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Expressed sequence tags-derived simple sequence repeats (EST-SSRs) are related to functional genes and can be useful in crop breeding. Parental lines selected in sweet potato (Ipomoea batatas (L.) Lam.) breeding including controlled hybridization and polycross may be originated from a limited number of genetic sources. We surveyed genetic variation of three breeding populations (hybrid, landrace, and polycross) of 89 cultivated sweet potato varieties derived from controlled hybridization (41 hybrids) and polycross (38 varieties) breeding population and landrace (10 varieties) maintained by various geographic regions and main agronomic traits of local farmers, using 23 EST-SSRs. Six wild sweet potato (I. trifida) samples were also included in the study. High genetic diversity in the three types of breeding populations was detected. High proportions of shared alleles leading to low levels of differentiation between breeding populations were discovered. The neighbor-joining tree and individual assignments showed intermingling of varieties among the three breeding populations. Additionally, genetic clustering showed little power of grouping varieties of different breeding populations into separate clades. These results indicate limits of sweet potato breeding. Nevertheless, ten alleles of nine loci showed variance contributed significantly to the delimitation of varieties in different breeding populations. [ABSTRACT FROM AUTHOR]

Inferring the evolutionary history of a group of closely related species can be challenging. Genetic diversity, structure, and multilocus phylogeny were studied to shed light on the evolutionary processes that shapes diversity in three closely related Lecanorchis species (L. cerina, L. suginoana, and L. thalassica). In this study, we surveyed nucleotide and genetic variation, respectively, using nuclear internal transcribed spacer 1 (nrITS1) and amplified fragment length polymorphism (AFLP) in individuals of Lecanorchis species. Both nrITS1 parsimonious and AFLP neighbor-joining trees showed paraphyly indicated that lineage sorting for these species may be incomplete. ITS1 haplotype sharing was found within L. cerina, within L. suginoana, and between L. suginoana and L. thalassica. Higher AFLP diversity was observed in L. cerina than that in L. suginoana and in L. thalassica, indicating larger population size in L. cerina. Two contrasting patterns of AFLP genetic differentiation between geographic neighbors relative to geographic distant populations were observed. Two major AFLP genetic components were found in individuals of Lecanorchis species examined. Individuals of L. cerina and of L. thalassica were classified into either component with high probabilities. Most individuals of L. suginoana were classified into one of these components, but two individuals showed apparent admixture of these components. The evidence of paraphyly, haplotype sharing, higher L. cerina diversity, sharing and admixture of genetic components, and the contrasting patterns of genetic differentiation suggest that both incomplete lineage sorting and secondary gene flow could have occurred in these closely related species, though at different temporal scale. [ABSTRACT FROM AUTHOR]