Skip to main content
SpringerLink
Log in

Prospects for the study of genetic variation among Moso bamboo wild-type and variants through genome resequencing

  • Original Article
  • Published:
Trees Aims and scope Submit manuscript

Abstract

Key message

A large number of genome regions exhibit high diversity among Moso bamboo species which can be used in marker-assisted selection programs to detect unique SNPs and Indels for variant fingerprinting to the bamboo development.

Abstract

Moso bamboo (Phyllostachys edulis (Carrière) J. Houz.) is one of the most important bamboo species worldwide. Since the sequencing of its reference genome, the interest in genome-wide structural variations (SV) of Moso bamboo cultivars and variants has grown. To investigate the genetic polymorphism of Moso bamboo, we selected one wild-type (WT) with normal colour internodes in green and two variants, one having yellow internodes with regularly interval green stripes (Ph. edulis (Carr.) Mitford cv. Viridisulcata) (PhV), and the other having green internodes with regularly interval yellow stripes (Ph. edulis (Carr.) Mitford cv. Luteosulcata) (PhL). We re-sequenced the genomes of three Moso bamboo species with an average genome coverage of at least 30x. A total of 4,700,803 unique single nucleotide polymorphisms (Uni-SNPs) and 268,150 unique InDels (Uni-Indels) were identified across the genome of three Moso bamboo species. Additionally, we detected 215,297 unique regions with SV and 65,935 unique regions with copy-number variations (CNVs) that could help to explain the divergence among the three accessions evaluated. A total of 24,303 new transposable elements (TEs) insertion sites were identified in three Moso bamboo species. Additionally, SNP mutations, InDel mutations and CNVs located in coding regions were enriched for gene ontology (GO) and Kyoto Encyclopaedia of Genes and Genomes (KEGG) pathways analysis. The analysis confirmed that allelic variations in genes were linked with many pathways such as ribosome biogenesis, caffeine metabolism, anion binding, carbohydrate derivative binding and ribonucleotide binding. The results presented a large number of highly diverse genomic regions of Moso bamboo indicating clear evolutionary separation of internode colour variants. A large number of allelic and SV identified in this study can be of potential use in variant fingerprinting and in breeding programs.

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

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6

Similar content being viewed by others

Abbreviations

WT:

Wild-type

PhV:

Ph. edulis (Carr.) Mitford cv. Viridisulcata

PhL:

Ph. edulis (Carr.) Mitford cv. Luteosulcata

SNPs:

Single nucleotide polymorphisms

CNVs:

Copy-number variations

SVs:

Structure variations

ts/tv:

Transition/transversion

dN/dS:

Non-synonymous mutation to synonymous mutation

GO:

Gene Ontology

KEGG:

Kyoto Encyclopaedia of Genes and Genomes

TEs:

Transposable elements

References

  • Abyzov A, Urban AE, Snyder M, Gerstein M (2011) CNVnator: an approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing. Genome Res 21(6):974–984

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • An MM, Guo C, Lin PP, Zhou MB (2016) Heterogeneous evolution of Ty3-gypsy retroelements among bamboo species. Genet Mol Res 15(3)

  • Barbazuk WB, Emrich SJ, Chen HD, Li L, Schnable PS (2007) SNP discovery via 454 transcriptome sequencing. Plant J 51:910–918

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Bennetzen JL, Wang H (2014) The contributions of transposable elements to the structure, function, and evolution of plant genomes. Annu Rev Plant Biol 65:505–530

    Article  CAS  PubMed  Google Scholar 

  • Causse M, Desplat N, Pascual L, Le Paslier MC, Sauvage C, Bauchet G, Bérard A, Bounon R, Tchoumakov M, Brunel D, Bouchet JP (2013) Whole-genome resequencing in tomato reveals variation associated with introgression and breeding events. BMC Genom 14:791

    Article  CAS  Google Scholar 

  • Chen J, Wrightsman TR, Wessler SR, Stajich JE (2017) RelocaTE2: a high-resolution transposable element insertion site mapping tool for population resequencing. Peer J 5:e2942. https://doi.org/10.7717/peerj.2942. (eCollection 2017)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Cook D, Bayless A, Wang K, Guo X, Song Q, Jiang J, Bent A (2014) Distinct copy number, coding sequence and locus methylation patterns underlie Rhg1-mediated soybean resistance to soybean cyst nematode. Plant Physiol 165:630–647

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Dou Y, Yu X (2008) Development and comparison of the world bamboo industry. World Agric 7:18–21

    Google Scholar 

  • Fan X, Abbott TE, Larson D, Chen K (2014) BreakDancer: identification of genomic structural variation from paired-end read mapping. Curr Protoc Bioinform 45:15.6.1–11

    Google Scholar 

  • Fu J (2001) Chinese Moso Bamboo: it’s importance. Bamboo 22:5–7

    Google Scholar 

  • Gan X, Stegle O, Behr J, Steffen JG, Drewe P, Hildebrand KL, Lyngsoe R, Schultheiss SJ, Osborne EJ, Sreedharan VT, Kahles A, Bohnert R, Jean G, Derwent P, Kersey P, Belfield EJ, Harberd NP, Kemen E, Toomajian C, Kover PX, Clark R, Rätsch G, Mott R (2011) Multiple reference genomes and transcriptomes for Arabidopsis thaliana. Nature 477:419–423

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Gui Y, Wang S, Quan L, Zhou C, Long S, Zheng H, Jin L, Zhang X, Ma N, Fan L (2007) Genome size and sequence composition of moso bamboo: a comparative study. Sci China Ser C Life Sci 50:1–6

    Article  CAS  Google Scholar 

  • Lai JS, Li RQ, Xu X, Jin WW, Xu ML, Zhao HN, Xiang ZK, Song WB, Ying K, Zhang M, Jiao YP, Ni PX, Zhang JG, Li D, Guo XS, Ye KX, Jian M, Wang B, Zheng HS, Liang HQ, Zhang XQ, Wang SC, Chen SJ, Li JS, Fu Y, Springer NM, Yang HM, Wang JA, Dai JR, Schnable PS, Wang J (2010) Genome-wide patterns of genetic variation among elite maize inbred lines. Nat Genet 42:1027–1030

    Article  CAS  PubMed  Google Scholar 

  • Lam HM, Xu X, Liu X, Chen W, Yang G, Wong FL, Li MW, He W, Qin N, Wang B, Li J, Jian M, Wang J, Shao G, Wang J, Sai-Ming Sun S, Zhang G (2010) Resequencing of 31 wild and cultivated soybean genomes identifies patterns of genetic diversity and selection. Nat Genet 42:1053–1059

    Article  CAS  PubMed  Google Scholar 

  • Li H, Durbin R (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25:1754–1760

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Liu Dedi X, Yufang L Lanying (2005) Discussion on the development of bamboo industry in Anji country. For Econ 25:25–29

    Google Scholar 

  • Mace ES, Tai S, Gilding EK, Li Y, Prentis PJ, Bian L (2013) Whole-genome sequencing reveals untapped genetic potential in Africa’s indigenous cereal crop sorghum. Nat Commun 4:2320

    Article  PubMed  Google Scholar 

  • Mao X, Cai T, Olyarchuk JG, Wei L (2005) Automated genome annotation and pathway identification using the KEGG Orthology (KO) as a controlled vocabulary. Bioinformatics 21:3787–3793

    Article  CAS  PubMed  Google Scholar 

  • Ossowski S, Schneeberger K, Clark RM, Lanz C, Warthmann N, Weigel D (2008) Sequencing of natural strains of Arabidopsis thaliana with short reads. Genome Res 18:2024–2033

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Peng Z, Lu Y, Li L, Zhao Q, Feng Q, Gao Z, Lu H, Hu T, Yao N, Liu K, Li Y, Fan D, Guo Y, Li W, Lu Y, Weng Q, Zhou C, Zhang L, Huang T, Zhao Y, Zhu C, Liu X, Yang X, Wang T, Miao K, Zhuang C, Cao X, Tang W, Liu G, Liu Y, Chen J, Liu Z, Yuan L, Liu Z, Huang X, Lu T, Fei B, Ning Z, Han B, Jiang Z (2013) The draft genome of the fast-growing non-timber forest species moso bamboo (Phyllostachys heterocycla). Nat Genet 45:456–461

    Article  CAS  PubMed  Google Scholar 

  • Subbaiyan GK, Waters DLE, Katiyar SK, Sadananda AR, Vaddadi S, Henry RJ (2012) Genome-wide DNA polymorphisms in elite indica rice inbreds discovered by whole-genome sequencing. Plant Biotech J 10:623–634

    Article  CAS  Google Scholar 

  • Tennessen JA (2008) Positive selection drives a correlation between non-synonymous/synonymous divergence and functional divergence. Bioinformatics 24(12):1421–1425

    Article  CAS  PubMed  Google Scholar 

  • Watanabe M, Ueda K, Manabe I, Akai T (1982) Flowering, seeding, germination and flowering periodicity of Phyllostachys pubescens. J Jpn For Soc 64:107–111

    Google Scholar 

  • Xu X, Liu X, Ge S, Jensen JD, Hu F, Li X (2012) Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes. Nat Biotechnol 30:105–111

    Article  CAS  Google Scholar 

  • Young MD, Wakefield MJ, Smyth GK, Oshlack A (2010) Gene ontology analysis for RNA-seq: accounting for selection bias. Genome Biol 11:R14

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zhong H, Zhou MB, Xu CM, Tang DQ (2010) Diversity and evolution of Pong-like elements in Bambusoideae subfamily. Biochem Syst Ecol 38:750–758

    Article  CAS  Google Scholar 

  • Zhou MB, Lu JJ, Zhong H, Liu XM, Tang DQ (2010a) Distribution and diversity of PIF-like transposable elements in the Bambusoideae subfamily. Plant Sci 179:257–266

    Article  CAS  Google Scholar 

  • Zhou MB, Lu JJ, Zhong H, Tang KX, Tang DQ (2010b) Distribution and polymorphism of mariner-like elements in the Bambusoideae subfamily. Plant Syst Evol 289:1–11

    Article  CAS  Google Scholar 

  • Zhou MB, Zhong H, Zhang QH, Tang KX, Tang DQ (2010c) Diversity and evolution of Ty1-copia retroelements in representative tribes of Bambusoideae subfamily. Genetica 138:861–868

    Article  PubMed  Google Scholar 

  • Zhou MB, Liu XM, Tang DQ (2011a) Transposable elements in Phyllostachys pubescens (Poaceae) genome survey sequences and the full-length cDNA sequences, and their association with simple-sequence repeats. Genet Mol Res 10(4):3026–3037

    Article  CAS  PubMed  Google Scholar 

  • Zhou MB, Zhong H, Tang DQ (2011b) Isolation and characterization of seventy-nine full-length mariner-like transposases in the Bambusoideae subfamily. J Plant Res 124:607–617

    Article  CAS  PubMed  Google Scholar 

  • Zhou Z, Jiang Y, Wang Z, Gou Z, Lyu J, Li W, Yu Y, Shu L, Zhao Y, Ma Y, Fang C, Shen Y, Liu T, Li C, Li Q, Wu M, Wang M, Wu Y, Dong Y, Wan W, Wang X, Ding Z, Gao Y, Xiang H, Zhu B, Lee S-H, Wang W, Tian Z (2015) Resequencing 302 wild and cultivated accessions identifies genes related to domestication and improvement in soybean. Nat Biotechnol 33:408–414

    Article  CAS  PubMed  Google Scholar 

  • Zhou M, Tao G, Pi P, Zhu Y, Bai Y, Meng X (2016) Genome-wide characterization and evolution analysis of miniature inverted-repeat transposable elements (MITEs) in moso bamboo (Phyllostachys heterocycla). Planta 244:775–787

    Article  CAS  PubMed  Google Scholar 

  • Zhou M, Hu B, Zhu Y (2017a) Genome-wide characterization and evolution analysis of long terminal repeat retroelements in moso bamboo (Phyllostachys edulis). Tree Genetics Genomes 13:43. https://doi.org/10.1007/s11295-017-1114-3

    Article  Google Scholar 

  • Zhou M, Zhu Y, Bai Y, Hänninen K, Meng X (2017b) Transcriptionally active LTR retroelement-related sequences and their relationship with small RNA in moso bamboo (Phyllostachys edulis). Mol Breeding 37:132. https://doi.org/10.1007/s11032-017-0733-6

    Article  CAS  Google Scholar 

Download references

Acknowledgements

This work was supported by the grant from the National Natural Science Foundation of China (Grant Nos. 31470615 and 31870656).

Author information

Authors and Affiliations

  1. The State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin’an, 311300, Zhejiang Province, People’s Republic of China

    Ming-bing Zhou, Jia-jun Wu, M. Ramakrishnan & Xian-wen Meng

  2. Zhejiang Provincial Collaborative Innovation Center for Bamboo Resources and High-Efficiency Utilization, Zhejiang A&F University, Lin’an, 311300, Zhejiang Province, People’s Republic of China

    Ming-bing Zhou

  3. Rice Breeding and Genetics Research Centre, ICAR-Indian Agricultural Research Institute, Aduthurai, Tamil Nadu, India

    K. K. Vinod

Authors
  1. Ming-bing Zhou
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Jia-jun Wu
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. M. Ramakrishnan
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Xian-wen Meng
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. K. K. Vinod
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

MBZ conceived and designed the study, JJW performed DNA extraction and sent the samples for sequencing, MBZ and XWM performed the bioinformatics resequencing data analysis workflow for SNPs, InDels, CNVs, SVs, TE insertions calling and interpretation data; RM performed data analysis, interpreted the results and wrote the manuscript; RM and KKV revised and edited the paper. All authors have read and approved the final manuscript.

Corresponding author

Correspondence to Ming-bing Zhou.

Ethics declarations

Conflict of interest

The authors declare that the research work was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Additional information

Communicated by Carlson.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary material 1 (DOCX 364 KB)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Zhou, Mb., Wu, Jj., Ramakrishnan, M. et al. Prospects for the study of genetic variation among Moso bamboo wild-type and variants through genome resequencing. Trees 33, 371–381 (2019). https://doi.org/10.1007/s00468-018-1783-z

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00468-018-1783-z

Keywords

Search

Navigation