Mining and characterizing EST-SSR markers from ESTs of Torreya grandis

Publication date: April 2016 Source:Biochemical Systematics and Ecology, Volume 65 Author(s): Guanmei Yi, Tingting Zhao, Zhinang Yin, Ping Tang, Yingjun Qiu, Xiaohong Yao Torreya grandis Fort. ex Lindl. cv. Merrillii (Taxaceae) is an important economic tree species grown for dried nuts in China. However, it was listed as national second-grade key protected wild plants due to overexploitation of wild resources. To enhance knowledge about genetic characteristics useful for the conservation and sustainable utilization of genetic resource of this species, microsatellite loci were developed by analyzing a reference transcriptome de novo assembled from RNA-seq data of T. grandis. A total of 1713 SSRs containing repeats from di-to pentanucleotides were detected in 46,000 unigenes. Trinucleotide (46.9%) was the most common repeat unit followed by the di (19.7%), pentanucleotides (15.1%), hexa (8.9%), and tetra (6.5%). From these, 108 primer pairs were designed, among which nineteen polymorphic microsatellites were developed and characterized. The number of alleles per locus ranged from 2 to 4, with an average of 2.6 alleles per locus. The observed and expected heterozygosity ranged from 0.10 to 1.00 and 0.13 to 0.70, respectively. Six loci showed significant departure from HWE after Bonferroni correction. The microsatellite markers described here will be useful for evaluating the genetic structure of T. grandis as well as to estimate fine-scale gene flow rates.

Source: Biochemical Systematics and Ecology - February 23, 2016 Category: Biochemistry Source Type: research