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Table 3 Haplotypes at the alcohol dehydrogenase (Adh1), stearoyl-ACP-desaturase and acetyl-CoA C-acyltransferase loci Adh1 haplotypes are based on concatenation of all three segments of Adh1 sequenced

From: SNP frequency, haplotype structure and linkage disequilibrium in elite maize inbred lines

Adh1
   SNP Position in AF123535 and genotype
Haplotype Frequency 16920 16933 16935 16951 16978 17873 17880 17904 18071
–072
21129 29729
–730
21178 21179 21180 21181
–185
21199
–532
21359 21513
–514
21576 21649
–50
21650
–736
21737
1 0.031 G G A A C C A C - G I C G C - - T T C I - G
2 0.031 A T G G T C A C - G I C G C - - T T C I - G
3 0.125 A T G G T C G T - T - T T G I I C - T - - -
4 0.250 A T G G T C G T - T - T T G I I C - T - I C
5 0.250 A T G G T C G T - T - T T G I I T - T - - -
6 0.312 A T G G T G G T I T - T T G I I C I T - - -
Stearoyl-ACP-desaturase
   SNP Position in GenBank accesion AF498430 and genotype
Haplotype Frequency 71 82 86 87 153 156 171 190–194 200              
1 0.222 A A T A C G A - T              
2 0.222 G A T A C A A I C              
3 0.055 G A T A C A A I T              
4 0.500 G C A T T A C - T              
Acetyl-CoA C-acyltransferase
   SNP Position in GenBank accesion AF498472 and genotype
Haplotype Frequency 38 73 100 111 143 161 239 245 247 250 251 257 266 270 279 290 295 330–391 449    
1 0.030 C C A G C G A C G C G C T A T T A - T    
2 0.470 C T T G C C A C C T G C A A T C A - C    
3 0.230 C T T G T C A C G T G C A A T C A - C    
4 0.260 T T A T C G G T C C A T A C C C T I C    
  1. Allelic sites at polymorphic sites are shown, together with their nucleotide positions. The insertion – deletion is represented as I. Missing data are denoted "?". Promoter region is separated from the rest of the gene by "^" (Adh1 only).
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