|
|
|
|
|
| Unravelling transcriptome changes between two distinct maize inbred lines using RNA-seq |
ZHOU Yu-qian1*, WANG Qin-yang2*, ZHAO Hai-liang2, GONG Dian-ming2, SUN Chuan-long2, REN Xue-mei2, LIU Zhong-xiang1, HE Hai-jun1, QIU Fa-zhan2 |
1 Crop Research Institute, Gansu Academy of Agricultural Sciences, Lanzhou 730070, P.R.China
2 National Key Laboratory of Crop Genetic Improvement/College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, P.R.China |
|
|
|
|
Abstract Seed size play a significant role in maize yield production. Two maize inbred lines with distinct seed size and weight, V671 (a large-seed inbred line) and Mc (a small-seed inbred line), were investigated by RNA-seq at 14 days after pollination (DAP), when maize endosperm undergoes an active transition from mitosis to storage accumulation. RNA-seq expression data showed that the small-seed line Mc had a higher storage accumulation activity, whereas the large-seed kernel line V671 possessed a higher DNA synthesis activity. An investigation of the pattern of increasing kernel width at serial DAPs showed that V671 experienced an increased kernel width later than did Mc, but the rate and duration of increase were longer in V671. SDS-PAGE of the storage proteins and quantitative RT-PCR of cell cycle-related genes and indole-3-acetic (IAA) synthesis genes certified that the transition from mitosis to storage accumulation starts earlier in Mc. We hypothesized that the difference in the mitosis-to-storage accumulation transition accounts for the larger seed size in V671 vs. Mc.
|
|
Received: 21 December 2017
Accepted:
|
| Fund: This research was supported by the National Natural Science Foundation of China (91735306), the National Basic Research Program of China (973 Program, 2014CB138203), and the National Key Research and Development Program of China (2016YFD0100103-19). |
|
Corresponding Authors:
Correspondence QIU Fa-zhan, Tel: +86-27-87286870, Fax: +86-27-87281006, E-mail: qiufazhan@mail.hzau.edu.cn
|
| About author: * These authors contributed equally to this study. |
Cite this article:
ZHOU Yu-qian, WANG Qin-yang, ZHAO Hai-liang, GONG Dian-ming, SUN Chuan-long, REN Xue-mei, LIU Zhong-xiang, HE Hai-jun, QIU Fa-zhan.
2018.
Unravelling transcriptome changes between two distinct maize inbred lines using RNA-seq. Journal of Integrative Agriculture, 17(07): 1574-1584.
|
Anders S, Huber W. 2010. Differential expression analysis for sequence count data. Genome Biology, 11, R106.
Chen Y, Xu Y, Luo W, Li W, Chen N, Zhang D, Chong K. 2013. The F-box protein OsFBK12 targets OsSAMS1 for degradation and affects pleiotropic phenotypes, including leaf senescence, in rice. Plant Physiology, 163, 1673–1685.
Du Z, Zhou X, Ling Y, Zhang Z, Su Z. 2010. AgriGO: A GO analysis toolkit for the agricultural community. Nucleic Acids Research, 38, W64–W70.
Garcia D, Fitz J G, Berger F. 2005. Maternal control of integument cell elongation and zygotic control of endosperm growth are coordinated to determine seed size in Arabidopsis. The Plant Cell, 17, 52–60.
Gonzalez N, Vanhaeren H, Inze D. 2012. Leaf size control: Complex coordination of cell division and expansion. Trends in Plant Science, 17, 332–340.
Ishimaru K, Hirotsu N, Madoka Y, Murakami N, Hara N, Onodera H, Kashiwagi T, Ujiie K, Shimizu B, Onishi A, Miyagawa H, Katoh E. 2013. Loss of function of the IAA-glucose hydrolase gene TGWss6 enhances rice grain weight and increases yield. Nature Genetics, 45, 707–711.
Jensen P J, Bandurski R S. 1994. Metabolism and synthesis of indole-3-acetic acid (IAA) in Zea mays (levels of IAA during kernel development and the use of in vitro endosperm systems for studying IAA biosynthesis). Plant Physiology, 106, 343–351.
Kesavan M, Song J T, Seo H S. 2013. Seed size: A priority trait in cereal crops. Plant Physiology, 147, 113–120.
Kim D, Pertea G, Trapnell C, Pimentel H, Kelley R, Salzberg S L. 2013. TopHat2: Accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biology, 14, R36.
Liu Y, Wang L, Sun C, Zhang Z, Zheng Y, Qiu F. 2014. Genetic analysis and major QTL detection for maize kernel size and weight in multi-environments. Theoretical and Applied Genetics, 127, 1019–1037.
Livak K J, Schmittgen T D. 2001. Analysis of relative gene expression data using real-time quantitative PCR and the 2(–Delta Delta C(T)) method. Methods, 25, 402–408.
Luo M, Dennis E S, Berger F, Peacock W J, Chaudhury A. 2005. MINISEED3 (MINI3), a WRKY family gene, and HAIKU2 (IKU2), a leucine-rich repeat (LRR) KINASE gene, are regulators of seed size in Arabidopsis. Proceedings of the National Academy of Sciences of the United States of America, 102, 17531–17536.
Lur H S, Setter T L. 1993. Role of auxin in maize endosperm development (timing of nuclear DNA endoreduplication, zein expression, and xytokinin). Plant Physiology, 103, 273–280.
Phillips K A, Skirpan A L, Liu X, Christensen A, Slewinski T L, Hudson C, Barazesh S, Cohen J D, Malcomber S, McSteen P. 2011. Vanishing tassel2 encodes a grass-specific tryptophan aminotransferase required for vegetative and reproductive development in maize. The Plant Cell, 23, 550–566.
Sabelli P A, Larkins B A. 2009. The contribution of cell cycle regulation to endosperm development. Sexual Plant Reproduction, 22, 207–219.
Schruff M C, Spielman M, Tiwari S, Adams S, Fenby N, Scott R J. 2006. The AUXIN RESPONSE FACTOR 2 gene of Arabidopsis links auxin signalling, cell division, and the size of seeds and other organs. Development (Cambridge, England), 133, 251–261.
Schweizer L, Yerk-Davis G L, Phillips R L, Srienc F, Jones R J. 1995. Dynamics of maize endosperm development and DNA endoreduplication. Proceedings of the National Academy of Sciences of the United States of America, 92, 7070–7074.
Sekhon R S, Hirsch C N, Childs K L, Breitzman M W, Kell P, Duvick S, Spalding E P, Buell C R, de Leon N, Kaeppler S M. 2014. Phenotypic and transcriptional analysis of divergently selected maize populations reveals the role of developmental timing in seed size determination. Plant Physiology, 165, 658–669.
Trapnell C, Roberts A, Goff L, Pertea G, Kim D, Kelley D R, Pimen- tel H, Salzberg S L, Rinn J L, Pachter L. 2012. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nature Protocols, 7, 562–578.
Wang A, Garcia D, Zhang H, Feng K, Chaudhury A, Berger F, Peacock W J, Dennis E S, Luo M. 2010. The VQ motif protein IKU1 regulates endosperm growth and seed size in Arabidopsis. The Plant Journal, 63, 670–679.
Wang E, Wang J, Zhu X, Hao W, Wang L, Li Q, Zhang L, He W, Lu B, Lin H, Ma H, Zhang G, He Z. 2008. Control of rice grain-filling and yield by a gene with a potential signature of domestication. Nature Genetics, 40, 1370–1374.
Weber H, Borisjuk L, Wobus U. 1996. Controlling seed development and seed size in Vicia faba: A role for seed coat-associated invertases and carbohydrate state. The Plant Journal, 10, 823–834.
Weng J, Gu S, Wan X, Gao H, Guo T, Su N, Lei C, Zhang X, Cheng Z, Guo X, Wang J, Jiang L, Zhai H, Wan J. 2008. Isolation and initial characterization of GW5, a major QTL associated with rice grain width and weight. Cell Research, 18, 1199–1209.
Wu T, Shen Y, Zheng M, Yang C, Chen Y, Feng Z, Liu X, Liu S, Chen Z, Lei C, Wang J, Jiang L, Wan J. 2014. Gene SGL, encoding a kinesin-like protein with transactivation activity, is involved in grain length and plant height in rice. Plant Cell Reports, 33, 235–244.
Wu X Y, Kuai B K, Jia J Z, Jing H C. 2012. Regulation of leaf senescence and crop genetic improvement. Journal of Integrative Plant Biology, 54, 936–952.
Wu Y, Messing J. 2012. RNA interference can rebalance the nitrogen sink of maize seeds without losing hard endosperm. PLoS ONE, 7, e32850.
Wu Y, Wang W, Messing J. 2012. Balancing of sulfur storage in maize seed. BMC Plant Biology, 12, 77.
Young M D, Wakefield M J, Smyth G K, Oshlack A. 2010. Gene ontology analysis for RNA-seq: Accounting for selection bias. Genome Biology, 11, R14.
Yue J, Li C, Zhao Q, Zhu D, Yu J. 2014. Seed-specific expression of a lysine-rich protein gene, GhLRP, from cotton significantly increases the lysine content in maize seeds. International Journal of Molecular Sciences, 15, 5350–5365.
|
| No Suggested Reading articles found! |
|
|
Viewed |
|
|
|
Full text
|
|
|
|
|
Abstract
|
|
|
|
|
Cited |
|
|
|
|
| |
Shared |
|
|
|
|
| |
Discussed |
|
|
|
|
