Journal of Applied Genetics

, Volume 60, Issue 1, pp 13–25 | Cite as

Genome-wide regulatory gene-derived SSRs reveal genetic differentiation and population structure in fiber flax genotypes

  • Dipnarayan SahaEmail author
  • Rajeev Singh Rana
  • Shantanab Das
  • Subhojit Datta
  • Jiban Mitra
  • Sylvie J. Cloutier
  • Frank M. You
Plant Genetics • Original Paper


We designed a set of 580 simple sequence repeat markers; 506 from transcription factor-coding genes, and 74 from long non-coding RNAs and designated them as regulatory gene-derived simple sequence repeat (ReG-SSR) markers. From this set, we could anchor 559 ReG-SSR markers on 15 flax chromosomes with an average marker distance of 0.56 Mb. Thirty-one polymorphic ReG-SSR primers, amplifying SSR loci length of at least 20 bp were chosen from 134 screened primers. This primer set was used to characterize a diversity panel of 93 flax accessions. The panel included 33 accessions from India, including released varieties, dual-purpose lines and landraces, and 60 fiber flax accessions from the global core collection. Thirty-one ReG-SSR markers generated 76 alleles, with an average of 2.5 alleles per primer and a mean allele frequency of 0.77. These markers recorded 0.32 average gene diversity, 0.26 polymorphism information content and 1.35% null alleles. All the 31 ReG-SSR loci were found selectively neutral and showed no evidence of population reduction. A model-based clustering analysis separated the flax accessions into two sub-populations—Indian and global, with some accessions showing admixtures. The distinct clustering pattern of the Indian accessions compared to the global accessions, conforms to the principal coordinate analysis, genetic dissimilarity-based unweighted neighbor-joining tree and analysis of molecular variance. Fourteen flax accessions with 99.3% allelic richness were found optimum to adopt in breeding programs. In summary, the genome-wide ReG-SSR markers will serve as a functional marker resource for genetic and phenotypic relationship studies, marker-assisted selections, and provide a basis for selection of accessions from the Indian and global gene pool in fiber flax breeding programs.


Bast fiber Flax Functional markers Genic SSRs Genetic diversity Linum usitatissimum Long non-coding RNA Transcription factors 



long non-coding RNA


Million tons


Principal coordinate analysis


polymorphism information content


Regulatory gene-derived simple sequence repeat


transcription factor


Funding information

The authors thank the Indian Council of Agricultural Research-Central Research Institute for Jute and Allied Fibres for providing the necessary infrastructure and funding support (Project No. CRIJAF-JB 10.3) to carry out this study.

Compliance with ethical standards

Statement of author contributions

D.S. conceptualized the study, analyzed all data, and drafted the Ms. R.S.R conducted PCR profiling with lncRNA-SSRs and scored all the bands. S.Das isolated genomic DNAs and carried out PCR profiling with TF-SSR primers. S.D. and J.M. provided technical guidance and edited the Ms. S.J.C. significantly contributed in several rounds of critical corrections of the whole Ms. for both content and English language. F.M.Y. conducted in silico anchoring of the ReG-SSR markers on flax chromosomes and edited the Ms. All authors approved the final Ms.

Conflict of interest

S.Das conducted this study as a partial fulfillment of his M.Sc. thesis submitted to the School of Agriculture and Rural Development, Ramakrishna Mission Vivekananda University, Ramakrishna Mission Ashrama, Narendrapur, Kolkata and declare no conflict of interest. The rest of the authors declare that they have no conflict of interest.

Ethical approval

This article does not contain any studies with human participants performed by any of the authors.

Supplementary material

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Copyright information

© Institute of Plant Genetics, Polish Academy of Sciences, Poznan 2018

Authors and Affiliations

  1. 1.ICAR–Central Research Institute for Jute and Allied FibresKolkataIndia
  2. 2.School of Agriculture and Rural DevelopmentRamakrishna Mission Vivekananda UniversityKolkataIndia
  3. 3.Ottawa Research and Development CentreAgriculture and Agri-Food CanadaOttawaCanada
  4. 4.Morden Research and Development CentreAgriculture and Agri-Food CanadaMordenCanada

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