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

Rice

Table 2 Haplotype characterization and 2AP concentration across U.S. breeding germplasm panel

					20374951^a	20,381,787	20,382,161	20,384,350	20,382,286	20,380,447	20,381,308	20,380,886
		2AP Concentration Test (ppm)^b			SNP1^c	SNP2	SNP3	SNP4	SNP5	SNP6	SNP7	SNP8
Hap Group	Number	n	Range	Mean (SE)^d	601^e	548	536	603	531	849	852	855
1	181	5	0–0	0	G	A	G	G	A	G	G	T
2	134	9	0–0.079	0.009 (0.005)	G	T	A	G	A	C	C	T
3	11	2	0–0	0	G	A	G	A	A	C	C	T
5	5	3	0–0.001	0.0002 (0.0002)	G	T	G	G	A	C	C	T
6 (aromatic)	27	17	0.356–3.165	1.30 (0.058)	T	T	A	G	A	C	C	T
7 or 9	11	3	0–0.009	0.003 (0.002)	G	A	G	G	A	C	C	T

^aSNP positions are based on IRGSPv.1 and are on Chromosome 8
^bppm, parts per million
^cRepresents the SNP ID used throughout manuscript
^dValues in the parentheses represent the standard error of the 2AP Concentration
^eRepresents the LSU KASP SNP ID