JIA-2021-2227 基于全基因组的mRNA和miRNA转录组分析为黄瓜花冠开放调控机制提供新的见解

Journal of Integrative Agriculture ›› 2022, Vol. 21 ›› Issue (9): 2603-2614.DOI: 10.1016/j.jia.2022.07.024

所属专题：园艺-分子生物合辑Horticulture — Genetics · Breeding

• • 上一篇下一篇

JIA-2021-2227 基于全基因组的mRNA和miRNA转录组分析为黄瓜花冠开放调控机制提供新的见解

收稿日期:2022-04-04 接受日期:2022-02-17 出版日期:2022-09-01 发布日期:2022-02-17

Genome-scale mRNA and miRNA transcriptomic insights into the regulatory mechanism of cucumber corolla opening

SONG Xiao-fei^1*, GE Dan-feng^2*, XIE Yang^1*, LI Xiao-li¹, SUN Cheng-zhen¹, CUI Hao-nan¹, ZHU Xue-yun¹, LIU Ren-yi², YAN Li-ying¹ #br#

¹ Hebei Key Laboratory of Horticultural Germplasm Excavation and Innovative Utilization, College of Horticultural Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao 066004, P.R.China
² Center for Agroforestry Mega Data Science, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, P.R.China

Received:2022-04-04 Accepted:2022-02-17 Online:2022-09-01 Published:2022-02-17
About author:Correspondence YAN Li-ying, E–mail: yanliying0665@hevttc.edu.cn; LIU Ren-yi, E–mail: ryliu@fafu.edu.cn * These authors contributed equally to this study.
Supported by:
This work was supported by the National Natural Science Foundation of China (31772327 and 31801877), and the Hebei Vegetable Innovation Projects of Modern Agricultural Industry Technology System, China (HBCT2018030209).

摘要/Abstract

摘要：

为探究黄瓜超级子房花冠开放的分子机制，本研究对超级子房和正常子房花冠发育过程中的mRNA和miRNA进行了测序分析。从4个发育时期共鉴定出234个差异表达miRNAs (DEMs)和291个差异表达靶基因(DE-target genes)，其中以黄蕾期的DEMs最多。另外，受5个以上DEMs调控的靶基因有30个，其中CsHD-Zip受28个DEMs调控，其次是DD2X为18个。miRNA_104、miRNA_157、miRNA_349、miRNA_242和miRNA_98在花冠发育过程中表达模式相近，且具有相同的靶基因CsCuRX。此外，通过qRT-PCR进一步对几个关键的候选DEMs及其靶基因进行了验证分析，结果表明miRNA_157-CsCuRX、miRNA_411-CsGH3.6和miRNA_161/297/257-CsHD-Zip可能与黄瓜超级子房花冠开放有关。

Abstract:

‘Corollas and spines’ is an important trait for fresh market cucumber. In a unique cucumber line, ‘6457’, the super ovary is much larger and corolla opening is delayed by 4–5 days, thus the resulting fruit has a flower that remains on the tip, which has a high commodity value. In this study, to better understand the molecular basis of corolla opening, mRNA and miRNA transcriptome analyses were performed during corolla development of the super and normal ovaries. A total of 234 differentially expressed miRNAs (DEMs) and 291 differentially expressed target genes (DE-target genes) were identified from four developmental stages, and the greatest number of DEMs was found at the yellow bud stage. Thirty of the DE-target genes were regulated by more than five DEMs, among which, CsHD-Zip was regulated by 28 DEMs, followed by DD2X (18). In addition, the expression patterns of miRNA_104, miRNA_157, miRNA_349, miRNA_242, and miRNA_98 were similar during corolla development, and they shared the same target gene, CsCuRX. Moreover, several critical candidate DEMs and DE-target genes were characterized and profiled by a qRT-PCR experiment. Three of the miRNAs, miRNA_157-CsCuRX, miRNA_411-CsGH3.6, and miRNA_161/297/257-CsHD-Zip, might be responsible for corolla opening in the cucumber super ovary. This integrated study on the transcriptional and post-transcriptional profiles can provide insights into the molecular regulatory mechanism underlying corolla opening in the cucumber.

Key words: cucumber , miRNA , corolla opening , super ovaries

. JIA-2021-2227 基于全基因组的mRNA和miRNA转录组分析为黄瓜花冠开放调控机制提供新的见解[J]. Journal of Integrative Agriculture, 2022, 21(9): 2603-2614.

SONG Xiao-fei, GE Dan-feng, XIE Yang, LI Xiao-li, SUN Cheng-zhen, CUI Hao-nan, ZHU Xue-yun, LIU Ren-yi, YAN Li-ying. Genome-scale mRNA and miRNA transcriptomic insights into the regulatory mechanism of cucumber corolla opening[J]. Journal of Integrative Agriculture, 2022, 21(9): 2603-2614.

参考文献

Aman M M, Bi X, Maria V K. 2018. FLOWERING LOCUS T3 controls spikelet initiation but not floral development. Plant Physiology, 178, 1170–1186.
Anders S, Pyl P T, Huber W. 2015. HTSeq - A Python framework to work with high-throughput sequencing data.
Bioinformatics, 31, 166–169.
Aukerman M J. 2003. Regulation of flowering time and floral organ identity by a microRNA and its APETALA2-like
target genes. The Plant Cell, 15, 2730–2741.
Belamkar V, Weeks N T, Bharti A K, Farmer A D, Graham M A, Cannon S B. 2014. Comprehensive characterization and RNA-Seq profiling of the HD-Zip transcription factor family in soybean (Glycine max) during dehydration and salt stress. BMC Genomics, 15, 950.
Cao L, Yu Y, Duanmu H, Chen C, Duan X, Zhu P, Chen R, Li Q, Zhu Y, Ding X. 2016. A novel Glycine soja homeodomain-leucine zipper (HD-Zip) I gene, Gshdz4, positively regulates bicarbonate tolerance and responds to osmotic stress in Arabidopsis. BMC Plant Biology, 16, 184.
Choi M, Davidson V L. 2011. Cupredoxins - A study of how proteins may evolve to use metals for bioenergetic processes. Metallomics, 3, 140–151.
D’Ario M, Griffiths-Jones S, Kim M. 2017. Small RNAs: Big impact on plant development. Trends in Plant Science, 22, 1056–1068 .
Dezar C A, Giacomelli J I, Manavella P A, Ré D A, Alves-Ferreira
M, Baldwin I T, Bonaventure G, Chan R L. 2011. HAHB10, a sunflower HD-Zip II transcription factor, participates in the induction of flowering and in the control of phytohormone-mediated responses to biotic stress. Journal of Experimental Botany, 62, 1061–1076.
Fu R, Liu W, Li Q, Li J, Wang L N, Ren Z H. 2013. Comprehensive analysis of the homeodomain-leucine zipper IV transcription factor family in Cucumis sativus. Genome, 56, 395–405.
Goyal A, Bharat M, Hwang K S, Lee S G. 2015. Identification of novel cupredoxin homologs using overlapped conserved residues based approach. Journal of Microbiology and Biotechnology, 25, 127–136.
Hart P J, Eisenberg D, Nersissian A M, Valentine J S, Herrmann R G, Nalbandyan R M. 1996. A missing link in cupredoxins: Crystal structure of cucumber stellacyanin at 1.6 Å resolution. Protein Science, 5, 2175–2183.
Iwakawa H O, Tomari Y. 2013. Molecular insights into microRNA-mediated translational repression in plants. Molecular Cell, 52, 591–601.
Kim D, Langmead B, Salzberg S L. 2015. HISAT: A fast spliced aligner with low memory requirements. Nature Methods, 12, 357–360.
Kuang Z, Wang Y, Li L, Yang X. 2019. miRDeep-P2: Accurate and fast analysis of the microRNA transcriptome in plants. Bioinformatics, 35, 2521–2522.
Li S J, Castillo-Gonzalez C, Yu B, Zhang X R. 2016. The functions of plant small RNAs in development and in stress responses. The Plant Journal, 90, 654–670.
Liu H, Yu H, Tang G, Huang T B. 2018. Small but powerful: Function of microRNAs in plant development. Plant Cell Reports, 37, 515–528.
Ma X, Xin Z, Wang Z, Yang Q, Lin T. 2015. Identification and comparative analysis of differentially expressed miRNAs in leaves of two wheat (Triticum aestivum L.) genotypes during dehydration stress. BMC Plant Biology, 15, 21.
Nakazawa M, Yabe N, Ichikawa T, Yamamoto Y Y, Yoshizumi T, Hasunuma K, Matsui M. 2001. DFL1, an auxin-responsive GH3 gene homologue, negatively regulates shoot cell elongation and lateral root formation, and positively regulates the light response of hypocotyl length. The Plant Journal, 25, 213–221.
Nitsch J P. 1952. Plant hormones in the development of fruits. Quarterly Review of Biology, 27, 33–57.
Panjabi P, Jagannath A, Bisht N C, Padmaja K L, Sharma S, Gupta V, Pradhan A K, Pental D. 2008. Comparative mapping of Brassica juncea and Arabidopsis thaliana using Intron Polymorphism (IP) markers: homoeologous relationships, diversification and evolution of the A, B and C Brassica genomes. BMC Genomics, 9, 113.
Robinson M D, McCarthy D J, Smyth G K. 2010. EdgeR: A Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics, 26, 139–140.
Rudich J, Baker L R, Sell H M 1977. Parthenocarpy in Cucumis sativus L. as affected by genetic parthenocarpy, thermo-photoperiod, and femaleness. Journal of the American Society for Horticultural Science , 102, 225–228.
Rueda E C, Dezar C A, Gonzalez D H, Chan R L. 2005. Hahb-10, a sunflower homeobox-leucine zipper gene, is regulated by light quality and quantity, and promotes early flowering when expressed in Arabidopsis. Plant and Cell Physiology, 46, 1954–1963.
Saetan W, Tian C, Yu J, Lin X, Li G. 2020. Comparative transcriptome analysis of gill tissue in response to hypoxia in silver sillago (Sillago sihama). Animals, 10, 13.
Zhang G Z, Jin S H, Li P, Jiang X Y, Li Y J, Hou B K. 2017. Ectopic expression of UGT84A2 delayed flowering by indole-3-butyric acid-mediated transcriptional repression of ARF6 and ARF8 genes in Arabidopsis. Plant Cell Reports, 36, 1995–2006.
Zhang X H, Lai Y S, Zhang W, Ahmad J, Qiu Y, Zhang X X, Duan M M, Liu T J, Song J P, Wang H P, Li X X. 2018. MicroRNAs and their targets in cucumber shoot apices in response to temperature and photoperiod. BMC Genomics, 19: 819.
Spanudakis E, Jackson S. 2014. The role of microRNAs in the control of flowering time. Journal of Experimental Botany, 65, 365–380.
Staswick P E, Serban B, Rowe M, Tiryaki I, Maldonado M T, Maldonado M C, Suza W. 2005. Characterization of an Arabidopsis enzyme family that conjugates amino acids to indole-3-acetic acid. The Plant Cell, 17, 616–627.
Sun C, Li Y, Zhao W, Song X, Lu M, Li X L, Li X X, Liu R Y, Yan L Y, Zhang X L. 2016. Integration of hormonal and nutritional cues orchestrates progressive corolla opening. Plant Physiology, 171, 1209–1229.
Teotia S, Tang G. 2015. To bloom or not to bloom: Role of microRNAs in plant flowering. Molecular Plant, 8, 359–377.
Tsukamoto Y, Harada T. 1957. Studies on the delaying of chrysanthemum flowering by the spray of the growth substance (2). Journal of the Japanese Society for Horticultural Science, 26, 54–58. (in Japanese)
Wang J W, Czech B, Weigel D. 2009. miR156-regulated SPL transcription factors define an endogenous flowering pathway in Arabidopsis thaliana. Cell, 138, 738–749.
Wu G, Park M Y, Conway S R, Wang J W, Weigel D, Poethig R S. 2009. The sequential action of miR156 and miR172 regulates developmental timing in Arabidopsis. Cell, 138, 750–759.
Wu H J, Ma Y K, Chen T, Wang M, Wang X J. 2012. PsRobot: A web-based plant small RNA meta-analysis toolbox. Nucleic Acids Research, 40, 22–28.
Xie Y, Ying J L, Xu L, Wang Y, Liu L W. 2020. Genome-wide sRNA and mRNA transcriptomic profiling insights into dynamic regulation of taproot thickening in radish (Raphanus sativus L.). BMC Plant Biology, 20, 373.
Zeng J, Ding Q, Hiroo F, He X Q. 2016. Fertilization independent endosperm genes repress NbGH3.6 and regulate the auxin level during shoot development in Nicotiana benthamiana. Journal of Experimental Botany, 8, 2207–2217.
Zhang S W, Li C H, Cao J, Zhang Y C, Zhang S Q, Xia Y F, Sun D Y, Sun Y. 2009. Altered architecture and enhanced drought tolerance in rice via the down-regulation of indole-3-acetic acid by TLD1/OsGH3.13 activation. Plant Physiology, 151, 1889–1901.
Zhang Z B, Xu C M, Gu X F, Liu J L, Sub-Academy H. 2016. Effect of flower dipping agents on cucumber fruit growth and quality. China Vegetables, 5, 16–19. (in Chinese)
Zhou Q, Shi J W, Li Z N, Zhang S S, Zhang S T, Zhang J Q, Bao M Z, Liu G F. 2021. miR156/157 targets SPLs to regulate flowering transition, plant architecture and flower organ size in petunia. Plant and Cell Physiology, 62, 839–857.
Zhu Q H, Helliwell C A. 2011. Regulation of flowering time and floral patterning by miR172. Journal of Experimental Botany, 62, 487–495.

相关文章 0

编辑推荐

Metrics