Table S1. Trait summary for Northern Leaf Blight resistance in the maize nested association mapping (NAM) population and individual NAM families

Transcription

1 SUPPLEMENTAL MATERIAL Supplemental Tables: Table S1. Trait summary for Northern Leaf Blight resistance in the maize nested association mapping (NAM) population and individual NAM families "#$%&' (')*'%$+,-' ''."/$+0'1' ''."/$+0'2' ''."/$+0'3' )4+5,6-' 27' '' 789' :183;'278<=' '' 1189' :187;'>3=' '' 2?81' BA7'C'B73' 19A' ' 1>8A' :>81;'>189=' ' ' :13;'7A8<=' DEF1?3'C'B73' 177' ' A83' :189;'238>=' ' 1>83' ' DEF229'C'B73' 1<1' ' :2;'2?81=' ' 1187' :28A;'2>8A=' ' 228<' :98A;'><8>=' DEF2>7'C'B73' 192' ' 78<' ' 1189' :18<;'3389=' ' 238?' DEF277'C'B73' :?8<;'138A=' ' 981' :1;'2?8A=' ' DEF322'C'B73' ' 1189' :28>;'3?8A=' ' 1787' :3;'>387=' ' 3?8?' :A8>;'<28<=' DEF333'C'B73' 193' ' ' 218<' ' 328>' 1<3' ' 78<' :?87;'2181=' ' 1181' ' DEF<A'C'B73' 19<' ' <87' :?87;'2<8A=' ' 1?83' :182;'>387=' ' 1983' GH3?1'C'B73' 192' ' 2?81' :982;'><=' ' 3?8>' :13;'<38>=' ' :2787;'7<=' I%1>G'C'B73' 197' ' 1>81' :>81;'318<=' ' ' 3<81' J$11'C'B73' 1<9' ' A8?' :?83;'2782=' ' :?83;'3A8A=' ' 238>' J$3'C'B73' 1A1' ' <8?' ' 989' :182;'2187=' ' 1<8>' :>82;'3>87=' J&21'C'B73' 1A1' ' ' 2>8>' ' 3789' :1782;'<?8<=' E1<2K'C'B73' 197' ' :1;'178>=' ' A8<' :?89;'298A=' ' E37K'C'B73' 197' ' 78?' :18<;'2281=' ' :18A;'3<83=' ' 1A81' E)17'C'B73' 17A' ' 1189' ' 1789' ' 2A89' :1?82;'<?=' E)19K'C'B73' 173' ' ' 1>89' ' 2<81' :<83;'<?89=' EL71'C'B73' 1A1' ' ' 238>' ' :1181;'7A82=' 192' ' 1283' ' 198<' :283;'>?8<=' ' 2A8>' 192' ' 789' :282;'218<=' ' 1282' :289;'3<=' ' 2289' NO>3'C'B73' 19?' ' 138<' :<83;'2<8<=' ' 2?87' ' 328>' NO7B'C'B73' 17<' ' ' :98>;'7387=' ' >98A' :1983;'7A83=' P3A'C'B73' 17>' ' 1<81' ' 2>8<' ' 3A8?' :178A;'738>=' QC3?3'C'B73' 199' ' 128<' ' 1A8>' :>81;'3781=' ' 328>' QR$9'C'B73' 192' '' 1287' :18>;'>18<=' '' 198A' '' 3?8A' :781;'7387=' MSE' ><<7' ' 118>' ' 1782' :?83;'7387=' ' 2982' #,"+' :#$+;#"C='

2 Table S2. Broad-sense heritability for resistance to Northern Leaf Blight in the maize nested association mapping (NAM) population and individual NAM families "#$%&'."/$+0'1'."/$+0'2'."/$+0'3' 'I+5,C' DEF322'?872'?87A'?87<'?893' I%1>G'?8<?'?872'?872'?877' E)17'?8<9'?871'?8<A'?879' E)19K'?872'?89?'?87<'?893' QC3?3'?8<>'?871'?8<>'?87<' ST08'U$/O$+' "#$%&'?8<3'?871'?8<9'?877' )4+5,6-'?89?'?897'?899'?8A?'

3 Table S3. Joint Linkage Model for Northern Leaf Blight Resistance in the maize nested association mapping population Model Effect Df Sum Sq F value Pr(>F) Chr. Marker Name factor(pop) < 2.2e- DaysToAnthesis E- 16 factor(pop):m E- 01 factor(pop):m E- 07 factor(pop):m E- 06 factor(pop):m E- 12 factor(pop):m E- 06 factor(pop):m E- 07 factor(pop):m E- 14 factor(pop):m E- 08 factor(pop):m E- 05 factor(pop):m E- 09 factor(pop):m E- 08 factor(pop):m E- 09 factor(pop):m < 2.2e- 05 factor(pop):m E- 16 factor(pop):m E- 06 factor(pop):m E- 12 factor(pop):m E- 12 factor(pop):m E- 12 factor(pop):m E- 12 factor(pop):m E- 14 factor(pop):m E- 06 factor(pop):m E- 06 factor(pop):m E- 15 factor(pop):m < 2.2e- 06 factor(pop):m E- 16 factor(pop):m < 2.2e- 16 factor(pop):m E- 16 factor(pop):m E- 05 factor(pop):m E- 06 Residuals NAM Marker Position (cm) Lower CI (cm) Upper CI (cm) BAC AGP Physical Map 1 PZB m AC c0365i PZA /2 m PZA m AC b0410i PZA m AC c0201i PZA m AC c0245c PZA m AC b0116l PZA m AC b0151l PZA m AC c0468p PZB /4 m PZA m AC b0498c PZA m AC c0276p PZA m AC b0457n PHM m PZA m PHM m AC b0318b PZA m AC c0337k PZA m AC c0422e PZA m AC b0395c PHM m AC c0190k PZA m AC b0623j PZA m AC c0411a PZA m AC c0207m PZA m AC c0447o PZA m AC c0206p PZA m AC b0358b PHM m AC c0384o PZA m AC c0384c PZA m AC c0325g PHM m

4 Supplemental Figures: % diseased leaf area CML277 Ki3 M162W CML69 CML52 M37W CML247 NC358 CML228 CML103 Ki11 Mo18W NC350 Mo17 CML322 Tzi8 Tx303 CML333 MS71 Oh43 B97 Il14H Ky21 P39 Hp301 Oh7B Fig. S1. Box-plot of trait variation of NLB resistance for individual families of NAM. The scale is percentage of total diseased leaf area at the third disease rating. For each family, the family median is shown as a bold line, the 25% and 75% percentiles with the box, and outliers with individual circles. Square-root transformation of the phenotype produced normal distributions for the families and were used for analysis (see text).

5 Family Average R 2 = Founder Phenotype Fig. S2. Comparison of NAM founder phenotypes and mean phenotype of progeny. For each NAM founder the observed phenotype was compared to the average observed phenotype for its respective family. Regression of the family means on the founder phenotype explained 80% of the variance.

6 Number of Alleles Allele Effect (change in % diseased leaf area) Fig. S3. Histogram of allele effects for all modeled alleles at QTL. The nested model give an estimated allele effect for each founder line at each QTL resulting in #QTL x #Founder estimates. The nesting of marker effects allows for pooling data among families to increase power in testing for QTL effects and estimating the total percentage of explained genetic variation accounted by the multiple SNP model of the NAM pop as a whole. Most of these allele effects are estimated to be close to zero and non-significant (grey). The significant positive and negative allele effects are shown in blue and red. Most observed effects were less than a 5% difference in diseased leaf area.

7 4 Allele Effect (change in % Diseased Leaf Area) CML103 P39 Ki3 Ky21 Ki11 Oh43 B97 Mo17 CML277 CML69 CML333 CML322 CML247 CML228 Hp301 M162W Tx303 Mo18W Tzi8 NC358 M37W NC350 MS71 Il14H CML52 Oh7B 4 Fig. S4. It was observed that many of the QTL (21 of 29) had allele effects that were estimated both above and below the B73 allele (the zero reference point). Shown here are the estimated allele effects for a single QTL (m616, Chr.5 at 69.5 cm, 88.6 Mb) showing both positive and negative alleles relative to B73. Confidence intervals (95%) are shown in brackets. We can conclude that there are at least three alleles at this locus by comparing to B73, and possibly more considering differences within both the positive and the negative allele groups.

8 Emperical Phenotype R 2 = Predicted Phenotype Fig. S5. Additive genetic model for NLB resistance gives accurate prediction of the observed phenotypes for the nested association mapping (NAM) population founders. Linear fit of predicted phenotypic values for each of the diverse founder inbred lines of NAM against the empirical phenotypic observations. Predicted phenotypes were determined by summing the allele effect for each respective founder line at all of the QTL identified while the empirical phenotypes are best linear unbiased predictions from three years of replicated field trials. Units are shown in percentage diseased leaf area.

9 m501 m Non Stiff Stalk m87 m m728 m Fig. S6. Test for allele origins showing QTL markers that had significant association with quantitative estimates of allele origins. The horizontal axis in each graph shows the origin of a given founder for either non-stiff stalk (first graph) or Tropical/Sub-tropical (remaining five graphs). The estimated allele effect is plotted on the vertical axis. The linear regression line is also shown.