Abstract
The transcriptome sequencing approach RNA-seq represents a powerful tool for transcriptional analysis and development of simple sequence repeat (SSR) markers for nonmodel crop. In the Perilla crop, analysis of the distribution of different repeat motifs showed that the most abundant type was dinucleotide repeats (62.0%), 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. In total, 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, 40 individuals from an F2 population of Perilla were selected for association analysis based on their leaf- and plant-related characteristics. An association analysis of 37 SSR markers and 9 leaf- and plant-related traits in the 40 individuals of the F2 population was conducted. From the analysis, we identified 12 SSR markers associated with leaf-related traits and 11 SSR markers associated with plant-related traits. 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.
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Acknowledgements
This study was supported by the Basic Science Research Program through the National Research Foundation of Korea (NRF) funded by the Ministry of Education, Science, and Technology (#2016R1D1A1B01006461) and the Cooperative Research Program for Agriculture Science & Technology Development (project no. PJ014227032019 and PJ0142272019), Rural Development Administration, Republic of Korea.
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JKL wrote the manuscript and designed the experiments. JYK and KJS performed the experiment and analyzed the data, and YJH helped to draft the manuscript. All authors commented on previous versions of the manuscript and approved the final manuscript.
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10681_2021_2867_MOESM1_ESM.docx
Supplement Fig. 1. An example of an SSR profile in nine Perilla accessions using the SSR primers KNUPF88 (a), KNUPF118 (b), KNUPF119 (c) and KNUPF125 (d). (DOCX 916 kb)
10681_2021_2867_MOESM3_ESM.docx
Supplement Table 2. Characteristics of the 39 SSR loci, including allele size, allele number, genetic diversity, polymorphism information content, and major allele frequency, among nine Perilla accessions. (DOCX 17 kb)
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Kim, J.Y., Sa, K.J., Ha, Y.J. et al. Genetic variation and association mapping in the F2 population of the Perilla crop (Perilla frutescens L.) using new developed Perilla SSR markers. Euphytica 217, 135 (2021). https://doi.org/10.1007/s10681-021-02867-z
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DOI: https://doi.org/10.1007/s10681-021-02867-z