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Summary of the statistical models used to test for marker-trait associations.

 
Model Statistical model Information captured in the model
Naïve y = Xα + ε y is related to X, without correction for structure (Q or PCA) or relatedness (K or K*)
K y = Xα + Kν + ε y is related to X, with correction for K
K* y = Xα + K*ν + ε y is related to X, with correction K*
Q y = Xα + Qβ + ε y is related to X, with correction for Q
PCA y = Xα + Pβ + ε y is related to X, with correction for PCA
Q + K y = Xα + Qβ + Kν + ε y is related to X, with correction for Q and K
Q + K* y = Xα + Qβ + K*ν + ε y is related to X, with correction for Q and K*
PCA + K y = Xα + Pβ + Kν + ε y is related to X, along with correction for PCA and K
PCA + K* y = Xα + Pβ + K*ν + ε y is related to X, along with correction for PCA and K*
PCA, principal component analysis.
Q is seven and three subpopulations for 2005 and 2006, respectively.
§Principal components (PCs) that explain ∼25% variance are four in both the years.



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Analysis of variance for iron deficiency chlorosis ratings for the two soybean populations grown at different locations.

 
Population
2005
2006
Source of variation df MS df MS
Location 4 104.39 3 133.49
Line 142 3.76 140 3.15
Location × line 569 0.25 420 0.33
Replication × location 15 2.11 12 2.08
Error 2130 0.19 1680 0.17
***Significant difference p ≤ 0.001.
MS, mean square,



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Test statistics for the nine models used to discover single nucleotide polymorphism (SNP) and iron deficiency chlorosis (IDC) tolerance marker–trait associations.

 
2005
2006
Model Percent p-values < 0.05 MSD Model Percent p-values < 0.05 MSD
Q + K* 15.51 0.017 PCA + K* 18.72 0.015
PCA 17.48 0.026 Q 23.39 0035
PCA + K 18.07 0.028 PCA 23.85 0.036
Q 20.86 0.032 Q + K 23.86 0.037
Q + K 22.03 0.034 PCA + K 24.45 0.038
Naïve 42.66 0.075 Naïve 38.59 0.067
K* 43.71 0.076 K 38.75 0.068
PCA + K* 50.59 0.203 K* 76.03 0.276
K 85.42 0.302 Q + K* 73.97 0.281
MSD, mean square deviation.
PCA, principal component analysis.



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Single nucleotide polymorphism (SNP) marker loci significantly associated with iron deficiency chlorosis (IDC) tolerance in both 2005 and 2006 populations.

 
BARC SNP marker Chromosome SNP position (bp) Genetic position (cM) Minor allele Major allele
BARC-029969-06762 2 2,454,206 18.801 A C
BARC-044603-08734 3 45,007,967 85.822 T A
BARC-060109-16388 3 45,391,018 86.907 A G
BARC-016535-02085 3 45,416,307 88.225 G A
BARC-010457-00640 6 45,281,692 108.504 T A
BARC-039383-07310 7 7,151,246 39.939 C A
BARC-025897-05144 13 27,145,239 49.424 A G
BARC-055499-13329 13 31,472,325 61.354 G A
BARC-059723-16418 19 40,357,687 56.404 A G



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Test statistics for single nucleotide polymorphism (SNP) loci significantly associated with iron deficiency chlorosis (IDC) tolerance in the 2005 and 2006 populations.

 
2005
2006
BARC SNP marker Chromosome –log10(p) pFDR R2 (%) Minor allele frequency Minor allele mean Major allele mean –log10(p) pFDR R2 (%) Minor allele frequency Minor allele mean Major allele mean
BARC-029969-06762 2 2.707 0.046 11.8 49.0 3.0 2.7 7.531 0.000 24.3 40.4 2.9 2.5
BARC-044603-08734 3 3.661 0.022 14.9 40.6 2.7 3.0 4.898 0.001 15.7 45.4 2.5 2.8
BARC-060109-16388 3 3.321 0.024 16.3 46.2 2.7 3.0 3.781 0.003 13.9 47.5 2.5 2.8
BARC-016535-02085 3 2.886 0.046 15.3 46.9 2.7 3.0 3.781 0.003 13.9 47.5 2.5 2.8
BARC-010457-00640 6 2.185 0.076 0.1 39.9 2.8 2.9 4.018 0.002 2.6 44.7 2.6 2.7
BARC-039383-07310 7 3.114 0.034 17.8 21.7 2.5 3.0 4.548 0.002 13.5 21.3 2.3 2.7
BARC-025897-05144 13 2.309 0.067 15.2 38.5 3.1 2.7 4.008 0.002 15.9 37.6 2.9 2.5
BARC-055499-13329 13 2.420 0.058 9.4 31.5 3.1 2.8 2.602 0.021 13.4 27.0 2.9 2.6
BARC-059723-16418 19 3.415 0.022 15.4 44.8 2.7 3.0 4.124 0.002 10.7 31.2 2.4 2.8
pFDR, positive false discovery rate.



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Significant (positive false discovery rate [pFDR] < 0.1) Universal Soy Linkage Panel (USLP) 1.0 markers that are the immediate neighbor to a gene known to be involved in iron metabolism. Markers without statistical information did not converge.

 
2005
2006
BARC marker Chromosome SNP position (bp) –log10 (p) pFDR R2 (%) –log10 (p) pFDR R2 (%) At gene Gm gene model Start of model (bp) Distance from SNP (bp) E-value Percent identity
BARC-060109-16388 3 45,391,018 3.32 0.02 16.26 3.78 0.00 13.94 NAS3 Glyma03g39050 45,279,921 111,097 5.00 E × 10–109 62.9
BARC-053261-11776 5 937,302 2.21 0.08 0.72 AHA2 Glyma05g01460 960,820 23,518 0 81.1
BARC-021775-04203 5 41,114,078 0.08 0.53 0.07 2.47 0.03 9.30 BTI2-ITP Glyma05g37300 40,906,083 207,995 1.00 E × 10–95 65.7
BARC-054331-12480 7 8,652,831 1.72 0.09 4.78 BTI2-ITP Glyma07g10870 9,082,076 429,245 2.00 E × 10–45 36.8
BARC-049147-10810 9 35,895,343 0.44 0.38 0.73 2.07 0.05 1.50 YSL7 Glyma09g29410 36,298,317 402,974 0 54.6
BARC-062275-17736 11 38,020,165 0.02 0.56 1.64 2.63 0.02 0.18 FER4 Glyma11g35610 37,245,783 774,382 7.00 E × 10–103 73.2
BARC-017917-02456 13 30,457,599 2.17 0.08 7.83 FRD3 Glyma13g27300 30,477,485 19,886 2.00 E × 10–137 54.7
BARC-043041-08509 15 48,694,193 2.71 0.05 12.66 0.94 0.26 9.24 IRT1 Glyma15g41620 48,764,845 70,652 8.00 E × 10–80 43.5
BARC-030595-06910 16 3,039,691 0.09 0.53 4.55 1.93 0.06 7.72 FRO2 Glyma16g03770 3,142,668 102,977 0 57.7
BARC-011625-00310 16 36,544,010 0.26 0.45 0.47 2.28 0.04 2.79 YSL7 Glyma16g33840 36,609,082 65,072 0 73.4
BARC-043087-08524 17 4,899,023 3.44 0.02 0.25 1.37 0.16 1.35 AHA2 Glyma17g06930 4,977,823 78,800 0 87.7
BARC-012289-01799 18 1,957,710 1.78 0.08 2.07 FER4 Glyma18g02800 1,821,344 136,366 6.00 E × 10–102 75.1
BARC-016867-02359 18 56,429,447 1.26 0.19 2.77 2.11 0.05 6.63 FRO2 Glyma18g47060 56,712,622 283,175 0 52.2
BARC-059723-16418 19 40,357,687 3.42 0.02 15.41 4.12 0.00 10.68 OPT1 Glyma19g32400 40,140,993 216,694 3.00 E × 10–146 47.4
BARC-042281-08231 20 343,106 0.22 0.47 2.33 1.96 0.06 8.58 YSL7 Glyma20g00690 418,225 75,119 0 62.8
SNP, single nucleotide polymorphism.
At, Arabidopsis thaliana (L.) Heynh.
§Gm, Glycine max (L.) Merr.