Supplementary Materials

Selective trade-offs maintain alleles underpinning complex trait variation in plants

Ashley Troth, Joshua R. Puzey, Rebecca S. Kim, John H. Willis, John K. Kelly

Materials/Methods, Supplementary Text, Tables, Figures, and/or References

Download Supplement
  • Materials and Methods¬†
  • Captions for tables S1 to S5¬†
  • References¬†
Table S1
The 45 polymorphisms (SNPs and small indels) that were genome-wide significant from permutation are reported. These are distilled into 27 distinct loci (Locus ID column) by combining closely linked and strongly correlated sites. Four of the 27 loci exhibit strong correlation despite being unlinked (see Supplemental Table 2) and so only one was used in Figure 1 of main paper. (n=24 there).
Table S2
Associations are reported among the 45 polymorphisms (SNPs and small indels) that were genome-wide significant from permutation. Calculations of the LD (as both D and r2) were based only on lines where both loci are scored. The count of these informative lines (No. haplotypes) was required to be >=100. p1 and p2 refer to frequency of the reference base at each locus among scored haplotypes.
Table S3
The description of structural polymorphisms (from Lumpy) that were significant (p < 10-5) for effects on greenhouse phenotypes. If more than one trait is effected by a single locus, the results for each trait are reported on a different line.
Table S4
Estimates of phenotypic effect in the greenhouse are reported for the meiotic drive locus on chromosome 11. Across lines, genotypes counts are 111 dd, 6 Dd, and 48 DD, where D refers to the driving allele.
Table S5
Estimates of phenotypic and fitness effect in the field experiment (2014-2016) are reported for the meiotic drive locus on chromosome 11. The same conventions are used as in Table S4.