Mapping the sex determination region in the Salix F1 hybrid common parent population confirms a ZW system in six diverse species

Abstract

Within the genus Salix, there are approximately 350 species native primarily to the northern hemisphere and adapted to a wide range of habitats. This diversity can be exploited to mine novel alleles conferring variation important for production as a bioenergy crop, but also to identify evolutionarily important genes, such as those involved in sex determination. To leverage this diversity, we created a mapping population by crossing six Salix species (S. viminalis, S. suchowensis, S. integra, S. koriyanagi, S. udensis, and S. alberti) to common male and female S. purpurea parents. Each family was genotyped via genotyping-by-sequencing and assessed for kinship and population structure as well as the construction of 16 backcross linkage maps to be used as a genetic resource for breeding and selection. Analyses of population structure resolved both the parents and F1 progeny to their respective phylogenetic section and indicated that the S. alberti parent was misidentified and was most likely S. suchowensis. Sex determining regions were identified on Salix chromosome 15 in the female-informative maps for seven of the eight families indicating that these species share a common female heterogametic ZW sex system. The eighth family, S. integra × S. purpurea, was entirely female and had a truncated chromosome 15. Beyond sex determination, the Salix F1 hybrid common parent population (Salix F1 HCP) introduced here will be useful in characterizing genetic factors underlying complex traits, aid in marker-assisted selection, and support genome assemblies for this promising bioenergy crop.

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

“…S4). Linkage map markers for the 94006 genotype were obtained from Wilkerson et al (2022) and include one marker, S15_7998352, that is located in the misassembled region [2]. In a BLASTN analysis, the flanking regions of this marker align to HiC_scaffold_7 (Chr17), while the nearest markers on the 94006 linkage map, which are tightly linked, align to HiC_scaffold_15 (Chr15), confirming that this region, including GATA15, is indeed a Chr15W region misassembled onto Chr17.…”

“…Commonly cultivated shrub willow species include European natives S. purpurea and S. viminalis, the Chinese species S. suchowensis, Japanese natives S. integra and S. udensis, and S. koriyanagi from Korea [1,14,15]. Together, these six aforementioned species represent a broad range of genetic diversity across the section Vetrix, including two subsections: Helix (S. purpurea, S. suchowensis, S. integra, S. koriyanagi) and Vimen (S. viminalis, S. udensis) [2,14]. Due to both the dynamic nature of the SDR within this genus and the unique mechanism of sex determination in S. purpurea [12], there is an interest in comparing the gene content of the sex determination regions across shrub willow species, in order confirm the two-gene model from S. purpurea and to identify any additional shifts in sex determination genes during the evolution of this clade.…”

“…A male S. purpurea, (94001, the father of 'Fish Creek'), two female (P294, P295) and one male (P63) S. suchowensis, one female S. integra (P336), one male (04-FF-016) and one female (SH3) S. koriyanagi, one female (07-MBG-5027) and one male ('Jorr') S. viminalis, and a male S. udensis (04-BN-051) were also sequenced. These particular genotypes are of interest since previous research has reported F1 crosses to S. purpurea 94001 and 94006 for each of these genotypes along with linkage maps, phenotypic analysis, and QTL mapping in the progeny [2].…”

“…Salicaceae is almost entirely dioecious, and contains approximately 30 species of Populus and over 300 species of Salix [1] yet, both the location of the sex determination system (SDR) as well as the sex inheritance mechanism (ZW vs XY) differ across clades within this family. In the shrub willows (section Vetrix), the sex determination region has been localized in to Chr15, with a ZW system of inheritance [2][3][4][5], while Chr15XY is predominant in the section Salix, including S. arbutifolia [6], and a Chr07 XY sex determination system has been identified in the tree willows (section Protitea) S. nigra [7], S. chaenomeloides [6], and S. dunnii [8]. In Populus, Chr19 XY, Chr19 ZW, and Chr14 XY sexdetermination systems have all been reported [9].…”

An unusual origin of a ZW sex chromosome system

“…We con rmed an XY to ZW transition within the same pair of sex chromosomes (homologous transition) in Salix. It appears that the ZW sex determination system in most of the subgenus Vetrix (shrub willows) have been derived from this transition because all of the studied species in this subgenus have a 15ZW sex chromosome system 35,37,39 . Combined with the previous discovery of an XY to ZW transition between lineages of P. tremula and P. alba, shifts in heterogamety occurred at least twice in Salicaceae 26 .…”