Allele mining, amplicon sequencing and computational prediction of Solanum melongena L. FT/TFL1 gene homologs uncovers putative variants associated to seed dormancy and germination

Abstract

The FT/TFL1 gene homolog family plays a crucial role in the regulation of floral induction, seed dormancy and germination in angiosperms. Despite its importance, the FT/TFL1 gene homologs in eggplant (Solanum melongena L.) have not been characterized to date. In this study, we performed a genome-wide identification of FT/TFL1 genes in eggplant using in silico genome mining. The presence of these genes was validated in four economically important eggplant cultivars (Surya, EP-47 Annamalai, Pant Samrat and Arka Nidhi) through Pacbio RSII amplicon sequencing. Our results revealed the presence of 12 FT/TFL1 gene homologs in eggplant, with evidence of diversification among FT-like genes suggesting their possible adaptations towards various environmental stimuli. The amplicon sequencing also revealed the presence of two alleles for certain genes (SmCEN-1, SmCEN-2, SmMFT-1 and SmMFT-2) of which SmMFT-2 was associated with seed dormancy and germination. This association was further supported by the observation that seed dormancy is rarely reported in domesticated eggplant cultivars, but is commonly observed in wild species. A survey of the genetic regions in domesticated cultivars and a related wild species, S. incanum, showed that the alternative allele of S. incanum was present in some members of the Pant Samrat cultivar, but was absent in most other cultivars. This difference could contribute to the differences in seed traits between wild and domesticated eggplants.

Ethyl Methanesulphonate (EMS)-Mediated Mutagenesis Induces Genetic and Morphological Variations in Eggplant (Solanum melongena L.)

“…Of the 95 M2 plants, 16 were chosen to undergo screening for potential changes in their genetic makeup. Within this group, six genes belonging to the Flowering Locus T (FT)/Terminal Flower 1 (TFL1) family [26] were selected for further analysis. These genes included TFL1/Centroradialis (CEN)-like genes, namely SmTFL1, SmCEN-1, SmCEN-2 and SmCEN-4, as well as SmMFT-1 and SmMFT-2, which are members of the Mother of FT and TFL1 (MFT) gene cluster of the FT/TFL1 gene family.…”

“…We attempted to screen for mutations induced by EMS mutagenesis by targeting six selected genes belonging to the FT/TFL1 family [26]. The amplicons of the genes were derived from the control and mutant samples and were subjected to Pacio RSIItargeted amplicon sequencing.…”

“…The mutations were then identified by comparing the mutant sequences with their respective controls. The full-length sequences of the genes from the start to stop codons (inclusive of exons and introns) derived from the control samples of the Surya cultivar have been deposited in NCBI Genbank under the following accession numbers: SmTFL1 (OQ025058) (2620 bp), SmCEN-1 (OQ025060) (1015 bp), SmCEN-2 (OQ025061) (2596 bp), SmCEN-4 (OQ025057) (1488 bp), SmMFT-1 (OQ025063) (2134 bp) and SmMFT-2 (OQ025065) (981 bp) [26]. After analyzing the data, we identified a heterozygous mutation in the 5 untranslated sequence region of the SmMFT-2 gene from a mutant sample.…”

Identification of Quantitative Trait Loci and Candidate Genes Controlling Seed Dormancy in Eggplant (Solanum melongena L.)

“…Ali et al [18] suggested that aqueous garlic (Allium sativum), SA, and methyl jasmonate (MeJA) can promote seed germination and seedling growth in eggplant. Subramaniam [19] identified some candidate genes related to dormancy traits by comparing the FT/TFL1 gene family in terms of seed dormancy using multiple genomes.…”