中国农业科学 ›› 2021, Vol. 54 ›› Issue (11): 2249-2260.doi: 10.3864/j.issn.0578-1752.2021.11.001
王继庆1(),任毅1,时晓磊1,王丽丽1,张新忠2,苏力坛·姑扎丽阿依1,谢磊1,耿洪伟1(
)
收稿日期:
2020-10-31
接受日期:
2020-12-28
出版日期:
2021-06-01
发布日期:
2021-06-09
通讯作者:
耿洪伟
作者简介:
王继庆,E-mail:基金资助:
WANG JiQing1(),REN Yi1,SHI XiaoLei1,WANG LiLi1,ZHANG XinZhong2,SULITAN· GuZhaLiAYi1,XIE Lei1,GENG HongWei1(
)
Received:
2020-10-31
Accepted:
2020-12-28
Online:
2021-06-01
Published:
2021-06-09
Contact:
HongWei GENG
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。
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.
表1
不同环境中212份冬小麦籽粒SOD活性统计分析"
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 | ||
---|---|---|---|---|---|---|---|
2016—2017 | 2017—2018 | 2018—2019 | |||||
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*** |
表2
不同麦区冬小麦籽粒SOD活性"
环境 Environment | 来源 Origin | ||||
---|---|---|---|---|---|
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 |
表3
标记的分布、物理图谱长度及标记的多态性"
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 |
表4
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 |
表5
筛选获得候选基因信息"
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] |
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] |
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] |
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