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

	Subpopulation Ancestry^b								20374951^a	20,381,787	20,382,161	20,384,350	20,382,286	20,380,447	20,381,308	20,380,886	20,382,480
	Subpopulation Ancestry^b								SNP1^c	SNP2	SNP3	SNP4	SNP5	SNP6	SNP7	SNP8	SNP9
Hap Group	Aus	Indica	Admix^d	ARO.	TEJ.	TRJ.	Japx	Total	601^e	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

^aSNP positions are based on IRGSPv.1
^bSubpopulation assignments based on SNP-Seek assignments, with all Indica subgroups classified as Indica
^cRepresents the SNP ID used throughout manuscript
^dAdmix, admixture; ARO, aromatic; TEJ, temperate japonica; TRJ, tropical japonica; Japx, japonica admixture
^eRepresents the LSU KASP SNP ID. SNP9 was not developed into a KASP assay