Genome-Wide Association Study of Cooked Rice Textural Attributes and Starch Physicochemical Properties in indica Rice

doi:10.1016/j.rsci.2024.02.008

Abstract

Abstract:

Rice cooking and eating qualities (CEQ) are mainly determined by cooked rice textural parameters and starch physicochemical properties. However, the genetic bases of grain texture and starch properties in rice have not been fully understood. We conducted a genome-wide association study for apparent amylose content (AAC), starch pasting viscosities, and cooked rice textural parameters using 279 indica rice accessions from the 3 000 Rice Genome Project. We identified 26 QTLs in the whole population and detected single nucleotide polymorphisms (SNPs) with the lowest P-value at the Waxy (Wx) locus for all traits except pasting temperature and cohesiveness. Additionally, we detected significant SNPs at the SUBSTANDARD STARCH GRAIN6 (SSG6) locus for AAC, setback (SB), hardness, adhesiveness, chewiness (CHEW), gumminess (GUM), and resilience. We subsequently divided the population using a SNP adjacent to the Waxy locus, and identified 23 QTLs and 12 QTLs in two sub-panels, Wx^T and Wx^A, respectively. In these sub-panels, SSG6 was also identified to be associated with pasting parameters, including peak viscosity, hot paste viscosity, cold paste viscosity, and consistency viscosity. Furthermore, a candidate gene encoding monosaccharide transporter 5 (OsMST5) was identified to be associated with AAC, breakdown, SB, CHEW, and GUM. In total, 39 QTLs were co-localized with known genes or previously reported QTLs. These identified genes and QTLs provide valuable information for genetic manipulation to improve rice CEQ.

Key words: cooking and eating quality, genome-wide association study, rice, Waxy gene

Deng Bowen, Zhang Yanni, Zhang Fan, Wang Wensheng, Xu Jianlong, Zhang Yu, Bao Jinsong. Genome-Wide Association Study of Cooked Rice Textural Attributes and Starch Physicochemical Properties in indica Rice[J]. Rice Science, 2024, 31(3): 300-316.

Figures/Tables 9

References 68

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Parameter	Whole panel				Wx^T panel				Wx^A panel
Parameter	Mean ± SD	Range	Skewness	Kurtosis	Mean ± SD	Range	Skewness	Kurtosis	Mean ± SD	Range	Skewness	Kurtosis
AAC (%)	22.41 ± 6.52	2.90‒30.04	-0.89	-0.30	25.74 ± 4.21	3.68‒30.04	-2.57	7.59	15.07 ± 4.77	2.90‒28.71	0.17	1.15
PV (RVU)	285.03 ± 54.58	106.88‒403.46	-0.81	0.91	274.58 ± 55.06	106.88‒401.75	-1.02	0.92	308.53 ± 47.9	201.42‒403.46	-0.33	-0.61
HPV (RVU)	180.91 ± 44.78	82.25‒299.59	0.18	-0.80	194.75 ± 46.18	82.25‒299.59	-0.35	-0.62	153.26 ± 23.61	93.38‒239.71	0.38	1.39
CPV (RVU)	321.62 ± 78.37	136.25‒491.59	0.02	-0.99	351.65 ± 73.21	154.92‒491.59	-0.60	-0.33	256.58 ± 43.26	136.25‒441.21	0.58	4.39
BD (RVU)	104.12 ± 49.91	22.63‒247.58	0.48	-0.71	79.83 ± 36.21	22.63‒201.79	0.98	0.95	155.27 ± 37.2	63.59‒247.58	-0.23	-0.30
CS (RVU)	140.70 ± 41.84	23.84‒244.51	-0.16	-0.39	156.90 ± 35.33	29.30‒244.51	-0.48	0.47	103.32 ± 30.42	23.84‒201.51	0.33	2.15
SB (RVU)	36.78 ± 80.88	-179.04‒202.17	-0.51	-0.84	77.07 ± 54.21	-112.54‒202.17	-1.32	2.50	-51.95 ± 56.72	-179.04‒137.92	0.89	1.39
PT (ºC)	76.89 ± 4.17	68.10‒85.00	-0.19	-1.21	76.62 ± 4.38	68.10‒84.70	-0.28	-1.38	77.24 ± 3.82	70.80‒85.00	0.31	-1.20
HD (gf)	217.07 ± 51.74	107.84‒311.66	-0.32	-1.02	241.79 ± 38.91	107.84‒311.66	-1.04	1.55	163.60 ± 32.42	114.77‒263.67	0.88	0.55
ADH (gf·s)	18.62 ± 20.93	0.00‒115.89	1.55	2.37	9.34 ± 13.00	0.00‒64.15	2.64	6.99	38.68 ± 21.71	0.09‒115.89	1.00	1.47
SPR	0.56 ± 0.06	0.37‒0.77	0.02	0.47	0.58 ± 0.05	0.37‒0.68	-0.48	1.18	0.53 ± 0.05	0.44‒0.77	1.59	5.79
CHEW (gf)	60.82 ± 20.98	15.25‒123.41	0.21	-0.45	69.51 ± 17.68	15.25‒123.41	0.00	0.73	41.79 ± 13.03	21.79‒89.49	1.33	2.32
GUM (gf)	105.35 ± 29.19	41.27‒179.89	0.01	-0.70	118.16 ± 23.66	41.27‒179.89	-0.35	0.89	77.50 ± 18.21	48.30‒142.88	1.17	1.81
COH	0.48 ± 0.05	0.35‒0.65	0.28	0.17	0.49 ± 0.06	0.35‒0.65	0.15	0.20	0.47 ± 0.04	0.39‒0.58	0.42	-0.16
RES	0.11 ± 0.03	0.04‒0.19	0.20	-0.36	0.12 ± 0.02	0.07‒0.19	0.06	0.34	0.09 ± 0.02	0.04‒0.16	1.19	3.31

Parameter	Whole panel				Wx^T panel				Wx^A panel
Parameter	Mean ± SD	Range	Skewness	Kurtosis	Mean ± SD	Range	Skewness	Kurtosis	Mean ± SD	Range	Skewness	Kurtosis
AAC (%)	22.41 ± 6.52	2.90‒30.04	-0.89	-0.30	25.74 ± 4.21	3.68‒30.04	-2.57	7.59	15.07 ± 4.77	2.90‒28.71	0.17	1.15
PV (RVU)	285.03 ± 54.58	106.88‒403.46	-0.81	0.91	274.58 ± 55.06	106.88‒401.75	-1.02	0.92	308.53 ± 47.9	201.42‒403.46	-0.33	-0.61
HPV (RVU)	180.91 ± 44.78	82.25‒299.59	0.18	-0.80	194.75 ± 46.18	82.25‒299.59	-0.35	-0.62	153.26 ± 23.61	93.38‒239.71	0.38	1.39
CPV (RVU)	321.62 ± 78.37	136.25‒491.59	0.02	-0.99	351.65 ± 73.21	154.92‒491.59	-0.60	-0.33	256.58 ± 43.26	136.25‒441.21	0.58	4.39
BD (RVU)	104.12 ± 49.91	22.63‒247.58	0.48	-0.71	79.83 ± 36.21	22.63‒201.79	0.98	0.95	155.27 ± 37.2	63.59‒247.58	-0.23	-0.30
CS (RVU)	140.70 ± 41.84	23.84‒244.51	-0.16	-0.39	156.90 ± 35.33	29.30‒244.51	-0.48	0.47	103.32 ± 30.42	23.84‒201.51	0.33	2.15
SB (RVU)	36.78 ± 80.88	-179.04‒202.17	-0.51	-0.84	77.07 ± 54.21	-112.54‒202.17	-1.32	2.50	-51.95 ± 56.72	-179.04‒137.92	0.89	1.39
PT (ºC)	76.89 ± 4.17	68.10‒85.00	-0.19	-1.21	76.62 ± 4.38	68.10‒84.70	-0.28	-1.38	77.24 ± 3.82	70.80‒85.00	0.31	-1.20
HD (gf)	217.07 ± 51.74	107.84‒311.66	-0.32	-1.02	241.79 ± 38.91	107.84‒311.66	-1.04	1.55	163.60 ± 32.42	114.77‒263.67	0.88	0.55
ADH (gf·s)	18.62 ± 20.93	0.00‒115.89	1.55	2.37	9.34 ± 13.00	0.00‒64.15	2.64	6.99	38.68 ± 21.71	0.09‒115.89	1.00	1.47
SPR	0.56 ± 0.06	0.37‒0.77	0.02	0.47	0.58 ± 0.05	0.37‒0.68	-0.48	1.18	0.53 ± 0.05	0.44‒0.77	1.59	5.79
CHEW (gf)	60.82 ± 20.98	15.25‒123.41	0.21	-0.45	69.51 ± 17.68	15.25‒123.41	0.00	0.73	41.79 ± 13.03	21.79‒89.49	1.33	2.32
GUM (gf)	105.35 ± 29.19	41.27‒179.89	0.01	-0.70	118.16 ± 23.66	41.27‒179.89	-0.35	0.89	77.50 ± 18.21	48.30‒142.88	1.17	1.81
COH	0.48 ± 0.05	0.35‒0.65	0.28	0.17	0.49 ± 0.06	0.35‒0.65	0.15	0.20	0.47 ± 0.04	0.39‒0.58	0.42	-0.16
RES	0.11 ± 0.03	0.04‒0.19	0.20	-0.36	0.12 ± 0.02	0.07‒0.19	0.06	0.34	0.09 ± 0.02	0.04‒0.16	1.19	3.31

Parameter	AAC	PV	HPV	CPV	BD	CS	SB	PT	HD	ADH	SPR	CHEW	GUM	COH
PV	-0.296**
HPV	0.469**	0.509**
CPV	0.668**	0.306**	0.911**
BD	-0.745**	0.633**	-0.344**	-0.486**
CS	0.748**	0.026	0.634**	0.896**	-0.540**
SB	0.848**	-0.374**	0.544**	0.767**	-0.897**	0.855**
PT	-0.063	0.207**	-0.031	0.003	0.253**	0.037	-0.139*
HD	0.861**	-0.339**	0.461**	0.615**	-0.768**	0.661**	0.804**	0.005
ADH	-0.747**	0.319**	-0.403**	-0.588**	0.696**	-0.674**	-0.768**	0.038	-0.629**
SPR	0.536**	-0.048	0.372**	0.482**	-0.383**	0.506**	0.491**	0.046	0.571**	-0.342**
CHEW	0.768**	-0.206**	0.465**	0.612**	-0.632**	0.651**	0.715**	-0.013	0.862**	-0.574**	0.816**
GUM	0.807**	-0.266**	0.453**	0.607**	-0.685**	0.655**	0.749**	-0.020	0.911**	-0.611**	0.700**	0.979**
COH	0.209**	0.033	0.147*	0.211**	-0.096	0.237**	0.176**	-0.027	0.178**	-0.197**	0.563**	0.606**	0.558**
RES	0.707**	-0.169**	0.446**	0.611**	-0.577**	0.670**	0.690**	-0.093	0.641**	-0.680**	0.668**	0.863**	0.857**	0.766**

Parameter	AAC	PV	HPV	CPV	BD	CS	SB	PT	HD	ADH	SPR	CHEW	GUM	COH
PV	-0.296**
HPV	0.469**	0.509**
CPV	0.668**	0.306**	0.911**
BD	-0.745**	0.633**	-0.344**	-0.486**
CS	0.748**	0.026	0.634**	0.896**	-0.540**
SB	0.848**	-0.374**	0.544**	0.767**	-0.897**	0.855**
PT	-0.063	0.207**	-0.031	0.003	0.253**	0.037	-0.139*
HD	0.861**	-0.339**	0.461**	0.615**	-0.768**	0.661**	0.804**	0.005
ADH	-0.747**	0.319**	-0.403**	-0.588**	0.696**	-0.674**	-0.768**	0.038	-0.629**
SPR	0.536**	-0.048	0.372**	0.482**	-0.383**	0.506**	0.491**	0.046	0.571**	-0.342**
CHEW	0.768**	-0.206**	0.465**	0.612**	-0.632**	0.651**	0.715**	-0.013	0.862**	-0.574**	0.816**
GUM	0.807**	-0.266**	0.453**	0.607**	-0.685**	0.655**	0.749**	-0.020	0.911**	-0.611**	0.700**	0.979**
COH	0.209**	0.033	0.147*	0.211**	-0.096	0.237**	0.176**	-0.027	0.178**	-0.197**	0.563**	0.606**	0.558**
RES	0.707**	-0.169**	0.446**	0.611**	-0.577**	0.670**	0.690**	-0.093	0.641**	-0.680**	0.668**	0.863**	0.857**	0.766**

Trait	Chr.	Position (bp)	PVE (%)	P-value	Candidate locus	Known gene
AAC	5	28 105 720	11.3	7.71E-07	LOC_Os05g48990‒LOC_Os05g49000
	6	1 657 731	32.8	6.07E-24	LOC_Os06g04040‒LOC_Os06g04060	SSG6
	6	1 777 598	34.7	2.56E-29	LOC_Os06g04200	Wx
PV	6	1 769 242	17.7	3.22E-13	LOC_Os06g04200	Wx
HPV	6	1 768 998	43.9	8.56E-33	LOC_Os06g04200	Wx
CPV	3	6 712 794	7.8	9.98E-07	LOC_Os03g12620‒LOC_Os03g12630
	6	1 768 998	47.6	2.17E-37	LOC_Os06g04200	Wx
BD	6	1 769 141	24.8	6.91E-19	LOC_Os06g04200	Wx
CS	6	1 768 998	34.8	1.92E-25	LOC_Os06g04200	Wx
SB	6	1 769 141	31.9	1.83E-24	LOC_Os06g04200	Wx
	6	1 633 040	25.4	3.19E-18	LOC_Os06g03990	SSG6
PT	6	6 752 888	28.9	3.14E-19	LOC_Os06g12450	SSIIa
HD	6	1 770 024	27.6	3.20E-18	LOC_Os06g04200	Wx
	6	1 633 260	19.6	1.03E-13	LOC_Os06g03990	SSG6
ADH	3	16 160 642	12.1	1.58E-08	LOC_Os03g28110
	5	27 224 506	15.0	7.79E-08	LOC_Os05g47520‒LOC_Os05g47530
	6	1 765 761	27.7	6.44E-18	LOC_Os06g04200	Wx
	6	1 631 244	23.1	1.50E-15	LOC_Os06g03990	SSG6
	7	28 487 354	11.9	1.11E-07	LOC_Os07g47680‒LOC_Os07g47690
SPR	6	1 765 976	15.3	6.33E-10	LOC_Os06g04200	Wx
CHEW	6	1 769 141	25.1	4.54E-17	LOC_Os06g04200	Wx
	6	1 633 260	18.8	8.28E-13	LOC_Os06g03990	SSG6
GUM	6	1 770 024	26.7	2.70E-17	LOC_Os06g04200	Wx
	6	1 633 260	19.7	2.27E-13	LOC_Os06g03990	SSG6
RES	6	1 769 141	27.7	2.14E-18	LOC_Os06g04200	Wx
	6	1 628 937	22.8	7.98E-16	LOC_Os06g03990	SSG6