Genome-Wide Association Studies Reveal New Genetic Targets for Five Panicle Traits of International Rice Varieties

doi:10.1016/S1672-6308(14)60302-4

Abstract

Abstract:

Narrow genetic background is a key limiting factor in breeding stable high-yielding rice. The introduction and utilization of international rice core germplasm is an important way to increase the genetic diversity of domestic rice varieties. We conducted a genome-wide association study on 5 panicle traits of 315 rice accessions introduced from the international rice micro-core germplasm bank. Based on the tests from Yangzhou of China and Arkansas of American, environment exhibited a significant impacts on panicle length and primary branch number, while grain length, grain width and grain length/width ratio were insensitive to environment changes. We discovered a total of 7, 5, 10, 8 and 6 chromosomal regions or single nucleotide polymorphism marker loci that were significantly associated with primary branch number, panicle length, grain length, grain width and grain length/width ratio, respectively. Among them, eleven regions were associated with grain shape and one region associated with primary branch number, showing the good consistence in two different environments. Significant linear correlation was discovered between the average trait value and the number of favorable alleles carried by the varieties in all associated loci. Among the associated loci, varieties in aromatic and tropical japonica sub-groups possessed most favorable alleles, while those in temperate japonica sub-group contained the least. The domestic varieties mainly harbored unfavorable alleles in six of the associated loci being detected. On the contrary, 15 varieties from 11 different countries harbored more favorable alleles (as many as 30 or more) than the others. Remarkably, all these 15 varieties belonged to the tropical japonica sub-group. In conclusion, our study demonstrates that varieties in the tropical japonica sub-group had high potentials for breeding stable high-yielding rice. Based on this discovery, we proposed a new approach for improving the panicle traits of domestic rice by using tropical japonica varieties.

Key words: international rice core germplasm, panicle trait, genome-wide association study, favorable allele, breeding utilization

Ya-fang Zhang, Yu-yin Ma, Zong-xiang Chen, Jie Zou, Tian-xiao Chen, Qian-qian Li, Xue-biao Pan, Shi-min Zuo. Genome-Wide Association Studies Reveal New Genetic Targets for Five Panicle Traits of International Rice Varieties[J]. Rice Science, 2015, 22(5): 217-226.

Figures/Tables 7

References 31

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Trait	Location	ADM (49)	ARO (8)	AUS (52)	IND (53)	TEJ (78)	TRJ (75)
Panicle length (cm)	Arkansas, America	24.6 ± 3.6 A	30.3 ± 2.0 A	24.9 ± 2.8 A	25.8 ± 2.6 A	21.3 ± 2.7 A	25.0 ± 3.1 A
Panicle length (cm)	Yangzhou, China	27.9 ± 4.7 B	32.8 ± 4.1 A	28.2 ± 3.5 B	27.1 ± 3.7 A	24.5 ± 4.7 B	30.1 ± 4.5 B
Primary branch number	Arkansas, America	9.9 ± 1.7 A	8.4 ± 1.2 A	8.6 ± 1.3 A	9.9 ± 1.3 A	9.7 ± 1.5 A	11.2 ± 1.8 A
Primary branch number	Yangzhou, China	12.1 ± 2.2 B	13.1 ± 0.8 B	12.1 ± 1.9 B	12.8 ± 1.7 B	11.4 ± 2.4 B	14.3 ± 2.4 B
Grain length (cm)	Arkansas, America	8.6 ± 0.9 A	9.4 ± 0.6 A	8.0 ± 0.8 A	8.2 ± 0.7 A	7.9 ± 0.8 A	9.0 ± 0.8 A
Grain length (cm)	Yangzhou, China	8.7 ± 0.9 A	9.4 ± 0.7 A	8.2 ± 0.7 A	8.3 ± 0.7 A	7.9 ± 0.8 A	9.0 ± 0.7 A
Grain width (mm)	Arkansas, America	3.2 ± 0.3 A	2.6 ± 0.3 A	2.9 ± 0.3 A	2.9 ± 0.2 A	3.5 ± 0.2 A	3.0 ± 0.4 A
Grain width (mm)	Yangzhou, China	3.2 ± 0.4 A	2.7 ± 0.3 A	2.9 ± 0.4 A	3.0 ± 0.3 A	3.5 ± 0.3 A	3.0 ± 0.4 A
Grain length/width ratio	Arkansas, America	2.7 ± 0.5 A	3.6 ± 0.5 A	2.8 ± 0.5 A	2.8 ± 0.4 A	2.2 ± 0.3 A	3.0 ± 0.5 A
Grain length/width ratio	Yangzhou, China	2.7 ± 0.5 A	3.5 ± 0.5 A	2.9 ± 0.6 A	2.8 ± 0.5 A	2.3 ± 0.3 A	3.1 ± 0.5 A

Trait	Location	ADM (49)	ARO (8)	AUS (52)	IND (53)	TEJ (78)	TRJ (75)
Panicle length (cm)	Arkansas, America	24.6 ± 3.6 A	30.3 ± 2.0 A	24.9 ± 2.8 A	25.8 ± 2.6 A	21.3 ± 2.7 A	25.0 ± 3.1 A
Panicle length (cm)	Yangzhou, China	27.9 ± 4.7 B	32.8 ± 4.1 A	28.2 ± 3.5 B	27.1 ± 3.7 A	24.5 ± 4.7 B	30.1 ± 4.5 B
Primary branch number	Arkansas, America	9.9 ± 1.7 A	8.4 ± 1.2 A	8.6 ± 1.3 A	9.9 ± 1.3 A	9.7 ± 1.5 A	11.2 ± 1.8 A
Primary branch number	Yangzhou, China	12.1 ± 2.2 B	13.1 ± 0.8 B	12.1 ± 1.9 B	12.8 ± 1.7 B	11.4 ± 2.4 B	14.3 ± 2.4 B
Grain length (cm)	Arkansas, America	8.6 ± 0.9 A	9.4 ± 0.6 A	8.0 ± 0.8 A	8.2 ± 0.7 A	7.9 ± 0.8 A	9.0 ± 0.8 A
Grain length (cm)	Yangzhou, China	8.7 ± 0.9 A	9.4 ± 0.7 A	8.2 ± 0.7 A	8.3 ± 0.7 A	7.9 ± 0.8 A	9.0 ± 0.7 A
Grain width (mm)	Arkansas, America	3.2 ± 0.3 A	2.6 ± 0.3 A	2.9 ± 0.3 A	2.9 ± 0.2 A	3.5 ± 0.2 A	3.0 ± 0.4 A
Grain width (mm)	Yangzhou, China	3.2 ± 0.4 A	2.7 ± 0.3 A	2.9 ± 0.4 A	3.0 ± 0.3 A	3.5 ± 0.3 A	3.0 ± 0.4 A
Grain length/width ratio	Arkansas, America	2.7 ± 0.5 A	3.6 ± 0.5 A	2.8 ± 0.5 A	2.8 ± 0.4 A	2.2 ± 0.3 A	3.0 ± 0.5 A
Grain length/width ratio	Yangzhou, China	2.7 ± 0.5 A	3.5 ± 0.5 A	2.9 ± 0.6 A	2.8 ± 0.5 A	2.3 ± 0.3 A	3.1 ± 0.5 A

Trait	SNP ID	Chromosome	Position (bp)	Major allele	Minor allele	Minor allele frequency	P value	Marker R²	Phenotypic difference
Trait	SNP ID	Chromosome	Position (bp)	Major allele	Minor allele	Minor allele frequency	P value	Marker R²	between alleles
PL	id3002504	3	4 364 855	A	G	0.31	3.24E-06	7.38	4.23
	id3006008	3	11 627 714	T	C	0.22	2.70E-06	8.88	4.94
	id6003381	6	4 846 082	A	T	0.37	1.90E-07	8.04	4.3
	id8003039	8	9 380 990	C	T	0.26	3.02E-06	6.5	4.46
	ud10001221	10	21 175 430	G	C	0.14	9.57E-08	8.35	5.57
	id12006578	12	19 520 927	T	C	0.5	6.53E-07	7.32	1.74
	id12009010	12	24 997 487	A	C	0.31	6.84E-06	6.04	4.35
PBN	id1002477	1	3 096 543	A	T	0.26	9.76E-07	7.14	-2.27
	id1003789	1	4 545 468	C	T	0.28	2.01E-06	6.66	-2.15
	id4010535	4	31 070 028	A	G	0.37	1.57E-05	5.76	-1.9
	id6014585	6	26 364 670	A	T	0.29	3.26E-06	6.44	1.99
	id11011548	11	28 322 308	T	G	0.07	4.94E-06	6.23	3.02
GL	ud3000463	3	8113 668	A	T	0.45	3.46E-12	8.74	0.32
	id3008053	3	16 074 273	C	T	0.36	9.41E-15	11.79	0.64
	id3009175	3	18 788 035	G	A	0.27	1.27E-13	11.25	0.9
	id5002706	5	5 339 063	C	T	0.24	1.69E-13	10.29	0.93
	wd6000477	6	9 123 484	C	T	0.18	4.78E-11	7.59	1.01
	ud7001337	7	18 964 116	G	C	0.28	5.56E-12	9.05	0.87
	id8005966	8	21 416 851	G	T	0.27	7.11E-12	8.88	0.83
	id10001788	10	5 878 902	A	G	0.26	3.18E-13	11.34	0.95
	wd10002564	10	11 284 071	C	T	0.16	1.98E-12	9.07	1.09
	id12006498	12	19 402 914	C	A	0.43	6.25E-12	9.33	-0.84
GW	id1024648	1	38 923 066	A	T	0.41	1.55E-05	6.35	0.47
	id2015723	2	34 819 747	T	C	0.28	2.88E-06	6.47	0.33
	id3008699	3	17 806 411	G	C	0.49	8.27E-06	6.01	-0.48
	id5002708	5	5 340 574	A	T	0.11	1.93E-08	9.35	0.48
	id6011831	6	22 951 051	C	T	0.13	5.71E-08	11.95	0.55
	id7003644	7	22 056 571	A	G	0.44	6.02E-07	7.34	0.46
	dd11000032	11	21 706 131	A	G	0.19	3.68E-07	7.63	-0.18
	id12007136	12	21 630 274	G	A	0.06	3.63E-06	6.43	0.56
GLWR	wd3000595	3	16 759 297	T	C	0.23	1.30E-05	6.01	0.1
	id4012361	4	34 949 006	G	A	0.15	1.10E-05	5.71	-0.03
	id5002751	5	5 396 733	G	C	0.47	3.42E-07	7.65	0.65
	id6011831	6	22 951 051	C	T	0.13	6.04E-06	8.47	-0.83
	id7003917	7	22 787 412	A	G	0.12	1.24E-06	6.95	-0.77
	id11001567	11	3 956 750	A	G	0.45	7.99E-06	6.09	-0.39

Trait	SNP ID	Chromosome	Position (bp)	Major allele	Minor allele	Minor allele frequency	P value	Marker R²	Phenotypic difference
Trait	SNP ID	Chromosome	Position (bp)	Major allele	Minor allele	Minor allele frequency	P value	Marker R²	between alleles
PL	id3002504	3	4 364 855	A	G	0.31	3.24E-06	7.38	4.23
	id3006008	3	11 627 714	T	C	0.22	2.70E-06	8.88	4.94
	id6003381	6	4 846 082	A	T	0.37	1.90E-07	8.04	4.3
	id8003039	8	9 380 990	C	T	0.26	3.02E-06	6.5	4.46
	ud10001221	10	21 175 430	G	C	0.14	9.57E-08	8.35	5.57
	id12006578	12	19 520 927	T	C	0.5	6.53E-07	7.32	1.74
	id12009010	12	24 997 487	A	C	0.31	6.84E-06	6.04	4.35
PBN	id1002477	1	3 096 543	A	T	0.26	9.76E-07	7.14	-2.27
	id1003789	1	4 545 468	C	T	0.28	2.01E-06	6.66	-2.15
	id4010535	4	31 070 028	A	G	0.37	1.57E-05	5.76	-1.9
	id6014585	6	26 364 670	A	T	0.29	3.26E-06	6.44	1.99
	id11011548	11	28 322 308	T	G	0.07	4.94E-06	6.23	3.02
GL	ud3000463	3	8113 668	A	T	0.45	3.46E-12	8.74	0.32
	id3008053	3	16 074 273	C	T	0.36	9.41E-15	11.79	0.64
	id3009175	3	18 788 035	G	A	0.27	1.27E-13	11.25	0.9
	id5002706	5	5 339 063	C	T	0.24	1.69E-13	10.29	0.93
	wd6000477	6	9 123 484	C	T	0.18	4.78E-11	7.59	1.01
	ud7001337	7	18 964 116	G	C	0.28	5.56E-12	9.05	0.87
	id8005966	8	21 416 851	G	T	0.27	7.11E-12	8.88	0.83
	id10001788	10	5 878 902	A	G	0.26	3.18E-13	11.34	0.95
	wd10002564	10	11 284 071	C	T	0.16	1.98E-12	9.07	1.09
	id12006498	12	19 402 914	C	A	0.43	6.25E-12	9.33	-0.84
GW	id1024648	1	38 923 066	A	T	0.41	1.55E-05	6.35	0.47
	id2015723	2	34 819 747	T	C	0.28	2.88E-06	6.47	0.33
	id3008699	3	17 806 411	G	C	0.49	8.27E-06	6.01	-0.48
	id5002708	5	5 340 574	A	T	0.11	1.93E-08	9.35	0.48
	id6011831	6	22 951 051	C	T	0.13	5.71E-08	11.95	0.55
	id7003644	7	22 056 571	A	G	0.44	6.02E-07	7.34	0.46
	dd11000032	11	21 706 131	A	G	0.19	3.68E-07	7.63	-0.18
	id12007136	12	21 630 274	G	A	0.06	3.63E-06	6.43	0.56
GLWR	wd3000595	3	16 759 297	T	C	0.23	1.30E-05	6.01	0.1
	id4012361	4	34 949 006	G	A	0.15	1.10E-05	5.71	-0.03
	id5002751	5	5 396 733	G	C	0.47	3.42E-07	7.65	0.65
	id6011831	6	22 951 051	C	T	0.13	6.04E-06	8.47	-0.83
	id7003917	7	22 787 412	A	G	0.12	1.24E-06	6.95	-0.77
	id11001567	11	3 956 750	A	G	0.45	7.99E-06	6.09	-0.39