Genome-wide Association Analysis of Total Protein Content in Rice Seeds

doi:10.7668/hbnxb.20195550

Abstract

Abstract:

In order to cultivate good quality rice,it utilized 139 rice germplasm resources from home and abroad as materials to analyze the total protein content of rice grains in 2022-2023,combined with 255 501 SNP markers obtained from whole-genome sequencing(depth of coverage of 10×),and performed genome-wide linkage analysis by using a general linear model to avoid the influence of false positives to select the genes with the highest thresholds for haplotype analysis.The genes related to the total protein content of rice grains were predicted based on the results of previous studies and gene function annotation,and the relative expression of the predicted genes was analyzed by Real-time Fluorescence PCR.The results showed that the total protein content of 139 rice seeds belonged to moderate variation,with coefficients of variation of 21.66% and 20.65%,respectively,which conformed to the normal distribution.Through genome-wide association analysis,a total of 55 significant SNPs were obtained in both environments,distributed on chromosomes 1,2,4,5,6,8,11,and 12,of which 16 consecutive and with upstream and downstream intervals of no more than 100 kb SNPs were distributed on chromosome 11.Further haplotype analysis of genes with strong correlation between the upstream and downstream intervals within 50 kb(±50 kb)of the loci of significant SNPs on chromosome 11 was conducted,combined with the results of functional annotation of the genes and the analysis of the relative expression of the seed grain at the irrigating stage,we preliminarily hypothesized that LOC_Os11g08460 was associated with the total protein content of the seed grain of rice,which encodes the Dnak/Hsp70s protein family.In conclusion,candidate gene prediction and haplotype analysis of total protein content of 139 rice germplasm resources using genome-wide association analysis can provide new genes for genetic improvement of rice quality and accelerate the process of rice improvement.

Key words: Rice, Grain, Total protein content, Genome-wide association study, Candidate gene

CLC Number:

MAO Xinyuan, DU Huaidong, DONG Yue, YU Xueran, WANG Jingwen, LI Peifu. Genome-wide Association Analysis of Total Protein Content in Rice Seeds[J]. Acta Agriculturae Boreali-Sinica, 2025, 40(4): 49-56. doi: 10.7668/hbnxb.20195550.

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Figures/Tables 7

References 41

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年份 Year	最小值/ (mg/g) Min	最大值/ (mg/g) Max	平均值/ (mg/g) Mean	标准差 s	变异系数/% CV	偏度 Skewness	峰度 Kurt	变动幅度/ (mg/g) Range
2022	6.43	16.67	9.05	1.90	21.66	1.72	3.41	6.43~16.67
2023	5.30	16.57	7.38	1.41	20.65	2.97	15.06	5.30~16.57

年份 Year	最小值/ (mg/g) Min	最大值/ (mg/g) Max	平均值/ (mg/g) Mean	标准差 s	变异系数/% CV	偏度 Skewness	峰度 Kurt	变动幅度/ (mg/g) Range
2022	6.43	16.67	9.05	1.90	21.66	1.72	3.41	6.43~16.67
2023	5.30	16.57	7.38	1.41	20.65	2.97	15.06	5.30~16.57

染色体 Chromosomes	物理位置/ bp Position	参考碱基 Reference	变异碱基 Alternative	-log₁₀(P)		染色体 Chromosomes		物理位置/ bp Position		参考碱基 Reference		变异碱基 Alternative		-log₁₀(P)
染色体 Chromosomes	物理位置/ bp Position	参考碱基 Reference	变异碱基 Alternative	2022	2023	染色体 Chromosomes		物理位置/ bp Position		参考碱基 Reference		变异碱基 Alternative		2022		2023
1	15 943 095	C	T	5.408 95	8.662 69	6	20 860 782		T		C		5.881 02		6.644 74
2	15 531 086	A	C	5.408 95	8.66 269	8	12 953 794		C		T		7.178 92		5.409 98
2	15 531 107	T	C	5.408 95	8.662 69	8	18 034 363		C		T		6.246 40		8.158 39
2	15 531 186	A	G	5.488 26	8.149 23	8	20 089 392		C		A		5.484 96		7.659 35
2	15 531 403	T	C	5.488 26	8.149 23	11	4 445 181		T		G		5.484 96		7.659 35
2	15 531 406	T	C	5.488 26	8.149 23	11	4 466 969		G		T		6.335 17		9.714 24
2	15 531 437	T	G	5.488 26	8.149 23	11	4 466 970		G		T		6.335 17		9.714 24
4	8 057 160	G	T	5.498 58	7.946 54	11	4 466 972		A		C		6.335 17		9.714 24
5	4 188 417	A	T	6.422 26	8.582 57	11	4 466 975		C		G		6.335 17		9.714 24
5	4 188 421	C	T	6.422 26	8.582 57	11	4 466 977		C		T		6.335 17		9.714 24
5	4 188 442	C	T	6.422 26	8.582 57	11	4 466 981		T		C		6.335 17		9.714 24
5	4 188 473	C	T	5.488 26	8.149 23	11	4 467 072		T		C		5.408 95		8.662 69
5	4 188 486	G	A	5.488 26	8.149 23	11	4 467 081		T		C		5.408 95		8.662 69
5	13 183 123	C	T	5.488 26	8.149 23	11	4 467 091		T		C		5.408 95		8.662 69
5	13 183 909	A	T	5.484 96	7.659 35	11	4 467 106		G		A		5.408 95		8.662 69
5	22 205 616	C	T	5.488 26	8.149 23	11	4 467 526		C		G		5.600 99		7.493 62
5	22 205 656	C	T	5.488 26	8.149 23	11	4 467 535		T		C		6.235 40		10.235 35
6	20 860 681	C	A	7.457 26	8.282 49	11	4 467 537		C		T		6.235 40		10.235 35
6	20 860 684	G	C	7.457 26	8.282 49	11	4 467 538		A		G		6.235 40		10.235 35
6	20 860 691	C	T	6.500 28	6.975 52	11	4 485 603		C		T		5.408 95		8.662 69
6	20 860 692	A	G	6.500 28	6.975 52	11	4 625 931		G		A		5.484 96		7.659 35
6	20 860 699	A	G	7.158 24	6.043 19	12	2 024 745		G		C		6.290 67		10.215 25
6	20 860 700	A	G	7.158 24	6.04319	12	2 024 784		T		C		5.449 28		8.599 73
6	20 860 716	G	A	7.158 24	6.043 19	12	9 527 600		T		A		6.246 40		8.158 39
6	20 860 717	G	A	7.158 24	6.043 19	12	9 527 625		T		A		5.483 22		6.673 74
6	20 860 728	A	G	6.529 96	5.693 34	12	9 527 724		C		T		5.488 26		8.149 23
6	20 860 729	A	G	5.828 72	6.430 58	12	10 415 645		C		T		6.460 70		12.968 47
6	20 860 746	C	A	7.158 24	6.043 19

染色体 Chromosomes	物理位置/ bp Position	参考碱基 Reference	变异碱基 Alternative	-log₁₀(P)		染色体 Chromosomes		物理位置/ bp Position		参考碱基 Reference		变异碱基 Alternative		-log₁₀(P)
染色体 Chromosomes	物理位置/ bp Position	参考碱基 Reference	变异碱基 Alternative	2022	2023	染色体 Chromosomes		物理位置/ bp Position		参考碱基 Reference		变异碱基 Alternative		2022		2023
1	15 943 095	C	T	5.408 95	8.662 69	6	20 860 782		T		C		5.881 02		6.644 74
2	15 531 086	A	C	5.408 95	8.66 269	8	12 953 794		C		T		7.178 92		5.409 98
2	15 531 107	T	C	5.408 95	8.662 69	8	18 034 363		C		T		6.246 40		8.158 39
2	15 531 186	A	G	5.488 26	8.149 23	8	20 089 392		C		A		5.484 96		7.659 35
2	15 531 403	T	C	5.488 26	8.149 23	11	4 445 181		T		G		5.484 96		7.659 35
2	15 531 406	T	C	5.488 26	8.149 23	11	4 466 969		G		T		6.335 17		9.714 24
2	15 531 437	T	G	5.488 26	8.149 23	11	4 466 970		G		T		6.335 17		9.714 24
4	8 057 160	G	T	5.498 58	7.946 54	11	4 466 972		A		C		6.335 17		9.714 24
5	4 188 417	A	T	6.422 26	8.582 57	11	4 466 975		C		G		6.335 17		9.714 24
5	4 188 421	C	T	6.422 26	8.582 57	11	4 466 977		C		T		6.335 17		9.714 24
5	4 188 442	C	T	6.422 26	8.582 57	11	4 466 981		T		C		6.335 17		9.714 24
5	4 188 473	C	T	5.488 26	8.149 23	11	4 467 072		T		C		5.408 95		8.662 69
5	4 188 486	G	A	5.488 26	8.149 23	11	4 467 081		T		C		5.408 95		8.662 69
5	13 183 123	C	T	5.488 26	8.149 23	11	4 467 091		T		C		5.408 95		8.662 69
5	13 183 909	A	T	5.484 96	7.659 35	11	4 467 106		G		A		5.408 95		8.662 69
5	22 205 616	C	T	5.488 26	8.149 23	11	4 467 526		C		G		5.600 99		7.493 62
5	22 205 656	C	T	5.488 26	8.149 23	11	4 467 535		T		C		6.235 40		10.235 35
6	20 860 681	C	A	7.457 26	8.282 49	11	4 467 537		C		T		6.235 40		10.235 35
6	20 860 684	G	C	7.457 26	8.282 49	11	4 467 538		A		G		6.235 40		10.235 35
6	20 860 691	C	T	6.500 28	6.975 52	11	4 485 603		C		T		5.408 95		8.662 69
6	20 860 692	A	G	6.500 28	6.975 52	11	4 625 931		G		A		5.484 96		7.659 35
6	20 860 699	A	G	7.158 24	6.043 19	12	2 024 745		G		C		6.290 67		10.215 25
6	20 860 700	A	G	7.158 24	6.04319	12	2 024 784		T		C		5.449 28		8.599 73
6	20 860 716	G	A	7.158 24	6.043 19	12	9 527 600		T		A		6.246 40		8.158 39
6	20 860 717	G	A	7.158 24	6.043 19	12	9 527 625		T		A		5.483 22		6.673 74
6	20 860 728	A	G	6.529 96	5.693 34	12	9 527 724		C		T		5.488 26		8.149 23
6	20 860 729	A	G	5.828 72	6.430 58	12	10 415 645		C		T		6.460 70		12.968 47
6	20 860 746	C	A	7.158 24	6.043 19

候选基因 Candidate gene	功能注释 Description
LOC_Os11g08350	表达蛋白
LOC_Os11g08360	表达蛋白
LOC_Os11g08440	DnaK/Hsp70s蛋白家族
LOC_Os11g08445	DnaK/Hsp70s蛋白家族
LOC_Os11g08460	DnaK/Hsp70s蛋白家族
LOC_Os11g08470	DnaK/Hsp70s蛋白家族
LOC_Os11g08490	表达蛋白
LOC_Os11g08536	表达蛋白

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