Switchgrass Germplasm Genetic Diversity And Correlation Analysis Of Important Traits Loci

Switchgrass(Panicum virgatum L.)belonging to Poaceae(Gramineae)Panicum,is a tall tufted perennial warm-season type C4 plant.Switchgrass is constantly regarded as a huge potential energy plant,due to its energy conversion rate,strong water absorption rate,high utilization of nutritional value and environmentally friendly characteristics The early 1990s,the United States and Canada considered switchgrass as a model plant for the research on the production of bio-energy plant fuel ethanol.Currently,few studies have been focused on the association analysis for switchgrass.In this study,the association analysis has been conducted by combining the EST-SSR,ISSR,SCoT,and SNP markers and phenotypic traits,to obtain closely chain site with fine properties.Results from this study are as follows:(1)The genetic variation and relationship of 96 switchgrass germplasms were analyzed by SCoT molecular markers.Twenty SCoT primer pairs were used to amplify SCoT fragments for 138 switchgrass germplasms.The primers generated a total of 445 bands among which 402(96.00%)bands were found to be polymorphic.The value of locus polymorphism information contents(PIC)ranged from 0.184 to 0.426,with an average of 0.334.Marker index was 10.72.The genetic similarity coefficient among the germplasms ranged from 0.498 to 0.912,and the average content was 0.688,indicating that the genetic variation could be revealed using SCoT markers.138 switchgrass germplasms were clustered into upland and lowland groups by the cluster analysis.The results of POPGENE version 1.32 analysis showed that the genetic diversity index(H)and Shannon index(I)were 0.285 and 0.432,respectively,indicating that there was comparatively great genetic diversity and high genetic variation among the switchgrass germplasms.Analysis of molecular variance(AMOVA 1.55)indicated that 71.91%of total variability came within populations level,while 28.09%came among populations level.The results indicated that SCoT markers were feasible and effective to analyze the genetic diversity of switchgrass.(2)To search for molecular markers which closely related to the phenotype of switchgrass,and estimate the phenotypic effects,15 pairs of EST-SSR primers,16 pairs of ISSR primers,and 20 SCoT primers for 30 switchgrass germplasm resources were used to analyze the genetic diversity,population structure,and do association analysis with phenotypic traits.Genetic diversity analysis results showed that three markers were detected in 708 polymorphic loci,accounting for 89.28%of all all loci.Population structural analysis showed that 30 switchgrass germplasms were clustered into two subgroups,with 17 resources(56.67%)in POP1,and 13 resources(43.33%)in POP2;Association analysis showed that a total of 36 markers associated with phenotypic traits were detected significantly(P<0.01)in 2013 and 2014.Fifteen markers were detected significantly(P<0.01)in 2013,with the sum of rate for explain is 3.4177,the average explain is 0.2278,and the explain ranged from 0.0175(SCoT-463 marks)-0.5104(ISSR-130).Twenty-one markers were detected significantly(P<0.01)in 2014,with the sum of rate for explain is 4.2541,the average explain is 0.2026,and the explain ranged from 0.0512(ISSR-125)-0.2685(ISSR-113),indicating high polymorphism and certain extent of linkage disequilibrium were exited among sites.(3)Four genes named 4CL,PAL,COMT,and LACS of thirty switchgj’ass germplasm resources were used to cloned and sequenced.The results showed that three SNP variation sites were detected in 4CL gene.The phenotypic variation explanation of the site 116 for DBM2014 is 0.2040,the phenotypic variation explanation of the site 116 for DBM2013 is 15.3906,and the phenotypic variation explanation of the site 654 for DBM2013 is 37.3097.PAL gene were detected in two SNP variation sites,the phenotypic variation explanation of the site 391 for DBM2014 is 0.5565,the phenotypic variation explanation of the site 435 for DBM2013 is 11.9168.COMT gene were detected in a SNP mutations point,The phenotypic variation explanation of the site 678 for DBM2013 is 25.7427.LAC5 gene were detected six SNP variation sites,the phenotypic variation explanation of the site 218 for DBM2014 is 37.4163,the phenotypic variation explanation of the site 116 for DBM2014 is 37.4163,the phenotypic variation explanation of the site 419 for DBM2014 is 37.4163,the phenotypic variation explanation of the site 707 for TN2014 is 15.4397,the phenotypic variation explanation of the site 97 for TN2014 is 12.0097,The phenotypic variation explanation of the site 126 for TN2014 is 30.2732.The detected SNPs were the least for COMT and the detected SNPs were the most in LACS gene among the four genes.But it did not detecte SNPs associated with lignin trait.