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Bulk segregant analysis identifies SSR markers associated with leaf- and seed-related traits in Perilla crop (Perilla frutescens L.)

Genes & Genomics volume 43, pages 323–332 (2021)Cite this article

Abstract

Background

Bulk segregant analysis (BSA) is another method of identifying significant molecular markers linked to the target gene or region for specific traits. BSA is easier and less expensive than other methods; it does not require genetic map construction and needs fewer markers than the number needed to construct a genetic map for QTL mapping.

Objectives

The purpose of our study was to identify simple sequence repeat (SSR) markers linked with leaf- and seed-related traits in Perilla crop, and to allow the selection of better accessions in Perilla breeding programs with marker-assisted selection (MAS).

Methods

The genotypes of the 25 SSR markers and phenotypic data for the eight qualitative traits were used to confirm significant marker-trait associations (SMTAs) using TASSEL software. To detect SSR markers associated with leaf color, the 16 individuals of the F3 population were divided into three bulk groups based on the colors of the surface and reverse sides of the leaf, respectively: six in the green/green group, five in the green/purple group and five in the purple/purple group.

Results

This study detected 18 significant marker-trait associations (SMTAs) involving 12 SSR markers associated with six agronomic traits. The SSR markers KNUPF15, KNUPF21, KNUPF29, and KNUPF60 were associated with leaf surface color, and KNUPF11, KNUPF15, KNUPF21, and KNUPF60 were associated with leaf reverse side color. In addition, five SSR markers were associated with seed-related traits. KNUPF11 and KNUPF29 were associated with seed coat color, while KNUPF29 was associated with seed size. KNUPF12, KNUPF16, and KNUPF42 were associated with seed hardness. To verify the selected significant SSR markers associated with leaf color and seed-related traits, a UPGMA dendrogram for 11 individuals in the F3 population, which formed two bulk groups consisting of 6 green/green and 5 purple/purple individuals, was constructed using six SSR marker-related LC and RLC traits.

Conclusion

These results are very important for understanding the characteristics of Perilla leaves and seeds; they may also support opportunities to effectively preserve and utilize existing accessions and to allow Perilla breeders to improve crop quality by mean of MAS

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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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Author notes

  1. Su Eun Lim and Kyu Jin Sa contributed equally to this work.

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  1. Department of Applied Plant Sciences, College of Agriculture and Life Sciences, Kangwon National University, Chuncheon-si, 24341, Korea

    Su Eun Lim, Kyu Jin Sa & Ju Kyong Lee

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  1. Su Eun Lim
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Correspondence to Ju Kyong Lee.

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Su Eun Lim declares that he has no conflict of interest. Kyu Jin Sa declares that he has no conflict of interest. Ju Kyong Lee declares that he has no conflict of interest.

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Lim, S.E., Sa, K.J. & Lee, J.K. Bulk segregant analysis identifies SSR markers associated with leaf- and seed-related traits in Perilla crop (Perilla frutescens L.). Genes Genom 43, 323–332 (2021). https://doi.org/10.1007/s13258-021-01056-5

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Keywords

  • Perilla frutescens
  • Bulk segregant analysis
  • SSR marker
  • Association analysis