Integrative genomics reveals paths to sex dimorphism in Salix purpurea L

Brennan Hyden; Craig H. Carlson; Fred E. Gouker; Jeremy Schmutz; Kerrie Barry; Anna Lipzen; Aditi Sharma; Laura Sandor; Gerald A. Tuskan; Guanqiao Feng; Matthew S. Olson; Stephen P. DiFazio; Lawrence B. Smart

doi:10.1038/s41438-021-00606-y

Integrative genomics reveals paths to sex dimorphism in Salix purpurea L

Brennan Hyden, Craig H. Carlson, Fred E. Gouker, Jeremy Schmutz, Kerrie Barry, Anna Lipzen, Aditi Sharma, Laura Sandor, Gerald A. Tuskan, Guanqiao Feng, Matthew S. Olson, Stephen P. DiFazio, Lawrence B. Smart

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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.

Original language	English
Article number	170
Journal	Horticulture Research
Volume	8
Issue number	1
DOIs	https://doi.org/10.1038/s41438-021-00606-y
State	Published - Dec 2021

Funding

Support for this research was provided by grants (DEB-1542486, DEB-1542599) from the National Science Foundation and from the USDA National Institute for Food and Agriculture (2015-67009-23957). The work conducted by the DOE JGI is supported by the Office of Science of the US Department of Energy under Contract no. DE-AC02-05CH11231. Partial support for BLH was provided by a Cornell AgriTech Extension and Outreach Assistantship. The authors would like to thank Matt Christiansen, Curt Carter, Rebecca Wilk, Lauren Carlson, Jane Petzoldt, Dawn Fishback, and Sam Knopka for their technical assistance with sample collection and field-trial maintenance and Alex Harkess and Xiohan Yang for critical feedback on drafts of the paper.

Funders	Funder number
National Science Foundation	DEB-1542509, DEB-1542599, DEB-1542486
U.S. Department of Energy
National Institute of Food and Agriculture	2015-67009-23957
Office of Science	DE-AC02-05CH11231

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title = "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.",

author = "Brennan Hyden and Carlson, {Craig H.} and Gouker, {Fred E.} and Jeremy Schmutz and Kerrie Barry and Anna Lipzen and Aditi Sharma and Laura Sandor and Tuskan, {Gerald A.} and Guanqiao Feng and Olson, {Matthew S.} and DiFazio, {Stephen P.} and Smart, {Lawrence B.}",

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doi = "10.1038/s41438-021-00606-y",

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AU - Lipzen, Anna

AU - Sharma, Aditi

AU - Sandor, Laura

AU - Tuskan, Gerald A.

AU - Feng, Guanqiao

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AU - Smart, Lawrence B.

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Integrative genomics reveals paths to sex dimorphism in Salix purpurea L

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