Cultivar-specific SSR markers as revealed through fluorescence- labeling and capillary electrophoresis in sugarcane (Saccharum hybrids spp.)

Authors: LUZARAN, ROSALYN - Philippine Sugar Research Institute Foundation, Inc; Pan, Yong-Bao

Submitted to: Philippine Journal of Crop Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/10/2020
Publication Date: 8/20/2020
Citation: Luzaran, R.T., Pan, Y.-B. 2020. Cultivar-specific SSR markers as revealed through fluorescence- labeling and capillary electrophoresis in sugarcane (Saccharum hybrids spp.). Philippine Journal of Crop Science. 45(2):47-57.

Interpretive Summary: Breeding new and better sugarcane varieties is a sustainable way of increasing productivity, but it takes more than 10 years for cane breeders to produce a new cariety. Philippine Sugar Research Institute Foundation Inc. (PHILSURIN) took the first step to establish a germplasm collection through variety exchange programs with the USA, Australia, South Africa, China, France, Thailand, and Mauritius. The next step was to find out the extent of genetic variability among > 750 domestic and foreign sugarcane cultivars through phenotypic and molecular surveys. In this study, the diversity and relatedness among 41 parental varieties and 20 newly produced hybrids were assessed using 21 SSR primer pairs along with the CE/FD method. A total of 199 DNA bands were amplified through PCR, of which 90.45% were polymorphic. Number of DNA bands per primer pair ranged from 3 to 16 with an average of 8.57. Some bands were uniquely present or absent in a particular cultivar, which can be used as cultivar-specific DNA markers. Percentage of polymorphic bands (PPB) per primer pair varied from 72.72 to 100% with an average of 92.07%. Polymorphism information content (PIC) ranged from 0.19 to 0.89 with an average of 0.80. An UPGMA genetic method was used to cluster the 61 sugarcane varieties into two major and three minor groups, which were in agreement with the results from principal component analysis except for a few cultivars that were loosely distributed distantly from the larger group. Twenty SSR primer pairs amplified DNA bands that are useful in identifying commercial cultivars and other wild relatives of sugarcane in the PHILSURIN germplasm collection. The information generated from this study can also be employed in seed cane production certification, seed contaminant identification, and distinguishing among cultivars with similar phenotype.

Technical Abstract: Genetic diversity in sugarcane was investigated using 21 fluorescence-labeled polymorphic SSR markers and capillary electrophoresis system. Sixty-one sugarcane varieties from the Philippines were included in the study including 21 commercial cultivars with 13 parental materials and 20 new hybrids. A total of 199 alleles were amplified, of which 90.45% were polymorphic. Number of alleles recorded per primer pair ranged from 3 to 16 with an average of 8.57. Some alleles were uniquely present or absent in a particular cultivar that can be used as cultivar-specific markers for rapid discrimination. The percentage of polymorphic bands (PPB) per primer pair varied from 72.72 to 100% with an average of 92.07%. The polymorphism information content (PIC) value ranged from 0.19 to 0.89 with an average of 0.80. An unweighted pair group method analysis was used to cluster the 61 sugarcane varieties into two major groups and three minor clusters, which were in agreement with the results of principal component analysis except for a few cultivars that were loosely distributed distantly from the large group. Twenty SSR primer pairs generated fingerprint markers that are useful in identifying commercial cultivars and other wild relatives of sugarcane in the germplasm collection in the Philippines. The results can be extended by using additional SSR primer pairs. The information generated from this study can also be employed in seed cane production certification, seed contaminant identification, and distinguishing among cultivars with similar phenotype.