Genetic diversity and differentiation in citron watermelon [Citrullus lanatus var. citroides] landraces assessed by simple sequence repeat markers

Highlights

• Genetic diversity was assessed among diverse citron watermelon landraces using simple sequence repeats markers.

• Analysis of molecular variance revealed 21 and 78% of total genetic variance among and within individuals, respectively.

• Cluster analysis identified three distinct genetic groups.

• Considerable genetic diversity was detected among South African grown citron watermelon landraces useful for breeding and strategic conservation.

Abstract

Citron watermelon genetic resources are useful for dessert watermelon breeding. The objective of the present study was to assess the genetic diversity present among citron watermelon landrace collections of South Africa using simple sequence repeat (SSR) markers. Thirty four diverse citron watermelon landraces were genotyped using 10 SSR markers. The markers amplified a total of 72 alleles from the sampled populations. Number of alleles ranged from 2 to 17 with a mean of 7.2 per locus. Number of effective alleles ranged from 1.03 to 6.74 with a mean of 3.54. The mean observed and expected heterozygosity were 0.48 and 0.60, respectively. The mean inbreeding coefficient was 0.18 suggesting high levels of heterozygosity among the collections. The mean polymorphic information content (PIC) of the SSR loci was 0.60 suggesting their value in genetic diversity analysis of watermelon. Analysis of molecular variance revealed highly significant difference (P < 0.001) among and within individuals. Among and within individuals variance contributed 21 and 78% of the total genetic variance. Cluster analysis separated the genotypes into three distinct genetic groups revealing the presence of wide genetic variation among the citron watermelon genotypes studied. The study identified 5 distinct genotypes from cluster I, 7 from cluster II and 5 from cluster III. These are recommended for further phenotyping using horticultural attributes for effective breeding and strategic conservation.

Introduction

Watermelon is a viny creeping crop belonging to the Cucurbitaceae family. Chomicki and Renner (2015) using molecular phylogenetic analysis proposed six species under the genus Citrullus namely C. lanatus, C. mucosospermus, C. colocynthis, C. ecirrhosus, C. rehmii, and C. naudinianus. The authors further ascribed species C. amarus Schrad. to the citron watermelon. The Citrullus species are mainly found in the temperate regions of Africa, central Asia and the Mediterranean Region (Levi et al., 2001a; Whitaker and Davis, 1962). The species C. lanatus encompasses two botanical varieties: lanatus (dessert watermelon) and citroides (citron watermelon). The southern Africa region is reported to be the center of diversity and probably center of origin of most of the species of Citrullus (Dane and Lang, 2004; Robinson and Decker-Walters, 1997; Rubatzky, 2001). Contrastingly, Chomicki and Renner (2015) reported West Africa to be the origin of the egusi-type dessert watermelon.

Citron watermelon is also known as “cow-melon” or “tsamma” melon (Robinson and Decker-Walters, 1997). Typically, it’s fruits are used to prepare jam (Van Wyke and Gericke, 2000). The orange and yellow fleshed fruits of some citron watermelon varieties serve for human food after cooking and for livestock feed (Laghetti and Hammer, 2007, Nantoumé et al., 2013). Also, young and succulent leaves of the crop are used as vegetable in sub-Saharan Africa (Fox and Norwood, 1982, Schippers, 2002, Maggs-Kolling and Christiansen, 2003) and seeds can be roasted and eaten as snack. Citron watermelon is considerably drought resilient crop (Akashi et al., 2001, Yoshimura et al., 2008, Mo et al., 2015) making an ideal source of genes for drought tolerance breeding in cultivated dessert watermelon (Mo et al., 2015, Rhee et al., 2015). Further, it is used as a rootstock for dessert watermelon breeding (Edelstein et al., 2014) owing to its resistance to economically important diseases including root-knot nematodes (Meloidogyne incognita), bacterial fruit blotch (Pseudomonas avenae ssp. Citrulli) gummy stem blight [Didymella bryoniae (Auersw.) Rehm] and powdery mildew [Podosphaera xanthii (Castagne) Braun & Shishkoff] (Davis et al., 2007; Gusmini et al., 2005, Tetteh et al., 2010; Thies et al., 2015, Thies et al., 2010). Therefore, citron watermelon genotypes are useful sources of genetic variation for watermelon breeding and conservation. Dessert watermelon has a narrow genetic base (Levi et al., 2001b, Ocal et al., 2014). Conversely, citron watermelon shows wider genetic variation (Levi and Thomas, 2005, Dane and Liu, 2007) suggesting its genetic value as a source of valuable genes for breeding.

Several studies conducted in southern Africa reported the presence of genetic diversity in citron watermelon. In Namibia, Maggs-Kölling et al. (2000) used morphological traits and reported wide variation among citron watermelon genotypes. Genetic diversity studies conducted using simple sequence repeat (SSR), random amplified polymorphic DNA (RAPD) and high frequency oligonucleotides (HFO) markers on citron watermelon collections in southern African countries revealed a high genetic differentiation of the species (Levi et al., 2001a, Levi et al., 2012, Mujaju et al., 2010). Nantoumé et al. (2013) differentiated landraces of citron watermelon from Jarret et al. (1997) differentiated citron watermelon accessions acquired from Chad using SSR markers. SSR markers are co-dominant, a very important factor of their popularity for genetic diversity analysis studies (Ji et al., 2012).

Information is scanty regarding genetic diversity analysis of citron watermelon germplasm from South Africa. In the past, citron watermelon was a neglected and under-researched crop (Laghetti and Hammer, 2007). Various studies reported that South African citron watermelon germplasm has been used in disease resistance breeding programs in the USA (Gusmini et al., 2005, Tetteh et al., 2010, Wechter et al., 2012, Ma and Wehner, 2015, Thies et al., 2015). Conversely, local watermelon breeding programs are largely dependent on plant introductions (PI) from the United States Department of Agriculture (USDA) germplasm collections.

Small-holder farmers in South Africa grow unimproved citron watermelon landraces which exhibit great morphological diversity such as variation in fruit shape, exocarp colouring patterns and seed morphology (Hashizume et al., 2003). Citron watermelon landraces maintained by farmers could be useful genetic resources for breeding the cultivated dessert watermelon (Levi et al., 2011b, Levi et al., 2011a). There have been no prior studies on genetic clustering of South African citron watermelon collections using molecular data. Therefore, it is important to develop systematic genetic groupings using diverse genetic pool of watermelon well-adapted to local growing conditions. This will assist in developing varieties in a reduced timeline in South Africa or other breeding programs. The objective of this study was to assess the genetic diversity present among citron watermelon landrace collections of South Africa using simple sequence repeat markers and to select genetically unique genotypes for breeding and strategic conservation.