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Genetic diversity and genome-wide association analysis in Chinese hulless oat germplasm

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Abstract

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Genotyping-by-sequencing (GBS)-derived molecular markers reveal the distinct genetic population structure and relatively narrow genetic diversity of Chinese hulless oat landraces. Four markers linked to the naked grain gene (N1) are identified by genome-wide association study (GWAS).

Abstract

Interest in hulless oat (Avena sativa ssp. nuda), a variant of common oat (A. sativa) domesticated in Western Asia, has increased in recent years due to its free-threshing attribute and its domestication history. However, the genetic diversity and population structure of hulless oat, as well as the genetic mechanism of hullessness, are poorly understood. In this study, the genetic diversity and population structure of a worldwide sample of 805 oat lines including 186 hulless oats were investigated using genotyping-by-sequencing. Population structure analyses showed a strong genetic differentiation between hulless landraces vs other oat lines, including the modern hulless cultivars. The distinct subpopulation stratification of hulless landraces and their low genetic diversity suggests that a domestication bottleneck existed in hulless landraces. Additionally, low genetic diversity within European oats and strong differentiation between the spring oats and southern origin oat lines revealed by previous studies were also observed in this study. Genomic regions contributing to these genetic differentiations suggest that genetic loci related to growth habit and stress resistance may have been under intense selection, rather than the hulless-related genomic regions. Genome-wide association analysis detected four markers that were highly associated with hullessness. Three of these were mapped on linkage group Mrg21 at a genetic position between 195.7 and 212.1 cM, providing robust evidence that the dominant N1 locus located on Mrg21 is the single major factor controlling this trait.

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Acknowledgements

We gratefully acknowledge the professional and technical assistance provided by Charlene Wight.

Funding

This work was supported by the National Natural Science Foundation of China (Grant Nos. 31571739, 31801430) and the Sichuan International (Hong Kong/Macao/Taiwan) Innovation Cooperation in Science and Technology (Grant No. 2019YFH0125).

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  1. Honghai Yan and Pingping Zhou contributed equally to this work.

Authors and Affiliations

  1. Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China

    Honghai Yan, Pingping Zhou, Yun Peng & Yuanying Peng

  2. Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, 960 Carling Ave, Ottawa, ON, K1A0C6, Canada

    Wubishet A. Bekele & Nicholas A. Tinker

  3. Baicheng Academy of Agricultural Sciences, Baicheng, 137000, China

    Changzhong Ren

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  1. Honghai Yan
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Contributions

YYP and NAT conceived and designed the experiments. HY and PZ conducted experiments and analyzed the data, and HY drafted the manuscript. YP contributed to preparation of reagents and materials. RC contributed to interpretation of results. WAB, NAT and YYP assisted with the interpretation of results and revised the manuscript. All authors read and approved the final manuscript.

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Correspondence to Nicholas A. Tinker or Yuanying Peng.

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Supplementary file1 (XLSX 112 kb)

122_2020_3674_MOESM2_ESM.tif

Fig. S1 Number of haplotypes called by discovery (a) and production (b) modes after population-based filtering and the percentage of distribution of minor allele frequency (MAF) of these haplotypes in the panel of 158 Chinese hulless oat lines (CN Panel). Haplotypes with MAF < 0.05 were filtered out (TIF 686 kb)

Fig. S2 PCoA analysis based on markers called using Haplotag production mode (TIF 252 kb)

122_2020_3674_MOESM4_ESM.tif

Fig. S3 Percentage of distribution of minor allele frequency (MAF) of 8675 haplotypes called from 728 oat lines in the full panel. Haplotypes with MAF < 0.05 were filtered out (TIF 163 kb)

122_2020_3674_MOESM5_ESM.tif

Fig. S4 Grouping results of 158 Chinese hulless oats at K = 6. Oat lines with membership probability less than 0.6 of either subgroup were grouped into admixture group (AD) (TIF 830 kb)

Fig. S5 Neighbor-joining (NJ) tree of 158 Chinese hulless oats based on 3093 haplotypes (TIF 185 kb)

122_2020_3674_MOESM7_ESM.tif

Fig. S6 Plot of the eigenvalues of the first 15 principal coordinates (PCs) in an analysis of the full panel (TIF 54 kb)

122_2020_3674_MOESM8_ESM.pdf

Fig. S7 Heatmaps for linkage disequilibrium (LD) by using uncorrected value of r2 as well as corrected value of r2 by population structure (rs2), kinship (rk2), and both (rsk2) (PDF 1496 kb)

122_2020_3674_MOESM9_ESM.pdf

Fig. S8 Linkage disequilibrium (LD) decay rate in each individual chromosomes (linkage groups).Critical LD value is shown as horizontal broken lines at 0.167 (PDF 1592 kb)

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Yan, H., Zhou, P., Peng, Y. et al. Genetic diversity and genome-wide association analysis in Chinese hulless oat germplasm. Theor Appl Genet 133, 3365–3380 (2020). https://doi.org/10.1007/s00122-020-03674-1

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