Genome-Wide Association Analysis of Superoxide Dismutase (SOD) Activity in Wheat Grain
WANG JiQing,1, REN Yi1, SHI XiaoLei1, WANG LiLi1, ZHANG XinZhong2, SULITAN· GuZhaLiAYi1, XIE Lei1, GENG HongWei,11College of Agriculture, Xinjiang Agricultural University/Key Laboratory of Agricultural Biological Technology, Urumqi 830052 2Institute of Grain Crops, Xinjiang Academy of Agricultural Sciences, Urumqi 830091
Received:2020-10-31Accepted:2020-12-28Online:2021-06-01 作者简介 About authors 王继庆,E-mail:WANGjiqing0655@163.com。
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. Keywords:wheat grain;SOD activity;genome-wide association study;SNP;candidate genes
PDF (2452KB)元数据多维度评价相关文章导出EndNote|Ris|Bibtex收藏本文 本文引用格式 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 doi:10.3864/j.issn.0578-1752.2021.11.001 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 Acricultura Sinica, 2021, 54(11): 2249-2260 doi:10.3864/j.issn.0578-1752.2021.11.001
ZHANGJ F. Analyses on factors affecting wheat flour whiteness [D]. Yangzhou: Yangzhou University, 2005. (in Chinese) [本文引用: 1]
SCHIAVONM, LEINAUERB, SERENAM, MAIERB, SALLENAVER. Plant growth regulator and soil surfactants’ effects on saline and deficit irrigated warm-season grasses: II. Pigment content and superoxide dismutase activity Crop Science, 2014,54:2827-2836. DOI:10.2135/cropsci2013.10.0708URL [本文引用: 2]
BOWLERC, CAMPW V, MONTAGUM V, INZéD, ASADAP K. Superoxide dismutase in plants Critical Reviews in Plant Sciences, 1994,13(3):199-209. DOI:10.1080/07352689409701914URL [本文引用: 3]
DONGY M, DEX S, YIZ, CHENY W, YUNJ Z, TIANC G. Diversity of antioxidant content and its relationship to grain color and morphological characteristics in winter wheat grains Journal of Integrative Agriculture, 2014,13:1258-1267. DOI:10.1016/S2095-3119(13)60573-0URL [本文引用: 2]
BEKESF, GRASP, GUPTAR. Mixing properties as a measure of reversible reduction and oxidation of doughs Cereal Chemistry, 1994,71:44-50. [本文引用: 1]
NAKAMURAM, KURATAT. Effect of L-ascorbic acid and superoxide anion radical on the rheological properties of wheat flour water dough Cereal Chemistry, 1997,74:651-655. DOI:10.1094/CCHEM.1997.74.5.651URL [本文引用: 2]
LIN B, WANGX X, YUL, QUY, LEIH. Dough rheology properties and its application in the food processing industry Food Science and Technology, 2008,33(8):35-38. (in Chinese) [本文引用: 2]
BRUNEELC, LAGRAINB, BRIJSK, DELCOURJ A. Redox agents and N-ethylmaleimide affect the extractability of gluten proteins during fresh pasta processing(Article) Food Chemistry, 2011,127:905-911. DOI:10.1016/j.foodchem.2011.01.048URL [本文引用: 1]
ALEJANDRAM M, ELIZABETHC, AGUSTíNR, FRANCISCOA H, EDITHV D. Ferulated arabinoxylans and their gels: Functional properties and potential application as antioxidant and anticancer agent Oxidative Medicine and Cellular Longevity, 2018,2018:1-22. [本文引用: 1]
CHENGH Y, SONGS Q. Species and organ diversity in the effects of hydrogen peroxide on superoxide dismutase activity in vitro Journal of Integrative Plant Biology, 2006,48:672-678. DOI:10.1111/jipb.2006.48.issue-6URL [本文引用: 1]
BHARTIK A, PANDEYN, SHANKHDHARD, SRIVASTAVAP C, SHANKHDHARS C. Effect of different zinc levels on activity of superoxide dismutases & acid phosphatases and organic acid exudation on wheat genotypes Physiology and Molecular Biology of Plants, 2014,20:41-48. DOI:10.1007/s12298-013-0201-7URL [本文引用: 1]
EYIDO?ANF, ?KTEMH A, YüCELM. Superoxide dismutase activity in salt stressed wheat seedlings Acta Physiologiae Plantarum, 2003,25:263-269. DOI:10.1007/s11738-003-0007-2URL [本文引用: 1]
ZHAOY, SHENGY L, SONGY F, ZHANGJ K, WENGQ Y, YUANJ C, ZHAOZ H, LIUY H. Genome-wide identification and bio-informatics analysis of superoxide dismutase gene family in Setaria italica Journal of Agricultural Science and Technology, 2018,20(8):1-6. (in Chinese) [本文引用: 1]
WUG, WILENR W, ROBERTSONA J, GUSTAL V. Isolation, chromosomal localization, and differential expression of mitochondrial manganese superoxide dismutase and chloroplastic copper/zinc superoxide dismutase genes in wheat Plant physiology, 1999,120:513-520. DOI:10.1104/pp.120.2.513URL [本文引用: 1]
BAEKK H, SKINNERD Z, LINGP, CHENX. Molecular structure and organization of the wheat genomic manganese superoxide dismutase gene Genome, 2006,49:209-218. DOI:10.1139/g05-102URL [本文引用: 1]
ZHAOY L. QTLs Mapping and cloning of micronutrient-related genes in hexaploid wheat [D]. Beijing: Chinese Academy of Agricultural Sciences, 2005. (in Chinese) [本文引用: 1]
JIANGW, YANGL, HEY, ZHANGH, LIW, CHENH, MAD, YINJ. Genome-wide identification and transcriptional expression analysis of superoxide dismutase (SOD) family in wheat (Triticum aestivum) PeerJ, 2019,7:e8062. DOI:10.7717/peerj.8062URL [本文引用: 3]
KUMARR R, DUBEYK, GOSWAMIS, HASIJAS, PANDEYR, SINGHP K, SINGHB, SAREENS, RAIG K, SINGHG P, SINGHA K, CHINNUSAMYV, PRAVEENS. Heterologous expression and characterization of novel manganese superoxide dismutase (Mn-SOD) -A potential biochemical marker for heat stress-tolerance in wheat (Triticum aestivum) International Journal of Biological Macromolecules, 2020,161:1029-1039. DOI:10.1016/j.ijbiomac.2020.06.026URL [本文引用: 2]
GENGH W, XIAX C, ZHANGL P, QUY Y, HEZ H. Development of functional markers for a lipoxygenase gene TaLox-B1 on chromosome 4BS in common wheat Crop Science, 2012,52:568-576. DOI:10.2135/cropsci2011.07.0365URL [本文引用: 1]
SHIJ, ZHAIS N, LIUJ D, WEIJ X, BAIL, GAOW W, WENW E, HEZ H, XIAX C, GENGH W. Genome-wide association study of grain peroxidase activity in common wheat Scientia Agricultura Sinica, 2017,50(21):164-179. (in Chinese) [本文引用: 2]
QUM, QINL N, LIUY J, FANH C, ZHUS, WANGJ F. The comparison of two methods of testing superoxide dismutase activity Journal of Food Safety & Quality, 2014,5(10):3318-3323. (in Chinese) [本文引用: 1]
MENGL, LIH, ZHANGL, WANGJ. QTL IciMapping: Integrated software for genetic linkage map construction and quantitative trait locus mapping in biparental populations The Crop Journal, 2015,3:269-283. DOI:10.1016/j.cj.2015.01.001URL [本文引用: 1]
YUJ, PRESSOIRG, BRIGGSW H, BII V, YAMASAKIM, DOEBLEYJ F, MCMULLENM D, GAUTB S, NIELSEND M, HOLLANDJ B, KRESOVICHS, BUCKLERE S. A unified mixed-model method for association mapping that accounts for multiple levels of relatedness Nature Genetics, 2006,38:203-208. DOI:10.1038/ng1702URL [本文引用: 1]
ZHOUS Y, BIH H, CHENGX Y, ZHANGX R, RUNY X, WANGH H, MAOP J, LIH X, XUH X. Genome-wide association study of low-phosphorus tolerance related traits in wheat Journal of Plant Genetic Resources, 2020,21(2):431-445. (in Chinese) [本文引用: 1]
ZHAOY, WANGJ, YANGX F, LIX Y, ZHANGS H, TIANJ C, YANGX J. QTL analysis on polyphenol oxidase activity in wheat kernel Journal of Shandong Agricultural University (Natural Science Edition), 2015,46(2):189-193. (in Chinese) [本文引用: 1]
WANGM D, WEIZ H, ZHANGJ L, LIUL W, CHENH G. Changes of xylanase activity and xylanase lnhibitor activity in wheat at different growth stages Journal of Triticeae Crops, 2010,30(3):544-547. (in Chinese)
XIEJ, CHENN C, ZHANGB. Quality improvement of whole wheat flour with fungal α-amylase and glucose oxidase Journal of Southern Agriculture, 2012,43(6):843-846. (in Chinese) [本文引用: 1]
WUT, DONGY Q, XIAOY, WANGX L, YUANL Z, YUANR H, SUNY Z, ZHOUJ G. Study on the combining ability and heritability analysis of the main phenotypic traits in Chinese cabbage Journal of Henan Agricultural Sciences, 2018,47(12):102-109. (in Chinese) [本文引用: 1]
PUG L, XIAOQ W, CAIL J, LUOY F, ZOUX M. Variation and probability grading of main quantitative traits of walnut (Juglans regia L.) germplasm resources Journal of Hunan Agricultural University (Natural Science), 2015,60(6):647-650. (in Chinese) [本文引用: 1]
ZENGZ K, WANGZ H, WANGL M, PANGY H, HANZ P, GUOC, WANGC P. Water-saving physiological characteristics and comprehensive evaluation of new wheat varieties (lines) in northern winter wheat region Agricultural Research in the Arid Areas, 2019,37(5):137-143. (in Chinese) [本文引用: 1]
MENGZ L, YANX Q, ZHUQ, NIX F, ZHUW. Characteristics of wheat cultivation and problems of different winter wheat areas Modern Agricultural Science and Technology, 2018,47(4):44-45. (in Chinese) [本文引用: 1]
QIAOY Y. Effect of genotype by environment on wheat processing quality in Southwest China [D]. Chengdu: Sichuan Agricultural University, 2016. (in Chinese) [本文引用: 1]
WANH P, CHENC Y, CHENG, CAOX H, XIAM. Research status of genome-wide association study in soybean Journal of Jianghan University (Natural Science Edition), 2019,47(3):197-203. (in Chinese) [本文引用: 1]
STICHB, MELCHINGERA E. Comparison of mixed-model approaches for association mapping in rapeseed, potato, sugar beet, maize, and Arabidopsis BMC Genomics, 2009,10:1-14. DOI:10.1186/1471-2164-10-1URL [本文引用: 1]
JUX Y, ZHAOY, CHENG S, ZHANGS H, YANGX J. QTL mapping for antioxidant enzyme activity and malondialdehyde content in wheat seedling stage Journal of Hebei Agricultural University, 2017,40(3):1-7. (in Chinese) [本文引用: 1]
WEIX Y, LIS S, JIANGF S, GUOY, LIR J. QTL mapping for premature senescence and related physiological traits in wheat Acta Botanica Boreali-Occidentalia Sinica, 2007,28(3):485-489. (in Chinese) [本文引用: 1]
ZHANGH P, CHANGC, XIAOS H. Proteome analysis of ABA signal transduction in wheat embryo dormancy Acta Agronomica Sinica, 2006,88(5):690-697. (in Chinese) [本文引用: 1]
ZHANGX, TAOL, QIAOC, DUB H, GUOC H. Roles of glutathione s-transferase in plant tolerance to abiotic stresses China Biotechnology, 2017,37(3):92-98. (in Chinese) [本文引用: 1]
DUJ, ZHUZ, LIW C. Over-expression of exotic superoxide dismutase gene Mn-SOD and increase in stress resistance in maize Journal of Plant Physiology and Molecular Biology, 2006,32(1):57-63. (in Chinese) [本文引用: 1]