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Table 1 Haplotype characterization of the BADH2 gene across the global rice diversity panel

From: Characterization of Haplotype Diversity in the BADH2 Aroma Gene and Development of a KASP SNP Assay for Predicting Aroma in U.S. Rice

  Subpopulation Ancestryb 20374951a 20,381,787 20,382,161 20,384,350 20,382,286 20,380,447 20,381,308 20,380,886 20,382,480
SNP1c SNP2 SNP3 SNP4 SNP5 SNP6 SNP7 SNP8 SNP9
Hap Group Aus Indica Admixd ARO. TEJ. TRJ. Japx Total 601e 548 536 603 531 849 852 855 N/A
1 1 749 12 0 1 121 8 892 G A G G A G G T C
2 2 148 19 26 215 281 64 755 G T A G A C G T C
3 0 201 1 0 1 0 0 203 G A G A A C C T C
4 9 183 5 0 0 0 0 197 G A G G A G C T C
5 1 186 5 2 0 1 0 195 G T G G A C C T C
6 (aromatic) 0 65 9 38 3 53 3 171 T T A G A C C T C
7 97 11 6 0 0 0 0 114 G A G G A C C T C
8 0 89 2 1 0 2 0 94 G A G G G G G T C
9 63 13 6 3 0 0 0 85 G A G G A C C T C
10 1 39 6 0 2 4 0 52 G A G G A G G T T
11 3 22 6 0 0 0 0 31 G A G G A G C C C
R 22 42 6 2 0 2 0 74
U 2 41 16 3 2 3 2 69
Total 201 1789 99 75 224 467 77 2932          
  1. aSNP positions are based on IRGSPv.1
  2. bSubpopulation assignments based on SNP-Seek assignments, with all Indica subgroups classified as Indica
  3. cRepresents the SNP ID used throughout manuscript
  4. dAdmix, admixture; ARO, aromatic; TEJ, temperate japonica; TRJ, tropical japonica; Japx, japonica admixture
  5. eRepresents the LSU KASP SNP ID. SNP9 was not developed into a KASP assay