Integrative genomics reveals paths to sex dimorphism in Salix purpurea L

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.

Structural variation of a sex‐linked region confers monoecy and implicates GATA15 as a master regulator of sex in Salix purpurea

“…Moreover, of the candidate sex determination genes proposed by Hyden et al . (2021), only the GATA15 homolog (Sapur.15WG062800) is present and supported by RNA‐Seq gene expression data in 94003 and its monoecious progeny (Fig. 2).…”

“…Among the features missing from the 94003 Chr15W H is the entire palindromic region, characterized by Zhou et al . (2020), which contains several candidate genes for the regulation of sex, including homologs of ARR17 , AGO4 , and DRB1 (Zhou et al ., 2020; Hyden et al ., 2021). Moreover, of the candidate sex determination genes proposed by Hyden et al .…”

“…With regard to methylation, widespread differences were observed between catkins of 94003 and six diverse male and female S. purpurea genotypes. The role of methylation in sex determination in willow has been previously implicated, with nearly threefold differences in methylated regions between male and female catkins being reported (Hyden et al ., 2021). Among the differentially methylated promoter regions in 94003 are homologs of six known floral development genes: UNUSUAL FLORAL ORGANS ( UFO ), PISTILLATA ( PI ), AGL104 , AGL44 , AGL62 , and AGL32 .…”

“…These genes are of interest since their transcriptional regulation and role in floral development may indicate involvement in monoecious phenotypic expression. Sapur.005G143300 is a homolog of PISTILLATA , a gene necessary for male floral organ development with high expression in male catkins (Hyden et al ., 2021). Sapur.005G143300 shows exceptionally high expression in 94003 (monoecious : male log 2 FC = 5.21; monoecious : female log 2 FC = 11.43) while also being undermethylated relative to males and females in the distal promoter region 538–1036 bp upstream of the transcription start site (Table S1).…”

Gap-free X and Y chromosomes ofSalix arbutifoliareveal an evolutionary change from male to female heterogamety in willows, without a change in the sex-determining region

“…Genes with corrected P -values < 0.05 and |log2FoldChange| >1 (absolute value of log2FoldChange > 1) as identified by DESeq2 were classified as differentially expressed (DEGs). We also included gene expression data of male and female catkins from S. purpurea (Hyden et al, 2021) to help interpret the differential gene expression patterns.…”