Genotype-Specific Microsatellite (SSR) Markers for the Sugarcane Germplasm from the Karst Region of Guizhou, China

Abstract

Genetic variability among sugarcane genotypes from the Karst region of China was evaluated using genotype-specific microsatellite (SSR) markers. Eighteen sugarcane genotypes including 13 active cultivars and five elite QT-series clones bred locally were screened for genetic variability with 21 SSR primer pairs. All the primer pairs were highly polymorphic and amplified a total of 167 alleles with an average of eight alleles per primer pair. The average polymorphism information content (PIC) value was 0.86 with a range of 0.68 and 0.92. A UPGMA dendrogram categorized the 18 sugarcane genotypes into three major groups containing three, ten and five genotypes, respectively. No geographical affinity was observed among genotypes within the same group. Eight SSR primer pairs produced cultivar-specific alleles, of which five alleles were unique to the QT-series clones, namely, . The clone-specific SSR alleles will be useful in identifying elite QT-series clones for use in the sugarcane crossing programs in China.

Development and Use of Simple Sequence Repeats (SSRs) Markers for Sugarcane Breeding and Genetic Studies

“…Tena et al [75] used 22 SSR markers to amplify a total of 260 alleles in a study of introduced sugarcane accessions in Ethiopia to determine population relationships and differentiation. Fu et al [64] employed 18 sugarcane genotypes, including 13 active cultivars and five elite QT-series clones, to determine genetic variability with 21 SSR primer pairs.…”

“…QTL mapping typically employs populations resulting from a bi-parental cross [93]. In sugarcane, SSRs can be used to analyze QTLs that can contribute to the identification of candidate genes for traits of agronomic interest, including sugar yield, biotic and abiotic resistance, and overall quality [58,64,94]. Mapping and stability of QTLs is made difficult because many genetic and external factors influence the expression of the final phenotype, and studies therefore must include a high number of segregating genotypes to ensure precision [58,95].…”

SSR Marker-Assisted Management of Parental Germplasm in Sugarcane (Saccharum spp. hybrids) Breeding Programs

“…SSR markers have been used widely to study sugarcane genetic diversity and population structure [22][23][24], variety identity [25], genetic map [26,27], and genetic association [28][29][30]. Furthermore, fluorescence-labeled SSR markers combined with high-performance capillary electrophoresis (HPCE) have manifested better performance in genotyping of polyploid sugarcane, due to higher accuracy and better detection power [22][23][24][31][32][33][34][35][36][37]. Now, this paper reports a study that was designed to manage the parental germplasm of the sugarcane breeding programs in China through the microsatellite (SSR) DNA fingerprinting using fluorescence-labeled SSR primers and the high-performance capillary electrophoresis (HPCE) system.…”