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Table 4 Allele frequencies of significantly associated SNPs in the five major maize subpopulations and P -value of Fisher’s exact test of the null hypothesis of equal allele frequencies across subpopulations

From: Genome-wide association study of Fusarium ear rot disease in the U.S.A. maize inbred line collection

  

Resistance allele frequency (%) a

 

N b

Chromo-some

SNP physical position (bp)

SS c

NSS

TS

PC

SC

P- value

SS

NSS

TS

PC

SC

4

7,566,354

1.2

0.0

32.0

60.4

0.0

<2.2 × 10−16

164

171

222

48

51

4

7,618,125

0.6

0.0

30.7

47.9

0.0

<2.2 × 10−16

164

171

215

48

52

4

7,618,284

0.6

0.0

36.5

66.0

0.0

<2.2 × 10−16

159

168

211

47

51

4

9,353,851

0.6

0.6

31.9

0.0

0.0

<2.2 × 10−16

161

168

213

61

50

4

124,930,006

0.0

1.8

8.8

3.3

0.0

1.7 × 10−5

162

166

238

60

51

5

64,771,372

0.0

4.7

8.1

14.8

0.0

3.2 × 10−6

164

170

246

61

51

9

19,532,465

2.5

7.2

26.6

26.7

2.0

4.9 × 10−15

158

167

241

60

51

 

Ear rot mean (%)d

39.6

39.6

43.0

41.3

61.1

      
  1. aAt all SNP loci the minor allele is associated with increased disease resistance.
  2. bN, total number of lines within each subpopulation with marker calls at a particular SNP locus.
  3. cSS, stiff stalk; NSS, non-stiff stalk; TS, tropical/subtropical; PC, popcorn; SC, sweet corn.
  4. dOverall phenotypic ear rot means are the average of least squares means across members of each subpopulation.