Supplemental Material for Mollinari and Garcia, 2019 Marcelo Mollinari Antonio Augusto Franco Garcia 10.25387/g3.8218325.v1 https://gsajournals.figshare.com/articles/online_resource/Supplemental_Material_for_Mollinari_and_Garcia_2019/8218325 Supplementary Information for the manuscript: "Linkage analysis and haplotype phasing in experimental autopolyploid populations with high ploidy level using hidden Markov models"<div><br></div><div>1. File S1: Algebraic simplifications for transition probabilities</div><div>2. File S2: Algorithm for obtaining l<sub>P</sub> and l<sub>Q</sub> given two genotypic indices</div><div>3. File S3: Example of usage of the two-point and multipoint procedures to infer the linkage phase configuration in both parents and estimate recombination fractions in a sequence of markers in high-level autopolyploids.</div><div>4. Figure S4: Haplotypes for simulation study 1 - Simulated haplotypes with 10 markers and three ploidy levels, namely autotetraploid (m = 4), autohexaploid (m = 6) and autooctaploid (m = 8).</div><div>5. Figure S5: Haplotypes for simulation study 2 - Simulated haplotypes with 200 markers and two ploidy levels, namely autotetraploid (m = 4) and autohexaploid (m = 6).</div><div>6. Figure S6: Boxplots of the average Euclidean distances between the estimated and simulated distance vectors for simulation study 2</div><div>7. Figure S7: Examples autotetraploid and autohexapoloid maps estimated from datasets with three quadrivalent formation rates: 0.00, 0.25 and 0.50</div><div>8. File S8: Summary of results from B2721 population map construction</div><div>9. Figure S9: Simulated haplotypes for comparison between polymapR and HMM-based method</div>10. File S10: Results of comparison between polymapR and HMM-based method 2019-08-12 15:40:46 mapping analyses polyploid plants recombination fraction Genetics