Visitors   Views   Downloads

Development of polymorphic EST-SSR markers and characterization of the autotetraploid in sainfoin (Onobrychis viciifolia)

View preprint
121 days ago
Development of polymorphic EST-SSR markers and characterization of the autotetraploid in sainfoin (Onobrychis viciifolia) https://t.co/kFOLDMcacG
NOT PEER-REVIEWED
"PeerJ Preprints" is a venue for early communication or feedback before peer review. Data may be preliminary.

Supplemental Information

Figure 1: Tissues used in this study. Samples were collected as described in the Materials and Methods section.

(A) Callus cells. (B) An emerging tidbit. (C) A young inflorescence. (D) An inflorescence. (E) Mature inflorescence. (F) Developing seed pods. (G) Mature seed pods. (H) Roots. (I) A germinated seed. (J) Young stems. (K) Stems. (L) Mature stems. (M) A young compound leaf. (N) A mature compound leaf. Bar = 1 cm.

DOI: 10.7287/peerj.preprints.27232v1/supp-1

Figure 2: STRUCTURE analysis of the genetic structures of five vetch sainfoin

Six different colors represent six different clusters. Pink, cluster 1; Green, cluster 2; Cyan, cluster 3; Blue, cluster 4; Yellow, cluster 5; and Red, cluster 6. Genetic structure of eight individuals in each of the five sainfoin sample populations is inferred by STRUCTURE using the EST-SSR markers dataset.

DOI: 10.7287/peerj.preprints.27232v1/supp-2

Figure 3: Phylogenic relationships among the 40 wild sainfoin individuals

The phylogeny tree was constructed using a neighbor-joining dendrogram in the Darwin software. The starting dataset was represented by the 61 best EST-SSRs. I-V, group number representing five different sampling locations. 1-8, sample number representing eight individual samples in the same group.

DOI: 10.7287/peerj.preprints.27232v1/supp-3

Figure 4: Comparative analysis of the DNA fragment peak spectrum for two selected EST-SSR loci among the same unit of Onobrychis viciifolia

DOI: 10.7287/peerj.preprints.27232v1/supp-4

Table1 Summary of the de novo assembled sainfoin EST-SSRs

DOI: 10.7287/peerj.preprints.27232v1/supp-5

Table 2: Functional annotation of sainfiontranscriptome

DOI: 10.7287/peerj.preprints.27232v1/supp-6

Supplemental Figure S1: Length distribution of all unigenes

DOI: 10.7287/peerj.preprints.27232v1/supp-8

Supplemental Figure S2: COG analysis of the unigene sequences

DOI: 10.7287/peerj.preprints.27232v1/supp-9

Supplemental Figure S3: Summary of GO analysis of the unigene sequences

The y-axis on the right indicates the number of genes in a category. The y-axis on the left indicates the number of genes in a specific category.

DOI: 10.7287/peerj.preprints.27232v1/supp-10

Supplemental Figure S4: Statistics of the EST-SSR length distribution

DOI: 10.7287/peerj.preprints.27232v1/supp-11

Supplemental Figure S5: Gene ontology (GO) term enrichment status for SSR repeat-containing unigenes in sainfoin

DOI: 10.7287/peerj.preprints.27232v1/supp-12

Supplemental Figure S6: Variations of EST-SSR markers by PCR using the PCR primer set Vo61 and Vo157 and the 40 wild sainfoin individuals collected from the five different geographic locations

The letter M denotes a molecular marker of 300 and 200bp size (top to bottom).The red triangle indicates the individual plant used to cut the polyacrylamide gel, Vo61selected No. 2 individual from site 2, Vo157 selected No.1 individual from site 2.

DOI: 10.7287/peerj.preprints.27232v1/supp-13

Supplemental Table S1:Detailed information of EST-SSRs based on the number of nucleotide repeat units

DOI: 10.7287/peerj.preprints.27232v1/supp-14

Supplemental Table S2: Analysis of 200 primer pairs

DOI: 10.7287/peerj.preprints.27232v1/supp-15

Supplemental Table S3: Sampling of sainfoin for marker validation assays

DOI: 10.7287/peerj.preprints.27232v1/supp-16

Supplemental Table S4: Primer pairs used to analyze the 61 developed EST-SSR markers in sainfoin

DOI: 10.7287/peerj.preprints.27232v1/supp-17

Additional Information

Competing Interests

The authors declare there to be no conflict of interest.

Author Contributions

Shuheng Shen performed the experiments, analyzed the data, contributed reagents/materials/analysis tools, prepared figures and/or tables, authored or reviewed drafts of the paper, approved the final draft.

Xutian Chai performed the experiments, analyzed the data, prepared figures and/or tables.

Dong Luo analyzed the data.

Yanrong Wang conceived and designed the experiments, contributed reagents/materials/analysis tools.

Zhipeng Liu conceived and designed the experiments, contributed reagents/materials/analysis tools, prepared figures and/or tables, authored or reviewed drafts of the paper, approved the final draft.

Data Deposition

The following information was supplied regarding data availability:

NCBI SRA database (SRX3763386)

Funding

National Natural Science Foundation of China, Grant/Award Numbers: 31722055, 31672476, and 31730093; Fundamental Research Funds for the Central Universities, Grant/Award Numbers: lzujbky-2017-ot22 and lzujbky-2017-it08. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.


Add your feedback

Before adding feedback, consider if it can be asked as a question instead, and if so then use the Question tab. Pointing out typos is fine, but authors are encouraged to accept only substantially helpful feedback.

Some Markdown syntax is allowed: _italic_ **bold** ^superscript^ ~subscript~ %%blockquote%% [link text](link URL)
 
By posting this you agree to PeerJ's commenting policies