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Genotyping-by-sequencing empowered genetic diversity analysis of Jordanian oat wild relative Avena sterilis

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Abstract

Recent advances in next generation sequencing technologies make genotyping-by-sequencing (GBS) more feasible for molecular characterization of plant germplasm with complex and unsequenced genomes. Here we applied the GBS technology to assess the genetic diversity of 275 hexaploid oat wild relative (Avena sterilis) plants collected from 24 natural populations in Jordan. Total genomic DNAs were extracted and digested with restriction enzymes PstI and MspI. Three Illumina MiSeq sequencing runs generated 556 paired-end FASTQ files with 127,128,438 raw sequences. Bioinformatics analysis identified an informative matrix of 275 samples × 12,999 SNP markers. Analysis revealed 52.4% of SNP variation residing among 24 populations and eight major genetic clusters of the samples. Most samples were grouped together within their original populations. A significant association of pairwise population genetic distances was found with latitudinal or longitudinal differences. Two natural populations were highly differentiated from the others, and 30 highly distinct A. sterilis samples were identified from seven populations. These findings are useful for understanding genetic variability and conservation of natural A. sterilis populations, and they demonstrate the advances of the GBS application for germplasm characterization of crop wild relatives with complex genomes.

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Acknowledgements

The authors would like to thank NARC team for their assistance in this research: Israa Al-Hasanat, Abd-Alnaser Mousa, and Ziad Tahabsom and Kalid Abu Lila from biodiversity and medicinal plant department, and Safa Mazahreh and Doaa Abu-Hamoor from GIS Unit from NARC. We also are grateful to the technical assistance of Dallas Kessler and Axel Diederichsen in acquisition and identification of the wild oat collections and of Murari Singh in diversity analysis, and the useful comments raised by two anonymous journal reviewers on the early version of the manuscript. This research was partly funded by Agriculture and Agri-Food Canada A-base Program to YB Fu.

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Authors and Affiliations

  1. National Agricultural Research Centre NARC, P.O. Box 639, Baq’a, 19381, Jordan

    Nawal Al-Hajaj

  2. Plant Gene Resources of Canada, Saskatoon Research and Development Centre, Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK, S7N 0X2, Canada

    Gregory W. Peterson, Carolee Horbach & Yong-Bi Fu

  3. ICARDA, Dalia Building 2nd Floor, Bashir El Kassar Street, Verdun, Beirut, 1108-2010, Lebanon

    Khaled Al-Shamaa

  4. Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Ave, Ottawa, ON, K1A 0C6, Canada

    Nicholas A. Tinker

Authors
  1. Nawal Al-Hajaj
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  2. Gregory W. Peterson
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  3. Carolee Horbach
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  4. Khaled Al-Shamaa
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  5. Nicholas A. Tinker
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  6. Yong-Bi Fu
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Contributions

YBF and NA conceived the collaborative research. YBF designed the project. NA collected the germplasm in Jordan. GWP and CH conducted the GBS analysis. YBF, GWP and NAT conducted the GBS data analysis and genetic diversity analysis. KA contributed to the genetic diversity analysis. YBF and NA wrote the paper. All authors contributed to and approved the manuscript.

Corresponding authors

Correspondence to Nawal Al-Hajaj or Yong-Bi Fu.

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The authors declare that they have no conflict of interest.

Ethical standards

The experiment complies with the current laws of Jordan and Canada in which it was performed.

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Al-Hajaj, N., Peterson, G.W., Horbach, C. et al. Genotyping-by-sequencing empowered genetic diversity analysis of Jordanian oat wild relative Avena sterilis. Genet Resour Crop Evol 65, 2069–2082 (2018). https://doi.org/10.1007/s10722-018-0674-x

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