10.25387/g3.8218325.v1
Marcelo Mollinari
Antonio Augusto Franco Garcia
Supplemental Material for Mollinari and Garcia, 2019
2019
GSA Journals
mapping analyses
polyploid plants
recombination fraction
2019-08-12 15:40:46
article
https://gsajournals.figshare.com/articles/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