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

doi:10.1016/j.rsci.2024.02.008

摘要/Abstract

. [J]. Rice Science, 2024, 31(3): 300-316.

图/表 9

参考文献 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

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Metrics

Trait	Chr.	Position (bp)	P-value	PVE (%)	Candidate locus	Known gene
Wx^T panel
AAC	1	9 468 765	3.35E-07	13.5	LOC_Os01g16670‒ LOC_Os01g16690	OsYUC9
	3	21 069 124	1.78E-08	22.4	LOC_Os03g37940‒ LOC_Os03g37950
	6	1 970 080	3.33E-07	14.7	LOC_Os06g04550
	8	4 582 547	3.50E-09	22.1	LOC_Os08g08070	OsMST5
	10	11 299 091	2.07E-07	14.0	LOC_Os10g21920‒ LOC_Os10g21930
	12	13 955 846	1.45E-07	16.0	LOC_Os12g24450
PV	4	23 898 757	1.45E-07	15.6	LOC_Os04g40150‒ LOC_Os04g40170
	6	1 768 998	1.05E-12	26.4	LOC_Os06g04200	Wx
	6	1 621 298	3.17E-11	22.3	LOC_Os06g03980‒ LOC_Os06g03990	SSG6
HPV	6	1 768 998	9.16E-20	38.8	LOC_Os06g04200	Wx
	6	1 621 298	5.22E-14	27.1	LOC_Os06g03980‒ LOC_Os06g03990	SSG6
CPV	6	1 768 998	1.41E-20	40.6	LOC_Os06g04200	Wx
	6	1 621 298	4.96E-13	25.7	LOC_Os06g03980‒ LOC_Os06g03990	SSG6
BD	6	6 854 257	6.98E-09	16.2	LOC_Os06g12600‒ LOC_Os06g12610	SSIIa
	6	6 752 888	4.02E-07	13.8	LOC_Os06g12450	SSIIa
	8	4 584 642	3.07E-06	13.5	LOC_Os08g08070‒ LOC_Os08g08080	OsMST5
CS	6	1 768 998	5.36E-12	25.2	LOC_Os06g04200	Wx
	6	1 621 298	1.56E-07	15.7	LOC_Os06g03980‒ LOC_Os06g03990	SSG6
SB	6	1 970 080	1.67E-09	21.4	LOC_Os06g04550
	8	4 582 547	3.45E-09	18.4	LOC_Os08g08070	OsMST5
PT	6	6 752 888	5.45E-14	31.1	LOC_Os06g12450	SSIIa
HD	8	4 282 227	3.06E-07	21.1	LOC_Os08g07620‒ LOC_Os08g07630
ADH	8	25 957 150	4.39E-08	17.0	LOC_Os08g41054
Wx^A panel
AAC	1	4 901 428	1.10E-07	36.8	LOC_Os01g09560‒ LOC_Os01g09570
CS	9	22 391 230	2.72E-07	30.2	LOC_Os09g38990‒ LOC_Os09g39000
PT	6	6 752 888	7.36E-10	39.3	LOC_Os06g12450	SSIIa
HD	8	9 304 513	1.49E-08	17.5	LOC_Os08g15300
ADH	2	31 628 729	1.06E-08	24.1	LOC_Os02g51640‒ LOC_Os02g51650
	7	28 507 542	2.95E-08	25.7	LOC_Os07g47720‒ LOC_Os07g47730
SPR	2	556 675	1.60E-07	27.7	LOC_Os02g02000‒ LOC_Os02g02010
	6	11 318 610	2.63E-07	29.1	LOC_Os06g19800‒ LOC_Os06g19810
	11	4 936 393	1.63E-07	34.3	LOC_Os11g09200
CHEW	8	8 577 354	1.27E-07	21.3	LOC_Os08g14310‒ LOC_Os08g14320
	8	4 581 009	1.27E-06	16.0	LOC_Os08g08070	OsMST5
GUM	8	4 585 261	6.88E-07	13.6	LOC_Os08g08070‒ LOC_Os08g08080	OsMST5