Application of EST-SSR markers developed from the transcriptome of <i>Torreya grandis</i> (Taxaceae), a threatened nut-yielding conifer tree

et al. 2020

Front. Genet.

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, dinucleotide, 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. Seventyseven 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.

Section: Characterization Of Microsatellites In P Chienii Transcriptomesupporting

confidence: 84%

Section: Validation Of Microsatellite Markerssupporting

confidence: 71%

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

et al. 2020

Front. Genet.

“…More than half of the unigenes can be successfully annotated through seven databases (Nr, Nt, KOG, Swiss-Prot, Pfam, KO, and GO), of which 490 were simultaneously identified ( Table 1 ). Most of the annotated unigenes were unique in A. argotaenia compared to its closely related conifer Torreya grandis (Zeng et al, 2018). Moreover, the annotated results of NR database indicated that A. argotaenia exhibited only 27.5% unigene identity to another conifer Picea sitchensis .…”

Section: Discussionmentioning

confidence: 99%

Characterization and Application of EST-SSR Markers Developed From the Transcriptome of Amentotaxus argotaenia (Taxaceae), a Relict Vulnerable Conifer

Ruan

et al. 2019

Front. Genet.

Amentotaxus argotaenia (Taxaceae) is a vulnerable coniferous species with preference for shade and moist environment. Accurate estimation of genetic variation is crucial for its conservation, especially in the context of global warming. In this study, we acquired a transcriptome from A. argotaenia leaves using Illumina sequencing and de novo assembled 62,896 unigenes, of which 5510 EST-SSRs were detected. Twenty-two polymorphic EST-SSRs were successfully developed and further used to investigate genetic variation, linkage disequilibrium, and bottleneck signatures of A. argotaenia. The results showed that A. argotaenia had moderate genetic variation and high genetic differentiation, which may provide raw material to protect against climatic changes and accelerate local adaptation, respectively. No bottlenecks were found to occur in A. argotaenia. Our study not only showed that these EST markers are very effective in population genetic analysis but also lay a solid foundation for further investigating adaptive evolution and conservation strategies of A. argotaenia.

“…In general, markers with PIC> 0.5 are defined as highly polymorphic [ 40 ]. In our case, the average PIC value of the 13 EST-SSR markers used, except LaES18 and LaES27, was 0.654, higher than many EST-SSR markers developed from transcriptome sequences, such as for Torreya grandis (0.357) [ 41 ], Mucuna pruriens (0.24) [ 42 ] and Lagerstroemia spp (0.589) [ 43 ]. The high PIC values observed in our work hinted a high efficiency of these set of markers in genetic analysis.…”

Section: Discussionmentioning

confidence: 61%

Characterization, validation, and cross-species transferability of EST-SSR markers developed from Lycoris aurea and their application in genetic evaluation of Lycoris species

Jiang

et al. 2020

BMC Plant Biol

Background The Lycoris genus includes many ornamentally and medicinally important species. Polyploidization and hybridization are considered modes of speciation in this genus, implying great genetic diversity. However, the lack of effective molecular markers has limited the genetic analysis of this genus. Results In this study, mining of EST-SSR markers was performed using transcriptome sequences of L. aurea, and 839 primer pairs for non-redundant EST-SSRs were successfully designed. A subset of 60 pairs was randomly selected for validation, of which 44 pairs could amplify products of the expected size. Cross-species transferability of the 60 primer pairs among Lycoris species were assessed in L. radiata Hreb, L. sprengeri Comes ex Baker, L. chinensis Traub and L. anhuiensis, of which between 38 to 77% of the primers were able to amplify products in these Lycoris species. Furthermore, 20 and 10 amplification products were selected for sequencing verification in L. aurea and L. radiata respectively. All products were validated as expected SSRs. In addition, 15 SSRs, including 10 sequence-verified and 5 unverified SSRs were selected and used to evaluate the genetic diversity of seven L. radiata lines. Among these, there were three sterile lines, three fertile lines and one line represented by the offspring of one fertile line. Unweighted pair group method with arithmetic mean analysis (UPGMA) demonstrated that the outgroup, L. aurea was separated from L. radiata lines and that the seven L. radiata lines were clustered into two groups, consistent with their fertility. Interestingly, even a dendrogram with 34 individuals representing the seven L. radiata lines was almost consistent with fertility. Conclusions This study supplies a pool of potential 839 non-redundant SSR markers for genetic analysis of Lycoris genus, that present high amplification rate, transferability and efficiency, which will facilitate genetic analysis and breeding program in Lycoris.