Table 1.

lcyE associations across seasons. Association results for significant polymorphisms identified in the four regions sampled along the lcyE gene. Each polymorphism is labeled numerically by its position on the alignment relative to the exon 1 start codon. Followed by the favorable allele (bold)/unfavorable allele at the site. An initial scan for association using both β-carotene and the ratio of the two pathway branches was conducted using the mixed model incorporating population structure and kinship. Subsequently a simpler general linear model (GLM) was used to evaluate data sets from additional years, including population structure (Q), given the oligogenic behavior of the trait the change in flux estimates for 2003 do not include Q. Avg., average; n.c., nonconvergence; n.s., not significant.

lcyE association (P), mixed model oflcyE association as a ratio across environments (GLM) (P)Fold change in flux
β-Carotene/allRatio of branches
Environment (year) (2003) (2003) (2002) (2003) (2004) (2005) (2003)
Avg. observation no. Polymorphic site (157) (154) (44) (156) (154) (156)
5′ TE 1+4/2/3 5.42 × 10-4 3.96 × 10-11 0.024 8.05 × 10-11 0.008 8.61 × 10-9 6.5
216 G / T n.c. 1.35 × 10-10 0.059 1.24 × 10-10 0.003 2.93 × 10-10 2.8
2238 G / T 1.22 × 10-4 1.69 × 10-9 0.008 2.12 × 10-10 0.023 1.08 × 10-9 2.7
2312 A / T 1.70 × 10-3 n.c. n.s. 6.84 × 10-4 0.026 0.005 2.9
4184 G / A 3.06 × 10-4 n.c. 8.87 × 10-4 2.23 × 10-10 0.019 1.13 × 10-8 2.6
4315 C / G 1.84 × 10-4 7.01 × 10-10 0.012 3.07 × 10-9 5.75 × 10-4 6.79 × 10-7 2.6
3′Indel 8/0 4.80 × 10-3 2.75 × 10-9 n.s. 1.46 × 10-8 8.97 × 10-4 4.13 × 10-6 3.5