玉米盐胁迫相关性状全基因组关联分析及候选基因预测
收稿日期: 2021-08-13
修回日期: 2021-10-02
网络出版日期: 2021-12-07
基金资助
南通市科技项目和南通大学人才引进项目资助(MS22020033);南通大学人才引进项目资助编号(135420609055)
Genome-wide association study and candidate gene prediction of salt tolerance related traits in maize
Received date: 2021-08-13
Revised date: 2021-10-02
Online published: 2021-12-07
Supported by
Supported by the Science and Technology Project of Nantong City, China(MS22020033);Talent Introduction Project of Nantong University No(135420609055)
盐胁迫是影响玉米产量的重要因素,为探究玉米盐胁迫响应的遗传基础,本研究以150份遗传背景丰富的玉米自交系为材料,结合34,342个多态性SNP标记,利用混合线性模型对玉米两个盐胁迫相关性状进行全基因组关联分析。关联分析结果表明：共鉴定8个独立位点与盐胁迫相关性状显著关联,其中3个位点与枯萎度显著关联,分布在4号和9号染色体上,5个SNP位点与株高变化率显著关联,分布在1、2、3和6号染色体上。结合盐胁迫下基因的表达量数据和功能注释,筛选到11个候选基因,利用qRT-PCR验证其中7个基因在盐胁迫下表达量显著上调。本研究结果为玉米耐盐机理的解析奠定了基础,为玉米耐盐种质的培育提供新的靶基因。
单婷玉, 施雯, 王翌婷, 曹孜怡, 汪保华, 方辉 . 玉米盐胁迫相关性状全基因组关联分析及候选基因预测[J]. 遗传, 2021 , 43(12) : 1159 -1169 . DOI: 10.16288/j.yczz.21-298
Salt stress is an important factor that affects maize yield. In order to explore the genetic basis of salt tolerance in maize, a genome-wide association study (GWAS) using the mixed liner model was conducted on 150 maize inbred lines with rich genetic background and 34,342 polymorphism SNP markers. A total of 8 independent loci were identified that significantly associated with salt-tolerance traits, among which 3 loci were significantly associated with withering degree on chromosomes 4 and 9; and the remaining 5 loci were significantly associated with plant height change rate on chromosomes 1, 2, 3 and 6. Eleven candidate genes were identified according to the gene expression data under salt stress; and functional annotations verified 7 of them to be significantly up-regulated under salt stress by qRT-PCR. These findings lay a foundation for understanding the mechanism(s) of maize salt tolerance and provide new target genes for the breeding of maize salt tolerance germplasm.
Key words： maize; salt tolerance; mixed liner model; genome-wide association study
| [1] | Deinlein U, Stephan AB, Horie T, Luo W, Xu GH, Schroeder JI. Plant salt-tolerance mechanisms. Trends Plant Sci, 2014,19(6):371-379. |
| [2] | Hu T, Zhang GX, Zheng FC, Cao Y. Research progress in plant salt stress response. Mol Plant Breed, 2018,16(9):3006-3015. |
| [2] | 胡涛, 张鸽香, 郑福超, 曹钰. 植物盐胁迫响应的研究进展. 分子植物育种, 2018,16(9):3006-3015. |
| [3] | Munns R, Tester M. Mechanisms of salinity tolerance. Annu Rev Plant Biol, 2008,59:651-681. |
| [4] | Liang WJ, Ma XL, Wan P, Liu LY. Plant salt-tolerance mechanism: a review. Biochem Bioph Res Co, 2018,495(1):286-291. |
| [5] | Luo X, Wang BC, Gao S, Zhang F, Terzaghi W, Dai MQ. Genome-wide association study dissects the genetic bases of salt tolerance in maize seedlings. J Integr Plant Biol, 2019,61(6):658-674. |
| [6] | Prasad SR, Bagali PG, Hittalmani S, Shashidhar HE. Molecular mapping of quantitative trait loci associated with seedling tolerance to salt stress in rice (Oryza sativa L.). Curr Sci India, 2000,78(2):162-164. |
| [7] | Hamwieh A, Tuyen DD, Cong H, Benitez ER, Takahashi R, Xu DH. Identification and validation of a major QTL for salt tolerance in soybean. Euphytica, 2011,179(3):451-459. |
| [8] | Ren ZH, Zheng ZM, Chinnusamy V, Zhu JH, Cui XP, Iida K, Zhu JK. RAS1, a quantitative trait locus for salt tolerance and ABA sensitivity in Arabidopsis. Proc Natl Acad Sci USA, 2010,107(12):5669-5674. |
| [9] | Luo MJ, Zhao YX, Zhang RY, Xing JF, Duan MX, Li JN, Wang NS, Wang WG, Zhang SS, Chen ZH, Zhang HS, Shi Z, Song W, Zhao JR. Mapping of a major QTL for salt tolerance of mature field-grown maize plants based on SNP markers. BMC Plant Biol, 2017,17(1):140. |
| [10] | Luo MJ, Zhang YX, Chen K, Kong MS, Song W, Lu BS, Shi YX, Zhao YX, Zhao JR. Mapping of quantitative trait loci for seedling salt tolerance in maize. Mol Breeding, 2019,39(5):1-12. |
| [11] | Ren ZH, Gao JP, Li LG, Cai XL. Huang W, Chao DY, Zhu MZ, Wang ZY, Luan S, Liu HX. A rice quantitative trait locus for salt tolerance encodes a sodium transporter. Nat Genet, 2005,37(10):1141-1146. |
| [12] | Cui D, Wu D, Somarathna Y, Xu CY, Li S, Li P, Zhang H, Chen HB, Li Z. QTL mapping for salt tolerance based on SNP markers at the seedling stage in maize (Zea mays L.). Euphytica, 2015,203(2):273-283. |
| [13] | Zhang M, Cao YB, Wang ZP, Wang ZQ, Shi JP, Liang XY, Song WB, Chen QJ, Lai JS, Jiang CF. A retrotransposon in an HKT1 family sodium transporter causes variation of leaf Na + exclusion and salt tolerance in maize . New Phytol, 2018,217(3):1161-1176. |
| [14] | Zhang M, Liang XY, Wang LM, Cao YB, Song WB, Shi JP, Lai JS, Jiang CF. A HAK family Na + transporter confers natural variation of salt tolerance in maize . Nat Plants, 2019,5(12):1297-1308. |
| [15] | Cao YB, Zhang M, Liang XY, Li FR, Shi YL, Yang XH, Jiang CF. Natural variation of an EF-hand Ca 2+-binding- protein coding gene confers saline-alkaline tolerance in maize . Nat Commun, 2020,11(1):186. |
| [16] | Xie YH, Feng Y, Chen Q, Zhao FK, Zhou SJ, Ding Y, Song XL, Li P, Wang BH. Genome-wide association analysis of salt tolerance QTLs with SNP markers in maize (Zea mays L.). Genes Genomics, 2019,41(10):1135-1145. |
| [17] | Ganal MW, Durstewitz G, Polley A, Bérard A, Buckler ES, Charcosset A, Clarke JD, Graner E, Hansen M, Joets J, LePaslier M, McMullen MD, Montalent P, Rose M, Sch?n C, Sun Q, Walter H, Martin OC, Falque M. A large maize (Zea mays L.) SNP genotyping array: development and germplasm genotyping, and genetic mapping to compare with the B73 reference genome. PLoS One, 2011,6(12):e28334. |
| [18] | Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MAR, Bender D, Maller J, Sklar P, de Bakker PIW, Daly MJ, Sham PC. PLINK: a tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet, 2007,81(3):559-575. |
| [19] | Alexander D, Lange K. Enhancements to the ADMIXTURE algorithm for individual ancestry estimation. BMC Bioinformatics, 2011,12(1):1-6. |
| [20] | Bradbury PJ, Zhang ZW, Kroon DE, Casstevens TM, Ramdoss Y, Buckler ES. TASSEL: software for association mapping of complex traits in diverse samples. Bioinformatics, 2007,23(19):2633-2635. |
| [21] | Kumar S, Tamura K, Nei M. MEGA: molecular evolutionary genetics analysis software for microcomputers. Bioinformatics, 1994,10(2):189-191. |
| [22] | Yu JM, Pressoir G, Briggs WH, Bi IV, Yamasaki M, Doebley JF, McMullen MD, Gaut BS, Nielsen DM, Holland JB, Kresovich S, Buckle ES. A unified mixed- model method for association mapping that accounts for multiple levels of relatedness. Nat Genet, 2006,38(2):203-208. |
| [23] | Yu SB, Li JX, Xu CG, Tan YF, Gao YJ, Li XH, Zhang Q, Maroof MAF. Importance of epistasis as the genetic basis of heterosis in an elite rice hybrid. Proc Natl Acad Sci USA, 1997,94(17):9226-9231. |
| [24] | Wen WW, Liu HJ, Zhou Y, Jin M, Yang N, Li D, Luo J, Xiao YJ, Pan QC, Tohge T, Fernie AR, Yan JB. Combining quantitative genetics approaches with regulatory network analysis to dissect the complex metabolism of the maize kernel. Plant Physiol, 2016,170(1):136-146. |
| [25] | Li H, Peng ZY, Yang XH, Wang WD, Fu JJ, Wang JH, Han YJ, Chai YC, Guo TT, Yang N, Liu J, Warburton ML, Cheng YB, Hao XM, Zhang P, Zhao JY, Liu YJ, Wang GY, Li JS, Yan JB. Genome-wide association study dissects the genetic architecture of oil biosynthesis in maize kernels. Nat Genet, 2013,45(1):43-50. |
| [26] | Hoopes GM, Hamilton JP, Wood JC, Esteban E, Pasha A, Vaillancourt B, Provart NJ, Buell CR. An updated gene atlas for maize reveals organ-specific and stress-induced genes. Plant J, 2019,97(6):1154-1167. |
| [27] | Yang XH, Gao SB, Xu ST, Zhang ZX, Prasanna BM, Li L, Li JS, Yan JB. Characterization of a global germplasm collection and its potential utilization for analysis of complex quantitative traits in maize. Mol Breeding, 2011,28(4):511-526. |
| [28] | Yang XH, Yan JB, Zheng YP, Yu JM, Li JS. Reviews of association analysis for quantitative traits in plants. Acta Agron Sin, 2007,33(4):523-530. |
| [28] | 杨小红, 严建兵, 郑艳萍, 余建明, 李建生. 植物数量性状关联分析研究进展. 作物学报, 2007,33(4):523-530. |
| [29] | Meng YY, Wang ZY, Wang YQ, Wang CN, Zhu BT, Liu H, Ji WK, Wen JQ, Chu CC, Tadege M, Niu LF, Lin H. The MYB activator WHITE PETAL1 associates with MtTT8 and MtWD40-1 to regulate carotenoid-derived flower pigmentation in medicago truncatula. Plant Cell, 2019,31(11):2751-2767. |
| [30] | Wang J, Zhou L, Shi H, Chern M, Yu H, Yi H, He M, Yin JJ, Zhu XB, Li Y, Li WT, Liu JL, Wang JC, Chen XQ, Qing H, Wang YP, Liu GF, Wang WM, Li P, Wu XJ, Zhu LH, Zhou JM, Ronald PC, Li SG, Li JY, Chen WX. A single transcription factor promotes both yield and immunity in rice. Science, 2018,361(6406):1026-1028. |
| [31] | Ambawat S, Sharma P, Yadav NR, Yadav RC. MYB transcription factor genes as regulators for plant responses: an overview. Physiol Mol Biol Plants, 2013,19(3):307-321. |
| [32] | Qin YX, Wang MC, Tian YC, He WX, Han L, Xia GM. Over-expression of TaMYB33 encoding a novel wheat MYB transcription factor increases salt and drought tolerance in Arabidopsis. Mol Biol Rep, 2012,39(6):7183-7192. |
| [33] | He YN, Li W, Lv J, Jia YB, Wang MC, Xia GM. Ectopic expression of a wheat MYB transcription factor gene, TaMYB73, improves salinity stress tolerance in Arabidopsis thaliana. J Exp Bot, 2012,63(3):1511-1522. |
| [34] | Chen YH, Cao YY, Wang LJ, Li LM, Yang J, Zou MX. Identification of MYB transcription factor genes and their expression during abiotic stresses in maize. Biol Plantarum, 2018,62(2):222-230. |
| [35] | Wu JD, Jiang YL, Liang YN, Chen L, Chen WJ, Cheng BJ. Expression of the maize MYB transcription factor ZmMYB3R enhances drought and salt stress tolerance in transgenic plants. Plant Physiol Bioch, 2019,137:179-188. |
| [36] | Dong W, Liu XJ, Li DL, Gao TX, Song YG. Transcriptional profiling reveals that a MYB transcription factor MsMYB4 contributes to the salinity stress response of alfalfa. PLoS One, 2018,13(9):e0204033. |
| [37] | Guo HY, Wang YC, Wang LQ, Hu P, Wang YM, Jia YY, Zhang CR, Zhang Y, Zhang YM, Wang C, Yang CP. Expression of the MYB transcription factor gene Bpl MYB46 affects abiotic stress tolerance and secondary cell wall deposition in betula platyphylla. Plant Biotechnol J, 2017,15(1):107-121. |
| [38] | Yang N, Lu YL, Yang XH, Huang J, Zhou Y, Ali F, Wen WW, Liu J, Li JS, Yan JB. Genome wide association studies using a new nonparametric model reveal the genetic architecture of 17 agronomic traits in an enlarged maize association panel. PLoS Genet, 2014,10(9):e1004573. |
| [39] | Li N, Lin B, Wang H, Li XM, Yang FF, Ding XH, Yan JB, Chu ZH. Natural variation in ZmFBL41 confers banded leaf and sheath blight resistance in maize. Nat Genet, 2019,51(10):1540-1548. |
| [40] | Wang XL, Wang HW, Liu SX, Ferjani A, Li JS, Yan JB, Yang XH, Qin F. Genetic variation in ZmVPP1 contributes to drought tolerance in maize seedlings. Nat Genet, 2016,48(10):1233-1241. |
| [41] | Mao HD, Wang HW, Liu SX, Li ZG, Yang XH, Yan JB, Li JS, Tran LP, Qin F. A transposable element in a NAC gene is associated with drought tolerance in maize seedlings. Nat Commun, 2015,6:8326. |
| [42] | Luo MJ, Zhang YX, Li JN, Zhang PP, Chen K, Song W, Wang XQ, Yang JX, Lu XD, Lu YX, Zhao JR. Molecular dissection of maize seedling salt tolerance using a genome-wide association analysis method. Plant Biotechnol J, 2021,19(10):1937-1951. |
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