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Development of EST-SSR markers based on transcriptome sequencing for germplasm evaluation of 65 lilies (Lilium)

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Abstract

Background

Lilium genus consists of approximately 100 species and numerous varieties, many of which are interspecific hybrids, which result in a complicated genetic background. The germplasm identification, genetic relationship analysis, and breeding of Lilium rely on exploiting genetic information among different accessions. Hence, an attempt was made to develop new EST-SSR markers and study the molecular divergence among 65 genotypes of Lilium.

Methods and results

A total of 5509 EST-SSRs were identified from the high-throughput sequencing database of L. ‘Elodie’. After primer screening, six primer pairs with the most abundant polymorphic bands were selected from 100 primer pairs. Combined with the other 10 reported SSR primers, a total of 16 pairs detected genetic information with an average PIC value of 0.7583. The number of alleles per locus varied from four to 33, the expected heterozygosity varied from 0.3289 to 0.9231, and the observed heterozygosity varied from 0.2857 to 0.5122. Based on the phylogenic results, 22 Asiatic hybrids (A), seven Longiflorum × Asiatic hybrids (LA), as well as two native species were grouped. Eighteen Oriental hybrids (O) and nine Oriental × Trumpet (OT) hybrids, four native species, one LO, and one LL (L. pardalinum × L. longiflorum) variety were grouped.

Conclusions

Two major clusters were reported and a large number of genotypes were grouped based on UPGMA and STRUCTURE analysis methods. The PIC value as well as other parameters revealed that the EST-SSR markers selected were informative. In addition, the clustering pattern displayed better agreement with the cultivar’s pedigree. The newly identified SSRs in this study provides molecular markers for germplasm characterization and genetic diversity for Lilium.

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Funding

This work was supported by the Shanghai Agriculture Applied Technology Development Program, China (Grant No. X2020-02-08-00-12-F01463).

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Authors and Affiliations

  1. Shanghai Key Laboratory of Protected Horticultural Technology, Forestry and Pomology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, 201403, China

    Minmin Chen, Gongping Nie, Xin Li, Liuyan Yang, Youming Cai & Yongchun Zhang

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  1. Minmin Chen
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  2. Gongping Nie
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  3. Xin Li
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  4. Liuyan Yang
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  5. Youming Cai
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  6. Yongchun Zhang
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Contributions

MC and YZ conceived the theme of the study and designed the experiment; MC, GN and XL performed the experiment; MC, LY and YC analyzed the SSR data; MC wrote the manuscript. All co-authors read and approved the final manuscript.

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Correspondence to Yongchun Zhang.

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Chen, M., Nie, G., Li, X. et al. Development of EST-SSR markers based on transcriptome sequencing for germplasm evaluation of 65 lilies (Lilium). Mol Biol Rep 50, 3259–3269 (2023). https://doi.org/10.1007/s11033-022-08083-9

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