Skip to main content
SpringerLink
Log in

High-throughput sequencing reveals the molecular mechanisms determining the stay-green characteristic in soybeans

  • Published:
Journal of Biosciences Aims and scope Submit manuscript

Abstract

Senescence is an internally systematized degeneration process leading to death in plants. Leaf yellowing, one of the most prominent features of plant aging may lead to reduced crop yields. The molecular mechanism of responses to senescence in soybean leaves is not completely clear. In our research, two soybean varieties were selected with different stay-green traits: stay-green variety (BN106) and non-stay-green variety (KF14). RNA samples extracted from the leaves of two varieties were sequenced and compared using high-throughput sequencing. Six key enzyme genes in chlorophyll degradation pathways were studied to analyze the changes in their expression at seedling, flowering and maturation stage. Meanwhile, the construction of the genetic transformation process had been constructed to identify the function of putative gene by RNA-interference. A total of 4329 DEGs were involved in 52 functional groups and 254 KEGG pathways. Twelve genes encoding senescence-associated and inducible chloroplast stay-green protein showed significant differential expression. MDCase and PAO have a significant expression in BN106 that may be the key factors affecting the maintenance of green characteristics. In addition, the function of GmSGRs has been identified by genetic transformation. The loss of GmSGRs may cause soybean seeds to change from yellow to green. In summary, our results revealed fundamental information about the molecular mechanism of aging in soybeans with different stay-green characteristics. The work of genetic transformation lays a foundation for putative gene function studies that could contribute to postpone aging in soybeans.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Figure  1
Figure 2
Figure 3
Figure 4
Figure 5
Figure 6

Similar content being viewed by others

Abbreviations

bHLH:

basic helix-loop-helix

bZIP:

basic region/leucine zipper motif

CCE:

catabolic enzymes

DEG:

differential expressed genes

FER:

ferretin

FPKM:

fragments per kilobase million

GO:

gene ontology

HCAR:

7-hydroxymethyl chlorophyll a reductase

KEGG:

Kyoto encyclopedia of genes and genomes

LHCs:

light-harvesting complexes

NOL:

non-yellowing coloring like

NYC:

non-yellowing coloring

PaO:

pheophorbide a oxygenase

PPH:

pheophytinase

RCCR:

red chlorophyll catabolite reductase

SGR :

stay-green gene

References

  • Ainsworth EA, Yendrek CR, Skoneczka JA, et al. 2012 Accelerating yield potential in soybean: potential targets for biotechnological improvement. Plant. Cell Environ. 35 38–52

    CAS  PubMed  Google Scholar 

  • Apel K and Hirt H 2004 Reactive oxygen species: metabolism, oxidative stress, and signal transduction. Annu. Rev. Plant. Biol. 55 373–399

    CAS  PubMed  Google Scholar 

  • Armstead I, Donnison I, Aubry S, et al. 2006 From crop to model to crop: identifying the genetic basis of the staygreen mutation in the Lolium/Festuca forage and amenity grasses. New Phytol. 172 592–597

    PubMed  Google Scholar 

  • Audic S and Claverie JM 1997 The significance of digital gene expression profiles. Genome Res. 7 986–995

    CAS  PubMed  Google Scholar 

  • Barry CS, McQuinn R, Chung MY, et al. 2008 Amino acid substitutions in homologs of the STAY-GREEN protein are responsible for the green-flesh and chlorophyll retainer mutations of tomato and pepper. Plant Physiol. 147 179–187

    CAS  PubMed  PubMed Central  Google Scholar 

  • Benjamini Y and Yekutieli D 2001 The control of the false discovery rate in multiple testing under dependency. Ann. Stat. 29 1165–1188

    Google Scholar 

  • Berger H, Pachlinger R, Morozov I, Goller S, Narendja F, et al. 2006 The GATA factor AreA regulates localization and in vivo binding site occupancy of the nitrate activator NirA. Mol. Microbiol. 59 433–446

    CAS  PubMed  Google Scholar 

  • Besseau S, Li J and Palva ET 2012 WRKY54 and WRKY70 co-operate as negative regulators of leaf senescence in Arabidopsis thaliana. J. Exp. Bot. 63 2667–2679

    CAS  PubMed  PubMed Central  Google Scholar 

  • Borovsky Y and Paran I 2008 Chlorophyll breakdown during pepper fruit ripening in the chlorophyll retainer mutation is impaired at the homolog of the senescence-inducible stay-green gene. Theor. Appl. Genet. 117 235–240

    CAS  PubMed  Google Scholar 

  • Breeze E, Harrison E, McHattie S, et al. 2011 High-resolution temporal profiling of transcripts during Arabidopsis leaf senescence reveals a distinct chronology of processes and regulation. Plant Cell. 23 873–894

    CAS  PubMed  PubMed Central  Google Scholar 

  • Brown AV and Hudson KA 2017 Transcriptional profiling of mechanically and genetically sink-limited soybeans. Plant. Cell Environ. 40 2307–2318

    CAS  PubMed  Google Scholar 

  • Chang HX, Tan R, Hartman GL, Wen Z, Sang H, Domier LL and Chilvers MI 2019 Characterization of soybean STAY-GREEN genes in susceptibility to foliar chlorosis of sudden death syndrome. Plant Physiol. 180 711–717

    CAS  PubMed  PubMed Central  Google Scholar 

  • Chen L, Su ZZ, Huang L, Xia FN, Qi H, Xie LJ and Chen QF 2017 The AMP-activated protein kinase KIN10 is involved in the regulation of autophagy in Arabidopsis. Front. Plant. Sci. 8 1201

    PubMed  PubMed Central  Google Scholar 

  • Diaz-Mendoza, M, Velasco-Arroyo B, Santamaria ME, González-Melendi P, Martinez M and Diaz I 2016 Plant senescence and proteolysis: two processes with one destiny. Genet. Mol. Biol. 39 329–338

    CAS  PubMed  PubMed Central  Google Scholar 

  • Eckardt NA 2009 A new chlorophyll degradation pathway. Plant Cell. 21 700–700

    CAS  PubMed  PubMed Central  Google Scholar 

  • Eulgem T and Somssich IE 2007 Networks of WRKY transcription factors in defense signaling. Curr. Opin. Plant. Biol. 10 366–371

    CAS  PubMed  Google Scholar 

  • Fang C, Li C, Li W, et al. 2014 Concerted evolution of D1 and D2 to regulate chlorophyll degradation in soybean. Plant J. 77 700–712

    CAS  PubMed  Google Scholar 

  • Frugis G and Chua NH 2002 Ubiquitin-mediated proteolysis in plant hormone signal transduction. Trends Cell. Biol. 12 308–311

    CAS  PubMed  Google Scholar 

  • Gao L, Ding X, Li K, Liao W, Zhong Y, Ren R and Zhi H 2015 Characterization of Soybean mosaic virus resistance derived from inverted repeat-SMV-HC-Pro genes in multiple soybean cultivars. Theor. appl. Genet. 128 1489–1505.

    CAS  PubMed  Google Scholar 

  • Graham LE, Schippers JH, Dijkwel PP and Wagstaff C 2012 Ethylene and senescence processes. Ann. Plant. Rev. 44 275–304

    CAS  Google Scholar 

  • Gregersen PL 2011 Senescence and nutrient remobilization in crop plants; in Hawkesford MJ, Barraclough PB (eds) The molecular and physiological basis of nutrient use efficiency in crops (Blackwell, New York) pp 83–102

  • Guo YF and Gan SS 2012 Convergence and divergence in gene expression profiles induced by leaf senescence and 27 senescence-promoting hormonal, pathological and environmental stress treatments. Plant Cell. Environ. 35 644–655

    CAS  PubMed  Google Scholar 

  • Guo Y 2013 Towards systems biological understanding of leaf senescence. Plant Mol. Biol. 82 519–528

    CAS  PubMed  Google Scholar 

  • Horie Y, Ito H, Kusaba M, et al. 2009 Participation of chlorophyll b reductase in the initial step of the degradation of light-harvesting chlorophyll a/b-protein complexes in Arabidopsis. J. Biol. Chem. 284 17449–17456

    CAS  PubMed  PubMed Central  Google Scholar 

  • Hörtensteiner S and Kräutler B 2011 Chlorophyll breakdown in higher plants. BBA-Bioenergetics. 1807 977–988

    PubMed  Google Scholar 

  • Jakoby M, Weisshaar B, Dröge-Laser W, Vicente-Carbajosa J, Tiedemann J, et al. 2002 bZIP transcription factors in Arabidopsis. Trends Plant. Sci. 7 106–111

    CAS  PubMed  Google Scholar 

  • Jajic I, Sarna T, and Strzalka K 2015 Senescence, stress, and reactive oxygen species. Plants 4 393–411

    PubMed  PubMed Central  Google Scholar 

  • Jeong J and Guerinot ML 2009 Homing in on iron homeostasis in plants. Trends Plant. Sci. 14 280–285

    CAS  PubMed  Google Scholar 

  • Jiang H, Li M, Liang N, et al. 2007 Molecular cloning and function analysis of the stay-green gene in rice. Plant J. 52 197–209

    CAS  PubMed  Google Scholar 

  • Kanehisa M, Goto S, Kawashima S, Okuno Y and Hattori M 2004 The KEGG resource for deciphering the genome. Nucleic Acids Res. 32 277–280

    Google Scholar 

  • Kassahun B, Bidinger FR, Hash CT, et al. 2010 Stay-green expression in early generation sorghum [Sorghum bicolor (L.) Moench] QTL introgression lines. Euphytica 172 351–362

    Google Scholar 

  • Kosgey JR, Moot DJ, Fletcher AL, et al. 2013 Dry matter accumulation and post-silking N economy of ‘stay-green’maize (Zea mays L.) hybrids. Eur. J. Agron. 51 43–52

    Google Scholar 

  • Koyama T 2014 The roles of ethylene and transcription factors in the regulation of onset of leaf senescence. Front. Plant Sci. 5: 650–650

    PubMed  PubMed Central  Google Scholar 

  • Kusaba M, Tanaka A and Tanaka R 2013 Stay-green plants: what do they tell us about the molecular mechanism of leaf senescence. Photosynth. Res. 117 221–234

    CAS  PubMed  Google Scholar 

  • Lei Y, Zhou Z, Zhi T, Zhu Q and Ren C 2017 Sucrose enhances tyrosine-induced inhibition of growth in Arabidopsis seedlings. Agr. Sci. Tech. 18 753–755

    Google Scholar 

  • Li RJ, Wei H and Ying TL 2006 Arabidopsis cytosolic glutamine synthetase AtGLN1; 1 is a potential substrate of AtCRK3 involved in leaf senescence. Biochem. Bioph. Res. Co. 342 119–126

    CAS  Google Scholar 

  • Li Z, Wu S, Chen J, Wang X, Gao J, Ren G and Kuai B 2017 NYEs/SGRs-mediated chlorophyll degradation is critical for detoxification during seed maturation in Arabidopsis. Plant J. 92 650–661

    CAS  PubMed  Google Scholar 

  • Matile P, Hörtensteiner S, Thomas H 1999 Chlorophyll degradation. Annu. Rev. Plant. Biol. 50 67–95

    CAS  Google Scholar 

  • Miao Y, Laun T, Zimmermann P and Zentgraf U 2004 Targets of the WRKY53 transcription factor and its role during leaf senescence in Arabidopsis. Plant Mol. Biol. 55 853–867

    CAS  PubMed  Google Scholar 

  • Morita R, Sato Y, Masuda Y, et al. 2009 Defect in non‐yellow coloring 3, an α/β hydrolase-fold family protein, causes a stay-green phenotype during leaf senescence in rice. Plant J. 59 940–952

    CAS  PubMed  Google Scholar 

  • Nakano M, Yamada T, Masuda Y, et al. 2014 A green-cotyledon/stay-green mutant exemplifies the ancient whole-genome duplications in soybean. Plant Cell. Physiol. 55 1763–1771

    CAS  PubMed  Google Scholar 

  • Nakashima K, Takasaki H, Mizoi J, Shinozaki K and Yamaguchi SK 2012 NAC transcription factors in plant abiotic stress responses. BBA 1819 97–103.

    CAS  PubMed  Google Scholar 

  • Nayak SN, Agarwal G, Pandey MK, et al. 2017 Insights on host-pathogen interaction between groundnut (Arachis hypogaea) and Aspergillus flavus. In: InterDrought-V, February 21–25, 2017, Hyderabad, India

  • Ono Y, Wada S, Izumi M, et al. 2013 Evidence for contribution of autophagy to Rubisco degradation during leaf senescence in Arabidopsis thaliana. Plant. Cell. Environ. 36 1147–1159

    CAS  PubMed  Google Scholar 

  • Pfaffl MW 2001 A new mathematical model for relative quantification in real-time RT-PCR. Nucleic. Acids. Res. 29 e45

    CAS  PubMed  PubMed Central  Google Scholar 

  • Potschin M, Schlienger S, Bieker S and Zentgraf U 2014 Senescence networking: WRKY18 is an upstream regulator, a downstream target gene, and a protein interaction partner of WRKY53. J. Plant Growth Regul. 33 106–118

    CAS  Google Scholar 

  • Qin J, Ma X, Yi Z, Tang Z and Meng Y 2016 A transcriptome-wide study on the micro RNA-and the Argonaute 1-enriched small RNA-mediated regulatory networks involved in plant leaf senescence. Plant Biol. 18 197–205

    CAS  PubMed  Google Scholar 

  • Ranty B, Aldon D, Cotelle V, Galaud JP, Thuleau P and Mazars C 2016 Calcium sensors as key hubs in plant responses to biotic and abiotic stresses. Front. Plant Sci. 7 327

    PubMed  PubMed Central  Google Scholar 

  • Reddy NR, Ragimasalawada M, Sabbavarapu MM et al. 2014 Detection and validation of stay-green QTL in post-rainy sorghum involving widely adapted cultivar, M35–1 and a popular stay-green genotype B35. BMC Genomics 15 909

    Google Scholar 

  • Ren G, An K, Liao Y, et al. 2007 Identification of a novel chloroplast protein AtNYE1 regulating chlorophyll degradation during leaf senescence in Arabidopsis. Plant Physiol. 144 1429–1441

    CAS  PubMed  PubMed Central  Google Scholar 

  • Ren Y, Li Y, Jiang Y, Wu B and Miao Y 2017 Phosphorylation of WHIRLY1 by CIPK14 shifts its localization and dual functions in Arabidopsis. Mol. Plant 10 749–763

    CAS  PubMed  Google Scholar 

  • Rong H, Tang Y, Zhang H, et al. 2013 The Stay-Green Rice like (SGRL) gene regulates chlorophyll degradation in rice. J. Plant Physiol. 170 1367–1373

    CAS  PubMed  Google Scholar 

  • Ruan W and Lai M 2007 Actin, a reliable marker of internal control? Clin. Chim. Acta 385 1–5

    CAS  PubMed  Google Scholar 

  • Sakuraba Y, Schelbert S, Park S Y, et al. 2012 STAY-GREEN and chlorophyll catabolic enzymes interact at light-harvesting complex II for chlorophyll detoxification during leaf senescence in Arabidopsis. Plant Cell. 24 507–518

    CAS  PubMed  PubMed Central  Google Scholar 

  • Sakuraba Y, Kim YS, Yoo SC, et al. 2013 7-Hydroxymethyl chlorophyll a reductase functions in metabolic channeling of chlorophyll breakdown intermediates during leaf senescence. Biochem. Bioph. Res. Co. 430 32–37

    CAS  Google Scholar 

  • Sakuraba Y, Park SY, Kim YS, et al. 2014 Arabidopsis STAY-GREEN2 is a negative regulator of chlorophyll degradation during leaf senescence. Mol. Plant 7 1288–1302

    CAS  PubMed  Google Scholar 

  • Sakuraba Y, Park SY and Paek NC 2015 The divergent roles of STAYGREEN (SGR) homologs in chlorophyll degradation. Mol. Cell. 38 390

    CAS  Google Scholar 

  • Shen YH, Lu BG, Feng L, et al. 2017 Isolation of ripening-related genes from ethylene/1-MCP treated papaya through RNA-seq. BMC Genomics 18 671

    PubMed  PubMed Central  Google Scholar 

  • Shimoda Y, Ito H and Tanaka A 2016 Arabidopsis STAY-GREEN, Mendel’s green cotyledon gene, encodes magnesium-dechelatase. Plant Cell 28 2147–2160

    CAS  PubMed  PubMed Central  Google Scholar 

  • Shi S, Miao H, Du X, Gu J and Xiao K 2016 GmSGR1, a stay-green gene in soybean (Glycine max L.), plays an important role in regulating early leaf-yellowing phenotype and plant productivity under nitrogen deprivation. Acta Physiol. Plant 38 97

  • Singh KB, Foley RC and Oñate-Sánchez L 2002 Transcription factors in plant defense and stress responses. Curr. Opin. Plant Biol. 5 430–436

    CAS  PubMed  Google Scholar 

  • Spano G, Di Fonzo N, Perrotta C, et al. 2003 Physiological characterization of ‘stay-green’mutants in durum wheat. J. Exp. Bot. 54 1415–1420

    CAS  PubMed  Google Scholar 

  • Stracke R, Werber M and Weisshaar B 2001 The R2R3-MYB gene family in Arabidopsis thaliana. Curr. Opin. Plant Biol. 4 447–456

    CAS  PubMed  Google Scholar 

  • Teixeira RN, Ligterink W, França-Neto JDB, et al. 2016 Gene expression profiling of the green seed problem in soybean. BMC Plant Biol. 16 37

    PubMed  PubMed Central  Google Scholar 

  • Thomas H and Howarth CJ 2000 Five ways to stay-green. J. Exp. Bot. 51 329–337

    CAS  PubMed  Google Scholar 

  • Thomas H, Ougham H, Canter P, et al. 2002 What stay‐green mutants tell us about nitrogen remobilization in leaf senescence. J. Exp. Bot. 53 801–808

    CAS  PubMed  Google Scholar 

  • Thorrez L, Van Deun K, Tranchevent LC, et al. 2008 Using ribosomal protein genes as reference: a tale of caution. PLoS One 3 e1854

    PubMed  PubMed Central  Google Scholar 

  • Vandesompele J, De Preter K, Pattyn F, Poppr B, Van Roy N, et al. 2002 Accurate normalization of real-time quantitative RT-PCR date by geometric averaging of multiple internal control genes. Genome. Biol. https://doi.org/10.1186/gb-2002-3-7-research0034

    Article  PubMed  PubMed Central  Google Scholar 

  • Watanabe S, Nakagawa A, Izumi S, Shimada H and Sakamoto A 2010 RNA interference-mediated suppression of xanthine dehydrogenase reveals the role of purine metabolism in drought tolerance in Arabidopsis. FEBS. Lett. 584 1181–1186

    CAS  PubMed  Google Scholar 

  • Winkel-Shirley B 2002 Biosynthesis of flavonoids and effects of stress. Curr. Opin. Plant Biol. 5 218–223

    CAS  PubMed  Google Scholar 

  • Woo HR, Masclaux-Daubresse C and Lim PO 2018 Plant senescence: how plants know when and how to die. J. Exp. Bot. 69 715–718

    CAS  PubMed  PubMed Central  Google Scholar 

  • Wu L, Wang S, Tian L, et al. 2018 Comparative proteomic analysis of the maize responses to early leaf senescence induced by preventing pollination. J. Proteomics. 177 75–87

    CAS  PubMed  Google Scholar 

  • Yan J, He C, Wang J, et al. 2004 Overexpression of the Arabidopsis 14–3-3 protein GF14λ in cotton leads to a ‘stay-green’ phenotype and improves stress tolerance under moderate drought conditions. Plant Cell Physiol. 45 1007–1014

    CAS  PubMed  Google Scholar 

  • Xia W and Hou M 2018 Macrophage migration inhibitory factor rescues mesenchymal stem cells from doxorubicin-induced senescence though the PI3K-Akt signaling pathway. Int. J. Mol. Med. 41 1127–1137

    CAS  PubMed  Google Scholar 

  • YongZhong L, Qing L and Nengguo T 2006 Efficient isolation of RNA from fruit peel and pulp of ripening navel orange (Citrus sinensis Osbeck). J. Huazhong Agric. Univ. 25 300–304

    Google Scholar 

  • Zhou C, Han L, Pislariu C, et al. 2011a From model to crop: functional analysis of a STAY-GREEN gene in the model legume Medicago truncatula and effective use of the gene for alfalfa improvement. Plant Physiol. 157 1483–1496

    CAS  PubMed  PubMed Central  Google Scholar 

  • Zhou X, Jiang Y and Yu D 2011b WRKY22 transcription factor mediates dark-induced leaf senescence in Arabidopsis. Mol. Cell. 31 303–313

    CAS  Google Scholar 

  • Zwack PJ and Rashotte AM 2013 Cytokinin inhibition of leaf senescence. Plant Signal. Behav. 8 e24737

    PubMed  PubMed Central  Google Scholar 

Download references

Acknowledgements

The authors thank the National Science Foundation for Young Scientists of China (31301200), the National Natural Science Foundation of China (31371648), the General Plan for Scientific Research Projects of Beijing Education Commission (KM201810020006), and the Beijing Agricultural College Teacher’s Research Fund Project (SXQN2016104) for their support.

Author information

Author notes

  1. These authors contributed equally to this work.

Authors and Affiliations

  1. Beijing Key Laboratory of New Technology in Agricultural Application, College of Plant Science and Technology, Beijing University of Agriculture, Beijing, 102206, China

    Cheng Wang, Run Zhi Li, Ye Wang, Yang Ying Liu, Xin Zhang & Hao Xie

  2. Department of Plant Genetics and Breeding, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China

    Le Gao

Authors
  1. Cheng Wang
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Le Gao
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Run Zhi Li
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Ye Wang
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Yang Ying Liu
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Xin Zhang
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Hao Xie
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Hao Xie.

Additional information

Corresponding editor: Manchikatla Venkat Rajam

Electronic supplementary material

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Wang, C., Gao, L., Li, R.Z. et al. High-throughput sequencing reveals the molecular mechanisms determining the stay-green characteristic in soybeans. J Biosci 45, 103 (2020). https://doi.org/10.1007/s12038-020-00074-x

Download citation

  • Received:

  • Accepted:

  • Published:

  • DOI: https://doi.org/10.1007/s12038-020-00074-x

Keywords

Search

Navigation