Genetic analysis and molecular characterization of Chinese sesame (Sesamum indicum L.) cultivars using insertion-deletion (InDel) and simple sequence repeat (SSR) markers

Abstract

Background: Sesame is an important and ancient oil crop in tropical and subtropical areas. China is one of the most important sesame producing countries with many germplasm accessions and excellent cultivars. Domestication and modern plant breeding have presumably narrowed the genetic basis of cultivated sesame. Several modern sesame cultivars were bred with a limited number of landrace cultivars in their pedigree. The genetic variation was subsequently reduced by genetic drift and selection. Characterization of genetic diversity of these cultivars by molecular markers is of great value to assist parental line selection and breeding strategy design.

Results: Three hundred and forty nine simple sequence repeat (SSR) and 79 insertion-deletion (InDel) markers were developed from cDNA library and reduced-representation sequencing of a sesame cultivar Zhongzhi 14, respectively. Combined with previously published SSR markers, 88 polymorphic markers were used to assess the genetic diversity, phylogenetic relationships, population structure, and allele distribution among 130 Chinese sesame accessions including 82 cultivars, 44 landraces and 4 wild germplasm accessions. A total of 325 alleles were detected, with the average gene diversity of 0.432. Model-based structure analysis revealed the presence of five subgroups belonging to two main groups, which were consistent with the results from principal coordinate analysis (PCA), phylogenetic clustering and analysis of molecular variance (AMOVA). Several missing or unique alleles were identified from particular types, subgroups or families, even though they share one or both parental/progenitor lines.

Conclusions: This report presented a by far most comprehensive characterization of the molecular and genetic diversity of sesame cultivars in China. InDels are more polymorphic than SSRs, but their ability for deciphering genetic diversity compared to the later. Improved sesame cultivars have narrower genetic basis than landraces, reflecting the effect of genetic drift or selection during breeding processes. Comparative analysis of allele distribution revealed genetic divergence between improved cultivars and landraces, as well as between cultivars released in different years. These results will be useful for assessing cultivars and for marker-assisted breeding in sesame.

Figure 1

Comparison the distribution of observed heterozygosity (H _e ) (A), polymorphic information content (PIC) (B), minor allele frequency (MAF) (C) and F-statistics (F _st ) (D) between SSR and InDel markers.

Figure 2

Box and Whisker box of summary statistics for 325 SSR or InDel loci in five different subsets by types (A, B) or releasing period of cultivars (C, D). A and C gene diversity; B and D polymorphic information content (PIC). WIC[L], White seeded Improved cultivars or Inbred lines; WLR, White seeded Landraces; BIC, Black seeded Improved cultivars; BLR, Black seeded Landraces; LR refer to white or black seeded Landraces and four wild accessions; Y1970s, Y1980s, Y1990s, Y2000s and Y2010s refer to improved cultivars released in or prior to the 1970s, in the 1980s, 1990s, 2000s and 2010s, respectively.

Figure 3

Analysis of the population structure based on 88 SSR or InDel markers. A Estimated LnP(D) and ∆k of total 130 sesame lines over five runs for each k value. B Estimated LnP(D) and ∆k of 98 lines in G1 over five runs for each k value. C Estimated LnP(D) and ∆k of 21 lines in G2 over five runs for each k value. D Estimated population structure in 130 sesame lines assessed by STRUCTURE. Each individual is represented by a thin vertical bar, partitioned into up to k colored segments.

Figure 4

Representation of genetic structure of 130 sesame lines based on Neighbor-joining phylogenetic tree (NJ-tree) (A) and Principal component analysis (PCA) (B). P1, P2, P3, P4, P5 and Pmix are subgroups identified by STRUCTURE assigned with the maximum membership probability. For NJ-tree and PCA plot, the different colored lines or plots represent the different subgroups inferred by STRUCTURE analysis. P1 yellow, P2 red, P3 blue, P4 green, P5 pink, Pmix black.

Figure 5

X-Y plots for allele frequencies in pairwise comparisons of sesame accessions. A WIC(L) versus WLR, B BIC versus BLR, C Y1980s versus Y1970s, D Y1990s versus Y1980s, E Y2000s versus Y1990s, F Y2010s versus Y2000s, respectively.