Construction of a linkage map based on retrotransposon insertion polymorphisms in sweetpotato via high-throughput sequencing

Yuki Monden, Takuya Hara, Yoshihiro Okada, Osamu Jahana, Akira Kobayashi, Hiroaki Tabuchi, Shoko Onaga, Makoto Tahara

Research output: Contribution to journalArticle

12 Citations (Scopus)

Abstract

Sweetpotato (Ipomoea batatas L.) is an outcrossing hexaploid species with a large number of chromosomes (2n = 6x = 90). Although sweetpotato is one of the world’s most important crops, genetic analysis of the species has been hindered by its genetic complexity combined with the lack of a whole genome sequence. In the present study, we constructed a genetic linkage map based on retrotransposon insertion polymorphisms using a mapping population derived from a cross between ‘Purple Sweet Lord’ (PSL) and ‘90IDN-47’ cultivars. High-throughput sequencing and subsequent data analyses identified many Rtsp-1 retrotransposon insertion sites, and their allele dosages (simplex, duplex, triplex, or double-simplex) were determined based on segregation ratios in the mapping population. Using a pseudo-testcross strategy, 43 and 47 linkage groups were generated for PSL and 90IDN-47, respectively. Interestingly, most of these insertions (~90%) were present in a simplex manner, indicating their utility for linkage map construction in polyploid species. Additionally, our approach led to savings of time and labor for genotyping. Although the number of markers herein was insufficient for map-based cloning, our trial analysis exhibited the utility of retrotransposon-based markers for linkage map construction in sweetpotato.

Original languageEnglish
Pages (from-to)145-153
Number of pages9
JournalBreeding Science
Volume65
Issue number2
DOIs
Publication statusPublished - 2015

Fingerprint

Retroelements
retrotransposons
chromosome mapping
genetic polymorphism
Ipomoea batatas
Genetic Linkage
Polyploidy
testcrosses
outcrossing
hexaploidy
linkage groups
polyploidy
genotyping
Population
genetic techniques and protocols
Organism Cloning
molecular cloning
labor
Chromosomes
Alleles

Keywords

  • High-throughput sequencing
  • Linkage map
  • Polyploidy
  • Pseudo-testcross
  • Retrotransposon
  • Sweetpotato

ASJC Scopus subject areas

  • Agronomy and Crop Science
  • Genetics
  • Plant Science

Cite this

Construction of a linkage map based on retrotransposon insertion polymorphisms in sweetpotato via high-throughput sequencing. / Monden, Yuki; Hara, Takuya; Okada, Yoshihiro; Jahana, Osamu; Kobayashi, Akira; Tabuchi, Hiroaki; Onaga, Shoko; Tahara, Makoto.

In: Breeding Science, Vol. 65, No. 2, 2015, p. 145-153.

Research output: Contribution to journalArticle

Monden, Yuki ; Hara, Takuya ; Okada, Yoshihiro ; Jahana, Osamu ; Kobayashi, Akira ; Tabuchi, Hiroaki ; Onaga, Shoko ; Tahara, Makoto. / Construction of a linkage map based on retrotransposon insertion polymorphisms in sweetpotato via high-throughput sequencing. In: Breeding Science. 2015 ; Vol. 65, No. 2. pp. 145-153.
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