Characteristics of Microsatellites Mined from Transcriptome Data and the Development of Novel Markers in Paeonia lactiflora

Expression Profiles of Microsatellites in Fruit Tissues of Akebia trifoliata and Development of Efficient EST-SSR Markers

Akebia trifoliata, a member of the family Lardizabalaceae, has high exploitation potential for multiple economic purposes, so genetic improvements to meet requirements for commercial demand are needed. However, this progress is largely impeded by a lack of effective selection markers. In this study, we obtained 271.49 Gb of clean transcriptomic data from 12 samples (three tissues at four developmental stages) of A. trifoliata fruit. We identified 175,604, 194,370, and 207,906 SSRs from the de novo assembled 416,363, 463,756, and 491,680 unigene sequences obtained from the flesh, seed, and rind tissues, respectively. The profile and proportion of SSR motifs expressed in each fruit tissue and developmental stage were remarkably similar, but many trinucleotide repeats had differential expression levels among different tissues or at different developmental stages. In addition, we successfully designed 16,869 functional EST-SSR primers according to the annotated unigenes. Finally, 94 and 72 primer pairs out of 100 randomly selected primer pairs produced clear bands and polymorphic bands, respectively. These results were also used to elucidate the expression profiles of different tissues at various stages. Additionally, we provided a set of effective, polymorphic, and reliable EST-SSR markers sufficient for accelerating the discovery of metabolic and pathway-specific functional genes for genetic improvement and increased commercial productivity.

Anthocyanin Accumulation and Differential Expression of the Biosynthetic Genes Result in a Discrepancy in the Red Color of Herbaceous Peony (Paeonia lactiflora Pall.) Flowers

Herbaceous peony (Paeonia lactiflora Pall.) is an ornamental plant with huge potential in the international flower market. Similar to the flowers of most other ornamental plants, the top sellers of P. lactiflora are those with red or pink flowers. However, most studies on flower colors have focused on the novel colors and have neglected the most common red flowers. In this study, a red cultivar of P. lactiflora (‘Dafugui’) and a pink cultivar (‘Qingwen’) were selected in order to study the discrepancy in the red color of the flowers. The results demonstrate that these two cultivars have the same compositions as anthocyanins, flavones, and flavonols but different contents. ‘Dafugui’ was found to have a high accumulation of upstream substances due to the higher expression of the early genes encoding phenylalanine ammonialyase (PlPAL) and flavonoid 3′-hydroxylase (PlF3′H). Moreover, the anthocyanidin synthase gene (PlANS) and UDP-glucose flavonoid 3-O-glucosyltransferase gene (PlUF3GT) encoding enzymes catalyze these upstream substances into anthocyanins, resulting in more redness in ‘Dafugui’ than in ‘Qingwen’. Our study thus provides a better understanding of the anthocyanin accumulation and coloring mechanism of P. lactiflora and can serve as a theoretical basis for breeding more red flowers using genetic engineering techniques to cater to consumers’ preferences.

Characterization and Development of Microsatellite Markers in Pseudotaxus chienii (Taxaceae) Based on Transcriptome Sequencing

Pseudotaxus chienii (Taxaceae) is an endangered conifer species endemic to China. However, a lack of suitable molecular markers hinders the genomic and genetic studies on this species. Here, we characterized and developed the microsatellite markers from a newly sequenced P. chienii transcriptome. A total of 21,835 microsatellite loci were detected from 161,131 non-redundant unigene sequences, and the frequency of SSRs was 13.55%, with an average of one SSR loci per 9.18 kb. Mono-nucleotide, di-nucleotide, and tri-nucleotide were the dominant repeat types, accounting for 50.06, 13.49, and 29.39% of the total SSRs, respectively. In terms of distribution location, the coding regions (CDS) with few microsatellites and mainly consisted of tri-nucleotides. There were significant differences in the length of microsatellite among genic regions and motif types. Functional annotation showed that the unigenes containing microsatellites had a wide range of biological functions, most of which were related to basic metabolism, and a few might be involved in expression regulation of gene and response to environmental stress. In addition, 375 primer pairs were randomly selected and synthesized for the amplification and validation of microsatellite markers. Seventy-seven primer pairs were successfully amplified and 40 primer pairs were found to be polymorphic. Finally, 20 pairs of primers with high polymorphism were selected to assess the genetic diversity in four P. chienii populations. In addition, the newly developed microsatellite markers exhibited high transferability (70%) in Amentotaxus argotaenia. Our study could enable further genetic diversity analysis and functional gene mining on Taxaceae.