Genome-wide association mapping uncovers sex-associated copy number variation markers and female hemizygous regions on the W chromosome in Salix viminalis

Abstract

Background Sex chromosomes are in some species largely undifferentiated (homomorphic) with restricted sex determination regions. Homomorphic but different sex chromosomes are found in the closely related genera Populus and Salix indicating flexible sex determination systems, ideal for studies of processes involved in sex chromosome evolution. We have performed genome-wide association studies of sex and analysed sex chromosomes in a population of 265 wild collected Salix viminalis accessions and studied the sex determining locus. Results A total of 19,592 markers were used in association analyses using both Fisher’s exact tests and a single-marker mixed linear model, which resulted in 48 and 41 sex-associated (SA) markers respectively. Across all 48 SA markers, females were much more often heterozygous than males, which is expected if females were the heterogametic sex. The majority of the SA markers were, based on positions in the S. purpurea genome, located on chromosome 15, previously demonstrated to be the sex chromosome. Interestingly, when mapping the genotyping-by-sequencing sequence tag harbouring the two SA markers with the highest significance to the S. viminalis genomic scaffolds, five regions of very high similarity were found: three on a scaffold that represents a part of chromosome 15, one on a scaffold that represents a part of chromosome 9 and one on a scaffold not anchored to the genome. Based on segregation differences of the alleles at the two marker positions and on differences in PCR amplification between females and males we conclude that females had multiple copies of this DNA fragment (chromosome 9 and 15), whereas males only had one (chromosome 9). We therefore postulate that the female specific sequences have been copied from chromosome 9 and inserted on chromosome 15, subsequently developing into a hemizygous W chromosome linked region. Conclusions Our results support that sex determination in S. viminalis is controlled by one locus on chromosome 15. The segregation patterns observed at the SA markers furthermore confirm that S. viminalis females are the heterogametic sex. We also identified a translocation from chromosome 9 to the W chromosome.

<em>De Novo</em> Assembly and Annotation of 11 Diverse Shrub Willow (<em>Salix</em>) Genomes Reveals Novel Gene Organization in Sex-Linked Regions

“…Of particular interest is the lack of ARR17 or GATA15 homologs on Chr15 in the S. koriyanagi and S. viminalis female genomes. The missing ARR17 in S. viminalis is inconsistent with earlier studies on S. viminalis by Hallingback et al [24] and Almeidia et al [30], which both identified one copy of ARR17 on the S. viminalis Chr15W. The differing number of candidate sex determination genes between species, particularly ARR17 and GATA15, indicates that the mechanism of sex determination may be quite labile within the Vetrix lineage of willows, despite its apparent conservation within the tree willows and the poplars.…”

Recurrent neo-sex chromosome evolution in kiwifruit

“…including in the family Salicaceae 13,14 ), and in the genus Fragaria (strawberries), in which a 13-kb transposable "cassette" has moved a currently unidentified female-determining gene(s) to different genomic locations 15 .…”

Evolution of a ZW sex chromosome system in willows

“…Prior to the transition, at least five duplicates of small segments of the RR17 gene (‘partial duplicates’) were present on the Y chromosome. The function of these RR17 partial duplicates in Salix is still under investigation 26 , 35 , 37 ; however, inverted repeats of RR17 partial duplicates regulate sex determination via siRNA intermediates in Populus tremula 25 , 26 , which is in the sister genus to Salix , and RR17 partial duplicates in Salix arbutifolia , which also has a 15XY sex determination system, generate siRNAs 25 , 30 , 41 . Interestingly, there is currently no evidence of siRNA expression of RR17 partial duplicates in S. purpurea , so this masculinizing component of the XY system may have been lost or modified in the transition to ZW 39 .…”