Transcriptome-Derived Microsatellite Markers for Population Diversity Analysis in Archidendron Clypearia (Jack) I.C. Nielsen

Abstract Genomic resources including transcriptomic sequences and molecular markers remain scarce in the medicinally important woody legume genus Archidendron F. Mueller. Here we conducted transcriptome sequencing, genic microsatellite marker development, and population diversity analysis in Archidendron clypearia (Jack) I.C. Nielsen. Flower and flower bud transcriptomes were de novo assembled into 173,172 transcripts, with an average transcript length of 1597.3 bp and an N50 length of 2427 bp. A total of 34,701 microsatellite loci were identified from 26,716 (15.4%) transcripts. Primer pairs were designed for 718 microsatellite loci, of which 456 (63.5%) were polymorphic. Of the 456 polymorphic markers, 391 (85.7%) and 402 (88.1%) were transferable to A. lucidum (Benth.) I.C. Nielsen and A. multifoliolatum (H.Q. Wen) T.L. Wu, respectively. Using a subset of 15 microsatellite markers, relatively high genetic diversity was detected over two A. clypearia populations, with overall mean expected heterozygosity (He) being 0.707 and demonstrating the necessity of conservation. Relatively low differentiation between the two populations was revealed despite the distant separation (about 700 km), with overall inbreeding coefficient of sub-population to the total population (Fst) being 8.7%. This suggests that A. clypearia has mainly an outcrossing mating system and weak genetic structure. These results will offer valuable resources and information for further genetic studies and practical applications in Archidendron and the related taxa.