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Genome-Wide Association Studies (GWAS) for Yield and Weevil Resistance in Sweet potato (Ipomoea batatas (L.) Lam)

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We apply the GWAS to sweet potato genome, and identified the SNPs associated with yield and weevil resistance.

Abstract

The sweet potato (Ipomoea batatas (L.) Lam) is a highly heterozygous, outcrossing, polyploid species, which presents challenges for genetic analysis. Therefore, we considered that genome-wide association studies (GWAS) may be applied to the study of the sweet potato genome. The yield of two sweet potato varieties [Purple Sweet Lord (PSL) and 90IDN-47] was assessed at two locations (Kumamoto and Okinawa prefectures) in Japan in 2013 and the yield scores were used for GWAS. The results showed that there were several single nucleotide polymorphisms (SNP) above the significance thresholds in PSL; two peaks were detected in Kumamoto and Okinawa on the Ib03-3 and Ib01-4 linkage groups of PSL, respectively. As for 90IDN-47, one relatively high peak was detected in Kumamoto on the Ib13-8 linkage group. Interestingly, although high peaks above significance thresholds were detected in Kumamoto and Okinawa in PSL, the peaks were located in different linkage groups. This result suggests that the genetic regions controlling yield may change in response to environmental conditions. Additionally, we investigated the degree of weevil damage to the plants, which is the greatest problem in sweet potato cultivation in Okinawa. In this experiment, no SNPs were identified above the significance thresholds. However, one relatively high peak was found in the 90IDN-47 genotype, which showed resistance to weevils. On the other hand, one relatively high peak was also detected in the PSL genotype, which showed susceptibility to weevils. These results suggest that two regions could affect weevil resistance and may contain the gene(s) controlling weevil resistance.

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Acknowledgements

A part of this study was supported by a grant from the Ministry of Agriculture, Forestry, and Fisheries of Japan (Genomics-based Technology for Agricultural Improvement, SFC-3003).

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Authors and Affiliations

  1. Kyushu Okinawa Agricultural Research Center, NARO, 820 Makabe, Itoman, Okinawa, 901-0336, Japan

    Yoshihiro Okada

  2. Graduate School of Environmental and Life Science, Okayama University, 1-1-1 Tsushimanaka Kitaku, Okayama, Okayama, 700-8530, Japan

    Yuki Monden, Kanoko Nokihara & Makoto Tahara

  3. Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba, 292-0818, Japan

    Kenta Shirasawa & Sachiko Isobe

Authors
  1. Yoshihiro Okada
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  2. Yuki Monden
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  3. Kanoko Nokihara
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  4. Kenta Shirasawa
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  5. Sachiko Isobe
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  6. Makoto Tahara
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Contributions

YO, KS, SI, MT and YM conceived and designed research. YO, KS and YM performed the experiment. KS, KN and YM analyzed the data. YO and YM wrote the manuscript. All authors read and approved the manuscript.

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Correspondence to Yoshihiro Okada.

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The authors declare that they have no conflicts of interest.

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Communicated by Sang-Soo Kwak.

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Okada, Y., Monden, Y., Nokihara, K. et al. Genome-Wide Association Studies (GWAS) for Yield and Weevil Resistance in Sweet potato (Ipomoea batatas (L.) Lam). Plant Cell Rep 38, 1383–1392 (2019). https://doi.org/10.1007/s00299-019-02445-7

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