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Development of an X-specific marker and identification of YY individuals in spinach

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Abstract

Spinach is a popular vegetable native to central and western Asia. It is dioecious with a pair of nascent sex chromosomes. The difficulties of working with the non-recombining sex determination region of XY individuals have hindered the progress toward sequencing sex chromosomes of most dioecious species. Here we present important advances toward characterizing the non-recombining sex chromosomes in spinach. Of nearly 400 spinach accessions screened, we identified a single accession of spinach in which androdioecious XY individuals segregate YY spinach. The male and female genomes of the spinach cultivar Shami and USDA accession PI 664497 were sequenced at 12–17 × coverage. X-specific sequences were identified by comparing the depth of coverage differences between male and female alignments to a female draft genome. YY individuals were used as a negative control to validate X-specific markers found by depth of coverage analysis. Of 19 possible X chromosome sequences found by depth of coverage analysis, one was verified to be X-specific by a PCR-based marker, SpoX, which amplified genomic DNA from XX and XY, but not YY templates. Androdioecious XY individuals of accession PI 217425 (Cornell #9) were used to develop inbred lines, and at S7 generation, all XY individuals were androdioecious and all YY individuals were pure male. The sex reversal of the XY mutant to hermaphrodite is strong evidence that the sex chromosomes in spinach have a two-gene sex determination system. These results are crucial towards sequencing the X and Y chromosomes to advance sex chromosome research in spinach.

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Acknowledgements

The authors would like to thank Dr. David Brenner at the USDA-GRIN in Ames, Iowa, for facilitating access to the spinach germplasm collection, and Christina Fliege and Dr. Matt Hudson for allowing access to growth chambers. We appreciate Lixian Huang’s work to construct DNA sequencing libraries. This work was supported by the grant 2015N20002-1 from the Department of Science and Technology of Fujian Province to RM; National Science Foundation (NSF) Plant Genome Research Program Awards DBI-0922545 and DBI-1546890 to R.M.

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Authors and Affiliations

  1. FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China

    William H. Wadlington & Ray Ming

  2. Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA

    William H. Wadlington & Ray Ming

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  1. William H. Wadlington
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  2. Ray Ming
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Correspondence to Ray Ming.

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On behalf of both authors, the corresponding author states that there is no conflict of interest.

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Communicated by Michael J. Havey.

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Wadlington, W.H., Ming, R. Development of an X-specific marker and identification of YY individuals in spinach. Theor Appl Genet 131, 1987–1994 (2018). https://doi.org/10.1007/s00122-018-3127-1

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