Comparative transcript profiling of the fertile and sterile flower buds of pol CMS in B. napus

BMC Genomics

Tingdong Fu¹  Chaozhi Ma¹  Jinxing Tu¹  Jinxiong Shen¹  Jing Wen¹  Bin Yi¹  Zonghui Yang¹  Hong An¹ 

[1] National Key Lab of Crop Geneticc Improvement, National Center of Crop Molecular Breeding Technology, National Center of Oil Crop Improvement (Wuhan), College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, P. R. China

关键词: Transcriptome;    Anther;    pol CMS;    Brassica napus;   

Others  :  1217560
DOI  :  10.1186/1471-2164-15-258

 received in 2013-11-25, accepted in 2014-03-26,  发布年份 2014

【 摘 要 】

Background

The Polima (pol) system of cytoplasmic male sterility (CMS) and its fertility restoration gene Rfp have been used in hybrid breeding in Brassica napus, which has greatly improved the yield of rapeseed. However, the mechanism of the male sterility transition in pol CMS remains to be determined.

Results

To investigate the transcriptome during the male sterility transition in pol CMS, a near-isogenic line (NIL) of pol CMS was constructed. The phenotypic features and sterility stage were confirmed by anatomical analysis. Subsequently, we compared the genomic expression profiles of fertile and sterile young flower buds by RNA-Seq. A total of 105,481,136 sequences were successfully obtained. These reads were assembled into 112,770 unigenes, which composed the transcriptome of the bud. Among these unigenes, 72,408 (64.21%) were annotated using public protein databases and classified into functional clusters. In addition, we investigated the changes in expression of the fertile and sterile buds; the RNA-seq data showed 1,148 unigenes had significantly different expression and they were mainly distributed in metabolic and protein synthesis pathways. Additionally, some unigenes controlling anther development were dramatically down-regulated in sterile buds.

Conclusions

These results suggested that an energy deficiency caused by orf224/atp6 may inhibit a series of genes that regulate pollen development through nuclear-mitochondrial interaction. This results in the sterility of pol CMS by leading to the failure of sporogenous cell differentiation. This study may provide assistance for detailed molecular analysis and a better understanding of pol CMS in B. napus.

【 授权许可】

   
2014 An et al.; licensee BioMed Central Ltd.

【 图 表 】

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【 参考文献 】

• [1]Han-zhong W: Review and future development of rapeseed industry in china. Chin J Oil Crop Sci 2010, 32(2):3.
• [2]Chen J, Guan R, Chang S, Du T, Zhang H, Xing H: Substoichiometrically different mitotypes coexist in mitochondrial genomes of Brassica napus L. PLoS One 2011, 6(3):e17662.
• [3]Luo D, Xu H, Liu Z, Guo J, Li H, Chen L, Fang C, Zhang Q, Bai M, Yao N, Wu H, Ji C, Zheng H, Chen Y, Ye S, Li X, Zhao X, Li R, Liu Y: A detrimental mitochondrial-nuclear interaction causes cytoplasmic male sterility in rice. Nat Genet 2013, 45:573-577.
• [4]Woodson JD, Chory J: Coordination of gene expression between organellar and nuclear genomes. Nat Rev Genet 2008, 9(5):383-395.
• [5]L’Homme Y, Stahl RJ, Li XQ, Hameed A, Brown GG: Brassica nap cytoplasmic male sterility is associated with expression of a mtDNA region containing a chimeric gene similar to the pol CMS-associated orf224 gene. Curr Gen 1997, 31(4):325-335.
• [6]Yuan M, Yang GS, Fu TD, Li Y: Transcriptional control of orf224/atp6 by the pol CMS restorer Rfp gene in Brassica napus L. Yi Chuan Xue Bao 2003, 30(5):469-473.
• [7]Singh M, Hamel N, Menassa R, Li XQ, Young B, Jean M, Landry BS, Brown GG: Nuclear genes associated with a single Brassica CMS restorer locus influence transcripts of three different mitochondrial gene regions. Genetics 1996, 143(1):505-516.
• [8]Singh M, Brown GG: Suppression of cytoplasmic male sterility by nuclear genes alters expression of a novel mitochondrial gene region. Plant Cell 1991, 3(12):1349-1362.
• [9]Schuster SC: Next-generation sequencing transforms today’s biology. Nat Methods 2008, 5(1):16-18.
• [10]Torti S, Fornara F, Vincent C, Andres F, Nordstrom K, Gobel U, Knoll D, Schoof H, Coupland G: Analysis of the Arabidopsis shoot meristem transcriptome during floral transition identifies distinct regulatory patterns and a leucine-rich repeat protein that promotes flowering. Plant Cell 2012, 24(2):444-462.
• [11]Chen C, Farmer AD, Langley RJ, Mudge J, Crow JA, May GD, Huntley J, Smith AG, Retzel EF: Meiosis-specific gene discovery in plants: RNA-Seq applied to isolated Arabidopsis male meiocytes. BMC Plant Biol 2010, 10:280. BioMed Central Full Text
• [12]Feng C, Chen M, Xu CJ, Bai L, Yin XR, Li X, Allan AC, Ferguson IB, Chen KS: Transcriptomic analysis of Chinese bayberry (Myrica rubra) fruit development and ripening using RNA-Seq. BMC Genomics 2012, 13:19. BioMed Central Full Text
• [13]Logacheva MD, Kasianov AS, Vinogradov DV, Samigullin TH, Gelfand MS, Makeev VJ, Penin AA: De novo sequencing and characterization of floral transcriptome in two species of buckwheat (Fagopyrum). BMC Genomics 2011, 12:30. BioMed Central Full Text
• [14]Yu K, Xu Q, Da X, Guo F, Ding Y, Deng X: Transcriptome changes during fruit development and ripening of sweet orange (Citrus sinensis). BMC Genomics 2012, 13(1):10. BioMed Central Full Text
• [15]Lulin H, Xiao Y, Pei S, Wen T, Shangqin H: The first Illumina-based de novo transcriptome sequencing and analysis of safflower flowers. PLoS One 2012, 7(6):e38653.
• [16]Yan X, Dong C, Yu J, Liu W, Jiang C, Liu J, Hu Q, Fang X, Wei W: 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. BMC Genomics 2013, 14:26. BioMed Central Full Text
• [17]Wang Z, Gerstein M, Snyder M: RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet 2009, 10(1):57-63.
• [18]Hahn DA, Ragland GJ, Shoemaker DD, Denlinger DL: Gene discovery using massively parallel pyrosequencing to develop ESTs for the flesh fly Sarcophaga crassipalpis. BMC Genomics 2009, 10:234. BioMed Central Full Text
• [19]Trick M, Long Y, Meng J, Bancroft I: Single nucleotide polymorphism (SNP) discovery in the polyploid Brassica napus using Solexa transcriptome sequencing. Plant Biotechnol J 2009, 7(4):334-346.
• [20]Harper AL, Trick M, Higgins J, Fraser F, Clissold L, Wells R, Hattori C, Werner P, Bancroft I: Associative transcriptomics of traits in the polyploid crop species Brassica napus. Nat Biotechnol 2012, 30:798-802.
• [21]Roulin A, Auer PL, Libault M, Schlueter J, Farmer A, May G, Stacey G, Doerge RW, Jackson SA: The fate of duplicated genes in a polyploid plant genome. Plant J 2012, 73(1):143-153.
• [22]Pont C, Murat F, Confolent C, Balzergue S, Salse J: RNA-seq in grain unveils fate of neo- and paleopolyploidization events in bread wheat (Triticum aestivum L.). Genome Biol 2011, 12(12):R119. BioMed Central Full Text
• [23]Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, Adiconis X, Fan L, Raychowdhury R, Zeng Q, Chen Z, Mauceli E, Hacohen N, Gnirke A, Rhind N, Palma F, Birren BW, Nusbaum C, Lindblad-Toh K, Friedman N, Regev A: Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol 2011, 29(7):644-652.
• [24]Wang XW, Luan JB, Li JM, Bao YY, Zhang CX, Liu SS: De novo characterization of a whitefly transcriptome and analysis of its gene expression during development. BMC Genomics 2010, 11:400. BioMed Central Full Text
• [25]Sanders PM, Bui AQ, Weterings K, Mclntire KN, Hsu YC, Lee PY, Truong MT, Beals TP, Goldberg RB: Anther developmental defects in Arabidopsis thaliana male-sterile mutants. Sex Plant Reprod 1999, 11(6):297-322.
• [26]Unte US, Sorensen AM, Pesaresi P, Gandikota M, Leister D, Saedler H, Huijser P: SPL8, An SBP-Box gene that affects pollen sac development in Arabidopsis. Plant Cell Online 2003, 15(4):1009-1019.
• [27]Scott RJ, Spielman M, Dickinson HG: Stamen structure and function. Plant Cell 2004, 16(Suppl):S46-60.
• [28]Wilson ZA, Zhang DB: From Arabidopsis to rice: pathways in pollen development. J Exp Bot 2009, 60(5):1479-1492.
• [29]Ma H: Molecular genetic analyses of microsporogenesis and microgametogenesis in flowering plants. Annu Rev Plant Biol 2005, 56:393-434.
• [30]Moriya Y, Itoh M, Okuda S, Yoshizawa AC, Kanehisa M: KAAS: an automatic genome annotation and pathway reconstruction server. Nucleic Acids Res 2007, 35:W182-185.
• [31]Conesa A, Gotz S, Garcia-Gomez JM, Terol J, Talon M, Robles M: Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics 2005, 21(18):3674-3676.
• [32]Ito T, Wellmer F, Yu H, Das P, Ito N, Alves-Ferreira M, Riechmann JL, Meyerowitz EM: The homeotic protein AGAMOUS controls microsporogenesis by regulation of SPOROCYTELESS. Nature 2004, 430(6997):356-360.
• [33]Yang WC, Ye D, Xu J, Sundaresan V: The SPOROCYTELESS gene of Arabidopsis is required for initiation of sporogenesis and encodes a novel nuclear protein. Genes Dev 1999, 13(16):2108-2117.
• [34]Wei M, Song M, Fan S, Yu S: Transcriptomic analysis of differentially expressed genes during anther development in genetic male sterile and wild type cotton by digital gene-expression profiling. BMC Genomics 2013, 14(1):97. BioMed Central Full Text
• [35]Chase CD: Cytoplasmic male sterility: a window to the world of plant mitochondrial-nuclear interactions. Trends Genet 2007, 23(2):81-90.
• [36]Jing B, Heng S, Tong D, Wan Z, Fu T, Tu J, Ma C, Yi B, Wen J, Shen J: A male sterility-associated cytotoxic protein ORF288 in Brassica juncea causes aborted pollen development. J Exp Bot 2012, 63(3):1285-1295.
• [37]Fujii S, Yamada M, Fujita M, Itabashi E, Hamada K, Yano K, Kurata N, Toriyama K: Cytoplasmic-nuclear genomic barriers in rice pollen development revealed by comparison of global gene expression profiles among five independent cytoplasmic male sterile lines. Plant Cell Physiol 2010, 51(4):610-620.
• [38]Yang J, Liu X, Yang X, Zhang M: Mitochondrially-targeted expression of a cytoplasmic male sterility-associated orf220 gene causes male sterility in Brassica juncea. BMC Plant Biol 2010, 10:231. BioMed Central Full Text
• [39]Xu J, Yang C, Yuan Z, Zhang D, Gondwe MY, Ding Z, Liang W, Zhang D, Wilson ZA: The ABORTED MICROSPORES regulatory network is required for postmeiotic male reproductive development in Arabidopsis thaliana. Plant Cell 2010, 22(1):91-107.
• [40]Feng B, Lu D, Ma X, Peng Y, Sun Y, Ning G, Ma H: Regulation of the Arabidopsis anther transcriptome by DYT1 for pollen development. Plant J 2012, 72(4):612-624.
• [41]Shen Y, Zhang Z, Lin H, Liu H, Chen J, Peng H, Cao M, Rong T, Pan G: Cytoplasmic male sterility-regulated novel microRNAs from maize. Funct Integr Genom 2011, 11(1):179-191.
• [42]Yang J, Liu X, Xu B, Zhao N, Yang X, Zhang M: Identification of miRNAs and their targets using high-throughput sequencing and degradome analysis in cytoplasmic male-sterile and its maintainer fertile lines of brassica juncea. BMC Genomics 2013, 14:9. BioMed Central Full Text
• [43]Cox MP, Peterson DA, Biggs PJ: SolexaQA: At-a-glance quality assessment of Illumina second-generation sequencing data. BMC Bioinformatics 2010, 11:485. BioMed Central Full Text
• [44]Pertea G, Huang X, Liang F, Antonescu V, Sultana R, Karamycheva S, Lee Y, White J, Cheung F, Parvizi B, Tsai J, Quackenbush J: TIGR Gene Indices clustering tools (TGICL): a software system for fast clustering of large EST datasets. Bioinformatics 2003, 19(5):651-652.
• [45]Trapnell C, Pachter L, Salzberg SL: TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 2009, 25(9):1105-1111.
• [46]Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, van Baren MJ, Salzberg SL, Wold BJ, Pachter L: Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol 2010, 28(5):511-515.