Quantitative trait loci responsible for the difference in γ-oryzanol content in brown rice between japonica-type and indica-type rice cultivars

Figures & data

Figure 1. High-performance liquid chromatogram profile representing several components of γ-oryzanol (A to D) extracted from brown rice.

Figure 2. Frequency distributions of total γ-oryzanol content of brown rice among (A) recombinant inbred lines from Asominori/IR24 and (B) backcross inbred lines from Sasanishiki/Habataki//Sasanishiki. Horizontal bar indicates SD.

Table 1. QTLs for total γ-oryzanol content in brown rice detected from a set of recombinant inbred lines from Asominori/IR24 and that of backcross inbred lines from Sasanishiki/Habataki//Sasanishiki.

Population	QTL	Chromosome	Position (cM)	Nearest marker (cM)	LOD score	R^2	Additive effect
AIRIL	qOZ1c	1	117.6	R758 (134.2)	4.67	.161	−42.3
	qOZ5a	5	32.0	R569 (44.7)	3.58	.120	34.1
	qOZ9	9	52.4	C609 (53.4)	3.22	.106	−31.6
SHBIL	qOZ1a	1	47.2	S11122 (47.2)	5.46	.159	−55.7
	qOZ1b	1	69.0	Y5714L (69.0)	4.52	.134	−52.8
	qOZ5b	5	68.0	R372 (68.7)	3.78	.105	49.8
	qOZ7	7	91.7	C847 (91.7)	3.35	.094	44.0
	qOZ12	12	106.1	G1406 (103.1)	3.36	.115	40.2

Notes: Population: AIRIL and SHBIL, Recombinant inbred lines derived from Asominori (japonica-type)/IR24 (indica-type), and backcross inbred lines derived from Sasanishiki (japonica-type)/Habataki (indica-type)//Sasanishiki, respectively. Additive effect: Positive and negative values indicate that alleles from japonica-type parents increase and decrease the content, respectively.

Figure 3. Total γ-oryzanol content of brown rice in chromosome segment substitution lines (CSSLs) with IR24 segments in Asominori background (AIS), and those with Asominori segments in IR24 background (IAS), together with their parents. White, black and hatched bars indicate CSSLs with no significant differences from Asominori, from IR24 and with significant difference from the respective background parents (p < .001), respectively.

Figure 4. Total γ-oryzanol contents of brown rice in chromosome segment substitution lines (CSSLs) with Habataki segments in Sasanishiki background (SL), together with their parents. White, black and hatched bars indicate CSSLs with no significant differences from Sasanishiki, from Habataki and with significant difference from background parent, Sasanishiki (p < .001), respectively.

Table 2. Expected performance of a chromosome segment substitution line (CSSL) involving a QTL for total γ-oryzanol content in brown rice.

Allele at a QTL in the segment in a CSSL	Background of a CSSL
	Parent A	Parent B
Increasing allele from parent A	=	+
Decreasing allele from parent B	−	=
Increasing allele from parent B	+	=
Decreasing allele from parent A	=	−

Note: +, −, and = indicate that this CSSL is expected to show higher, lower, and similar contents compared with the corresponding background parent, respectively.

Table 3. Candidate regions of QTL for total γ-oryzanol content in brown rice suggested from three sets of chromosome segment substitution lines.

Population	Chromosome	Candidate region of QTL for γ-oryzanol {Marker interval (cM)}	Allele with increasing effect from
AIS and IAS	9	XNpb13 (40.9) − R2638 (43.2)	IR24
	10	XNpb37 (40.2) − C405 (92.8)	IR24
	12	C1069 (4.6) − R1684 (12.2)	IR24
SL	1	RM8105 (19.9) − RM3233 (26.1)	Habataki
	4	RM3534 (105.1) − RM2431 (129.6)	Sasanishiki
	6	RM1370 (118.9) − RM5463 (124.4)	Habataki
	10	RM3773 (58.9) − RM6673 (83.8)	Habataki
	11	RM5824 (56.8) − RM1355 (66.6)	Sasanishiki
	12	RM6905 (41.8) − RM3813 (87.6)	Sasanishiki

Notes: Population: AIS, IAS and SL, chromosome segment substitution lines with IR24 (indica-type) segment in Asominori (japonica-type) background, with Asominori segment in IR24 background and with Habataki (indica-type) segment in Sasanishiki (japonica-type) background, respectively. Candidate regions were deduced from the performance and chromosome segment constitutions of CSSLs in Supplemental Figures S1 and S2.

Table 4. Loci for enzymes involved in sterol syntheses located to near the detected QTLs for total γ-oryzanol content in brown rice (within 5 Mbp), searched at https://plantreactome/gramene.org/PathwayBrowser/ (secondary metabolite biosynthesis, sterol biosynthesis, and phenylplopanoid biosynthesis).

Enzyme			QTL nearby
Name	Locus ID	Position (×10^6 bp)	Name	Position (×10^6 bp)
Δ^14-sterol reductase	Os01g25189	14.22	qOZ1b	13.44
Cycloartenol synthase	Os05g14800	8.41	qOZ5a	4.25
Sterol 14-demethylase	Os05g34380	20.38	qOZ5b	18.32
Sterol 14-demethylase	Os07g37980	22.79	qOZ7	26.11
Sterol 14-demethylase	Os07g37970	22.79	qOZ7	26.11

Note: Position: Positions of QTLs were converted from these map positions in high-density rice genetic map to physical map positions on rice genome (searched at https://shigen.ng.ac.jp/rice/oryzabase/), by intrapolation between the nearest flanking markers.