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Research Article
Ju Kyong Lee
Kangwon National University
Corresponding Author
ORCiD: https://orcid.org/0000-0002-2769-0799
License:
This work is licensed under a CC BY 4.0 License. Read Full License
The transcriptome sequencing approach RNA-seq represents a powerful tool for transcriptional analysis and development of SSR markers for nonmodel crop. In the Perilla crop, analysis of the distribution of different repeat motifs showed that dinucleotide repeats were the most abundant (62.0%) type, followed by trinucleotide repeats (35.3%), with the two together comprising 97.3% of the eSSR repeats. In this study, we developed 39 new SSR primer sets by the transcriptome sequencing approach RNA-sEq. A total of 130 alleles were detected segregating in nine Perilla accessions with an average of 3.3 alleles per locus, ranging from 125 to 360 bp. The number of alleles per locus ranged from two to six. To detect SSR markers associated with morphological characteristics of Perilla crop, a total of 40 individuals from the F2 population of Perilla were selected for association analysis based on their leaf- and plant-related characteristics. In an association analysis of 37 SSR markers and 9 leaf- and plant-related traits in the 40 individuals of the F2 population, we identified 12 and 11 SSR markers associated with leaf-related traits and plant-related traits, respectively. Therefore, the new Perilla SSR primers described in this study could be helpful in identifying genetic diversity and genetic mapping, designating important genes/QTLs for Perilla crop breeding programs, and allowing Perilla breeders to improve leaf and plant quality through marker-assisted selection (MAS) breeding programs.
Keywords
Perilla frutescens, transcriptome, RNA-seq, SSR marker, F2 population, association analysis
Figure 1
Figure 2
This is a list of supplementary files associated with this preprint. Click to download.
- SupplementFig.1.docx
An example of an SSR profile in nine Perilla accessions using the SSR primers KNUPF88 (a), KNUPF118 (b), KNUPF119 (c) and KNUPF125 (d).
- SupplementTable1.docx
Information on the 39 newly developed SSR primer sets used in the study.
- SupplementTable2.docx
Characteristics of the 39 SSR loci, including allele size, allele number, genetic diversity, polymorphism information content, and major allele frequency, among nine Perilla accessions.
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CURRENT STATUS: Under Review
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Posted 05 Apr, 2021
No community comments so far
Editorial decision: Major revisions
On 03 May, 2021
Reviewers invited
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Received 31 Mar, 2021
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A new preprint design is coming!
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This preprint is under consideration at Euphytica. A preprint is a preliminary version of a manuscript that has not completed peer review at a journal. Research Square does not conduct peer review prior to posting preprints. The posting of a preprint on this server should not be interpreted as an endorsement of its validity or suitability for dissemination as established information or for guiding clinical practice.
Learn more about In Review
Research Article
Ju Kyong Lee
Kangwon National University
Corresponding Author
ORCiD: https://orcid.org/0000-0002-2769-0799
Badges
Prescreen
This manuscript passed our Prescreen assessment
Complete author information
Appropriate declaration statements
Potential risks to human health
Prescreen
Peer Review Timeline
CURRENT STATUS: Under Review
Version 1
Posted 05 Apr, 2021
No community comments so far
Editorial decision: Major revisions
On 03 May, 2021
Reviewers invited
Invitations sent on 31 Mar, 2021
Reviews received
Received 31 Mar, 2021
Editor assigned
On 19 Mar, 2021
First submitted
On 18 Mar, 2021
Metrics
Comments: 0
PDF Downloads: ...
HTML Views: ...
License:
This work is licensed under a CC BY 4.0 License. Read Full License
The transcriptome sequencing approach RNA-seq represents a powerful tool for transcriptional analysis and development of SSR markers for nonmodel crop. In the Perilla crop, analysis of the distribution of different repeat motifs showed that dinucleotide repeats were the most abundant (62.0%) type, followed by trinucleotide repeats (35.3%), with the two together comprising 97.3% of the eSSR repeats. In this study, we developed 39 new SSR primer sets by the transcriptome sequencing approach RNA-sEq. A total of 130 alleles were detected segregating in nine Perilla accessions with an average of 3.3 alleles per locus, ranging from 125 to 360 bp. The number of alleles per locus ranged from two to six. To detect SSR markers associated with morphological characteristics of Perilla crop, a total of 40 individuals from the F2 population of Perilla were selected for association analysis based on their leaf- and plant-related characteristics. In an association analysis of 37 SSR markers and 9 leaf- and plant-related traits in the 40 individuals of the F2 population, we identified 12 and 11 SSR markers associated with leaf-related traits and plant-related traits, respectively. Therefore, the new Perilla SSR primers described in this study could be helpful in identifying genetic diversity and genetic mapping, designating important genes/QTLs for Perilla crop breeding programs, and allowing Perilla breeders to improve leaf and plant quality through marker-assisted selection (MAS) breeding programs.
Figure 1
Figure 2
This is a list of supplementary files associated with this preprint. Click to download.
- SupplementFig.1.docx
An example of an SSR profile in nine Perilla accessions using the SSR primers KNUPF88 (a), KNUPF118 (b), KNUPF119 (c) and KNUPF125 (d).
- SupplementTable1.docx
Information on the 39 newly developed SSR primer sets used in the study.
- SupplementTable2.docx
Characteristics of the 39 SSR loci, including allele size, allele number, genetic diversity, polymorphism information content, and major allele frequency, among nine Perilla accessions.
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