Genome-Wide Association Study of Nitrogen Use Efficiency and Agronomic Traits in Upland Rice

doi:10.1016/j.rsci.2021.05.008

Abstract

Abstract:

Genome-wide association study (GWAS) was performed for 16 agronomic traits including nitrogen use efficiency (NUE) and yield-related components using a panel of 190 mainly japonica rice varieties and a set of 38 390 single nucleotide polymorphism (SNP) markers. This panel was evaluated under rainfed upland conditions in Madagascar in two consecutive cropping seasons with two contrasted nitrogen input levels. Using another set of five grain traits, we identified previously known genes (GW5, GS3, Awn1 and Glabrous1), thus validating the pertinence and accuracy of our datasets for GWAS. A total of 369 significant associations were detected between SNPs and agronomic traits, gathered into 46 distinct haplotype groups and 28 isolated markers. Few association signals were identified for the complex quantitative trait NUE, however, larger number of quantitative trait loci (QTLs) were detected for its component traits, with 10 and 2 association signals for nitrogen utilization efficiency and nitrogen uptake efficiency, respectively. Several detected association signals co-localized with genes involved in nitrogen transport or nitrogen remobilization within 100 kb. The present study thus confirmed the potential of GWAS to identify candidate genes and new loci associated with agronomic traits. However, because of the quantitative and complex nature of NUE-related traits, GWAS might have not captured a large number of QTLs with limited effects.

Key words: genome-wide association study, nitrogen use efficiency, agronomic trait, upland rice

Rakotoson Tatiana, Dusserre Julie, Letourmy Philippe, Frouin Julien, Ramonta Ratsimiala Isabelle, Victorine Rakotoarisoa Noronirina, Cao Tuong-Vi, Vom Brocke Kirsten, Ramanantsoanirina Alain, Ahmadi Nourollah, Raboin Louis-Marie. Genome-Wide Association Study of Nitrogen Use Efficiency and Agronomic Traits in Upland Rice[J]. Rice Science, 2021, 28(4): 379-390.

Figures/Tables 10

References 65

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Code	Trait	Formulas	Units
AL	Awn length	Length of awn using a scale of 1 (no awn) to 9 (very long awn)	-
DTF	Days to flowering	Days from sowing to flowering	days
FG	Filled grain	100 × number of filled spikelets /total number of spikelets	%
GNC	Grain N content	Grain N concentration of 6 hills at maturity	%
GL	Grain Length	Length of grain	mm
GP	Grain Pilosity	Pilosity of grain using a scale of 1 (glabrous) to 9 (very hairy)	-
GT	Grain Thickness	Thickness of grain	mm
GW	Grain Width	Width of grain	mm
GY	Grain yield	PANM2 × SPIPAN × FG × TGW × 10	kg/hm²
HI	Harvest index	GY / (GY + SY)	-
NHI	Nitrogen harvest index	GNC × GY / TNUP x 100	-
NUE	Nitrogen use efficiency	GY / N supply	kg/kg
NUPE	Nitrogen uptake efficiency	TNUP / N supply	kg/kg
NUTE	Nitrogen utilization efficiency	GY / TNUP	kg/kg
PANM2	Number of panicles per m²	Number of panicle of 6 hills / 0.24	-
PH	Plant height	Height of plant from soil surface to the tip of main panicle	cm
SNC	Straw N content	Straw N concentration of 6 hills at maturity	%
SPIPAN	Number of spikelets per panicle	Number of spikelets of 6 hills / number of panicle of 6 hills	-
SY	Straw yield	10 × Biomass of 6 hills / 0.24	kg/hm²
TGW	1000-grain weight	Weight of 200 filled spikelets × 5	g
TNUP	Total plant N uptake	(GY × GNC/100) + (SY × SNC/100)	kg/hm²

Code	Trait	Formulas	Units
AL	Awn length	Length of awn using a scale of 1 (no awn) to 9 (very long awn)	-
DTF	Days to flowering	Days from sowing to flowering	days
FG	Filled grain	100 × number of filled spikelets /total number of spikelets	%
GNC	Grain N content	Grain N concentration of 6 hills at maturity	%
GL	Grain Length	Length of grain	mm
GP	Grain Pilosity	Pilosity of grain using a scale of 1 (glabrous) to 9 (very hairy)	-
GT	Grain Thickness	Thickness of grain	mm
GW	Grain Width	Width of grain	mm
GY	Grain yield	PANM2 × SPIPAN × FG × TGW × 10	kg/hm²
HI	Harvest index	GY / (GY + SY)	-
NHI	Nitrogen harvest index	GNC × GY / TNUP x 100	-
NUE	Nitrogen use efficiency	GY / N supply	kg/kg
NUPE	Nitrogen uptake efficiency	TNUP / N supply	kg/kg
NUTE	Nitrogen utilization efficiency	GY / TNUP	kg/kg
PANM2	Number of panicles per m²	Number of panicle of 6 hills / 0.24	-
PH	Plant height	Height of plant from soil surface to the tip of main panicle	cm
SNC	Straw N content	Straw N concentration of 6 hills at maturity	%
SPIPAN	Number of spikelets per panicle	Number of spikelets of 6 hills / number of panicle of 6 hills	-
SY	Straw yield	10 × Biomass of 6 hills / 0.24	kg/hm²
TGW	1000-grain weight	Weight of 200 filled spikelets × 5	g
TNUP	Total plant N uptake	(GY × GNC/100) + (SY × SNC/100)	kg/hm²

Chr.	SNP position	Trait	Max	Min	LOD	R² (%)	Q_min	Candidate gene within 100 kb
1	594 602	GNC	179	11	4.22	9.0	0.68	OsNRT2.1
1	594 602	GNC	179	11	4.22	9.0	0.68	OsNIP4.1
1	2 961 416	FG, DTF, NHI, HI	172	18	4.97	10.3	0.03	OsCrRLK1L4
1	2 972 214	NHI, DTF, HI	171	19	5.09	10.6	0.03
1	2 972 304	DTF, NHI	178	12	4.77	8.8	0.13
1	3 028 472	DTF, SY, NHI, HI	177	13	5.25	10.4	0.03
1	3 031 975	NUTE, NHI, HI	178	12	5.51	11.0	0.03
1	3 034 970	NUTE, NHI, HI	181	9	6.00	11.8	0.02
1	4 825 760	NUTE, NHI, HI	181	9	7.26	14.9	0.00
1	4 958 939	NHI	173	17	4.07	7.5	0.17	OsDOS
1	7 309 207	SNC	104	86	4.09	8.7	0.55	OsTIP4;2
1	29 135 405	GNC, NUTE	179	11	4.76	10.4	0.13	OsNRT2.3a
1	29 212 814	GNC	177	13	4.01	8.5	0.13	CBSCLC2
1	33 331 630	SY	155	35	4.23	8.8	0.47	OsGH3.1
1	35 227 489	TNUP	141	49	4.03	8.2	0.73	OsAAT7
2	2 843 055	DTF	136	54	4.19	9.0	0.28	lc2; OsVIL2
2	24 480 078	TGW	155	35	4.17	7.3	0.19	OsMPS
2	24 510 877	TGW	121	69	4.09	8.1	0.19	OsMPS
3	1 352 456	DTF	157	33	8.15	19.9	0.00	DTH3
3	1 356 326	DTF	164	26	8.12	19.9	0.00	DTH3
3	1 395 165	DTF, FG, NUTE	160	30	7.01	16.7	0.00	OsCrRLK1L6
3	1 424 348	DTF	154	36	8.81	21.9	0.00	OsCrRLK1L6
3	3 425 919	PH	167	23	4.88	6.7	0.20	oscow1; nal7
3	3 602 444	PH	175	15	4.27	5.7	0.20
3	3 677 867	PH	174	16	4.23	5.6	0.23
3	3 728 449	PH	175	15	4.27	5.7	0.20	OsDof12
3	3 845 920	DTF	176	14	5.34	12.1	0.03	OsSUT1
3	16 174 183	TGW, GL	135	55	5.46	11.8	0.03	GS3
3	16 174 184	TGW, GL	135	55	5.46	11.8	0.03
3	16 414 381	TGW	147	43	4.23	8.4	0.20
3	16 790 082	TGW, GL	152	38	6.17	13.6	0.02
4	31 050 939	PANM2	155	35	5.85	10.1	0.02	osks1
4	31 070 568	PANM2	172	18	4.69	8.3	0.05	osks2
4	31 243 064	PANM2	144	46	4.54	9.6	0.09	15 masked associations with PANM2
4	31 250 082	PANM2	141	49	5.92	10.8	0.02	nal1, GPS, SPIKE, LSCHL4
4	31 450 557	PANM2, PH	159	31	5.70	11.6	0.03	Six masked associations with PANM2
5	3 506 138	GW	157	33	5.09	9.2	0.10	GS5
5	5 309 762	GW	158	32	4.05	6.8	0.18	GW5
5	5 361 979	GW	113	77	4.55	7.7	0.07
5	5 362 675	GW	112	78	6.01	10.7	0.01
5	5 362 698	GW	114	76	6.08	11.1	0.01
5	5 365 520	GW	114	76	4.02	7.0	0.18
5	5 391 748	GW	122	68	6.48	11.7	0.01	Five masked associations with PANM2
6	21 981 979	TNUP	157	33	4.15	8.7	0.38	d35
6	21 982 001	TNUP	157	33	4.15	8.7	0.38
6	22 028 211	TNUP	161	29	4.10	8.5	0.38
6	22 047 685	TNUP	161	29	4.10	8.5	0.38
6	22 089 331	TNUP, NUPE	162	28	4.48	9.5	0.38
9	1 504 274	GL	169	21	4.19	8.6	0.15
9	1 504 282	GL	169	21	4.19	8.6	0.15
9	1 824 735	NUTE	169	21	4.10	8.4	0.08	rFCA
11	19 200 467	GY, NUE, NUTE, NHI, HI	180	10	5.53	11.6	0.03	tld1-D
11	19 365 597	NUTE, NHI, HI	181	9	4.72	8.7	0.13	tld1-D
12	9 914 173	NHI	126	64	4.46	8.3	0.14	rbcS, OsRBCS2
12	10 531 085	NHI	126	64	4.84	9.2	0.13	rbcS, OsRBCS2

Chr.	SNP position	Trait	Max	Min	LOD	R² (%)	Q_min	Candidate gene within 100 kb
1	594 602	GNC	179	11	4.22	9.0	0.68	OsNRT2.1
1	594 602	GNC	179	11	4.22	9.0	0.68	OsNIP4.1
1	2 961 416	FG, DTF, NHI, HI	172	18	4.97	10.3	0.03	OsCrRLK1L4
1	2 972 214	NHI, DTF, HI	171	19	5.09	10.6	0.03
1	2 972 304	DTF, NHI	178	12	4.77	8.8	0.13
1	3 028 472	DTF, SY, NHI, HI	177	13	5.25	10.4	0.03
1	3 031 975	NUTE, NHI, HI	178	12	5.51	11.0	0.03
1	3 034 970	NUTE, NHI, HI	181	9	6.00	11.8	0.02
1	4 825 760	NUTE, NHI, HI	181	9	7.26	14.9	0.00
1	4 958 939	NHI	173	17	4.07	7.5	0.17	OsDOS
1	7 309 207	SNC	104	86	4.09	8.7	0.55	OsTIP4;2
1	29 135 405	GNC, NUTE	179	11	4.76	10.4	0.13	OsNRT2.3a
1	29 212 814	GNC	177	13	4.01	8.5	0.13	CBSCLC2
1	33 331 630	SY	155	35	4.23	8.8	0.47	OsGH3.1
1	35 227 489	TNUP	141	49	4.03	8.2	0.73	OsAAT7
2	2 843 055	DTF	136	54	4.19	9.0	0.28	lc2; OsVIL2
2	24 480 078	TGW	155	35	4.17	7.3	0.19	OsMPS
2	24 510 877	TGW	121	69	4.09	8.1	0.19	OsMPS
3	1 352 456	DTF	157	33	8.15	19.9	0.00	DTH3
3	1 356 326	DTF	164	26	8.12	19.9	0.00	DTH3
3	1 395 165	DTF, FG, NUTE	160	30	7.01	16.7	0.00	OsCrRLK1L6
3	1 424 348	DTF	154	36	8.81	21.9	0.00	OsCrRLK1L6
3	3 425 919	PH	167	23	4.88	6.7	0.20	oscow1; nal7
3	3 602 444	PH	175	15	4.27	5.7	0.20
3	3 677 867	PH	174	16	4.23	5.6	0.23
3	3 728 449	PH	175	15	4.27	5.7	0.20	OsDof12
3	3 845 920	DTF	176	14	5.34	12.1	0.03	OsSUT1
3	16 174 183	TGW, GL	135	55	5.46	11.8	0.03	GS3
3	16 174 184	TGW, GL	135	55	5.46	11.8	0.03
3	16 414 381	TGW	147	43	4.23	8.4	0.20
3	16 790 082	TGW, GL	152	38	6.17	13.6	0.02
4	31 050 939	PANM2	155	35	5.85	10.1	0.02	osks1
4	31 070 568	PANM2	172	18	4.69	8.3	0.05	osks2
4	31 243 064	PANM2	144	46	4.54	9.6	0.09	15 masked associations with PANM2
4	31 250 082	PANM2	141	49	5.92	10.8	0.02	nal1, GPS, SPIKE, LSCHL4
4	31 450 557	PANM2, PH	159	31	5.70	11.6	0.03	Six masked associations with PANM2
5	3 506 138	GW	157	33	5.09	9.2	0.10	GS5
5	5 309 762	GW	158	32	4.05	6.8	0.18	GW5
5	5 361 979	GW	113	77	4.55	7.7	0.07
5	5 362 675	GW	112	78	6.01	10.7	0.01
5	5 362 698	GW	114	76	6.08	11.1	0.01
5	5 365 520	GW	114	76	4.02	7.0	0.18
5	5 391 748	GW	122	68	6.48	11.7	0.01	Five masked associations with PANM2
6	21 981 979	TNUP	157	33	4.15	8.7	0.38	d35
6	21 982 001	TNUP	157	33	4.15	8.7	0.38
6	22 028 211	TNUP	161	29	4.10	8.5	0.38
6	22 047 685	TNUP	161	29	4.10	8.5	0.38
6	22 089 331	TNUP, NUPE	162	28	4.48	9.5	0.38
9	1 504 274	GL	169	21	4.19	8.6	0.15
9	1 504 282	GL	169	21	4.19	8.6	0.15
9	1 824 735	NUTE	169	21	4.10	8.4	0.08	rFCA
11	19 200 467	GY, NUE, NUTE, NHI, HI	180	10	5.53	11.6	0.03	tld1-D
11	19 365 597	NUTE, NHI, HI	181	9	4.72	8.7	0.13	tld1-D
12	9 914 173	NHI	126	64	4.46	8.3	0.14	rbcS, OsRBCS2
12	10 531 085	NHI	126	64	4.84	9.2	0.13	rbcS, OsRBCS2

Parameter	Haplotype	GY	PANM2	SPIPAN	FG	TGW	DTF	GL	GW	GT	PH	SY	HI	NUE	NUPE	NUTE	SNC	GNC	TNUP	NHI
SNP			57	3	18	26	12	28	27	10	24	9	49	4	5	28	2	26	10	31
GY													1	3		1				1
PANM2	3	1									3
SPIPAN	3		1
FG	7		2	1			2						1			1				1
TGW	7			1				3
DTF	4				4							1	4			1				5
GL	4					2
GW	6			1		1				1
GT	2								1
PH	8		1		2		1		1	1
SY	4				2		1		1				1							1
HI	12	2	1		2	1	2				3	1		1	1	6				21
NUE	2	2	1										2			1				1
NUPE	2	1	1										1	1					5
NUTE	10	2	1		4		3	1				1	4	2	1			13		6
SNC	1				1
GNC	5	1									1		1	1	1	3
TNUP	3	1	1									1	1	1	2	1		1
NHI	9	1			2		2				2	1	6	1		4		1