Sapindus mukorossi Gaertn. and S. delavayi Franchet are among the most valuable species in the genus Sapindus for their commercially exploitable plant oils and chemicals. However, few studies have addressed genetic variation and improvement for either species. We evaluated the genetic diversity of germplasm from selected plus trees within a wide region and established the relationship between fruit traits and molecular markers. An association analysis based on inter-simple sequence repeats(ISSRs)provided a genetic basis for studies of fruit traits. A total of 247 loci were detected by scanning 61 trees of S. mukorossi and S. delavayi using 16 ISSR markers. Genetic diversity parameters were estimated for selected superior trees(or germplasm) and S. mukorossi and S. delavayi were categorized into two main groups, as well as into four groups within S. mukorossi. An association analysis between the ISSR markers and 14 fruit traits used the TASSEL MLM model. A genetic structure analysis differentiated S.mukorossi and S. delavayi. Eighteen ISSR loci associated with 13 fruit traits(P<0.005) were identified, with 13, 1,and 4 loci associated with seed oil production, fruit saponin production, and fruit quality, respectively. Using this information, a core collection was selected with adequate genetic diversity and good seed oil characters. Our results demonstrate the feasibility of effectively estimating fruit trait associations in Sapindus using ISSR markers, and the method is applicable and valuable for select germplasm conservation. The markers obtained in this study are potentially useful for molecular-assisted breeding of Sapindus spp.
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