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Genetic reticulation and interrelationships among citrullus species as revealed by joint analysis of shared AFLPs and species-specific SSR alleles

Published online by Cambridge University Press:  22 July 2009

Padmavathi Nimmakayala ,
Yan R. Tomason ,
Jooha Jeong ,
Sathish K. Ponniah ,
Anoji Karunathilake ,
Amnon Levi ,
Ramasamy Perumal  and
Umesh K. Reddy
Padmavathi Nimmakayala*
Affiliation:
Department of Biology and Gus R. Douglass Institute, West Virginia State University, Institute, WV25112, USA
Yan R. Tomason
Affiliation:
Department of Biology and Gus R. Douglass Institute, West Virginia State University, Institute, WV25112, USA Department of Selection and Seed Production, Dnepropetrovsk State Agrarian University, Voroshilov 25, Dnepropetrovsk49600, Ukraine
Jooha Jeong
Affiliation:
Department of Biology and Gus R. Douglass Institute, West Virginia State University, Institute, WV25112, USA
Sathish K. Ponniah
Affiliation:
Department of Biology and Gus R. Douglass Institute, West Virginia State University, Institute, WV25112, USA
Anoji Karunathilake
Affiliation:
Department of Biology and Gus R. Douglass Institute, West Virginia State University, Institute, WV25112, USA
Amnon Levi
Affiliation:
USDA, ARS, US Vegetable Laboratory, 2875 Savannah Highway, Charleston, SC29414, USA
Ramasamy Perumal
Affiliation:
Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX77843-2132, USA
Umesh K. Reddy
Affiliation:
Department of Biology and Gus R. Douglass Institute, West Virginia State University, Institute, WV25112, USA
*
*Corresponding author. E-mail: padma@wvstateu.edu
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Abstract

Thirty-one accessions of Citrullus spp. belonging to Citrullus lanatus var. lanatus, C. lanatus var. citroides and Citrullus colocynthis were subjected to phylogenetic analysis using combined datasets of amplified fragment length polymorphisms (AFLPs) and simple sequence repeats (SSRs). Tree topologies inferred by neighbour-joining analysis have resolved the phylogenic relationships among the species with special reference to established taxonomic classification. In this study, we have clearly resolved species boundaries of various taxa of citroides, lanatus and colocynthis into three well-supported clusters. Clustering pattern of principal component analysis with the shared polymorphisms using the subsets of data between any two taxon combinations helped to elucidate the introgression and interrelationships among the species. We report two major groups of C. lanatus taxa, one of which has undergone wide introgressions with the taxa of C. lanatus var. citroides and C. colocynthis. In this paper, we identified 583 AFLP bands that are polymorphic within the var. lanatus of C. lanatus, which is the largest set ever reported. The species-specific diagnostic SSRs and polymorphic AFLPs that are informative within and between the taxa reported in this paper would be immensely useful for future studies of these economically important genera.

Keywords

AFLPCitrullus speciesmicrosatellitesmolecular phylogenywatermelon
Type
Research Article
Information
Plant Genetic Resources , Volume 8 , Issue 1 , April 2010 , pp. 16 - 25
Copyright
Copyright © NIAB 2009

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References

Avise, JC (2000) Phylogeography: The History and Formation of Species. Cambridge, MA: Harvard University Press.CrossRefGoogle Scholar
Bates, DM and Robinson, RW (1995) Cucumbers melon and watermelons. In: Smart, J and Simmonds, NW (eds) Evolution of Crop Plants. 2nd edn., London, UK: Longman, pp. 89–96.Google Scholar
Biles, CL, Martyn, RD and Wilson, HD (1989) Isozymes and general proteins from various watermelon cultivars and tissue types. Horticultual Science 24: 810–812.Google Scholar
Burkill, HM (1985) The Useful Plants of West Tropical Africa. vol. 1, 2nd edn. Richmond, Surrey, UK: Royal Botanic Gardens, Kew.Google Scholar
Dane, F (2002) Chloroplast DNA investigations in Citrullus using PCR-RFLP analysis. Cucurbitaceae 2002: 100–108.Google Scholar
Dane, F and Lang, P (2004) Sequence variation at cpDNA regions of watermelon and related species: implications for the evolution of Citrullus haplotypes. Am J Bot 91: 1922–1929.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.CrossRefGoogle Scholar
Dane, F, Lang, P and Bakhtiyarova, R (2004) Comparative analysis of chloroplast DNA variability in wild and cultivated Citrullus species. Theoretical and Applied Genetics 108: 958–966.CrossRefGoogle ScholarPubMed
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
Ellstrand, NC, Prentice, HC and Hancock, JF (1999) Gene flow and introgression from domesticated plants into their wild relatives. Annual Review of Ecological Systems 30: 539–563.CrossRefGoogle Scholar
Ellul, P, Lelivelt, C, Naval, MM, Noguera, FJ, Sanchez, S, Atarés, A, Moreno, V, Corella, P and Dirks, R (2007) Watermelon biotechnology. Agriculture and Forestry, Transgenic Crops. vol. 60. Berlin/Heidelberg, Germany: Springer Verlag Publication, pp. 129–165.Google Scholar
Eriksen, B and Töpel, MH (2006) Molecular phylogeography and hybridization in members of the circumpolar Potentilla sect. Niveae (Rosaceae). American Journal of Botany 93: 460–469.CrossRefGoogle ScholarPubMed
Falush, D, Stephens, M and Pritchard, JK (2003) Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies. Genetics 164: 1567–1587.CrossRefGoogle ScholarPubMed
Falush, D, Stephens, M and Pritchard, J (2007) Inference of population structure using multilocus genotype data: dominant markers and null alleles. Molecular Ecology Notes 7(4): 574–578.CrossRefGoogle ScholarPubMed
Gillaspie, AG Jr, Hopkins, MS Jr and Dean, RE (2005) Determining genetic diversity between lines of Vigna unguiculata subspecies by AFLP and SSR markers. Genetic Resources and Crop Evolution 52: 245–247.CrossRefGoogle Scholar
Guerra-Sanz, JM (2002) Citrullus simple sequence repeats markers from sequence databases. Molecular Ecology Notes 2: 223–225.CrossRefGoogle Scholar
Harris, SA (1995) Systematic and randomly amplified polymorphic DNA in the genus Leucaena (Leguminosae, Mimosoideae). Plant Systematics and Evolution 197: 197–208.CrossRefGoogle Scholar
Hillis, DM (1994) Homology in molecular biology. In: Hall, BK (ed.) Homology: The Hierarchical Basis of Comparative Biology. San Diego, CA: Academic Press, pp. 339–368.Google Scholar
Jaccard, P (1908) Nouvelles recherches sur la distribution florale. Bull Soc Vaudoise Sci Nat 44: 223–270.Google Scholar
Jarret, RL, Merrick, LC, Holms, T, Evans, J and Aradhya, MK (1997) Simple sequence repeats in watermelon (Citrullus lanatus (Thunb.) Matsum & Nakai). Genome 40: 433–441.CrossRefGoogle ScholarPubMed
Jeffrey, C (2001) Cucurbitaceae (citrullus). In: Hanelt, P (ed.) Mansfeld's Encyclopedia of Agricultural and Horticultural Crops. New York: Springer, pp. 1533–1537.Google Scholar
Koopman, WJM, Wissemann, V and Cock, KD (2008) AFLP markers as a tool to reconstruct complex relationships: a case study in Rosa (Rosaceae). American Journal of Botany 95: 353–366.CrossRefGoogle ScholarPubMed
Kyndt, T, Romeijnpeeters, E, Droogenbroeck, BV, Romeromotochi, JP, Gheysen, G and Goetghebeur, P (2005) Species relationships in the genus Vasconcellea (Caricaceae) based on molecular and morphological evidence. American Journal of Botany 92: 1033–1044.CrossRefGoogle ScholarPubMed
Lee, SJ, Shin, JS, Park, KW and Hong, YP (1996) Detection of genetic diversity using RAPD-PCR and sugar analysis in watermelon [Citrullus lanantus (Thunb.) Mansf.] germplasm. Theoretical and Applied Genetics 92: 719–725.CrossRefGoogle ScholarPubMed
Levi, A, Thomas, CE, Keinathand, AP and Wehner, TC (2001 a) Genetic diversity among watermelon (Citrullus lanatus and Citrullus colocynthis) accessions. Genetic Resources and Crop Evolution 48: 559–566.CrossRefGoogle Scholar
Levi, A, Thomas, CE and Wehner, TC (2001 b) Low genetic diversity indicates the need to broaden the genetic base of cultivated watermelon. Horticultural Science 36: 1096–1101.Google Scholar
Levi, A, Thomas, CE, Newman, M, Reddy, OUK, Zhang, X and Xu, Y (2004) ISSR and AFLP markers differ among American watermelon cultivars with limited genetic diversity. Journal of American Society of Horticultural Science 129(4): 553–558.CrossRefGoogle Scholar
Mallick, MFR and Masui, M (1986) Origin, distribution and taxonomy of melons. Scientia Horticulturae 28: 215–261.CrossRefGoogle Scholar
Maluf, MP, Silvestrini, M, Ruggiero, LMC, Filho, OG and Colombo, CA (2005) Genetic diversity of cultivated Coffea arabica inbred lines assessed by RAPD, AFLP and SSR marker systems. Scientia Agricola 62: 366–373.CrossRefGoogle Scholar
Maggs-Kölling, G, Madsen, S and Christiansen, JL (2000) A phenetic analysis of morphological variation in Citrullus lanatus in Namibia. Genet Resour Crop Evol 47: 385–393.CrossRefGoogle Scholar
Meeuse, ADJ (1962) The Cucurbitaceae of southern Africa. Bothalia 8: 1–111.CrossRefGoogle Scholar
Navot, N and Zamir, D (1987) Isozyme and seed protein phylogeny of the genus Citrullus (Cucurbitaceae). Plant Systematics and Evolution 156: 61–68.CrossRefGoogle Scholar
Perumal, R, Krishnaramanujam, R, Menz, MA, Katilé, S, Dahlberg, J, Magill, CW and Rooney, WL (2007) Genetic diversity among sorghum races and working groups based on AFLPs and SSRs. Crop Science 47: 1375–1383.CrossRefGoogle Scholar
Pimentel, M, Sahuquillo, E and Catalán, P (2007) Genetic diversity and spatial correlation patterns unravel the biogeographical history of the European sweet vernal grasses (Anthoxanthum L. Poaceae). Molecular Phylogenetics and Evolution 44(2): 667–684.CrossRefGoogle ScholarPubMed
Pitrat, M, Chauvet, M and Foury, C (1999) Diversity, history and production of cultivated cucurbits. Acta Horticulture 492: 21–28.CrossRefGoogle Scholar
Pritchard, JK, Stephens, M and Donnelly, P (2000) Inference of population structure using multilocus genotype data. Genetics 155: 945–959.CrossRefGoogle ScholarPubMed
Ramakrishnan, AP, Meyer, SE, Waters, J, Stevens, MR, Coleman, CE and Fairbanks, DJ (2004) Correlation between molecular markers and adaptively significant genetic variation in Bromus tectorum (Poaceae), an inbreeding annual grass. American Journal of Botany 91: 797–803.CrossRefGoogle Scholar
Reddy, OUK, Pepper, AE, Abdurakhmonov, I, Saha, S, Jenkins, JN, Brooks, T, Bolek, Y and El-Zik, KM (2001) New dinucleotide and trinucleotide microsatellite marker resources for cotton genome research. The Journal of Cotton Science 5: 103–113.Google Scholar
Robinson, RW and Decker-Walters, DS (1997) Cucurbits. Wallingford, UK: CAB International.Google Scholar
Rohlf, FJ (1987) NTSYSpc. Numerical Taxonomy and Multivariate Analysis System, Version 1.30, Exeter Software, Setauket, NY, USA.Google Scholar
Saini, N, Jain, N, Jain, S and Jain, RK (2004) Assessment of genetic diversity within and among Basmati and non-Basmati rice varieties using AFLP, ISSR and SSR markers. Euphytica 140: 133–146.CrossRefGoogle Scholar
Saitou, N and Nei, M (1987) The neighborjoining method: a new method for reconstructing phylogenetic trees. Molecular Biology and Evolution 4: 406–425.Google Scholar
Schmidt, K and Jensen, K (2000) Genetic structure and AFLP variation of remnant populations in the rare plant Pedicularis palustris (Scrophulariaceae) and its relation to population size and reproductive components. American Journal of Botany 87: 678–689.CrossRefGoogle ScholarPubMed
Schönswetter, P, Suda, J, Popp, M, Weissschneeweiss, H and Brochmann, C (2007) Circumpolar phylogeography of Juncus biglumis (Juncaceae) inferred from AFLP fingerprints, cpDNA sequences, nuclear DNA content and chromosome numbers. Molecular Phylogenetics and Evolution 42: 92–103.CrossRefGoogle ScholarPubMed
Spooner, DM, Mclean, K, Ramsay, G, Waugh, R and Bryan, GJ (2005) A single domestication for potato based on multilocus amplified fragment length polymorphism genotyping. Proceedings of the National Academy of Sciences of the United States of America 102(41): 14694–14699.CrossRefGoogle ScholarPubMed
Špunarová, M, Ovesná, J, TvarŮžek, L, Kučera, L, Špunar, J and Hollerová, I (2005) The use of molecular markers for characterisation of spring barley for breeding to Fusarium head blight resistance. Plant Soil and Environment 51(11): 483–490.CrossRefGoogle Scholar
Sullivan, JP, Lavoue, S, Arnegard, ME and Hopkins, CD (2004) AFLPs resolve phylogeny and reveal mitochondrial introgression within a species flock of African electric fish (Mormyroidea: Teleostei). Evolution 58: 825–841.Google ScholarPubMed
Taylor, FW (1985) The potential for the commercial utilization of indigenous plants in Bostwana. In: Wickens, GE, Goodin, JR and Field, DV (eds) Plants for Arid Lands. London, UK: George Allen & Unwin.Google Scholar
Thaler, R, Brandstätter, A, Meranera, A, Chabicovskia, M, Parsonc, W, Zelgerd, R, Dallaviad, J and Dallinge, R (2008) Molecular phylogeny and population structure of the codling moth (Cydia pomonella) in Central Europe: II. AFLP analysis reflects humanaided local adaptation of a global pest species. Molecular Phylogenetics and Evolution 48(3): 838–849.CrossRefGoogle ScholarPubMed
Travis, SE, Maschinski, J and Keim, P (1996) An analysis of genetic variation in Astragalus cremnophylax var. cremnophylax, a critically endangered plant, using AFLP markers. Molecular Ecology 5: 735–745.CrossRefGoogle ScholarPubMed
Vos, P, Hogers, R, Bleeker, M, Reijans, M, van de Lee, T, Hornes, M, Fritjers, A, Pot, J, Paleman, J, Kuiper, M and Zabeau, M (1995) AFLP: A new technique for DNA fingerprinting. Nucleic Acids Research 23, (21): 4407–4414.CrossRefGoogle ScholarPubMed
Wehner, TC (2007) Watermelon. In: Prohens J and Nuez F (eds) Handbook of plant breeding; Vegetables I: Asteraceae, Brassicaceae, Chenopodiaceae, and Cucurbitaceae. New York, NY: Springer Science Business LLC, pp. 381–418.Google Scholar
Zamir, D, Navot, N and Rudich, J (1984) Enzyme polymorphism in Citrullus lanatus and C. colocynthis in Israel and Sinai. Plant Systematics and Evolution 146: 163–170.CrossRefGoogle Scholar
Zhang, XP, Rhodes, BB and Skorupska, HS (1994) RAPD molecular markers in watermelon. Cucurbit Genetic Cooperative Report 17: 116119.Google Scholar
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