Molecular Genetics and Genomics

, Volume 293, Issue 2, pp 557–568 | Cite as

Molecular insights into the non-recombining nature of the spinach male-determining region

  • Tomohiro Kudoh
  • Mitsuhiko Takahashi
  • Takayuki Osabe
  • Atsushi Toyoda
  • Hideki Hirakawa
  • Yutaka Suzuki
  • Nobuko Ohmido
  • Yasuyuki OnoderaEmail author
Original Article


Spinach (Spinacia oleracea L.) is a dioecious plant with male heterogametic sex determination and homomorphic sex chromosomes (XY). The dioecism is utilized for producing commercial hybrid seeds, and hence understanding the molecular-genetic basis of the species’ sex determining locus is an important issue for spinach breeding. In this study, seven dominant DNA markers were shown to completely co-segregate with the male-determining gene in segregating spinach populations comprising > 1500 plants. In addition, these seven dominant DNA markers were completely associated with the male-determining gene in over 100 spinach germplasm accessions and cultivars. These observations suggest that, in spinach, a Y-chromosomal region around the male-determining locus does not (or almost not) recombine with a counterpart region on the X chromosome. Using five of the seven DNA markers, five bacterial artificial chromosome (BAC) clone contigs with a total length of approximately 690 kbp were constructed. Full sequencing of six representative BAC clones (total insert length 504 kbp) from the five contigs and a transcriptome analysis by RNA-seq revealed that the Y-chromosomal region around the male-determining locus contains large amounts of repetitive elements, suggesting that the region might be poor in gene content. Most of the repeats found in this region are novel Ty1-copia-like and its derivative elements that accumulate predominantly in heterochromatic regions. Our findings may provide valuable insight into spinach genome structure and clues for future research into the evolution of the sex determining locus.


Spinach Dioecy Sex chromosomes LTR-retrotransposon 



The authors thank Tohoku Seed Co. Ltd. (Utsunomiya, Tochigi, Japan) very much for providing the spinach breeding lines used in this study. We appreciate the technical assistance provided by Mrs. H. Yokomoto. The work presented here was supported by the Interuniversity Bio-Backup Project (IBBP) as an application code (Hokkaido 0001). We used the DNA Sequencing Facility of Research Faculty of Agriculture, Hokkaido University.


This work was supported by the Japan Society for the Promotion of Science (Grants-in-Aid for Scientific Research (KAKENHI) Grant Numbers 26292001 and 16H06279), Ministry of Education, Culture, Sports, Science and Technology (KAKENHI Grant Number 221S0002), and the Takeda Science Foundation.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Data availability

The BAC clone sequences (AP017636–AP017641) and the RNA-seq reads (DRA006107) generated during and/or analyzed during the current study are available in the DNA Data Bank of Japan (DDBJ). The primer sequences of the SP_0018 marker developed by Tohoku Seed Co., Ltd. is not publicly available because it remains a trade secret.

Supplementary material

438_2017_1405_MOESM1_ESM.pdf (4.5 mb)
Supplementary material 1 (PDF 4580 KB)


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Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2017

Authors and Affiliations

  1. 1.The Research Faculty of AgricultureHokkaido UniversitySapporoJapan
  2. 2.Center for Information BiologyNational Institute of GeneticsMishimaJapan
  3. 3.The Department of Technology DevelopmentKazusa DNA Research InstituteKisarazuJapan
  4. 4.The Department of Computational Biology and Medical Sciences, Graduate School of Frontier SciencesThe University of TokyoKashiwaJapan
  5. 5.Graduate School of Human Development and EnvironmentKobe UniversityKobeJapan

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