Genomic Analysis of the Sex Determining Region of the Sex Chromosomes in Spinach

Spinacia oleracea (spinach) has been studied for sex determination since the 1950's. However, no sex determination genes have been identified from this species. Like with many dioecious species, research on the spinach Y chromosome has been hampered due to the inherent difficulties of working with the XY system: namely the lack of recombination of the sex determining region in X and Y chromosomes, and also the difficulty of separating homologous X and Y sequences from whole genome assemblies. Both of these problems can be worked around by using YY individuals for sequencing and also for generating recombined Y chromosomes. By utilizing an accession of spinach which bears both male and female-fertile hermaphroditic flowers on XY plants (andromonoecious), we were able to generate inbred YY plants for whole genome sequencing with PacBio. The sequence of Y-linked primers were used to identify Y-linked contigs in the YY assembly. The Y-linked contigs were found to be homologous to X-linked sequences identified from an XX assembly by depth of coverage analysis. For the genetic map of the Y, a hybrid YY parent with different haplotypes of the spinach Y chromosome was generated and backcrossed to 5 females. The XY progeny will show recombination in the Y-linked traits that are variant between the two Y haplotypes. Together these experiments have the