Table 2 Summary of marker-trait associations of maximum significance
TraitVariantaChrombcMbMAFc−log(P)dEffecteFreqf
Glossy spikemorex_contig_40051:2172_A/Gg1H0.10.12101.70.46N/A
Glossy sheathmorex_contig_41718:9777_CG/Cg3H96.60.02Inf0.50N/A
Black hullmorex_contig_1573652:70_A/G1H116.50.01Inf0.51N/A
morex_contig_38907:1672_G/Ag1H116.60.01Inf0.50N/A
morex_contig_53289:2443_G/Ag1H116.80.01Inf0.50N/A
morex_contig_42987:7765_T/Cg1H117.70.01Inf0.50N/A
morex_contig_5603:2020_T/Cg1H117.80.01Inf0.50N/A
morex_contig_243581:952_C/Gg1H118.10.01Inf0.50N/A
morex_contig_1576759:813_C/Tg1H118.30.01Inf0.50N/A
morex_contig_5976:324_G/Ag1H119.00.01Inf0.50N/A
morex_contig_39431:11917_G/Ag1H119.40.01Inf0.50N/A
GPCmorex_contig_43675:8617_T/C1H50.60.174.9−0.140.13
morex_contig_47454:1292_C/T1H119.70.016.8−0.370.95
morex_contig_44650:4992_C/T3H25.30.024.8−0.180.17
morex_contig_41236:9829_G/A3H37.40.024.9−0.100.06
morex_contig_99201:2611_C/T4H27.50.105.60.170.90
morex_contig_46131:3154_TA/T4H27.80.014.8−0.050.08
morex_contig_47914:307_C/T4H43.50.024.90.360.09
morex_contig_246786:1453_AACGTACGC/A4H44.90.035.0−0.200.59
morex_contig_156722:1830_G/A4H51.60.034.80.330.11
morex_contig_45564:4922_A/G4H52.20.074.5−0.070.06
morex_contig_52783:3343_C/T4H63.40.024.5−0.270.06
morex_contig_1575414:1899_A/G4H67.10.034.50.290.13
morex_contig_146580:705_T/A4H76.30.015.0−0.300.56
morex_contig_42454:4904_G/A4H78.70.044.80.230.11
morex_contig_7108:5074_G/Tg6H50.00.175.80.370.96
  • All significant marker-trait associations can be found in File S1. Markers for a single QTL of maximum significance are reported for qualitative traits. For grain protein content, QTL on the same chromosome were considered unique loci if there was a >5-cM gap between significant markers, and markers of maximum significance with both positive and negative effects are reported for each QTL. Chrom, chromosome; Freq, frequency; Inf, markers which cosegregate with the trait values; GPC, grain protein content.

  • a Variants significantly associated with trait. Association determined by an FDR >0.05 significance threshold, and a frequency of detection >0.05 in 100 bootstrap samplings of 25 individuals from each family for the trait protein.

  • b Chromosome and cM positions of Morex contig containing the variant as determined by the Mascher et al. (2013b) POPSEQ map.

  • c MAF of variant in the AB-NAM population.

  • d −log(P) averaged across significant bootstrap tests.

  • e Relative effect of non-Rasmusson allele, averaged across significant bootstrap tests.

  • f Frequency of significant association with variant detected in 100 bootstrap samples.

  • g Additional variants in the same bin with identical segregation pattern can be found in File S1.