Construction Of DNA Fingerprinting And Analysis Of Genetic Diversity And Population Structure With SSR Markers For Major Released Varieties And Wild Germplasm Resources Of Sugarcane From China

Sugarcane(Saccharum spp.hybrids)is an important sugar and renewable bio-energy crop with a high aneu-polyploidy and complex genome.Sugarcane is prone to mis-identification during germplasm exchange and clones propagation activities.The characteristics of complex genome and narrow genetic base of sugarcane enhance the difficulty of selecting elite varieties in sugarcane breeding program.It is essential that developing an accurate molecular-marker tool for protecting new sugarcane variety rights and enriching the genetic base of hybrid parents.Simple Sequence Repeat(SSR)are widely used in plant genetics and breeding programs because of SSR markers are co-dominant,multi-allelic,and relatively abundant with an excellent genome coverage.Hence,in this study,two objectives were achieved using 21 SSR DNA markers and two fingerprinting systems,i.e.,capillary electrophoresis(CE)and polyacrylamide gel electrophoresis(PAGE).Firstly,we established the molecular identities(ID)of 91 nationally or provincially released Chinese sugarcane varieties and to evaluate the extent of genetic diversity among these varieties.A total of 151 SSR alleles together with 20 new alleles were detected by CE and 117 SSR alleles were detected by PAGE.Primer pairs SMC336BS,SMC31CUQ,and SMC597CS amplified more than eight alleles detectable by either CE or PAGE.Polymorphism information content(PIC)values of the SSR markers varied from 0.71-0.98 with an average of 0.90 for CE,or from 0.55-0.95 with an average of 0.84 for PAGE.UPGMA method classified the 91 varieties based on the CE data into four major groups with pair-wise similarity coefficients ranging from 61%to 93%.Secondly,we investigated the genetic structure and diversity within and among species of the highly complex polyploid genus Saccharum and Erianthus populations including 45 accessions from six wild species(S.officinarum,S.spontaneum,S.robustum,S.barberi,S.sinense,and E.arundinaceus)along with eight Saccharum spp.hybrids using the same SSR DNA marker and two fingerprinting systems as used in our first objective of our study.A total of 167 polymorphic SSR alleles involved 38 new alleles were identified by CE,but only 120 alleles by PAGE.The mean value of polymorphic information content(PIC)was 0.94 for CE and 0.92 for PAGE,respectively.The 45 accessions were classified into seven groups at species level of Saccharum and Erianthus population based on phylogenetic analysis and principle component analysis(PCA).Besides,we proposed that six core pairs of SSR primers(SMC31CUQ,SMC336BS,SMC597CS,SMC703BS,mSSCIR3 and mSSCIR43)would be widely used in genotype identification and genetic diversity assessment of Saccharum species and Saccharum spp.hybrids.Thus,the information from this study can be used in genetic resource management.