Phenotypic and molecular characterization of a core collection of Saccharum spontaneum L. in China

Authors: XU, CHAO-HUA - Yunnan Academy Of Agriculture Sciences; LIU, XIN-LONG - Yunnan Academy Of Agriculture Sciences; BURNER, DAVID - Yunnan Academy Of Agriculture Sciences; ABBAS, ZAHEER - Yunnan Academy Of Agriculture Sciences; Pan, Yong-Bao; ELGAMAL, IBRAHIM - Yunnan Academy Of Agriculture Sciences; LU, XIN - Yunnan Academy Of Agriculture Sciences; SU, HUO-SHENG - Yunnan Academy Of Agriculture Sciences

Submitted to: Sugar Tech
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/16/2019
Publication Date: 2/20/2020
Citation: Xu, C., Liu, X., Burner, D.M., Abbas, Z., Pan, Y.-B., Elgamal, I.S., Lu, X., Su, H. 2020. Phenotypic and molecular characterization of a core collection of Saccharum spontaneum L. in China. Sugar Tech. 22(1):76–88. https://doi.org/10.1007/s12355-019-00761-6.
DOI: https://doi.org/10.1007/s12355-019-00761-6

Interpretive Summary: Modern sugarcane cultivars share a narrow genetic background that needs to be expanded by crossing cultivars with related wild species. Saccharum spontaneum L. is one progenitor species of sugarcane that contributes high vigor, stubbling, and tolerance to biotic and abiotic stresses. Although more than 500 wild S. spontaneum clones have been collected, these clones have not been fully characterized and utilized. The objective of this study was to evaluate a primary core collection of 92 S. spontaneum clones from a germplasm collection at Kaiyuan, Yunnan, China with 29 phenotypic traits and 15 single sequence repeat (SSR) markers. The results demonstrated that there were considerable genetic variations among the 92 S. spontaneum clones. Statistical and genetic analysis identified two major traits related to sugar yield and juice quality, indicated that geographic location was not a good predictor of clonal divergence, and proved that the primary core collection of S. spontaneum was constructed correctly. Although the phenotypic trait data and SSR data were useful for discriminating the genetic variations in the wild S. spontaneum species, a weak, non-significant correlation between phenotypic and SSR data was also observed. This discrepancy between phenotypic and SSR clusters requires a further study, perhaps using additional SSR markers developed from the genome sequence of S. spontaneum rather than that of sugarcane. Overall results suggested that a combination of SSR markers and phenotypic traits can be used to effectively assess the extent of genetic diversity within a S. spontaneum collection so as to help the sugarcane breeders identify diverse germplasm for use in their breeding programs.

Technical Abstract: The narrow genetic base among modern sugarcane varieties (Saccharum spp. hybrids) is stimulating research on the genetic diversity of related wild species in order to optimize breeding strategies. Saccharum spontaneum L. is one of the progenitor species of sugarcane that displays a considerable level of phenotypic variation, vigor, ratooning ability, and tolerance to biotic and abiotic stresses. The objective of this study was to assess the level of genetic diversity within a primary core collection of 92 S. spontaneum clones based on 29 phenotypic traits and 15 single sequence repeat (SSR) marker data. The results demonstrated that there was a considerable level of genetic diversity within a 92-accession primary core collection of S. spontaneum. Principal component analysis (PCA) and heatmap analysis by HemI (Heatmap Illustrator, version 1.0) identified two major traits related to yield and juice. High level of economic characters of S. spontaneum can be first exploited in breeding programs for sugarcane genetic improvement. Dendrogram analysis showed that geographic location was not a good predictor of clonal divergence either within or among the populations. The NE172 genetic distance varied from 0.072 to 0.964 between accessions. The results further proved that the primary core collection of S. spontaneum was constructed correctly in a previous study. Clustering analyses of phenotypic traits and SSR data were useful for discriminating the genetic variations in S. spontaneum, however, there was a weak, non-significant correlation (r=-0.059, p=0.151) between phenotypic and SSR data. The discrepancy between phenotypic and SSR clusters requires a further study, perhaps using additional SSR markers developed from the genome sequence of S. spontaneum rather than that of sugarcane. Our results suggested that a combination of SSR markers and phenotypic traits can be an effective means of assessing the genetic diversity within S. spontaneum so as to help the sugarcane breeders identify diverse germplasm for use in their breeding programs.