Abstract
PremiseNuclear microsatellite markers were developed for Linum bienne, the sister species of the crop L. usitatissimum, to provide molecular genetic tools for the investigation of L. bienne genetic diversity and structure.Methods and ResultsFifty microsatellite loci were identified in L. bienne by means of genome skimming, and 44 loci successfully amplified. Of these, 16 loci evenly spread across the L. usitatissimum reference nuclear genome were used for genotyping six L. bienne populations. Excluding one monomorphic locus, the number of alleles per locus ranged from two to 12. Four out of six populations harbored private alleles. The levels of expected and observed heterozygosity were 0.076 to 0.667 and 0.000 to 1.000, respectively. All 16 loci successfully cross‐amplified in L. usitatissimum.ConclusionsThe 16 microsatellite loci developed here can be used for population genetic studies in L. bienne, and 28 additional loci that successfully amplified are available for further testing.
Highlights
Departamento de Ecología Integrativa, Estación Biológica de Doñana (EBD), Consejo Superior de Investigaciones Científicas (CSIC), 41092, Seville, Spain
16 loci evenly spread across the L. usitatissimum reference nuclear genome were used for genotyping six L. bienne populations
All 16 loci successfully cross-amplified in L. usitatissimum
Summary
We employed the approach used by Viruel et al (2018), in which contigs are mined for microsatellite loci after a de novo assembly. DNA extractions for seven L. bienne individuals from different locations (Appendix 1) and corresponding whole genome shotgun libraries were prepared following the methods in Viruel et al (2019). Contigs containing microsatellite loci were filtered in R version 3.5.2 (R Core Team, 2018) using a custom-made script. Polymorphic loci were identified by BLASTing all contigs mapping to the L. usitatissimum reference genome for seven L. bienne individuals against the filtered contigs containing microsatellite loci, using BLAST version 2.2.31 (Altschul et al, 1990). 50 loci (Appendix 2) were left after filtering in R version 3.5.2 (R Core Team, 2018) based on BLAST output. Microsatellite loci with the following features were retained: ≥4 repeats of the base motif,
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
