SSR-based genetic identity of sugarcane clones and its potential application in breeding and variety extension

Authors: WANG, ZHOUTAO - Collaborator; Pan, Yong-Bao; LUO, JUN - Collaborator; YOU, QIAN - Collaborator; XU, LIPING - Collaborator; ZHANG, HUA - Collaborator; QUE, YOUXIONG - Collaborator

Submitted to: Sugar Tech
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/14/2019
Publication Date: 1/10/2020
Citation: Wang, Z., Pan, Y.-B., Luo, J., You, Q., Xu, L., Zhang, H., Que, Y. 2020. SSR-based genetic identity of sugarcane clones and its potential application in breeding and variety extension. Sugar Tech. 22(3):367-378. https://doi.org/10.1007/s12355-019-00788-9.
DOI: https://doi.org/10.1007/s12355-019-00788-9

Interpretive Summary: Sugarcane breeders identify new cultivars through outfield tests at multiple locations based on four years's data on cane and sugar yields, disease resistance and wide adaptability. During these tests, variety identity remains an essential issue. In this study, microsatellite DNA marker-based molecular identity was constructed for 68 sugarcane clones to supplement their morphological descriptors. The 68 clones are going through three cycles of nationwide regional tests and four cycles of integrated demonstrations. In total, 141 DNA fingerprints of 100 to 350 base pairs in length were amplified through PCR and the distribution of 139 fingerprints (98.6%) was variable among the 68 clones. Genetic variability analysis of the distribution pattern divided the 68 sugarcane clones into five groups, namely, I, II, III, IV, and V. Group I only had one clone YT 00-318. A small subgroup of Group V was identifiable at the genetic similarity coefficient of 0.890 that contained a check variety ROC 22 and four other clones. These four clones shared some excellent agronomic traits with ROC 22, shcu as wide adaptability, high cane and sugar yields, etc and therefore might have a high chance of commercial release. A statistical analysis placed the 68 clones into four quadrants based on the degree of genetic homogeneity, but not on the geographic origins. An SSR DNA fingerprint map was also drawn for the 68 clones for use by the sugarcane breeders to identify and maintain these clones in their sugarcane breeding programs.

Technical Abstract: Sugarcane variety regional test and integrated demonstration play an important role in identifying new varieties of high yield, disease resistance and wide adaptability. In this study, 15 SSR primer pairs were used to assess the genetic diversity among 68 sugarcane clones involved in three cycles of national regional tests and four cycles of integrated demonstrations in China. In total, 141 DNA fragments of 100 to 350 bp in length were identified, of which 139 fragments (98.58 %) were polymorphic among the 68 sugarcane clones. Clustering analysis of UPGMA algorithm based on the Nei genetic similarity coefficient divided the 68 sugarcane clones into five groups. Group I only had one clone YT 00-318 due to its high heterogeneity. Group II, III, VI and V contained 4, 6, 5 and 52 sugarcane clones, respectively. A small subgroup A in group V was identified at the genetic similarity coefficient 0.890 that contained ROC 22, FN 07-3206, FN 40, GT 09-12 and LC 07-150. ROC 22 was a check variety with wide adaptability, high cane yield, high sugar, and several other excellent characteristics; the other four clones might have a high potential of release by sharing the same excellent traits. Principal component analysis showed that the 68 sugarcane clones within quadrants I, II, III and IV showed a high homogeneity, and no series of clones obviously gathered together. The SSR fingerprint information of the 68 sugarcane clones has been drawn into a SSR fingerprint map for the identification of sugarcane clones in Chinese sugarcane breeding programs.