Research Article

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

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Science  03 Aug 2018:
Vol. 361, Issue 6401, pp. 475-478
DOI: 10.1126/science.aat5760
  • Fig. 1 Trait-associated alleles exhibit strong associations.

    (A) The effect of the reference allele (base or indel) on days to flower is a strong positive predictor of its effects on flower size (blue) and plant height (green). (B) The effect of the minor allele at each locus on days to flower (black), height (green), and flower size (blue) is plotted against frequency in the lines. Here, effects are standardized by the standard deviation of the trait.

  • Fig. 2 SNPs and small indels with a trait association test of P < 10−5 in the greenhouse GWAS as ascertained in pooled samples from two natural populations, IM and Quarry.

    (A) Density plots for the difference in frequency of the minor base (within the inbred line set) between Quarry and IM. Solid red curve, distribution for trait-associated sites; dashed black curve, distribution for all sites. (B) Allelic effect on flower size PC1 (in the greenhouse experiment) is a positive predictor of allele frequency divergence between Quarry and IM.

  • Fig. 3 Effects of minor frequency alleles on fitness components vary between years.

    The estimated effects of the minor allele on (A) viability, (B) log(seed set of survivors), and (C) total seed set (dead included) is plotted against allele frequency for plants in 2014 (blue) and 2016 (green). These are loci from the 10−5 set that exhibited effects on flower size PC1.

  • Fig. 4 The effects of all trait-associated polymorphisms (P < 10−5 in the greenhouse GWAS) on survival and total seed set.

    (A and B) Selection in 2014 (negative on flower size). (C and D) Selection in 2016 (positive on flower size). Viability is the response variable in (A) and (C), total seed in (B) and (D). The subset of polymorphisms that are significant for flower size PC1 are red. Here, effects are attributed to the reference allele at each polymorphism.

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

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    • 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.

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