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Genes 2018, 9(2), 97; https://doi.org/10.3390/genes9020097

Exploration and Exploitation of Novel SSR Markers for Candidate Transcription Factor Genes in Lilium Species

1
Department of Horticulture, Sunchon National University, 255 Jungang-ro, Suncheon, Jeonnam 57922, Korea
2
University-Industry Cooperation Foundation, Sunchon National University, 255 Jungang-ro, Suncheon, Jeonnam 57922, Korea
3
University-Industry Cooperation Foundation, Sunchon National University, 255 Jungang-ro, Suncheon, Jeonnam 57922, Korea
*
Author to whom correspondence should be addressed.
Received: 5 January 2018 / Revised: 7 February 2018 / Accepted: 12 February 2018 / Published: 14 February 2018
(This article belongs to the Section Plant Genetics and Genomics)
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Abstract

Lilies (Lilium sp.) are commercially important horticultural crops widely cultivated for their flowers and bulbs. Here, we conducted large-scale data mining of the lily transcriptome to develop transcription factor (TF)-associated microsatellite markers (TFSSRs). Among 216,768 unigenes extracted from our sequence data, 6966 unigenes harbored simple sequence repeats (SSRs). Seventy-one SSRs were associated with TF genes, and these were used to design primers and validate their potential as markers. These 71 SSRs were accomplished with 31 transcription factor families; including bHLH, MYB, C2H2, ERF, C3H, NAC, bZIP, and so on. Fourteen highly polymorphic SSRs were selected based on Polymorphic Information Content (PIC) values and used to study genetic diversity and population structure in lily accessions. Higher genetic diversity was observed in Longiflorum compared to Oriental and Asiatic populations. Lily accessions were divided into three sub-populations based in our structure analysis, and an un-rooted neighbor-joining tree effectively separated the accessions according to Asiatic, Oriental, and Longiflorum subgroups. Finally, we showed that 46 of the SSR-associated genes were differentially expressed in response to Botrytis elliptica infection. Thus, our newly developed TFSSR markers represent a powerful tool for large-scale genotyping, high-density and comparative mapping, marker-aided backcrossing, and molecular diversity analysis of Lilium sp. View Full-Text
Keywords: transcription factor; SSR markers; genetic diversity; Lilium species transcription factor; SSR markers; genetic diversity; Lilium species
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Biswas, M.K.; Nath, U.K.; Howlader, J.; Bagchi, M.; Natarajan, S.; Kayum, M.A.; Kim, H.-T.; Park, J.-I.; Kang, J.-G.; Nou, I.-S. Exploration and Exploitation of Novel SSR Markers for Candidate Transcription Factor Genes in Lilium Species. Genes 2018, 9, 97.

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