Association Analysis Of Main Agronomic Traits Of Sugarcane Cultivated Varieties Using AFLP And SSR Markers

The experiment is divided into two parts.The first part is the development and screening of SSR markers.We scanned the target genome sequences from NCBI by using MISA software,and found a total of 7231 SSR loci in 43Mb of the sugarcane cultivar "R570" genome sequence,with an average of 1 SSR site per 5947bp.The SSR motifs with two or three nucleotides are the most dominant types in the sugarcane genome,which is consistent with the results published in the similar studies of other crops.232 pairs of SSR primers were designed and synthesized in this study.232 primers were screened on 12 sugarcane varieties,and 48 pairs of primers with good quality of amplification and polymorphism were selected for further analysis use.These 48 pairs of SSR primers revealed a total of 212 polymorphic loci on 12 sugarcane varieties with an average of 4.41 polymorphic loci per pair of primers.Finally,only nine of these 48 pairs of SSR primers se were used in the association analysis in the second part of this study.In the second part of this study,a total of 80 sugarcane varieties from around the world were obtained from the National Nursery of Sugarcane Germplasm Resources?Kaiyuan,China?.Ten important agronomic traits?including sprouting number,total number of plants,tiller number,tiller rate,effective stalk number in Mu,effective stalk number/4m,brix,plant height,stalk diameter and stalk weight?have been cxamined on these varieties.The whole genome scans were performed with 64 combinations of AFLP primers and 9 pairs of SSR primers.We used the generalized linear model?GLM?to analyze the association between the phenotype and genotype data.Through the analyses of phenotypic variation,molecular genetic polymorphism and population structure,a total of 703 loci were identified as significant correlated with target traits.111 AFLP loci were found to be highly significantly correlated with target traits,and 27 SSR loci were found to be significantly correlated with the traits,of which 10 SSR loci was identified as highly significantly associated with the traits.1.Descriptive statistics and variance analysis of phenotypic traits o showed that P values of ten traits between 80 materials were less than 0.001,indicating that the difference between 80 varieties is extremely significant,and the phenotypic polymorphism is very high in the association mapping population.2.The correlation analysis of phenotypic traits showed that there was a significant positive correlation between the traits of plant height,stalk diameter and stalk weight,no significant correlation was found between Brix and other traits except for stalk diameter.3.15159 polymorphic loci were detected from 64 combinations of AFLP primers on 80 sugarcane varieties.4141 of them were selected by their high quality?64.7 per combination of primers?,and 151 polymorphic loci were detected by using the 9 pairs of SSR primers.4.Based on these molecular data,the 80 varieties were divided into 6 groups by using the STRUCTURE 2.3.4 software?designated for population structure analysis use?.This result is similiar to that obtained with NTSYS2.1e based on UPGMA,indicating that the result of population structure analysis is reliable5.Association analysis between genotypes and phenotypic traits showed that there more number of loci significantly associated with brix than that significantly associated with other characters.The percentages that the identified markers can explain the brix variation varied from 13.09%to 25.86%,of which eight markers explained each more than 20%ofthe brix variation.The highest value of 25.86%is associated with the AFLP marker E-ACT/M-CAT₂93bps.The association analysis with SSR markers showed that 27 loci were significantly associated with the traits?P<0.01?,and FZW89₁00bp and FZW202₂01bp were significantly correlated with the total number of plant and tiller number,respectively.The FZW97₂70bp locus was significantly correlated with the traits of brix and stalk weight.Ten SSR loci were identified as highly significantly correlated with phenotypic traits?P<0.001?.Of which,three loci FZW107₁06bp,FZW202₁01bp and FZW202₁95bp explained a percentage of 35.59%,37.62%,and 30.17%respectively of brix variation.