Isolation and characterization of polymorphic microsatellite markers in Toxicodendron vernicifluum

Abstract

A total 20 074 230 sequencing reads were generated by Illumina HiSeq<sup>™ </sup>2500 from three different Toxicodendron vernicifluum tissue samples. In total, 48 693 unigenes with an average length of 703.34 bp were obtained by de novo assembly. 3392 potential EST-SSRs (expressed sequence tag-simple sequence repeat) were identified as potential molecular markers from unigenes with lengths exceeding 1 kb. A total of 80 pairs of PCR primers were randomly selected to validate the assembly quality and develop EST-SSR markers from genomic DNA. Of these primer pairs, 14 primer pairs successfully amplified DNA fragments and detected significant amounts of polymorphism within the lacquer tree population in Langao, Shaanxi province, China. There were high genetic diversities (number of alleles per locus (A) = 2.93, polymorphic information content (PIC) = 0.53, observed heterozygosity (Ho) = 0.62 and expected heterozygosity (He) = 0.85) in the lacquer tree natural population. The four loci were significantly deviated from Hardy-Weinberg equilibrium. These results suggested high homozygosity in the population and low or deficiency in heterozygosity (inbreeding coefficient (Fis) = 0.27). These polymorphic EST-SSR markers will provide the base for further studies of genetic structure and breeding in T. vernicifluum.

Complete Chloroplast Genome Sequence of Chinese Lacquer Tree (Toxicodendron vernicifluum, Anacardiaceae) and Its Phylogenetic Significance

“…However, controversy still surrounded the delimitation of the cultivars based on morphological and anatomic traits [22]. Although some researchers have used different types of molecular markers, such as nuclear microsatellites (nSSRs) and amplified fragment length polymorphism (AFLP), to describe the genetic variation of both natural populations and cultivars of T. vernicifluum [23,24], the information on the genetic diversity and structure of the species was still limited by small sample size, narrow sampling range, and a few number of molecular markers. us, more studies on both nuclear and plastid genomes are expected to provide more useful markers to reveal the genetic variation pattern of T. vernicifluum and its cultivars in the future.…”

De novo assembly and transcriptome characterization of an endemic species of Vietnam, Panax vietnamensis Ha et Grushv., including the development of EST-SSR markers for population genetics

“…The samples were crushed by Mixer mill MM 400 (Retsch) in liquid nitrogen. DNA quality and concentration were validated according to Vu et al [18]. The concentration was then diluted to 10ng/µl.…”

“…Simple sequence repeats (SSRs) markers are useful tools for research in plant genetics, breeding, identi cation of individuals, species and varieties, and to generate genetic maps because of the allelic sequence diversity as they are widely spread in the genome and have high levels of the polymorphism, co-dominant inheritance, abundance, maximum reproducibility, multi-allelic variation, and good genome coverage [12][13][14][15][16][17][18]. The expressed sequence tags (EST) availability, enhanced SSR identi cation possibility in some woody plants [19].…”

De novo assembly and transcriptome characterization of an endemic species of Vietnam, Panax vietnamensis Ha et Grushv., including the development of EST-SSR markers for population genetics

“…Total RNA was extracted from each sample (roots, leaves and stems) by the OmniPlant RNA Kit (DNase I) for Illumina sequencing. RNA quality and quantity were validated by Nanodrop and 1.2% agarose gel electrophoresis [18]. Total RNA (equal amount of each sample) was pooled together and sent to Breeding Biotechnologies Co., Ltd., for transcriptome sequencing using Illumina HiSeq™ 4000.…”

“…SSRs markers are useful tools for research in plant genetics, breeding, identification of individuals, species and varieties, and to generate genetic maps because of the allelic sequence diversity as they are widely spread in the genome and have high levels of the polymorphism, co-dominant inheritance, abundance, maximum reproducibility, multi-allelic variation, and good genome coverage [12][13][14][15][16][17][18]. The expressed sequence tags (EST) availability, enhanced SSR identification possibility in some woody plants [19].…”