小麦籽粒超氧化物歧化酶（SOD）活性全基因组关联分析

doi:10.3864/j.issn.0578-1752.2021.11.001

摘要/Abstract

摘要：

【目的】小麦籽粒超氧化物歧化酶活性对小麦面粉色泽和营养品质具有重要影响,挖掘与小麦籽粒超氧化物歧化酶（superoxide dismutase,SOD）活性显著关联位点及候选基因,为揭示小麦籽粒SOD活性的遗传机理和小麦面粉色泽的遗传改良奠定基础。【方法】采用氮蓝四唑（nitro-blue tetrazolium,NBT）光化还原法对3个环境下种植的212份普通小麦品种（系）进行SOD活性检测,结合90K SNP芯片的16 705个高质量SNP标记对小麦籽粒SOD活性进行全基因组关联分析（genome-wide association study,GWAS）,并对稳定遗传的显著关联位点进行候选基因的挖掘。【结果】不同环境下,各小麦品种（系）间的SOD活性表现出丰富的表型变异,变异系数为4.34%—5.23%,相关系数介于0.60—0.90（P<0.001）。多态性信息含量（polymorphic information content,PIC）为0.24—0.29。全基因组连锁不平衡（linkage disequilibrium,LD）衰减距离为7 Mb。群体结构分析表明,供试材料可分为3个亚群。GWAS分析结果显示,共检测到29个与SOD活性显著关联位点（P≤0.001）,分布在1A、1B、2A、2B、2D、3B、3D、4B、4D、5A、5B、5D、6A、6B、6D和7B染色体上,单个位点可解释5.47%—32.43%的表型变异,其中14个位点在2个及以上环境下均被检测到。9个显著关联位点在3个环境下被同时检测到,分布于1B、2B、4B、5A、5B、6B和6D染色体,贡献率为6.21%—16.62%。对稳定遗传的显著关联位点进行候选基因的挖掘,共挖掘TraesCS2B01G567600、TraesCS3D01G069900、TraesCS3D01G070200、TraesCS5B01G525700、TraesCS5B01G373700、TraesCS6A01G021400和TraesCS6D01G431500等7个SOD基因和TraesCS5A01G263500、TraesCS6B01G707800等2个与SOD活性相关的候选基因,候选基因的功能主要与抑制细胞活性氧积累及参与抗氧化剂再生过程有关。【结论】检测到与小麦籽粒SOD活性显著关联的29个SNP位点,共筛选出7个SOD基因和2个与SOD活性有关的候选基因。

关键词: 小麦籽粒, SOD活性, 全基因组关联分析, SNP, 候选基因

Abstract:

【Objective】The activity of superoxide dismutase (SOD) in wheat grains has a significant effect on the color and nutritional quality of wheat flour. Identification of associated loci and candidate genes for SOD activity in wheat grains is important for discovering the genetic mechanism of SOD activity in wheat grains and genetic improvement of wheat flour color. 【Method】The SOD activity of 212 common wheat varieties (lines) planted in 3 environments was detected by photoreduction method of nitro-blue tetrazolium (NBT), and the genome-wide association study (GWAS) of SOD activity in wheat grains was carried out by 16 705 high-quality SNP markers of 90K SNP chip, and candidate genes of significantly associated loci of stable inheritance were identified. 【Result】The phenotypic variation of SOD activity among wheat varieties (lines) was significant in different environments, with the coefficient of variation ranging from 4.34% to 5.23%, the correlation coefficient ranging from 0.60 to 0.90 (P<0.001). Polymorphic information content (PIC) ranging from 0.24 to 0.29 and the whole genome linkage disequilibrium (LD) attenuation distance of 7 Mb. The analysis of population structure showed that the tested materials could be divided into 3 subgroups. GWAS analysis showed that 29 loci (P≤0.001) were significantly associated with SOD activity, which were distributed on chromosomes 1A, 1B, 2A, 2B, 2D, 3B, 3D, 4B, 4D, 5A, 5B, 5D, 6A, 6B, 6D and 7B. A single locus can explain the phenotypic variation(R²) between 5.47% and 32.43%, of which 14 loci were detected in 2 or more environments. Nine significant associated loci were detected in three environments, distributed on chromosomes 1B, 2B, 4B, 5A, 5B, 6B and 6D, with a contribution rate of 6.21%-16.62%. SOD genes of TraesCS2B01G567600, TraesCS3D01G069900, TraesCS3D01G070200, TraesCS5B01G525700, TraesCS6A01G021400 and TraesCS6D01G431500, and SOD-activity-related candidate genes of TraesCS5A01G263500 and TraesCS6B01G707800 were used to identify the candidate genes of significantly associated loci of stable inheritance. The functions of the candidate genes were mainly related to the inhibition of cell reactive oxygen species accumulation and the participation in antioxidant regeneration. 【Conclusion】Twenty-nine SNP loci associated with SOD activity in wheat grains were detected, and 7 SOD genes and 2 candidate genes related to SOD activity were screened out.

Key words: wheat grain, SOD activity, genome-wide association study, SNP, candidate genes

王继庆,任毅,时晓磊,王丽丽,张新忠,苏力坛·姑扎丽阿依,谢磊,耿洪伟. 小麦籽粒超氧化物歧化酶（SOD）活性全基因组关联分析[J]. 中国农业科学, 2021, 54(11): 2249-2260.

WANG JiQing,REN Yi,SHI XiaoLei,WANG LiLi,ZHANG XinZhong,SULITAN· GuZhaLiAYi,XIE Lei,GENG HongWei. Genome-Wide Association Analysis of Superoxide Dismutase (SOD) Activity in Wheat Grain[J]. Scientia Agricultura Sinica, 2021, 54(11): 2249-2260.

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链接本文: https://www.chinaagrisci.com/CN/10.3864/j.issn.0578-1752.2021.11.001

https://www.chinaagrisci.com/CN/Y2021/V54/I11/2249

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SNP-GWAS检测到的SOD活性显著相关的位点"

标记 Marker	染色体 Chromosome	物理位置 Position (bp)	环境 Environment	P值 P value	贡献率 R² (%)
Ex_c12584_2014	1A	435061794	A	5.77E-04	5.94
BS00109991_51	1A	536439240—536614333	A	7.90E-04—8.82E-04	7.02—7.07
Ra_c5683_2584	1A	551460924	A	9.44E-04	5.38
Kukri_c8533_1398	1B	49886407	E2	9.60E-04	8.43
Ra_c11303_359	1B	379383435	E2	9.78E-04	8.46
BS00022411_51	1B	629159210	E1/E3/A	2.88E-05—2.97E-04	8.93—11.10
Tdurum_contig92425_1574	2A	779977420	E2/A	6.80E-06—2.13E-04	8.52—16.45
BS00038217_51	2B	99961034	E1	6.35E-04	8.66
RFL_Contig1987_3440	2B	555840884	E1/E3/A	7.00E-05—3.92E-04	8.83—11.28
BS00026037_51	2B	793151228	E1/E3/A	1.24E-04—5.25E-04	14.23—16.62
BS00049876_51	2D	12891888	A	7.40E-04	7.36
Kukri_c40882_76	3B	19250811—19390877	E1	4.50E-04—6.44E-04	6.04—6.38
CAP8_c9373_277	3D	21005688	E1/A	3.13E-04—5.86E-04	5.81—6.81
Tdurum_contig12116_297	4B	60543887	E1/E3/A	4.52E-05—3.71E-04	8.40—10.97
Excalibur_c29496_799	4D	475027917	E1	3.96E-04	7.68
BS00022191_51	5A	476402782	E1/E3/A	6.11E-05—3.21E-04	8.57—10.77
BS00024602_51	5A	499660243	E3/A	2.64E-04—4.51E-04	26.29—32.43
Kukri_c14889_1086	5A	540052370—540611794	E1	3.04E-04—9.20E-04	6.22—9.17
tplb0061l23_1365	5B	506768500	A	6.90E-04	7.18
BobWhite_rep_c62475_70	5B	531199416	E1/E3/A	6.96E-05—5.30E-04	7.93—11.03
RAC875_c33791_320	5B	679804074	E1/E3/A	8.46E-06—7.05E-04	6.91—10.13
RAC875_c49940_385	5D	399290149	E1/A	3.21E-04—9.48E-04	5.37—6.69
RAC875_c13610_1239	6A	1497847—2402603	E2/A	8.61E-06—6.32E-04	6.29—17.00
BS00037162_51	6A	617689729	A	8.99E-04	7.93
BS00082893_51	6B	166226—169518	E2	2.24E-04—5.29E-04	13.18—13.22
Kukri_c49331_77	6B	664266146—667884621	E1/E3/A	4.25E-05—7.81E-04	6.21—11.61
Kukri_c338_109	6B	708660893	E3	7.10E-04	9.40%
Excalibur_c57840_227	6D	456465650	E1/E3/A	7.43E-05—4.78E-04	8.21—10.83
Kukri_c16814_103	7B	700830992	E1	9.32E-04	5.69

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环境 Environment	均值±标准差 Mean±SD	变幅 Range	变异系数 CV	相关系数Correlation coefficient			遗传力 h²
环境 Environment	均值±标准差 Mean±SD	变幅 Range	变异系数 CV	2016—2017	2017—2018	2018—2019	遗传力 h²
2016—2017	1784.14±73.31	1348.71—2025.14	4.34				0.79
2017—2018	1798.26±97.28	1316.83—2016.18	5.23	0.60***
2018—2019	1774.25±78.14	1348.26—2021.86	4.85	0.64***	0.62***
均值Mean	1781.28±73.40	1407.32—1988.93	4.72	0.86***	0.90***	0.87***

环境 Environment	来源 Origin
环境 Environment	北部冬麦区 Northern winter wheat region	西南冬麦区 Southwest winter wheat region	黄淮冬麦区 Huanghuai winter wheat region	长江中下游冬麦区 Middle/lower reaches of the Yangtze River winter wheat region	国外品种 Foreign varieties
2016—2017	1795.17	1782.41	1769.27	1733.88	1789.64
2017—2018	1804.36	1772.71	1790.38	1800.16	1800.91
2018—2019	1806.25	1799.82	1761.35	1747.94	1779.12
总计Total	1801.74	1787.21	1771.19	1759.67	1788.26

染色体 Chromosome	标记数目 No. of markers	长度 Length (Mb)	标记密度 Density of marker	遗传多样性 Genetic diversity	多态信息含量 PIC
1A	1262	592.38	0.47	0.32	0.26
1B	1293	688.60	0.53	0.34	0.27
1D	573	495.14	0.86	0.31	0.26
2A	1151	780.46	0.68	0.29	0.24
2B	1293	799.62	0.62	0.32	0.26
2D	481	650.94	1.35	0.31	0.25
3A	894	749.46	0.84	0.31	0.26
3B	1090	829.32	0.76	0.33	0.27
3D	234	613.92	2.62	0.29	0.24
4A	705	741.73	1.05	0.30	0.25
4B	571	672.56	1.18	0.32	0.26
4D	99	508.58	5.14	0.31	0.26
5A	960	709.43	0.74	0.36	0.29
5B	1157	712.82	0.62	0.35	0.28
5D	240	563.41	2.35	0.31	0.25
6A	1007	617.40	0.61	0.34	0.27
6B	1081	720.82	0.67	0.31	0.26
6D	319	472.61	1.48	0.31	0.25
7A	1174	736.44	0.63	0.30	0.25
7B	861	750.49	0.87	0.31	0.25
7D	260	637.17	2.45	0.29	0.24
A基因组 A genome	7153	4927.29	0.69	0.32	0.26
B基因组 B genome	7346	5174.23	0.70	0.33	0.27
D基因组 D genome	2206	3941.77	1.79	0.31	0.24
总计Total	16705	14043.30	0.84	0.32	0.26

位点 Marker	染色体 Chr.	物理位置 Position (bp)	基因 Gene	基因注释或编码蛋白 Gene annotation or coding protein
BS00026037_51	Chr.2B	758592689	TraesCS2B01G567600	超氧化物歧化酶Superoxide dismutase
CAP8_c9373_277	Chr.3D	30983003	TraesCS3D01G069900	铜、锌超氧化物歧化酶Superoxide dismutase [Cu-Zn]
CAP8_c9373_277	Chr.3D	31432328	TraesCS3D01G070200	铜、锌超氧化物歧化酶 Superoxide dismutase [Cu-Zn]
BS00022191_51	Chr.5A	476402782	TraesCS5A01G263500	锌指应激蛋白Zinc finger stress protein
BobWhite_rep_c62475_70	Chr.5B	531620481	TraesCS5B01G525700	铜、锌超氧化物歧化酶Superoxide dismutase [Cu-Zn]
BobWhite_rep_c62475_70	Chr.5B	551408544	TraesCS5B01G373700	铜、锌超氧化物歧化酶Superoxide dismutase [Cu-Zn]
RAC875_c13610_1239	Chr.6A	8971283	TraesCS6A01G021400	超氧化物歧化酶Superoxide dismutase
Kukri_c49331_77	Chr.6B	664393248	TraesCS6B01G707800	谷胱甘肽转移酶Glutathione transferase
Excalibur_c57840_227	Chr.6D	430047351	TraesCS6D01G431500	铜、锌超氧化物歧化酶Superoxide dismutase [Cu-Zn]