-ISSRs. Notulae Botanicae Horti Agrobotanici 39: 285–292.10.15835/nbha3926382CrossRefGoogle Scholar
Jakobsson, M and Rosenberg, NA (2007) CLUMPP: a cluster matching and permutation program for dealing with label switching and multimodality in analysis of population structure. Bioinformatics (Oxford, England) 23: 1801–1806.10.1093/bioinformatics/btm233CrossRefGoogle ScholarPubMed
Kim, KW, Chung, HK, Cho, GT, Ma, KH, Chandrabalan, D, Gwag, JG, Kim, TS, Cho, EG and Park, YJ (2007) Powercore: a program applying the advanced M strategy with a heuristic search for establishing allele mining sets. Bioinformatics (Oxford, England) 23: 2155–2162.CrossRefGoogle 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 and Genomics 32: 115–122.10.1007/s13258-008-0674-xCrossRefGoogle Scholar
Kyriacou, MC, Rouphael, Y, Colla, G, Zrenner, R and Schwarz, D (2017) Vegetable grafting: the implications of a growing agronomic imperative for vegetable fruit quality and nutritive value. Frontiers in Plant Science 8: 741. https://www.frontiersin.org/article/10.3389/fpls.2017.00741.CrossRefGoogle ScholarPubMed
Levi, A, Thies, JA, Wechter, WP, Harrison, HF, Simmons, AM, Reddy, UK, Nimmakayala, P and Fei, Z (2013) High frequency oligonucleotides: targeting active gene (HFO-TAG) markers revealed wide genetic diversity among Citrullus Spp. accessions useful for enhancing disease or pest resistance in watermelon cultivars. Genet Resources and Crop Evolution 60: 427–440.10.1007/s10722-012-9845-3CrossRefGoogle Scholar
Levi, A, Jarret, R, Kousik, S, Wechter, WP, Nimmakayala, P, Reddy, U (2017) Genetic resources of watermelon. In: Grumet, R, Katzir, N and Garcia-Mas, J (eds.) Genetics and Genomics of Cucurbitaceae, Plant Genetics and Genomics: Crops and Models. Cham, Switzerland: Springer International Publishing AG, pp. 87–110.CrossRefGoogle Scholar
Li, J, Schulz, B and Stich, B (2010) Population structure and genetic diversity in elite sugar beet germplasm investigated with SSR markers. Euphytica 175: 35–42.10.1007/s10681-010-0161-8CrossRefGoogle Scholar
Liu, KJ and Muse, SV (2005) Powermarker: an integrated analysis environment for genetic marker analysis. Bioinformatics (Oxford, England) 21: 2128–2129.CrossRefGoogle ScholarPubMed
Mahla, HR, Singh, JP and Roy, MM (2014) Seed Purpose Watermelon in Arid Zone. Jodhpur, Rajasthan, India: Central Arid Zone Research Institute, pp. 1–39.Google Scholar
Minsart, LA, Zoro, IA, Dje, Y, Baudoin, JP, Jacquemart, AL and Bertin, P (2011) Set up of simple sequence repeat markers and first investigation of the genetic diversity of West African watermelon (Citrullus lanatus ssp. vulgaris Oleaginous type). Genetic Resources and Crop Evolution 58: 805–814.CrossRefGoogle Scholar
Mujaju, C, Zborowska, A, Werlemark, G, Garkava-Gustavsson, L, Andersen, SB and Nybom, H (2011) Genetic diversity among and within watermelon (Citrullus lanatus) landraces in Southern Africa. Journal of Horticultural Science and Biotechnology 86: 353–358.CrossRefGoogle Scholar
Munisse, P, Jensen, BD and Andersen, SB (2013) Genetic differentiation of watermelon landraces in Mozambique using microsatellite markers. African Journal of Biotechnology 12: 5513–5521.Google Scholar
Nantoume, AD, Andersen, SB and Jensen, BD (2013) Genetic differentiation of watermelon landrace types in Mali revealed by microsatellite (SSR) markers. Genetic Resources and Crop Evolution 60: 2129–2141.CrossRefGoogle Scholar
Nei, M (1973) Analysis of gene diversity in subdivided populations. Proceedings of the National Academy of Sciences of the United States of America 70: 3321–3323.CrossRefGoogle ScholarPubMed
Nimmakayala, P, Abburi, VL, Bhandary, A, Abburi, L, Vajja, VG, Reddy, R, Malkaram, S, Venkatramana, P, Wijeratne, A, Tomason, YR, Levi, A, Wehner, TC and Reddy, UK (2014) Use of VeraCode 384-plex assays for watermelon diversity analysis and integrated genetic map of watermelon with single nucleotide polymorphisms and simple sequence repeats. Molecular Breeding 34: 537–548.CrossRefGoogle Scholar
Olsen, SR, Cole, CV, Watanabe, FS and Dean, LA (1954) Estimation of Available Phosphorus in Soils by Extraction with Sodium Bicarbonate. Washington: Circular of US Department of Agriculture. 939, 19.Google Scholar
Paris, HS, Daunay, MC and Janick, J (2013) Medieval iconography of watermelons in Mediterranean Europe. Annals of Botany 112: 867–879.CrossRefGoogle ScholarPubMed
Perrier, X and Jacquemoud-Collet, JP (2006) DARwin software. Available at: http://darwin.cirad.fr/.Google Scholar
Pritchard, JK, Stephens, M and Donnelly, P (2000) Inference of population structure from multilocus genotype data. Genetics 155: 945–959.Google ScholarPubMed
Rao, ES, Kadirvel, P, Symonds, RC, Geethanjali, S and Ebert, AW (2012) Using SSR markers to map genetic diversity and population structure of Solanum pimpinellifolium for development of a core collection. Plant Genet Resources 10: 38–48.CrossRefGoogle Scholar
Reddy, UK, Abburi, L, Abburi, VL, Saminathan, T, Cantrell, R, Vajja, VG, Reddy, R, Tomason, YR, Levi, A, Wehner, TC and Nimmakayala, P (2015) A genome-wide scan of selective sweeps and association mapping of fruit traits using microsatellite markers in watermelon. Journal of Heredity 106: 166–176.CrossRefGoogle ScholarPubMed
Ren, Y, Zhao, H, Kou, Q, Jiang, J, Guo, S, Zhang, H, Hou, W, Zou, X, Sun, H, Gong, G, Levi, A and Xu, Y (2012) A high resolution genetic map anchoring scaffolds of the sequenced watermelon genome. PLoS One 7: e29453.CrossRefGoogle ScholarPubMed
Renner, SS, Sousa, A and Chomicki, G (2017) Chromosome numbers, Sudanese wild forms, and classification of the watermelon genus Citrullus, with 50 names allocated to seven biological species. Taxonomy 66: 1393–1405.CrossRefGoogle Scholar
Shannon, CE and Weaver, W (1963) The Mathematical Theory of Communication. Urbana: University of Illinois Press. (First published in 1949).Google Scholar
Singh, D, Singh, R, Sandhu, JS and Chunneja, P (2017) Morphological and genetic diversity analysis Citrullus Landraces from India and their genetic interrelationship with continental watermelons. Scientia Horticulturae 218: 240–248.10.1016/j.scienta.2017.02.013CrossRefGoogle Scholar
Subbiah, BV and Asija, GL (1956) A rapid procedure for the estimation of available nitrogen in soils. Current Science 25: 259–260.Google Scholar
Wehner, TC (2008) Watermelon. In: Prohens, J and Nuez, F (eds.). Handbook of Plant Breeding; Vegetables I: Asteraceae, Brassicaceae, Chenopodiaceae, and Cucurbitaceae. New York: Springer Science Business LLC, pp. 381–418.10.1007/978-0-387-30443-4_12CrossRefGoogle Scholar
Wei, C, Chen, X, Wang, Z, Liu, Q, Li, H, Zhang, Y, Ma, J, Yang, J and Zhang, X (2017) Genetic mapping of the Lobed Leaf 1 (ClLL1) gene to a 127.6-kb region in watermelon (Citrullus lanatus L.). PLoS One 12: e0180741.10.1371/journal.pone.0180741CrossRefGoogle Scholar
Zhang, H, Wang, H, Guo, S, Ren, Y, Gong, G, Weng, Y and Xu, Y (2012) Identification and validation of a core set of microsatellite markers for genetic diversity analysis in watermelon, Citrullus lanatus thumb. Matsum. Nakai. Euphytica 186: 329–342.CrossRefGoogle Scholar
Zhang, H, Fan, J, Guo, S, Ren, Y, Gong, G, Zhang, J, Weng, Y, Davis, A and Xu, Y (2016) Genetic diversity, population structure and formation of core collection of 1197 Citrullus Accessions. HortScience 51: 23–29.CrossRefGoogle Scholar
Zhao, R (2015) A History of Food Culture in China. New York: SCPG Publishing Co.CrossRefGoogle Scholar
Zhao, W, Cho, GT, Ma, KH, Chung, JW, Gwag, JG and Park, YJ (2010) Development of an allele mining set in rice using a heuristic algorithm and SSR genotype data with least redundancy for the post-genomic era. Molecular Breeding 26: 639–651.10.1007/s11032-010-9400-xCrossRefGoogle Scholar
Zoltán, T, Gyulai, G, Szabó, Z, Horváth, L and Heszky, L (2007) Watermelon (Citrullus lanatus) production in Hungary from the Middle Ages (13th century). Hungarian Agricultural Research 4: 14–19.Google Scholar
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