作物学报 ›› 2022, Vol. 48 ›› Issue (11): 2733-2748.doi: 10.3724/SP.J.1006.2022.14168
杨亚杰(), 李昱樱, 申状状, 陈天, 荣二花, 吴玉香*()
YANG Ya-Jie(), LI Yu-Ying, SHEN Zhuang-Zhuang, CHEN Tian, RONG Er-Hua, WU Yu-Xiang*()
摘要:
通过转录组测序筛选草棉同源多倍体与二倍体相比差异表达基因, 为同源多倍体的表型变化及其染色体加倍过程中遗传物质的变化提供基因表达水平的依据。本研究以草棉二倍体(CK)和同源多倍体后代为材料, 通过流式细胞仪鉴定出同源三倍体(T)和同源四倍体(M)植株, 比较同源四倍体与二倍体的超氧化物歧化酶(SOD)、过氧化物酶(POD)、过氧化氢酶(CAT)、脯氨酸和可溶性蛋白含量生理指标, 并进行转录组测序分析。草棉同源四倍体叶片的SOD、POD、CAT、脯氨酸和可溶性蛋白含量均显著高于二倍体。DESeq差异分析结果表明, CK vs T、T vs M、CK vs M分别有4166 (2832个上调, 1334个下调)、4037 (1766个上调, 2271个下调)、4184 (2679个上调, 1505个下调)个DEGs, 有205个DEGs是不同倍性植株两两比较的3组间共同表达的。GO功能分析表明, DEGs在膜的固有成分、膜的组成部分、催化活性等途径差异显著。KEGG富集分析表明, DEGs在类黄酮生物合成、苯丙烷生物合成、光合作用-天线蛋白等通路较为活跃。通过富集分析筛选CK vs T和CK vs M中与倍性相关的DEGs发现, 多倍体在应激反应(62.46%和54.84%)、逆境反应(57.42%和53.85%)、细胞(70.16%和66.22%)、代谢(72.73%和66.14%)、生物活性物质和抗性(60.33%和63.37%)、光合(58.06%和63.16%)等方面的差异基因大都是上调表达, 这可能是导致多倍体优势的关键因子。Nr注释信息CK vs M中共获得27个与抗性相关的基因(19个上调, 8个下调), 11个与光合相关的基因(9个上调, 2个下调)。对不同倍性草棉与光合相关的27个DEGs进行聚类分析发现, 18个(66.67%)基因在四倍体中表达丰度最高。对3组间共同表达的205个DEGs进行Nr注释和表达情况分析发现, 有30个基因都表现为上调表达, 且在四倍体中表达量最高, 7个基因都表现为下调表达, 且在四倍体中表达量最低, 这37个基因可能是受DNA剂量影响或是与植株倍性相关的基因。研究结果进一步表明多倍体植株在抗性、生长势、新陈代谢以及光合速率方面均优于二倍体。
[1] |
Hutchinson J B, Silow R A, Stephens S G. The evolution of Gossypium and the differentiation of the cultivated cottons. Quart Rev Biol, 1949, 24: 143-144.
doi: 10.1086/396965 |
[2] |
Satya N J, Anukool S, Krishan M R, Alok R, Sunil K S, Tarannum N, Meenal S, Sumit K. B, Shrikant M, Mehar H A, Hemant K Y, Rakesh T, Samir V S. Development and characterization of genomic and expressed SSRs for levant cotton (Gossypium herbaceum L.). Theor Appl Genet, 2012, 124: 565-576.
doi: 10.1007/s00122-011-1729-y |
[3] |
Sattler M C, Carvalho C R, Clarindo W R. The polyploidy and its key role in plant breeding. Planta, 2016, 243: 281-296.
doi: 10.1007/s00425-015-2450-x |
[4] |
Bhattarai K, Areem A K, Deng Z. In vivo induction and characterization of polyploids in gerbera daisy. Sci Hortic, 2021, 282: 110054.
doi: 10.1016/j.scienta.2021.110054 |
[5] | 尚小红, 单忠英, 严华兵, 肖亮, 曹升, 周慧文. 木薯‘新选048’二倍体及其同源四倍体对干旱胁迫的生理响应. 植物生理学报, 2018, 54: 1064-1072. |
Shang X H, Shan Z Y, Yan H B, Xiao L, Cao S, Zhou H W. Physiological responses of cassava variety ‘Xinxuan 048’ diploid and autotetraploid to drought stress. Plant Physiol J, 2018, 54: 1064-1072. (in Chinese with English abstract) | |
[6] | 李昱樱, 申状状, 荣二花, 郑赟, 吴玉香. 草棉同源四倍体的诱导与鉴定. 山西农业大学学报(自然科学版), 2019, 39(6): 40-44. |
Li Y Y, Shen Z Z, Rong E H, Zheng Y, Wu Y X. Autotetraploid induction and identification of G. herbaceum. J Shanxi Agric Univ (Nat Sci Edn), 2019, 39(6): 40-44. (in Chinese with English abstract) | |
[7] | 姚娜, 刘秀明, 董园园, 王南, 孟璐璐, 李海燕. 转录组的测序方法及应用研究概述. 北方园艺, 2017, (12): 192-198. |
Yao N, Liu X M, Dong Y Y, Wang N, Meng L L, Li H Y. Advances in application and sequencing methods of transcriptome. Northern Hortic, 2017, (12): 192-198. (in Chinese with English abstract) | |
[8] |
Li H Y, Chen S M, Song A P, Wang H B, Fang W M, Guan Z Y, Jiang J F, Chen F D. RNA-Seq derived identification of differential transcription in the chrysanthemum leaf following inoculation with Alternaria tenuissima. BMC Genomics, 2014, 15: 9.
doi: 10.1186/1471-2164-15-9 |
[9] | 戚家明, 张东旭, 王少丽, 黄立斌, 夏丽丽, 董汪洋, 郑强, 刘青娥, 肖建中, 徐志文. 基于转录组测序数据对Weissella confusa XU1中低聚木糖代谢系统的分析. 微生物学报, 2020, 60: 912-923. |
Qi J M, Zhang D X, Wang S L, Huang L B, Xia L L, Dong W Y, Zheng Q, Liu Q E, Xiao J Z, Xu Z W. Transcriptome analysis of xylo-oligosaccharides utilization systems in Weissella confusa XU1. Acta Microbiol Sin, 2020, 60: 912-923. (in Chinese with English abstract) | |
[10] | 侯孟典, 王会, 钟金城, 柴志欣, 益西康珠, 王吉坤, 王嘉博. 基于转录组测序筛选黄牛低氧适应性相关差异基因. 华北农学报, 2020, 35(2): 217-227. |
Hou M D, Wang H, Zhong J C, Chai Z X, Yixikangzhu, Wang J K, Wang J B. Screening differential genes related to hypoxia adaptation in cattle by using transcriptome analysis. Acta Agric Boreali-Sin, 2020, 35(2): 217-227. (in Chinese with English abstract) | |
[11] | 黄伊子, 郭芾, 韩凝, 边红武. 基于RNA-seq的水稻根尖和侧根区伤组织诱导中生长素相关基因差异表达分析. 植物生理学报, 2020, 56: 1745-1755. |
Huang Y Z, Guo F, Han N, Bian H W. RNA-seq-based differential expression analysis of auxin-related genes during callus induction derived from root tip and lateral root region in rice (Oryza sativa). Plant Physiol J, 2020, 56: 1745-1755. (in Chinese with English abstract) | |
[12] | 申状状. 棉属远缘杂种的合成及性状鉴定与转录组分析. 山西农业大学硕士学位论文, 山西晋中, 2018. |
Shen Z Z. Synthesis, Identification and Transcriptome Analysis of Distant Hybrids in Gossypium. MS Thesis of Shanxi Agricultural University, Jinzhong, Shanxi, China, 2018. (in Chinese with English abstract) | |
[13] | 刘新星, 陈超. 基于短序列测序数据的四倍体拟南芥转录组研究. 中国生物工程杂志, 2011, 31(7): 45-53. |
Liu X X, Chen C. De novo assembly of allotetraploid Arabidopsis suecica transcriptome using short reads for gene discovery and marker identification. China Biotechnol, 2011, 31(7): 45-53. (in Chinese with English abstract) | |
[14] | 李萌, 郭烨, 刘松珊, 庞晓明, 李颖岳. 二倍体及其同源四倍体酸枣的生理特征和转录组分析. 北京林业大学学报, 2019, 41(7): 57-67. |
Li M, Guo Y, Liu S S, Pang X M, Li Y Y. Physiological characteristics and transcriptomics analysis in diploid Ziziphus jujuba Mill. var. spinosa and its autotetraploid. J Beijing For Univ, 2019, 41(7): 57-67. (in Chinese with English abstract) | |
[15] | 高真, 张成才, 罗丽娜, 张子璇, 王将, 向增旭. 茅苍术二倍体及其同源四倍体的生理特征与转录组差异分析. 南京农业大学学报, 2020, 43: 1024-1032. |
Gao Z, Zhang C C, Luo L N, Zhang Z X, Wang J, Xiang Z X. Physiological characteristics and transcriptome differences analysis of diploid and autotetraploid of Atractylodes lancea. J Nanjing Agric Univ, 2020, 43: 1024-1032. (in Chinese with English abstract) | |
[16] | 王娜, 赵资博, 高琼, 何守朴, 马晨辉, 彭振, 杜雄明. 陆地棉盐胁迫应答基因GhPEAMT1的克隆及功能分析. 中国农业科学, 2021, 54: 248-260. |
Wang N, Zhao Z B, Gao Q, He S P, Ma C H, Peng Z, Du X M. Cloning and functional analysis of salt stress response gene GhPEAMT1 in upland cotton. Sci Agric Sin, 2021, 54: 248-260. (in Chinese with English abstract) | |
[17] |
王晓阳, 王丽媛, 潘兆娥, 何守朴, 王骁, 龚文芳, 杜雄明. 亚洲棉短绒突变体纤维发育及其差异基因表达分析. 作物学报, 2020, 46: 645-660.
doi: 10.3724/SP.J.1006.2020.94133 |
Wang X Y, Wang L Y, Pan Z E, He S P, Wang X, Gong W F, Du X M. Analysis of differentially expressed genes and fiber development in Gossypium arboreum fuzzless mutant. Acta Agron Sin, 2020, 46: 645-660 (in Chinese with English abstract).
doi: 10.3724/SP.J.1006.2020.94133 |
|
[18] | 钱玉源, 刘祎, 张曦, 王燕, 王广恩, 崔淑芳, 李俊兰. 棉花种子质量突变体ims-15及其近等基因系种子发育期转录组分析. 华北农学报, 2021, 36(3): 50-59. |
Qian Y Y, Liu Y, Zhang X, Wang Y, Wang G E, Cui S F, Li J L. Transcriptome analysis of cotton seed weight mutant ims-15 and its near isogenic line during seed development. Acta Agric Boreali-Sin, 2021, 36(3): 50-59. (in Chinese with English abstract) | |
[19] | 王三根. 植物生理学实验教程. 北京: 科学出版社, 2017. pp 188-206. |
Wang S G. Plant Physiology Experiment. Beijing: Science Press, 2017. pp 188-206. (in Chinese) | |
[20] | 高俊凤. 植物生理学实验指导. 北京: 高等教育出版社, 2006. pp 140-148. |
Gao J F. Experimental Guidance of Plant Physiology. Beijing: Higher Education Press, 2006. pp 140-148. (in Chinese) | |
[21] | 何光源. 植物基因工程. 北京: 清华大学出版社, 2007. pp 74-82. |
He G Y. Plant Physiology. Beijing: Tsinghua University Press, 2007. pp 74-82. (in Chinese) | |
[22] | 周庭辉, 戴小枫. 棉花抗黄萎病生理与生化机制研究. 分子植物育种, 2006, 4: 593-600. |
Zhou T H, Dai X F. Research on physiological and biochemical mechanism of cotton against verticillium wilt. Mol Plant Breed, 2006, 4: 593-600. (in Chinese with English abstract) | |
[23] | Gange J M, Smalle J, Gingerich D J, Walker J M, Yoo S D, Yanagisawa S C, Vierstra R D, Newcomb E H. Arabidopsis EIN3-binding F-box 1 and 2 form ubiquitin-protein ligases that repress ethylene action and promote growth by directing EIN3 degradation Proc Natl Acad Sci USA, 2004, 101: 6803-6808. |
[24] |
王涛, 陈孟龙, 刘玲, 宁传丽, 蔡斌华, 章镇, 乔玉山. 植物多倍体化中基因组和基因表达的变化. 植物学报, 2015, 50: 504-515.
doi: 10.11983/CBB14097 |
Wang T, Chen M L, Liu L, Ning C L, Cai B H, Zhang Z, Qiao Y S. Changes in genome and gene expression during plant polyploidization. Chin Bull Bot, 2015, 50: 504-515. (in Chinese with English abstract) | |
[25] |
Xu C, Bai Y, Lin X, Zhao N, Hu L, Gong Z, Wendel J F, Liu B. Genome-wide disruption of gene expression in allopolyploids but not hybrids of rice subspecies. Mol Biol Evol, 2014, 31: 1066-1076.
doi: 10.1093/molbev/msu085 |
[26] | 柴小翠, 杨文涛, 汤琪, 马雪凤, 熊杰, 王平, 缪炜. 竹节参处理下嗜热四膜虫基因表达变化分析. 中国中药杂志, 2019, 44: 2580-2587. |
Chai X C, Yang W T, Tang Q, Ma X F, Xiong J, Wang P, Miao W. Analysis of gene expression of Tetrahymena thermophila treated with Panax japonicas. China J Chin Materia Med, 2019, 44: 2580-2587. (in Chinese with English abstract) | |
[27] | 蔡力. 二倍体和四倍体紫锥菊中叶形态结构及其光合效率的比较研究. 华南农业大学硕士学位论文, 广东广州, 2016. |
Cai L. Comparative Study of Morphological Structure and Photosynthetic Efficiency Between Diploid and Tetraploid Echinacea Purpurea. MS Thesis of South China Agriculture University, Guangzhou, Guangdong, China, 2016. (in Chinese with English abstract) | |
[28] | 周影影. 菘蓝同源多倍体及白菜菘蓝异源多倍体后代的细胞学及转录组学研究. 华中农业大学博士学位论文, 湖北武汉, 2014. |
Zhou Y Y. Cytology and Transcriptome Analysis of Isatis indigotica Autopolyploid and the Progeny of Brassica rapa-Isatis indigotica Allohexaploid. PhD Dissertation of Huazhong Agricultural University, Wuhan, Hubei, China, 2014. (in Chinese with English abstract) | |
[29] |
Tsukaya H. Does ploidy level directly control cell size? Counterevidence from Arabidopsis genetics. PLoS One, 2013, 8: e83729.
doi: 10.1371/journal.pone.0083729 |
[30] |
Cosgrove D J. Loosening of plant cell walls by expansions. Nature, 2000, 407: 321-326.
doi: 10.1038/35030000 |
[31] |
Han Z F, Qin Y X, Deng Y S, Kong F J, Wang Z W, Shen G F, Wang J H, Duan B, Li R Z. Expression profiles of a cytoplasmic male sterile line of Gossypium harknessii and its fertility restorer and maintainer lines revealed by RNA-Seq. Plant Physiol Biochem, 2017, 116: 106-115.
doi: 10.1016/j.plaphy.2017.04.018 |
[32] |
Siedlecka A, Wiklund S, Peronne M A, Micheli F, Lesniewska J, Sethson I, Edlund U, Richardl, Sundberg B, Mellerowicz E J. Pectin methyl esterase inhibits intrusive and symplastic cell growth in developing wood cells of Populus. Plant Physiol, 2008, 146: 554-565.
doi: 10.1104/pp.107.111963 pmid: 18065553 |
[33] |
Hongo S, Sato K, Yokoyama R, Nishitani K. Demethylesterification of the primary wall by PECTIN METHYLESTERASE35 provides mechanical support to the Arabidopsis stem. Plant Cell, 2012, 24: 2624-2634.
doi: 10.1105/tpc.112.099325 |
[34] | Chen J, Dong X, Li Q, Zhou X, Chen W. Biosynthesis of the active compounds of Isatis indigotica based on transcriptome sequencing and metabolites profiling. BioMed Central, 2013, 14: 857-869. |
[35] |
Gao A G, Hakimi S M, Mittanck C A, Wu Y, Woerner B M, Stark D M, Shah D M, Liang J, Rommens C M. Fungal pathogen protection in potato by expression of a plant defensin peptide. Nat Biotechnol, 2000, 18: 1307-1340.
pmid: 11101813 |
[36] |
Romeis T, Ludwig A A, Martin R, Jones J D G. Calcium- dependent protein kinases play an essential role in a plant defense response. EMBO J, 2001, 20: 5556-5567.
pmid: 11597999 |
[37] |
Rudd J J, Franklin-Tong V E. Unraveling response-specificity in Ca2+ signaling pathways in plant cells. New Phytol, 2001, 151: 7-33.
doi: 10.1046/j.1469-8137.2001.00173.x |
[38] | 姬万丽, 朱红菊, 路绪强, 赵胜杰, 何楠, 耿丽华, 刘文革. 四倍体西瓜抗枯萎病菌生理小种1的机理. 中国农业科学, 2018, 51: 3750-3765. |
Ji W L, Zhu H J, Lu X Q, Zhao S J, He N, Geng L H, Liu W G. The Mechanism of resistance to Fusarium oxysporum f. sp. niveum race 1 in tetraploid watermelon. Sci Agric Sin, 2018, 51: 3750-3765. (in Chinese with English abstract) | |
[39] | 万华方, 魏帅, 冯宇霞, 钱伟. 以六倍体(AnAnCnCnCoCo)为桥梁创制抗旱新型甘蓝型油菜(AnArCnCo). 中国农业科学, 2020, 53: 3226-3234. |
Wan H F, Wei S, Feng Y X, Qian W. Creating a new-type Brassica napus (AnArCnCo) with high drought-resistance employing hexaploid (AnAnCnCnCoCo) as a bridge. Sci Agric Sin, 2020, 53: 3226-3234. (in Chinese with English abstract) | |
[40] | 葛霞, 徐瑞, 李梅, 田甲春, 李守强, 程建新, 田世龙. 香芹酮对马铃薯种薯发芽的调控机制. 中国农业科学, 2020, 53: 4929-4939. |
Ge X, Xu R, Li M, Tian J C, Li S Q, Cheng J X, Tian S L. Regulation mechanism of carvone on seed potato sprouting. Sci Agric Sin, 2020, 53: 4929-4939. (in Chinese with English abstract) | |
[41] | 李玉青, 王清连, 韦春艳, 董涛, 陈全家, 周瑞阳. 棉花胞质雄性不育细胞形态学观察及生理生化特性的研究. 西南农业学报, 2020, 33(1): 58-63. |
Li Y Q, Wang Q L, Wei C Y, Dong T, Chen Q J, Zhou R Y. Morphological observation and physiological and biochemical characteristics of cotton cytoplasmic male sterile cells. Southwest China J Agric Sci, 2020, 33(1): 58-63. (in Chinese with English abstract) | |
[42] | 王忠. 植物生理学. 北京: 中国农业出版社, 2010. p 137. |
Wang Z. Plant Physiology. Beijing: China Agriculture Press, 2010. p 137. (in Chinese) | |
[43] | 于济, 沙伟, 张梅娟, 马天意. 植物磷酸烯醇式丙酮酸羧化酶的研究进展. 高师理科学刊, 2021, 41(2): 54-60. |
Yu J, Sha W, Zhang M J, Ma T Y. Research progress of plant phosphoenolpyruvate carboxylase. J Sci Teach Coll Univ, 2021, 41(2): 54-60. (in Chinese with English abstract) |
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[2] | 王瑞莉, 王刘艳, 雷维, 吴家怡, 史红松, 李晨阳, 唐章林, 李加纳, 周清元, 崔翠. 结合RNA-seq分析和QTL定位筛选甘蓝型油菜萌发期与铝毒胁迫相关的候选基因[J]. 作物学报, 2021, 47(12): 2407-2422. |
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