Population structure and genetic diversity analysis in sugarcane (Saccharum spp. hybrids) and six related Saccharum species

Authors: XIONG, HAIZHENG - University Of Arkansas; CHEN, YILIN - University Of Arkansas; GAO, SAN-JI - Fujian Agriculture And Forest University; Pan, Yong-Bao; SHI, AINONG - University Of Arkansas

Submitted to: Agronomy
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/1/2022
Publication Date: 2/6/2022
Citation: Xiong, H., Chen, Y., Gao, S., Pan, Y.-B., Shi, A. 2022. Population structure and genetic diversity analysis in sugarcane (Saccharum spp. hybrids) and six related Saccharum species. Agronomy. 12(2):412. https://doi.org/10.3390/agronomy12020412.
DOI: https://doi.org/10.3390/agronomy12020412

Interpretive Summary: Sugarcane is one of the most important commercial crops for sugar, ethanol and other byproducts production; therefore, it is of great significance to carry out genetic research. Knowledge of diversity and population structure is vital for managing germplasms and genetic breeding. In this study, 22 pairs of fluorescence-labeled highly polymorphic SSR primers and a capillary electrophoresis (CE) detection system were used to assess the diversity and population structure of 196 accessions, including 34 S. officinarum, 69 S. spontaneum, 17 S. robustum, 25 S. barberi, 13 S. sinense, 2 S. edule, and 36 sugarcane hybrids. A total of 624 polymorphic SSR fingerprints were amplified from the genomic DNA by PCR, separated by CE, and visualized by a genotyping software, of which 109 fragments were new. The presence or absence of these 624 fragments in each of the 196 accessions was recorded in an Excel spreadsheet. Three genetic analyses , namely, model-based clustering, principal component analysis, and phylogenetic analysis, were conducted. The results showed that these 196 accessions were grouped into either three or eight sub-populations. Furthermore, phylogenetic analysis indicated that most accessions in each species merged. The species S. barberi and S. sinense formed one group, while S. robustum, S. barberi, S. spontaneum and, S. edule merged with sugarcane hybrids into the second group. S. officinarum was the third group located between the other two groups. Lastly, two-way chi-square tests derived a total of 24 species-specific or species-associated SSR fragments, including four each for S. officinarum, S. spontaneum, S. barberi, and S. sinense, five for S. robustum. and three for sugarcane hybrids. These 24 species-specific or species-associated SSR fragments may have a wide application value in species identification in sugarcane and related germplasm. The results of this study will contribute to future genetic study of the Saccharum genus and provide information on how to use these sugarcane germplasm accessions in breeding and genetic base broadening.

Technical Abstract: Sugarcane (Saccharum spp. hybrids) is one of the most important commercial crops for sugar, ethanol and other byproducts production; therefore, it is of great significance to carry out genetic research. Assessing of the genetic population structure and diversity plays a vital role for managing genetic resources and gene mapping. In this study we used 22 pairs of fluorescence-labeled highly polymorphic SSR primers and a capillary electrophoresis (CE) detection system to assess the population structure among 196 sugarcane accessions, including 34 S. officinarum, 69 S. spontaneum, 17 S. robustum, 25 S. barberi, 13 S. sinense, 2 S. edule, and 36 Saccharum spp. hybrids. A total of 624 polymorphic SSR alleles were identified by CE with 109 new alleles. Three approaches (model-based clustering, principal component analysis, and phylogenetic analysis) were conducted for population structure and genetic diversity analyses and the results showed that these 196 accessions were grouped into either three or eight sub-populations (Q/q). Phylogenetic analysis indicated that most accessions in each species merged; the species S. barberi and S. sinense formed a group; the accessions of four species, namely, S. robustum, S. barberi, S. spontaneum and, S. edule merged with sugarcane hybrids into the second group; and S. officinarum was located between the two groups. Two-way chi-square tests derived a total of 24 species-specific or species-associated SSR alleles, including four each for S. officinarum, S. spontaneum, S. barberi, and S. sinense, five for S. robustum. and three for Saccharum spp. hybrids, which have a wide application value in sugarcane species identification. The results of this study would contribute to future genetic study of the Saccharum genus and provide information on how to use these sugarcane germplasm accessions in breeding and resource broadening.