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Genome survey sequencing of purple elephant grass (Pennisetum purpureum Schum ‘Zise’) and identification of its SSR markers

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Abstract

Elephant grass (Pennisetum purpureum) is a perennial grass in the Poaceae family with high tolerance and one of the best forage plants. Despite its economic importance, the inheritance information of P. purpureum has remained largely unknown. To obtain the whole reference genome, we first conducted a genome survey of P. purpureum. Next-generation sequencing (NGS) was used to perform the de novo whole genome sequencing. As a result, the estimated genome size of elephant grass was 2.01 Gb, with 71.36% repetitive elements. The heterozygosity was 1.02%, which indicates a highly heterozygous genome. The retroelements (9.36%) were the most repetitive elements, followed by DNA transposons (3.66%). In the meantime, 83,706 high-quality genomic simple sequence repeat (SSR) markers, in which the greatest SSR unit length was 3, were developed. Thirty pairs of SSR markers were randomly selected to verify the efficiency and all of them yielded clear amplification products, among which 28 pairs (93.3%) of the primers showed polymorphism. The genome data obtained in this research provided a large amount of gene resources for further investigating Pennisetum species.

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Acknowledgements

The authors gratefully acknowledge the financial support from the Modern Agro-industry Technology Research System (CARS-34), a Sichuan Province Breeding Research grant (2016NZ0098-11) and the Agricultural Industry System Sichuan Forage Innovation Team.

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Authors and Affiliations

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

    Chengran Wang, Ji Li, Sifan Zhou, Ting Liu, Xinquan Zhang & Linkai Huang

  2. Department of Horticulture, Virginia Tech, Blacksburg, VA, 24061, USA

    Haidong Yan

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  1. Chengran Wang
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  2. Haidong Yan
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  3. Ji Li
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Correspondence to Linkai Huang.

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Raw Illumina reads were deposited in the NCBI Sequence Read Archive (SRA): SRP129764.

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Wang, C., Yan, H., Li, J. et al. Genome survey sequencing of purple elephant grass (Pennisetum purpureum Schum ‘Zise’) and identification of its SSR markers. Mol Breeding 38, 94 (2018). https://doi.org/10.1007/s11032-018-0849-3

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