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Discovery and Utilization of EST-SSR Marker Resource for Genetic Diversity and Population Structure Analyses of a Subtropical Bamboo, Dendrocalamus hamiltonii

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Abstract

Dendrocalamus hamiltonii is a giant bamboo species native to Indian subcontinent with high economic importance. Nevertheless, highly outcross nature and flowering once in decades impose severe limitation in its propagation. Identification and mixed cultivation of genetically diverse genotypes may assist successful breeding and natural recombination of desirable traits. Characterization of existing genetic diversity and population structure are indispensable for efficient implementation of such strategies, which is facing a major challenge due to non-availability of sequence-based markers for the species. In this study, 8121 EST-SSR markers were mined from D. hamiltonii transcriptome data. Among all, tri-repeats were most represented (52%), with the abundance of CCG/CGG repeat motif. A set of 114 polymorphic markers encompassing epigenetic regulators, transcription factors, cell cycle regulators, signaling, and cell wall biogenesis, detected polymorphism and interaction (in silico) with important genes, that might have role in bamboo growth and development. Genetic diversity and population structure of the three D. hamiltonii populations (72 individuals) revealed moderate to high-level genetic diversity (mean alleles per locus: 5.8; mean PIC: 0.44) using neutral EST-SSR markers. AMOVA analysis suggests maximum diversity (59%) exists within population. High genetic differentiation (Gst = 0.338) and low gene flow (Nm = 0.49) were evident among populations. Further, PCoA, dendrogram, and Bayesian STRUCTURE analysis clustered three populations into two major groups based on geographical separations. In future, SSR marker resources created can be used for systematic breeding and implementation of conservation plans for sustainable utilization of bamboo complex.

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Acknowledgements

We acknowledge funding from CSIR research Grant MLP071. This is IHBT communication No. 4126.

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  1. Vikas Sharma

    Present address: Sant Baba Bhag Singh University, Khiala, Jalandhar, India

Authors and Affiliations

  1. Molecular Genetics & Genomics Lab, Department of Biotechnology, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, India

    Abhishek Bhandawat, Vikas Sharma, Pradeep Singh, Romit Seth, Akshay Nag & Ram Kumar Sharma

  2. Department of Biotechnology, Panjab University, Chandigarh, India

    Abhishek Bhandawat & Jagdeep Kaur

  3. Academy of Scientific and Innovative Research (AcSIR), CSIR-IHBT, Palampur, Himachal Pradesh, 176061, India

    Ram Kumar Sharma

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Contributions

AB, RKS: Conceived and designed the experiments; AB, V.S., RS: Performed the experiments; AB, AN, PS, RS: Analyzed the data; AB, RKS: wrote the paper; JK: Helped in data interpretations; RKS: Editing and approval of final version of manuscript.

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Correspondence to Ram Kumar Sharma.

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10528_2019_9914_MOESM1_ESM.tif

Fig. S1 Classification of Simple Sequence Repeats (SSRs) derived from D. hamiltonii transcriptome. Supplementary file1 (TIFF 2007 kb)

10528_2019_9914_MOESM2_ESM.tif

Fig. S2 Kyoto Encyclopedia of Gene and Genomes (KEGG) classification of SSR transcripts under four major categories A: cellular process, B: Environmental Information Processing, C: Genetic Information Processing and D: Metabolism. Supplementary file2 (DOCX 1565 kb)

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Fig. S3 Eukaryotic Cluster of Orthologous Groups (KOG) classification of SSR transcripts. Supplementary file3 (DOCX 1361 kb)

Fig. S4 Gene ontology classification of SSR containing transcripts in D. hamiltonii. Supplementary file4 (TIFF 1392 kb)

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Fig. S5 Gene ontology enrichment of SSR transcripts under biological process category. Supplementary file5 (TIFF 263 kb)

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Fig. S6 Gene ontology enrichment of SSR transcripts under molecular function category. Supplementary file6 (TIFF 156 kb)

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Fig. S7 Gene ontology enrichment of SSR transcripts under cellular component category. Supplementary file7 (TIFF 256 kb)

10528_2019_9914_MOESM8_ESM.tif

Fig. S8 BayeScan 2.0 plot of 231 alleles representing 40 SSR locus across 72 individuals from 3 populations from India. FST is plotted against the log10 of the posterior odds (PO). The vertical line shows the critical PO used for identifying outlier markers. Two markers on the right side of the vertical line are candidates for being under positive selection. Supplementary file8 (TIFF 14487 kb)

10528_2019_9914_MOESM9_ESM.tif

Fig. S9 Multiple sequence alignment of allelic variants of SSR locus: (a) DHTMS-45878; GAG-repeat, (b) DHTMS-1233; TCA-repeat, (c) DHTMS-22356; CTT-repeat. Region highlighted in green represents SSR locus, while dark region represents indels/point mutations. Supplementary file9 (TIFF 803 kb)

Fig. S10 In silico mapping of D. hamiltonii SSR locus on Supplementary file10 (TIFF 608 kb)

Table S1 Supplementary file11 (DOCX 25 kb)

Table S2 Supplementary file12 (XLS 4124 kb)

Table S3 Supplementary file13 (XLS 30 kb)

Table S4 Supplementary file14 (XLS 485 kb)

Table S5 Supplementary file15 (XLS 92 kb)

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Bhandawat, A., Sharma, V., Singh, P. et al. Discovery and Utilization of EST-SSR Marker Resource for Genetic Diversity and Population Structure Analyses of a Subtropical Bamboo, Dendrocalamus hamiltonii. Biochem Genet 57, 652–672 (2019). https://doi.org/10.1007/s10528-019-09914-4

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