细胞质雄性不育系转录组学研究进展

摘要/Abstract

摘要： 细胞质雄性不育是植物杂种优势利用的基础，也是研究线粒体基因与核基因之间相互作用的良好材料。采用DNA芯片和RNA测序技术进行转录组分析能够在同一个实验中分析和比较成千上万个基因，这为在基因组水平上更好地了解植物生长和发育机制以及遗传变异提供了可能。在细胞质雄性不育机理的研究上，通过转录组分析将获得详细的相关分子分析的信息，了解线粒体与核基因之间的相互调控作用方式，并有助于雄性败育机理的解析。

关键词: 细胞质雄性不育, 转录组学, 线粒体反向调控, 差异表达基因

Abstract: Cytoplasmic male sterility（CMS）is the basis of utilizing the heterosis of plants，and also favorable material for studying the interaction between mitochondrial genes and nuclear genes. Transcriptomics analysis using DNA microarray and RNA-Seq technology enabled the analysis and comparison of thousands of genes in one experiment. This allows it feasible to better understand fundamental aspects of growth and development，as well as genetic variation in plants on a genomic scale. Based on the mechanism of CMS lines，transcriptomics study may acquire the detailed relevant molecular analysis，understand the interaction mode between mitochondrial and nuclear genes，and be conducive to dissect the male sterility.

Key words: cytoplasmic male sterility, transcriptomics, mitochondrial retrograde regulation, differentially expressed gene

中图分类号:

10.13560/j.cnki.biotech.bull.1985.2016.12.001

杨鹏. 细胞质雄性不育系转录组学研究进展[J]. 生物技术通报, 2016, 32(12): 1-7.

YANG Peng. Research Advances on Transcriptomics of Plant Cytoplasmic Male Sterility Lines?[J]. Biotechnology Bulletin, 2016, 32(12): 1-7.

参考文献

[1] Young E, Hanson M. A fused mitochondrial gene associated with cytoplasmic male sterility is developmentally regulated[J] . Cell, 1987, 50：41-49.
[2] Linke B, Borner T. Mitochondrial effects on flower and pollen development[J] . Mitochondrion, 2005, 5：389-402.
[3] Hanson MR, Bentolila S. Interactions of mitochondrial and nuclear genes that affect male gametophyte development[J] . Plant Cell, 2004, 16（Suppl. 1）：S154-S169.
[4] Unseld M, Marienfeld JR, Brandt P, et al. The mitochondrial genome of Arabidopsis thaliana contains 57 genes in 366, 924 nucleotides[J] . Nature Genetics, 1997, 15（1）：57-61.
[5] Kubo T, Nishizawa S, Sugawara A, et al. The complete nucleotide sequence of the mitochondrial genome of sugar beet（Beta vulgaris L.）reveals a novel gene for tRNACys（GCA）[J] . Nucleic Acids Research, 2000, 28（13）：2571-2576.
[6] Notsu Y, Masood S, Nishikawa T, et al. The complete sequence of the rice（Oryza sativa L.）mitochondrial genome：frequent DNA sequence acquisition and loss during the evolution of flowering plants[J] . Molecular Genetics Genomics, 2002, 268（4）：434-445.
[7] Sugiyama Y, Watase Y, Nagase M. The complete nucleotide sequence and multipartite organization of the tobacco mitochondrial genome：comparative analysis of mitochondrial genomes in higher plants[J] . Molecular Genetics Genomics, 2005, 272（6）：603-615.
[8] Rhoads DM, Subbaiah CC. Mitochondrial retrograde regulation in plants[J] . Mitochondrion, 2007, 7（3）：177-194.
[9] Yurina NP, Odintsova MS. Signal transduction pathways of plant mitochondria：retrograde regulation[J] . Russian Journal of Plant Physiology, 2010, 57（1）：7-19.
[10] Newton KJ, Gabay-Laughnan S, Paepe RD. Mitochondrial mutations in plants[M] //Day DA, Millar AH, Whelan J（Eds.）, Advances in Photosynthesis and Respiration, 2004：121-141.
[11] Carlsson J, Lagercrantz U, Dundstr?m J, et al. Microarray analysis reveals altered expression of a large number of nuclear genes in developing cytoplasmic male sterile Brassica napus flowers[J] . Plant Journal, 2007, 49：452-456.
[12] Rhoads DM, Subbaiah CC. Mitochondrial retrograde regulation in plants[J] . Mitochondrion, 2007, 7（3）：177-194.
[13] Chase CD. Cytoplasmic male sterility：a window to the world of plant mitochondrial-nuclear interactions[J] . Trends in Genetics Tig, 2007, 23（2）：81-90.
[14] Yang JH, Zhang MF, Yu JQ. Relationship between cytoplasmic male sterility and SPL-like gene expression in stem mustard[J] . Physiologia Plantarum, 2008, 133（2）：426-434.
[15] DeRisi JL, Iyer VR, Brown PO. Exploring the metabolic and genetic control of gene expression on a genomic scale[J] . Science, 1997, 278（5338）：680-686.
[16] Schuster SC. Next-generation sequencing transforms today’s biology[J] . Nature Methods, 2008, 5（1）：16-18.
[17] Ansorge WJ. Next-generation DNA sequencing techniques[J] . New Biotechnology, 2009, 25（4）：195-203.
[18] Honys D, Twell D. Comparative analysis of the Arabidopsis pollen transcriptom[J] . Plant Physiology, 2003, 132（2）：640-652.
[19] Becker JD, Boavida LC, Carneiro J, et al. Transcriptional profiling of Arabidopsis tissues reveals the unique characteristics of the pollen transcriptome[J] . Plant Physiology, 2003, 133（2）：713-725.
[20] Wei MM, Song MZ, Fan SH, et al. Transcriptomic analysis of differentially expressed genes during anther development in genetic male sterile and wild type cotton by digital gene-expression profiling[J] . BMC Genomics, 2013, 14（1）：1-16.
[21] Zenoni S, Ferrarini A, Giacomelli E, et al. Characterization of transcriptional complexity during berry development in Vitis vinifera using RNA-seq[J] . Plant Physiology, 2010, 152（4）：1787-1795.
[22] Fujii S, Komatsu S, Toriyama K. Retrograde regulation of nuclear gene expression in CW-CMS of rice[J] . Plant Molecular Biology, 2007, 63（3）：405-417.
[23] Fujii S, Toriyama K. DCW11, down-regulated gene 11 in CW-type cytoplasmic male sterile rice, encoding mitochondrial protein phosphatase 2c is related to cytoplasmic male sterility[J] . Plant Cell Physiology, 2008, 49（4）：633-640.
[24] Dong XS, Kim WK, Lim YP, et al. Ogura-CMS in Chinese cabbage（Brassica rapa ssp. pekinensis）causes delayed expression of many nuclear genes[J] . Plant Science, 2013, 199-200：7-17.
[25] Suzuki H, Rodriguez-Uribe L, Xu JN, et al. Transcriptome analysis of cytoplasmic male sterility and restoration in CMS-D8 cotton[J] . Plant Cell Reports, 2013, 32（10）：1531-1542.
[26] Trick M, Long Y, Meng JL, et al. Single nucleotide polymorphism. SNP discovery in the polyploidy Brassica napus using Solexa transcriptome sequencing[J] . Plant Biotechnology Journal, 2009, 7（4）：334-346.
[27] Shi CY, Yang H, Wei CL, et al. Deep sequencing of the Camellia sinensis transcriptome revealed candidate genes for major metabolic pathways of tea-specific compounds[J] . BMC Genomics, 2011, 12（1）：1-19.
[28] Yu KQ, Xu Q, Da XL, et al. Transcriptome changes during fruit development and ripening of sweet orange（Citrus sinensis）[J] . BMC Genomics, 2012, 13（2）：10.
[29] Zhang XM, Zhao L, Larson-Rabin Z. De Novo sequencing and characterization of the floral transcriptome of Dendrocalamus latiflorus（poaceae：bambusoideae）[J] . PLoS One, 2012, 7（8）：e42082.
[30] Xu YJ, Gao S, Yang YJ, et al. Transcriptome sequencing and whole genome expression profiling of chrysanthemum under dehydration stress[J] . BMC Genomics, 2013, 14（1）：103-111.
[31] Hao DC, Ma P, Mu J, et al. De novo characterization of the root transcriptome of a traditional Chinese medicinal plant Polygonum cuspidatum[J] . Science China Life Science, 2012, 55（5）：452-466.
[32] Yang YH, Li MJ, Li XY, et al. Transcriptome-wide identification of the genes responding to replanting disease in Rehmannia glutinosa L. roots[J] . Molecular Biology Reports, 2015, 42（5）：881-892.
[33] Liu C, Ma N, Wang PY, et al. Transcriptome sequencing and de novo analysis of a cytoplasmic male sterile line and its near-isogenic restorer line in chili pepper（Capsicum annuum L.）[J] . PLoS One, 2013, 8（6）：e65209.
[34] Yan XH, Dong CH, Yu JY, et al. Transcriptome profile analysis of young floral buds of fertile and sterile plants from the self-pollinated offspring of the hybrid between novel restorer line NR1 and Nsa CMS line in Brassica napus[J] . BMC Genomics, 2013, 14（3）：1-16.
[35] Zheng BB, Wu XM, Ge XX, et al. Comparative transcript profiling of a male sterile cybrid pummelo and its fertile type revealed altered gene expression related to flower development[J] . PLoS One, 2013, 7（8）：e43758.
[36] Chen P, Ran SM, Li R, et al. Transcriptome de novo assembly and differentially expressed genes related to cytoplasmic male sterility in kenaf（Hibiscus cannabinus L.）[J] . Molecular Breeding, 2014, 34（4）：1 879-1891.
[37] An H, Yang ZH, Yi B, et al. Comparative transcript profiling of the fertile and sterile flower buds of pol CMS in B. napus[J] . BMC Genomics, 2014, 1592：1-10.
[38] 王娇. 棉花细胞质雄性不育的转录组学育代谢组学研究[D] . 南京：南京农业大学, 2013.
[39] Yang P, Han JF, Huang JL. Transcriptome sequencing and de novo analysis of cytoplasmic male sterility and maintenance in JA-CMS cotton[J] . PLoS One, 2014, 9（11）：e112320.
[40] Jazwinski SM, Kriete A. The yeast retrograde response as a model of intracellular signaling of mitochondrial dysfunction[J] . Frontiers Physiology, 2012, 3：139.
[41] Dewey RE, Levings III CS, Timothy DH. Novel recombinations in the maize mitochondrial genome produce a unique transcriptional unit in the texas male-sterile cytoplasm[J] . Cell, 1986, 44（3）：439-449.
[42] Gómez-Casati DF, Busi MV, Gonzalez-Schain N, et al. A mitocho-ndrial dysfunction induces the expression of nuclear-encoded com-plex I genes in engineered male sterile Arabidopsis thaliana[J] . FEBS Letter, 2002, 532（1-2）：70-74.
[43] Gutierres S, Sabar M, Lelandais C, et al. Lack of mitochondrial and nuclear-encoded subunits of complex I and alteration of the respiratory chain in Nicotiana sylvestris mitochondrial deletion mutants[J] . Proc Natl Acad Sci USA, 1997, 94（7）：3436-3441.
[44] Dutilleul C, Garmier M, Noctor G, et al. Leaf mitochondria modulate whole cell redox homeostasis, set antioxidant capacity, and determine stress resistance through altered signaling and diurnal regulation[J] . Plant Cell, 2003, 15（5）：1212-1226.
[45] Dutilleul C, Lelarge C, Prioul JL, et al. Mitochondria-driven changes in leaf NAD status exert a crucial influence in the cantrol of nitrate assimilation and the integration of carbon and nitrogen metabolism[J] . Plant Physiology, 2005, 139（1）：64-78.
[46] Xu P, Yang YW, Zhang ZZ, et al. Expression of the nuclear gene TaFAd is under mitochondrial retrograde regulation in anthers of male sterile wheat plants with timopheevii cytoplasm[J] . Journal of Experimental Botany, 2008, 59（6）：1375-1381.
[47] Vanlerberghe GC, Robson CA, Yip, JYH. Induction of mitochond-rial alternative oxidase in response to a cell signal pathway down-regulating the cytochrome pathway prevents programmed cell death[J] . Plant Physiology, 2002, 129（4）：1829-1842.
[48] Rhoads DM, Umbach AL, Subbaiah CC, et al. Mitochondrial reac-tive oxygen species. Contribution to oxidative stress and interorgan-ellar signaling[J] . Plant Physiology, 2006, 141（2）：357-366.
[49] Subbaiah CC, Bush DS, Sachs MM. Mitochondrial contribution to the anoxic Ca2+ signal in maize suspension-cultured cells[J] . Plant Physiology, 1998, 118（3）：759-771.
[50] Schwarzl?nder M, Finkemeier I. Mitochondrial energy and redox signaling in plants[J] . Antioxidants Redox Signalling, 2013, 189（6）：2122- 2144.
[51] Yang J, Zhang M, Yu J. Mitochondrial retrograde regulation tuning fork in nuclear genes expressions of higher plants[J] . Journal of Genetics and Genomics, 2008, 35（2）：65-71.
[52] Schwarzl?nder M, K?nig AC, Sweetlove LJ, et al. The impact of impaired mitochondrial function on retrograde signalling：A meta-analysis of transcriptomic responses[J] . Journal of Exprimental Botany, 2011, 63（4）：1735-1750.
[53] Birzele F, Schaub J, Rust W, et al. Into the unknown：expression profiling without genome sequence information in CHO by next gen-eration sequencing[J] . Nucleic Acids Research, 2010, 38（12）：3999-4010.
[54] Wei WL, Qi XQ, Wang LH, et al. Characterization of the sesame（Sesamum indicum L.）global transcriptome using Illumina paired-end sequencing and development of EST-SSR markers[J] . BMC Genomics, 2011, 12（5）：451-463.
[55] Huang MD, Hsing YI, Huang AH. Transcriptomes of the anther sporophyte：availability and uses[J] . Plant Cell Physiology, 2011, 52（9）：1459-1466.