Development and Characterization of Transcription Factor Gene-Derived Microsatellite (TFGM) Markers in Medicago truncatula and Their Transferability in Leguminous and Non-Leguminous Species

Abstract

Transcription factors (TFs) are critical adaptor molecules that regulate many plant processes by controlling gene expression. The recent increase in the availability of TF data has made TFs a valuable resource for genic functional microsatellite marker development. In the present study, we developed TF gene-derived microsatellite (TFGM) markers for Medicago truncatula and assessed their cross-species transferability. A total of 203 SSRs were identified from 1467 M. truncatula TF coding sequences, 87.68% of which were trinucleotide repeats, followed by mono-(4.93%) and hexanucleotide repeats (1.48%). Further, 142 TFGM markers showed a high level of transferability to the leguminous (55.63%-85.21%) and non-leguminous (28.17%-50.00%) species. Polymorphisms of 27 TFGM markers were evaluated in 44 alfalfa accessions. The allele number per marker ranged from two to eight with an average of 4.41, and the PIC values ranged from 0.08 to 0.84 with an average of 0.60. Considering the high polymorphism, these TFGM markers developed in our study will be valuable for genetic relationship assessments, marker-assisted selection and comparative genomic studies in leguminous and non-leguminous species.

Genome‐wide development of microRNA ‐based SSR markers in Medicago truncatula with their transferability analysis and utilization in related legume species

“…One hundred twenty-six (74.56%) of the 169 assayed Mt-mi-RNA-SSR markers provided consistent amplification in alfalfa ( Table 2). This result agrees with the previous study that high transferability possessed by the microsatellite markers developed from M. truncatula in alfalfa (85.21%) [34]. We further analyzed the transferability of these 169 Mt-mi-RNA-SSR markers in other five leguminous species, and high transferability also has been identified, such as 77.51% in Glycine max, 89.35% in Vicia sativa, 88.76% in Melilotus, 90.53% in Lotus corniculatus, and 89.…”

“…Chromosomes 3 and 4 contained the largest number of markers (35, 21.08%), while the fewest mapped on chromosome 1 (8, 4.82%) ( Figure 1). Previously, 4636 EST-SSR markers [33] and 130 transcription factor gene-derived SSR markers had been developed from M. truncatula based on 3828 EST sequences and 176 transcription factor sequences, respectively [34]. To determine the novelty of the 169 Mt-miRNA-SSR markers developed in this study, the 130 SSR-containing pri-miRNA sequences were cross-referenced with the 3828 EST sequences and 176 transcription factor sequences, respectively.…”

Genome-Wide Mining, Characterization and Development of miRNA-SSRs inArabidopsis thaliana

“…Targeted TFs could be utilized for developing next generation microsatellites, Transcription Factor Gene-Derived Microsatellite (TFGM) Markers which have potential in marker-assisted genetic improvement and genotyping applications through marker assisted selection (MAS) breeding program to develop the drought/heat responsive and nutrient efficient cultivars for cereal crops (Gupta and Prasad, 2009; Kujur et al 2013, 2014; Liu et al 2015). However in plants, (TFGM) markers have only been reported in chickpea and Medicago truncatula to date (Kujur et al 2013; Liu et al 2015).…”

Transferability and Polymorphism of SSR Markers Located in Flavonoid Pathway Genes in Fragaria and Rubus Species

“…In addition, in silico development of genic and EST-SSR markers can now be relatively easily done using publicly available nucleotide sequence databases. Genic SSRs in functional genes can be used as "functional genetic markers", and they have a much higher transferability across different taxa than random genomic SSRs [38]. Sargent et al [39] used primer pairs based on the binding sites in the Fragaria exons flanking polymorphic introns and found that their transferability was significantly higher compared to the random genomic SSRs.…”