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Construction of a high-density linkage map and graphical representation of the arrangement of transcriptome-based unigene markers on the chromosomes of onion, Allium cepa L.

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  • Satoshi Fujito, National Agricultural Research Centers Japan
  • ,
  • Turgut Yigit Akyol
  • Takuya Mukae, Yamaguchi University
  • ,
  • Tadayuki Wako, National Agricultural Research Centers Japan, Japan Ministry of Agriculture, Forestry and Fisheries
  • ,
  • Ken ichiro Yamashita, National Agricultural Research Centers Japan, NARO
  • ,
  • Hikaru Tsukazaki, National Agricultural Research Centers Japan
  • ,
  • Hideki Hirakawa, Kazusa DNA Research Institute
  • ,
  • Keisuke Tanaka, Tokyo University of Agriculture
  • ,
  • Yoko Mine, Tokyo University of Agriculture
  • ,
  • Shusei Sato, Tohoku University
  • ,
  • Masayoshi Shigyo, Yamaguchi University

Background: Genomic information for Allium cepa L. is limited as it is heterozygous and its genome is very large. To elucidate potential SNP markers obtained by NGS, we used a complete set of A. fistulosum L.-A. cepa monosomic addition lines (MALs) and doubled haploids (DHs). These were the parental lines of an A. cepa mapping population for transcriptome-based SNP genotyping. Results: We mapped the transcriptome sequence reads from a series of A. fistulosum-A. cepa MALs onto the unigene sequence of the doubled haploid shallot A. cepa Aggregatum group (DHA) and compared the MAL genotype call for parental bunching onion and shallot transcriptome mapping data. We identified SNP sites with at least four reads on 25,462 unigenes. They were anchored on eight A. cepa chromosomes. A single SNP site was identified on 3,278 unigenes and multiple SNPs were identified on 22,184 unigenes. The chromosome marker information was made public via the web database Allium TDB (http://alliumtdb.kazusa.or.jp/). To apply transcriptome based genotyping approach for genetic mapping, we gathered RNA sequence data from 96 lines of a DHA × doubled haploid bulb onion A. cepa common onion group (DHC) mapping population. After selecting co-dominant SNP sites, 16,872 SNPs were identified in 5,339 unigenes. Of these, at least two SNPs with identical genotypes were found in 1,435 unigenes. We developed a linkage map using genotype information from these unigenes. All unigene markers mapped onto the eight chromosomes and graphical genotyping was conducted based on the unigene order information. Another 2,963 unigenes were allocated onto the eight chromosomes. To confirm the accuracy of this transcriptome-based genetic linkage map, conventional PCR-based markers were used for linkage analysis. All SNP - and PCR-based markers were mapped onto the expected linkage groups and no inconsistency was found among these chromosomal locations. Conclusions: Effective transcriptome analysis with unique Allium resources successfully associated numerous chromosome markers with unigene information and a high-density A. cepa linkage map. The information on these unigene markers is valuable in genome sequencing and useful trait detection in Allium.

OriginalsprogEngelsk
Artikelnummer481
TidsskriftBMC Genomics
Vol/bind22
Nummer1
ISSN1471-2164
DOI
StatusUdgivet - dec. 2021

Bibliografisk note

Funding Information:
A part of the RNA-Sequencing experiments was supported by Cooperative Research Grant of the Genome Research for BioResource, NODAI Genome Research Center, Tokyo University of Agriculture in FY2014.

Funding Information:
This work was supported by JSPS KAKENHI Grant Number JP26292020 and a “Pilot program of International Collaborative Research (Collaborative research with Russia in agriculture)” under “Commissioned projects for promotion of strategic international collaborative research” for Utilizing Advanced Technologies in Agriculture, Forestry and Fisheries, administered by the Ministry of Agriculture, Forestry and Fisheries in Japan (1st stage 2017–2019, 2nd stage 2020–2022). The funding bodies played no role in the design of the study and collection, analysis, and interpretation of data and in writing the manuscript.

Publisher Copyright:
© 2021, The Author(s).

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