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. 2019 Jan 23;9(1):395.
doi: 10.1038/s41598-018-36630-7.

Genetic diversity and population structure analysis of Saccharum and Erianthus genera using microsatellite (SSR) markers

Ahmad Ali  1 , Yong-Bao Pan  2 , Qin-Nan Wang  3 , Jin-Da Wang  1 , Jun-Lü Chen  3 , San-Ji Gao  4
Affiliations

Genetic diversity and population structure analysis of Saccharum and Erianthus genera using microsatellite (SSR) markers

Ahmad Ali et al. Sci Rep. .

Abstract

In order to understand the genetic diversity and structure within and between the genera of Saccharum and Erianthus, 79 accessions from five species (S. officinarum, S. spontaneum, S. robustum, S. barberi, S. sinense), six accessions of E. arundinaceus, and 30 Saccharum spp. hybrids were analyzed using 21 pairs of fluorescence-labeled highly poloymorphic SSR primers and a capillary electrophoresis (CE) detection system. A total of 167 polymorphic SSR alleles were identified by CE with a mean value of polymorphic information content (PIC) of 0.92. Genetic diversity parameters among these 115 accessions revealed that Saccharum spp. hybrids were more diverse than those of Saccharum and Erianthus species. Based on the SSR data, the 115 accessions were classified into seven main phylogenetic groups, which corresponded to the Saccharum and Erianthus genera through phylogenetic analysis and principle component analysis (PCA). We propose that seven core SSR primer pairs, namely, SMC31CUQ, SMC336BS, SMC597CS, SMC703BS, SMC24DUQ, mSSCIR3, and mSSCIR43, may have a wide appicability in genotype identification of Saccharum species and Saccharum spp. hybrids. Thus, the information from this study contibites to manage sugarcane genetic resources.

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Conflict of interest statement

The authors declare no competing interests.

Figures

Figure 1
Figure 1
Statistical analysis of genetic variability among Saccharum, Erianthus and Saccharum spp. hybrids populations based on SSR data. Polymorphism index (PI) (a), Number of observed alleles (Na) (b), Number of effective alleles (Ne) (c), Shannon’s index (I) (d), and Nei’s genetic diversity (h) (e).
Figure 2
Figure 2
Three-dimensional principal component analysis (PCA) plot of Saccharum, Erianthus, and Saccharum spp. hybrids based on SSR data.
Figure 3
Figure 3
Phylogenetic trees of Saccharum, Erianthus, and Saccharum spp. hybrids based on SSR data. A distance tree was constructed in MEGA 6 using the UPGMA method. Robustness of the node of the phylogenetic tree was assessed from 1000 bootstrap replicates and bootstrap values of >60% are shown.
Figure 4
Figure 4
Two phylogenetic trees constrcuted using SSR data derived from 21 SSR primer pairs vs 7 SSR primer pairs with tanglegrams.
See this image and copyright information in PMC

References

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