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.
Highlights
(Lilium sp.) is one of the most important commercially-cultivated flowering plants and is widely grown in temperate and sub-tropical regions, including France, Chile, the USA, Japan, New Zealand, and the Netherlands, which is the world’s leading producer and exporter [1]
A total of 216,768 unigene sequences were screened from cDNA libraries of L. formolongi (Sinnapal), L. longiflorum (Easter lily), and L. longiflorum (White tower lily) transcriptome sequences to identify simple sequence repeats (SSRs) motifs, and the resulting 6966 SSR motifs were extracted (Table 1)
The unigenes that contained SSRs were used in BLAST searches of the Plant Transcription Factor Database to identify those likely to encode transcription factor (TF)
Summary
(Lilium sp.) is one of the most important commercially-cultivated flowering plants and is widely grown in temperate and sub-tropical regions, including France, Chile, the USA, Japan, New Zealand, and the Netherlands, which is the world’s leading producer and exporter [1]. Is a perennial monocotyledon belonging to the family Liliaceae, with the genus Lilium including more than 100 species distributed among seven sections (Archelirion, Leucolirion, Lilium, Martagon, Oxypetala, Pseudolirium, and Sinomartagon) [2,3,4]. Species belonging to the same section are cross-compatible and produce fertile hybrids [2]. They are highly heterozygous due to a series of interspecies crosses [2].
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