Development of SSR markers based on transcriptome data and association mapping analysis for fruit shell thickness associated traits in oil palm (Elaeis guineensis Jacq.)

Present study mainly aimed to ascertain the distribution characteristics of gene-based microsatellite loci and to develop polymorphic SSR markers from the already available transcriptome data of Elaeis guineensis Jacq, an important oil crop. From this study, we identified the sum of 5791 SSRs across 51,425 unigenes from the transcripts of oil palm. We were able to evaluate 331primer pairs and characterized 183 polymorphic gene-based SSR markers. We identified a total of 506 alleles from the 183 polymorphic SSR loci, with an average of 2.77 alleles per locus. The characterized gene-based SSR markers from the transcriptome data of oil palm exhibited moderate levels of polymorphism with a significant level of heterozygosity ranges from 0.096 to 0.594 (mean = 0.336 ± 0.11). Among the identified SSR markers, sixty polymorphic markers were used to analyze genotypes of 55 oil palm accessions selected from three different provinces of China. Association mapping analysis provided the information of four markers that are associated with fruit shell thickness trait of oil palm. Among the four markers identified from association analysis, one SSR marker obtained from Unigene17150 is strictly associated with the oil palm fruit shell thickness trait.