ISSR and AFLP Markers Differ among American Watermelon Cultivars with Limited Genetic Diversity

Abstract

<jats:p>Wide phenotypic diversity exists among American heirloom cultivars of watermelon (<jats:italic>Citrullus lanatus</jats:italic> var. <jats:italic>lanatus</jats:italic>). However, in published studies, low or no polymorphism was revealed among those heirlooms using isozyme or randomly amplified polymorphic DNA (RAPD) markers. In this study, experiments with inter-simple sequence repeat (ISSR) [also known as simple sequence repeat-(SSR-) anchored primers] and amplified fragment-length polymorphism (AFLP) markers produced high polymorphisms among watermelon heirloom cultivars. ISSR (111) and AFLP (118) markers (229 total) identified 80.2% to 97.8% genetic similarity among heirloom cultivars. The phylogenetic relations based on ISSR and AFLP markers are highly consistent with the parental records available for some of the heirloom cultivars, providing confidence in the dendogram constructed for heirlooms based on similarity values. As compared with RAPD markers, ISSRs and AFLPs are highly effective in differentiating among watermelon cultivars or elite lines with limited genetic diversity.</jats:p>

Effect of DNA methylation on molecular diversity of watermelon heirlooms and stability of methylation specific polymorphisms across the genealogies

“…The methylated bands that are polymorphic (MP) were used to construct Neighbor-Joining (NJ) phenograms to explore whether the patterns of genetic relationships were consistent with those determined previously (Levi et al 2004). The first and the second analyses included specific MPs of MspI and HpaII, respectively, to compare the tree topologies of complete methylation (MspI) versus hemi-methylation (HpaII).…”

“…There is wide phenotypic diversity in terms of growth habits, fruit traits and resistance to biotic and abiotic stress (Levi et al 2004). After using wide ranging DNA marker tools, Levi et al (2001Levi et al ( , 2004, concluded that there is a very narrow genetic diversity at the DNA sequence level.…”

“…There is wide phenotypic diversity in terms of growth habits, fruit traits and resistance to biotic and abiotic stress (Levi et al 2004). After using wide ranging DNA marker tools, Levi et al (2001Levi et al ( , 2004, concluded that there is a very narrow genetic diversity at the DNA sequence level. In order to exploit the cultivar phenotypic potential to the fullest extent, insights into other sources of variation such as epigenetic and functional diversity might be needed to understand the interplay between wide phenotypic diversity and narrow DNA sequence diversity.…”

“…Matsum. & Nakai] cultivars at the methylation level, and to estimate epigenetic diversity based on methylation profiles to compare with previously published DNA level diversity (Levi et al 2004).…”

Identification and validation of a core set of microsatellite markers for genetic diversity analysis in watermelon, Citrullus lanatus Thunb. Matsum. & Nakai

“…For example, of 1,309 RAPD markers, only 75 were polymorphic (5.9%) between two watermelon breeding lines (Harris et al 2008). Other marker systems such as AFLP (Che et al 2003;Levi et al 2004), SRAP (Levi et al 2006;Zhang et al 2008), EST-PCR (Levi et al 2009) and HFO-TAG produced slightly higher polymorphism among watermelon cultivars than the RAPD markers, but all in general were not breeder friendly. Results from these genetic assays were hardly comparable due to lack of a common core set of reference genotypes and the use of different marker systems.…”