High Density Genetic Map Construction And Molecular Markers Screening Of Stevia

Stevia is a kind of perennial herbaceous plants which is native to South American.Due to its glycoside characteristics of high sweetness and low thermal,stevia are attractive to people.China is the biggest country in stevia leaf producing and exporting in the world,whereas,no new varieties fit for the farmer acquirement.Restriction-site Associated DNA Sequencing(RAD-seq)can get rid of the limits of the reference genome,and can quickly identify high density single nucleotide polymorphisms(SNPs),which is very suitable for large genetic population research.In this study segregated populationbetween two parents of big leaf type and small leaf type was used for molecular marker mapping.A large scale of SNPs will be screened by the high through sequencing technology based on RAD tags.We used GATK for the detection of SNPs,developing 378 285 polymorphism loci of parents in total,and identifying the genotyping of offspring;We finished the screening towards SNP markers after three steps: abnormal base inspection,integrity filter and segregation distortion.Then software Joinmap 4.0 was used to divide linkage group and todevelop the high quality genetic markers after screening,sort the makers in the method of Maximum likelihood,and then correct and infer the markers with the help of smooth algorithm,meanwhile removing the marker loci at similarity of 1.After that,we sorted the all markers in the use of regression algorithm by the software Joinmap 4.0,and calculated the genetic distances by Function Kosambi.In the end,we constructed a high density genetic map of Stevia successfully.Through the map,we can find out that there are 2,521 markers in the male parent genetic map,with 1,632 cM genetic distance and 0.65 cM at average,9.34 cM gap at maximum.Totally there are3,363 markers in the female parent genetic map,with 1,367 cM genetic distance and 0.41 cM at average,6.06 cM gap at maximum.Integrating the whole linkage groups,we can have 5,839 markers,1,921 cM total genetic distance,0.33 c M average genetic distance and the max gap of9.35 cM.Ultimately,the chain relationship between markers was evaluated through the heat maps of adjacent ones.The construction of high density genetic map will be helpful for the marker assistant selection(MAS)technique in the stevia future breeding,and laid a foundation for further exploring molecular markers closely related to the important traits of stevia and molecular marker assisted breeding technology.This study will show a new method to conduct the genetic improvement and molecular breeding in the special crops.