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The first Illumina-based de novo transcriptome analysis and molecular marker development in Napier grass (Pennisetum purpureum)

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Abstract

Pennisetum purpureum belongs to the Pennisetum Rich genus in the family Poaceae. It is widely grown in subtropical and tropical regions as one of the most economically important cereal crops. Despite its importance, there is limited genomic data available for P. purpureum, which restricts genetic and breeding studies in this species. In the present study, the transcriptome of P. purpureum was assembled de novo and used to characterize two important P. purpureum cultivars: P. purpureum Schumab cv. Purple and P. purpureum cv. Mott. After assembly, a total of 197,466 unigenes were obtained for ‘Purple’ and ‘Mott’ and 103,454 of these unigenes were successfully annotated. From ‘Purple’ and ‘Mott,’ 214,648 SNPs and 21,213 EST-SSRs were identified in 40,259 unigenes and 18,587 unigenes respectively. Moreover, 50 EST-SSR primers and 6 SNP primers were designed to validate the identified markers. The transcriptomic data of present study from the two P. purpureum cultivars provides an abundant amount of available genomic information for Pennisetum. In addition, the identified SNPs and EST-SSRs will facilitate genetic and molecular studies within the Pennisetum genus.

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Acknowledgements

We thank Tomas Hasing Rodriguez who helped polish this manuscript.

Funding

The authors gratefully acknowledge the financial support from the National Project on Sci-Tec Foundation Resources Survey (2017FY100602), Sichuan Province Breeding Research Grant (2016NZ0098-11), and Modern Agricultural Industry System Sichuan Forage Innovation Team.

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Authors and Affiliations

  1. Department of Grassland Science, Faculty of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China

    Sifan Zhou, Chengran Wang, Haidong Yan, Peilin Chen, Linkai Huang, Xinquan Zhang, Yan Peng, Xiao Ma & Yanhong Yan

  2. Department of Plant Sciences, University of Tennessee, Knoxville, TN, 37996, USA

    Taylor P. Frazier

  3. National Animal Husbandry Service, Ministry of Agriculture, Beijing, 100026, China

    Zhihong Chen

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  1. Sifan Zhou
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  2. Chengran Wang
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Contributions

L.K.H. and X.Q.Z. designed research studies; S.F.Z., C.R.W., and H.D.Y. conducted experiments, acquired data, and analyzed data; L.K.H., X.Q.Z., Y.P., X.M., and Y.H.Y. provided the experimental equipment; S.F.Z. and P.L.C. wrote the manuscript; T.P.F. and Z.H.C. revised the manuscript.

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Correspondence to Linkai Huang.

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The authors declare that they have no conflict of interest.

Data archiving statement

Raw Illumina reads were deposited in NCBI SRA: SRP100008.

Electronic supplementary material

Fig. S1

The length distribution of CDSs mapped to known genes by BLAST. (PNG 89 kb)

High resolution image (TIFF 135890 kb)

Fig. S2

The length distribution of CDSs mapped to known genes by ESTScan. (PNG 85 kb)

High resolution image (TIFF 135890 kb)

Figure S3

UPGMA dendrogram based on Nei’s genetic diversity between the seventeen Pennisetum species. (PNG 258 kb)

High resolution image (TIFF 135890 kb)

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Zhou, S., Wang, C., Frazier, T.P. et al. The first Illumina-based de novo transcriptome analysis and molecular marker development in Napier grass (Pennisetum purpureum). Mol Breeding 38, 95 (2018). https://doi.org/10.1007/s11032-018-0852-8

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  • DOI: https://doi.org/10.1007/s11032-018-0852-8

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