Mining and characterization of genic-microsatellites associated with sucrose synthesis and their utility in population structure analysis in sugarcane

Abstract

Sucrose content is a highly valued trait in sugarcane breeding that is regulated by several genes. Tracking of multiple genes involved in the expression of a complex trait in a highly heterozygous crop like sugarcane during the breeding programme is a huge challenge. Trait tagging through expressed sequence tags (ESTs) derived molecular markers has been considered as powerful tool because they are encoded by functionally relevant elements of the genome and directly linked with the target traits. Functional markers related to sucrose content are very limited in sugarcane, which hindered the genetic improvement of this trait. Seventy-three sucrose rich and fifteen low sucrose clones chosen from twelve full-sib families were used for the study on the development and characterization of genic microsatellites associated with sucrose synthesis. A total of 186 alleles were obtained, with an average of 6.20 alleles per microsatellite marker. Polymorphism Information Content (PIC) values were ranged from 0.31 to 0.83, with a mean value of 0.61. The average values of gene diversity (GD) and resolving power (RP) were 0.60 and 5.14, respectively. The present study identified genic SSR markers for four major enzymes viz., CA076844187 (FK), CA155160295 (SREBF), CA163325191,213 (SREBF), TA38405-4547232 (PPFK), and CA135596178, 225 (DFPP) which could be useful to identify sucrose rich clones in the initial testing stages of the selection programme in sugarcane. Analysis of molecular variance (AMOVA) showed 74 per cent of the total variation within population and 26 per cent among population. The EST-SSR primers showed a high allelic polymorphism, as demonstrated by high genetic diversity estimates (I =1.17, Ho = 0.78). The low mean values of fixation index (FST = 0.078) and the high estimates of gene flow (Nm = 4.166) indicates the low level of population differentiation and maximum genetic exchange between two populations. Based on SSR marker data, eighty-eight clonal accessions were classified broadly into high and low sugar population which corresponded to the molecular diversity of the sucrose specific alleles through structure analysis and principal coordinate analysis. Key wordsSugarcane, sucrose content, genic-microsatellites, AMOVA, population structure