The use of chloroplast microsatellite markers for assessing cytoplasmic variation in a watermelon germplasm collection.

Fifteen chloroplast microsatellite (cpSSR) markers were tested to analyze cytoplasmic variation in a set of watermelon accessions containing 67 Chinese watermelon germplasms (CWGs) and 19 non-Chinese watermelon germplasms (NCGs), and 11 were polymorphic. These polymorphic cpSSR markers detected 2-4 alleles (mean = 2.8) in all the accessions, with diversity values ranging from 0.047 to 0.427 (mean = 0.252). Based on the polymorphic cpSSR loci, 17 distinct haplotypes were identified, of which six were from CWGs, seven were from NCGs, and four were shared by both of them. Most haplotypes from CWGs were nearly identical at the 11 cpSSR loci, but those from NCGs revealed higher variations. Of the haplotypes from CWGs, a predominant haplotype was found in 76.1% of CWGs, indicating that CWGs suffered a cytoplasmic bottleneck in domestication process and lost most of their cytoplasmic variability. To analyze the relationships among these 17 haplotypes, a dendrogram was constructed based on the cpSSR data using the unweighted pair-group method with arithmetic average (UPGMA). Three distinct groups were generated, revealing a genetic divergence between CWGs and NCGs. From this analysis, we obtained five rare haplotypes which had quite low genetic similarity to the others and would be useful for watermelon breeding in China. The results enriched the knowledge in genetic diversity of CWGs and could be informative for broadening the genetic base of watermelon.