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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.
Highlights
Evaluation and understanding of the genetic variation within the germplasm collection by using molecular markers is crucial for the effective conservation and use of genetic resources [1].Microsatellites or simple sequence repeats (SSRs) are PCR-based, multi-allelic, co-dominant genetic markers consisting of 1‒5 nucleotide core units that are tandemly repeated
Previous studies have shown that the results of SSR identification and primer design were related to the search criteria and sequence type [9,12], and the development of new functional microsatellite markers with relatively high polymorphic potential based on M. truncatula full-length Transcription factors (TFs) coding sequences will be essential and useful in various applications of genetics, genomics and breeding programs
A total of 1467 TF coding sequences of M. truncatula with an average length of bp were mined for SSRs and used to design the TF gene-derived microsatellite (TFGM) markers (Table 1)
Summary
Evaluation and understanding of the genetic variation within the germplasm collection by using molecular markers is crucial for the effective conservation and use of genetic resources [1]. Microsatellites or simple sequence repeats (SSRs) are PCR-based, multi-allelic, co-dominant genetic markers consisting of 1‒5 nucleotide core units that are tandemly repeated Because of their desirable genetic attributes, including hypervariability, co-dominant heritability, reliability, wide genomic distribution, chromosome-specific location and being multi-allelic, SSR markers have become the marker class of choice for population diversity studies, genetic map construction, marker-assisted selection and gene mapping [2]. Previous studies have shown that the results of SSR identification and primer design were related to the search criteria and sequence type [9,12], and the development of new functional microsatellite markers with relatively high polymorphic potential based on M. truncatula full-length TF coding sequences will be essential and useful in various applications of genetics, genomics and breeding programs. 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
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