Novel in silico EST-SSR markers and bioinformatic approaches to detect genetic variation among peach(Prunus persica L.)germplasm

Because there are thousands of peach cultivars,cultivar classification is a critical step before starting a breeding project.Various molecular markers such as simple sequence repeats(SSRs)can be used.In this study,67 polymorphic primers produced 302 bands.Higher values for SI index(1.903)suggested higher genetic variability in the genotype under investigation.Mean values for observed alleles(Na),expected heterozygosity(He),effective alleles(Ne),Nei’s information index(h),and polymorphic information content(PIC)were 4.5,0.83,5.45,0.83,and 0.81,respectively.The dendrogram constructed based on Jaccard’s similarity coefficients outlined four distinct clusters in the entire germplasm.In addition,an analysis of molecular variance(AMOVA)showed that70.68%of the total variation was due to within-population variation,while 29.32%was due to variation among populations.According to this research,all primers were successfully used for the peach accessions.The EST-SSR markers should be useful in peach breeding programs and other research.

Detection of QTL(quantitative trait loci) associated with wood density by evaluating genetic structure and linkage disequilibrium of teak

To find the quantitative trait loci associated with wood density in teak(Tectona grandis L.f.), 21 co-dominant markers including 13 site specific recombinase and 8 EST-based co-dominant markers designed from lignin biosynthesis genes were applied to 174 teak plus tree clones at the National Germplasm Bank, Chandrapur,India. The germplasm bank exhibited 10.6% coefficient of variation for wood densities with 84.5 ± 31.3 genetic polymorphism(%). The highly panmictic set of genotypes(FST= 0.035 ± 0.004) harbored 96.47 ± 0.40 genetic variability(%). The average allelic frequency of the 21 codominant markers was 0.65 ± 0.11 with 12.9% pairs of loci in significant LD(p\0.05, R^2 values [ 0.1), confirming their suitability for a strong marker-trait association study. The marker CCoAMT-1 was significantly(p\0.01) associated with wood density showing stability by both GLM and MLM models and explained 4.3% of the phenotypic effect. The marker from the EST representing CCoAMT can be further developed for gene-assisted selection of elite genotypes of teak with greater wood density. Therefore, we believe that the report will help accelerate the genetic improvement and advance the breeding program of the species.

Determination of the genetic diversity of vegetable soybean [Glycine max(L.) Merr.] using EST-SSR markers

The development of expressed sequence tag-derived simple sequence repeats(EST-SSRs) provided a useful tool for investigating plant genetic diversity.In the present study,22 polymorphic EST-SSRs from grain soybean were identified and used to assess the genetic diversity in 48 vegetable soybean accessions.Among the 22 EST-SSR loci,tri-nucleotides were the most abundant repeats,accounting for 50.00% of the total motifs.GAA was the most common motif among tri-nucleotide repeats,with a frequency of 18.18%.Polymorphic analysis identified a total of 71 alleles,with an average of 3.23 per locus.The polymorphism information content(PIC) values ranged from 0.144 to 0.630,with a mean of 0.386.Observed heterozygosity(H o) values varied from 0.0196 to 1.0000,with an average of 0.6092,while the expected heterozygosity(H e) values ranged from 0.1502 to 0.6840,with a mean value of 0.4616.Principal coordinate analysis and phylogenetic tree analysis indicated that the accessions could be assigned to different groups based to a large extent on their geographic distribution,and most accessions from China were clustered into the same groups.These results suggest that Chinese vegetable soybean accessions have a narrow genetic base.The results of this study indicate that EST-SSRs from grain soybean have high transferability to vegetable soybean,and that these new markers would be helpful in taxonomy,molecular breeding,and comparative mapping studies of vegetable soybean in the future.