Comparison of Spinach Sex Chromosomes with Sugar Beet Autosomes Reveals Extensive Synteny and Low Recombination at the Male-Determining Locus

Abstract

Spinach (Spinacia oleracea, 2n = 12) and sugar beet (Beta vulgaris, 2n = 18) are important crop members of the family Chenopodiaceae ss Sugar beet has a basic chromosome number of 9 and a cosexual breeding system, as do most members of the Chenopodiaceae ss. family. By contrast, spinach has a basic chromosome number of 6 and, although certain cultivars and genotypes produce monoecious plants, is considered to be a dioecious species. The loci determining male and monoecious sexual expression were mapped to different loci on the spinach sex chromosomes. In this study, a linkage map with 46 mapped protein-coding sequences was constructed for the spinach sex chromosomes. Comparison of the linkage map with a reference genome sequence of sugar beet revealed that the spinach sex chromosomes exhibited extensive synteny with sugar beet chromosomes 4 and 9. Tightly linked protein-coding genes linked to the male-determining locus in spinach corresponded to genes located in or around the putative pericentromeric and centromeric regions of sugar beet chromosomes 4 and 9, supporting the observation that recombination rates were low in the vicinity of the male-determining locus. The locus for monoecism was confined to a chromosomal segment corresponding to a region of approximately 1.7Mb on sugar beet chromosome 9, which may facilitate future positional cloning of the locus.

Young sex chromosomes in plants and animals

“…The sex‐linked regions in spinach species (a genus in which dioecy probably evolved from a monoecious ancestral state) may also have arisen in this way. The homomorphic XY chromosome pair exhibits extensive synteny with sugar beet ( Beta vulgaris ) chromosomes 4 and 9, and protein‐coding genes closely linked to the male‐determining locus in spinach are located in the putative pericentromeric and centromeric regions of these B. vulgaris chromosomes (Takahata et al ., ), whereas much of the pair recombines. High‐density mapping identified an 18 Mb region of linkage group 4, with 143 genes, as fully sex linked (Qian et al ., ); its location is consistent with a pericentromeric region, as is the low gene density of the region (Kudoh et al ., ).…”

Molecular evidence for recent divergence of X- and Y-linked gene pairs in Spinacia oleracea L.

“…As shown in S1 Table, three female and three male RNA samples (Female 1–3 and Male 1–3) were prepared from single plants, and one female and one male RNA sample (Female 5 and Male 5) were prepared using equal amounts of RNA isolated from five individuals. Eight cDNA libraries were prepared from the RNA samples according to a method described in Takahata et al [12] and sequenced using a HiSeq 2500 Instrument (Illumina, San Diego, CA, USA) configured to generate 100 bp paired-end reads.…”

“…The male-determining locus ( Y ) has been mapped to the largest chromosome. The spinach sex chromosomes containing X and Y , i.e., X and Y, are homomorphic, recombining across most of their length, excluding the region around the Y locus [10–12].…”

“…We recently showed that, in spinach, a Y-chromosomal region around the male-determining locus does not recombine with the counterpart region on the X chromosome [12, 26]. However, it is not clear whether the evolution of the non-recombining region on the spinach Y chromosome is directly associated with the establishment of dioecy in Spinacia , as predicted by the two-mutation (two-factor) model.…”

Genome Sequences of Spinach Deltapartitivirus 1, Spinach Amalgavirus 1, and Spinach Latent Virus Identified in Spinach Transcriptome

“…Breeding programs and genetic studies of spinach have investigated the development of varieties with desirable traits such as increased disease resistance and stress tolerance [1,2]. In addition, comprehensive genomic and transcriptomic studies of spinach have been actively performed to evaluate the genetic diversity of spinach and identify molecular resources, including a comparison of spinach sex chromosomes with sugar beet autosomes [3], a comparative transcriptomic analysis of cultivated and wild spinach varieties [4], and an expression profiling study of spinach leaves under heat stress [5].…”