Integrative genomics reveals paths to sex dimorphism inSalix purpureaL.

Abstract

Sex dimorphism and gene expression were studied in developing catkins in 159 F2 individuals from the bioenergy crop Salix purpurea, and potential mechanisms and pathways for regulating sex development were explored. Differential expression, eQTL, bisulfite sequencing, and network analysis were used to characterize sex dimorphism, detect candidate master regulator genes, and identify pathways through which the sex determination region (SDR) may mediate sex dimorphism. Eleven genes are presented as candidates for master regulators of sex, supported by gene expression and network analyses. These include genes putatively involved in hormone signaling, epigenetic modification, and regulation of transcription. eQTL analysis revealed a suite of transcription factors and genes involved in secondary metabolism and floral development that were predicted to be under direct control of the sex determination region. Furthermore, data from bisulfite sequencing and small RNA sequencing revealed strong differences in expression between males and females that would implicate both of these processes in sex dimorphism pathways. These data indicate that the mechanism of sex determination in Salix purpurea is likely different from that observed in the related genus Populus. This further demonstrates the dynamic nature of SDRs in plants, which involves a multitude of mechanisms of sex determination and a high rate of turnover.

Nonadditive gene expression is correlated with nonadditive phenotypic expression in interspecific triploid hybrids of willow (Salix spp.)

“…Recently, sex-specific long-read genome assemblies of S. purpurea have been completed ( S. purpurea v5.1, S. purpurea Fish Creek’ v.3.1, DOE-JGI, https://phytozome-next.jgi.doe.gov/ , last accessed 12/30/2021). The genome size is an estimated 330 Mb and contains approximately 35,125 protein-coding genes (57,462 transcripts), and has proven useful in read alignment, variant discovery, and candidate gene selection ( Hyden et al 2021 ). There have been a handful of studies in shrub willow that focused on genetic mapping ( Gunter et al 2003 ; Berlin et al 2010 ; Hanley and Karp 2014 ; Hällingbäck et al 2016 ; Zhou et al 2018 ; Carlson et al 2019 ) of quantitative trait loci (QTL) associated with biomass yield traits to aid in marker-assisted selection (MAS), but most have been low-resolution.…”

Nonadditive gene expression is correlated with nonadditive phenotypic expression in interspecific triploid hybrids of willow (Salix spp.)

“…The copyright holder for this preprint this version posted October 14, 2021. ; https://doi.org/10.1101/2021.10.13.464325 doi: bioRxiv preprint contains approximately 35,125 protein-coding genes (57,462 transcripts), and has proven useful in read alignment, variant discovery, and candidate gene selection (Hyden et al, 2021). There have been a handful of studies in shrub willow that focused on genetic mapping (Gunter et al 2003;Berlin et al 2010;Hanley and Karp 2016;Hällingback et al 2016;Zhou et al 2018;Carlson et al 2019) of quantitative trait loci (QTL) associated with biomass yield traits to aid in marker-assisted selection (MAS), but most have been low-resolution.…”

“…There have also been attempts at correlating cell wall biosynthesis genes with variation in biomass composition in Salix spp. (Serapiglia et al 2012), as well as correlating sex dimorphism (Gouker et al 2021) with gene expression and methylation patterns in F 2 S. purpurea (Hyden et al 2021). Thus far, family-based ASE in Salix is restricted to a single study of F 1 and F 2 intraspecific S. purpurea (Carlson et al 2017), where expression-level dominance comprised the greatest proportion of differentially expressed genes between the parents of both families.…”

“…Recently, sex specific long-read genome assemblies of S. purpurea have been completed ( Salix purpurea v5.1, S. purpurea ‘Fish Creek’ v.3.1, DOE-JGI, phytozome-next.jgi.doe.gov/). The genome size is an estimated 330 Mb and contains approximately 35,125 protein-coding genes (57,462 transcripts), and has proven useful in read alignment, variant discovery, and candidate gene selection (Hyden et al ., 2021). There have been a handful of studies in shrub willow that focused on genetic mapping (Gunter et al .…”

“…2012), as well as correlating sex dimorphism (Gouker et al . 2021) with gene expression and methylation patterns in F 2 S. purpurea (Hyden et al . 2021).…”