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Yamamoto E, Shirasawa K, Kimura T, et al. Genetic Mapping in Autohexaploid Sweet Potato with Low-Coverage NGS-Based Genotyping Data. G3 (Bethesda). 2020;10(8):2661-2670doi: 10.1534/g3.120.401433.
Yamamoto, E., Shirasawa, K., Kimura, T., Monden, Y., Tanaka, M., & Isobe, S. (2020). Genetic Mapping in Autohexaploid Sweet Potato with Low-Coverage NGS-Based Genotyping Data. G3 (Bethesda, Md.), 10(8), 2661-2670. https://doi.org/10.1534/g3.120.401433
Yamamoto, Eiji, et al. "Genetic Mapping in Autohexaploid Sweet Potato with Low-Coverage NGS-Based Genotyping Data." G3 (Bethesda, Md.) vol. 10,8 (2020): 2661-2670. doi: https://doi.org/10.1534/g3.120.401433
Yamamoto E, Shirasawa K, Kimura T, Monden Y, Tanaka M, Isobe S. Genetic Mapping in Autohexaploid Sweet Potato with Low-Coverage NGS-Based Genotyping Data. G3 (Bethesda). 2020 Aug 05;10(8):2661-2670. doi: 10.1534/g3.120.401433. PMID: 32482727; PMCID: PMC7407471.
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G3 (Bethesda). 2020 Aug 05;10(8):2661-2670. doi: 10.1534/g3.120.401433.

Genetic Mapping in Autohexaploid Sweet Potato with Low-Coverage NGS-Based Genotyping Data.

G3 (Bethesda, Md.)

Eiji Yamamoto, Kenta Shirasawa, Takumi Kimura, Yuki Monden, Masaru Tanaka, Sachiko Isobe

Affiliations

  1. Kazusa DNA Research Institute, Japan.
  2. Graduate School of Environmental and Life Science, Okayama University, Japan, and.
  3. Kyushu Okinawa Agricultural Research Center, National Agriculture and Food Research Organization, Japan.

PMID: 32482727 PMCID: PMC7407471 DOI: 10.1534/g3.120.401433

Abstract

Next-generation sequencing (NGS)-based genotyping methods can generate numerous genetic markers in a single experiment and have contributed to plant genetic mapping. However, for high precision genetic analysis, the complicated genetic segregation mode in polyploid organisms requires high-coverage NGS data and elaborate analytical algorithms. In the present study, we propose a simple strategy for the genetic mapping of polyploids using low-coverage NGS data. The validity of the strategy was investigated using simulated data. Previous studies indicated that accurate allele dosage estimation from low-coverage NGS data (read depth < 40) is difficult. Therefore, we used allele dosage probabilities calculated from read counts in association analyses to detect loci associated with phenotypic variations. The allele dosage probabilities showed significant detection power, although higher allele dosage estimation accuracy resulted in higher detection power. On the contrary, differences in the segregation patterns between the marker and causal genes resulted in a drastic decrease in detection power even if the marker and casual genes were in complete linkage and the allele dosage estimation was accurate. These results indicated that the use of a larger number of markers is advantageous, even if the accuracy of allele dosage estimation is low. Finally, we applied the strategy for the genetic mapping of autohexaploid sweet potato (

Copyright © 2020 Yamamoto et al.

Keywords: Allele dosage; Autopolyploid; Genetic mapping; NGS-based genotyping; Sweet potato

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