Biology subjects

DiFazio, S. P.

Publications and source records attributed to DiFazio, S. P..

4 recordsLinked to original sources

bioRxiv2021

Integrative genomics reveals paths to sex dimorphism in Salix purpurea L.

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.

genomics↗

bioRxiv2020

ISSRseq: an extensible, low-cost, and efficient method for reduced representation sequencing

O_LIThe capability to generate densely sampled single nucleotide polymorphism (SNP) data is essential in diverse subdisciplines of biology, including crop breeding, pathology, forensics, forestry, ecology, evolution, and conservation. However, the wet-lab expertise and bioinformatics training required to conduct genome-scale variant discovery remain limiting factors for investigators with limited resources. C_LIO_LIHere we present ISSRseq, a PCR-based method for reduced representation of genomic variation using simple sequence repeats as priming sites to sequence inter simple sequence repeat (ISSR) regions. Briefly, ISSR regions are amplified with single primers, pooled, used to construct sequencing libraries with a commercially-available kit, and sequenced on the Illumina platform. We also present a flexible bioinformatic pipeline that assembles ISSR loci, calls and hard filters variants, outputs data matrices in common formats, and conducts population analyses using R. C_LIO_LIUsing three angiosperm species as case studies, we demonstrate that ISSRseq is highly repeatable, necessitates only simple wet-lab skills and commonplace instrumentation, is flexible in terms of the number of single primers used, and can generate genomic-scale variant discovery on par with existing RRS methods which require more complex wet lab procedures. C_LIO_LIISSRseq represents a straightforward approach to SNP genotyping in any organism, and we predict that this method will be particularly useful for those studying population genomics and phylogeography of non-model organisms. Furthermore, the ease of ISSRseq relative to other RRS methods should prove useful to those lacking advanced expertise in wet lab methods or bioinformatics. C_LI

genomics↗

bioRxiv2020

A general model to explain repeated turnovers of sex determination in the Salicaceae

Dioecy, the presence of separate sexes on distinct individuals, has evolved repeatedly in multiple plant lineages. However, the specific mechanisms through which sex systems evolve and their commonalities among plant species remain poorly understood. With both XY and ZW sex systems, the family Salicaceae provides a system to uncover the evolutionary forces driving sex chromosome turnovers. In this study, we performed a genome-wide association study to characterize sex determination in two Populus species, P. euphratica and P. alba. Our results reveal an XY system of sex determination on chromosome 14 of P. euphratica, and a ZW system on chromosome 19 of P. alba. We further assembled the corresponding sex determination regions, and found that their sex chromosome turnovers may be driven by the repeated translocations of a Helitron-like transposon. During the translocation, this factor may have captured partial or intact sequences that are orthologous to a type-A cytokinin response regulator gene. Based on results from this and other recently published studies, we hypothesize that this gene may act as a master regulator of sex determination for the entire family. We propose a general model to explain how the XY and ZW sex systems in this family can be determined by the same RR gene. Our study provides new insights into the diversification of incipient sex chromosome in flowering plants by showing how transposition and rearrangement of a single gene can control sex in both XY and ZW systems.

genomics↗

bioRxiv2020

Sexual dimorphism and sex ratio bias in the dioecious willow Salix purpurea L.

PremiseSexual dimorphism in dioecious plant species is often not obvious or is absent. Dioecious species populations also often exhibit deviations from expected sex ratios. Previous studies on members of the Salicaceae family have shown strong, partial, and no sexual dimorphism. Some studies have shown sex-biased ratios in several Salix spp., however, S. purpurea has never been examined for evidence of sexual dimorphism or for the presence of sex-ratio bias, and therefore a comprehensive phenotypic study is needed to fill this knowledge gap. MethodsThis study examined a suite of morphological, phenological, physiological and wood composition traits from multi-environment and multi-year replicated field trials in a diversity panel of unrelated S. purpurea accessions and in full-sib F1 and F2 families produced through controlled cross pollinations to test for sexual dimorphism and sex ratio bias. Key ResultsSignificant evidence of sexual dimorphism was found in vegetative traits with greater means for many traits in male genotypes compared to females across three populations of S. purpurea, measured across multiple years that were highly predictive of biomass yield. Male plants exhibited greater nitrogen accumulation under fertilizer amendment as measured by SPAD in the diversity panel, and males showed greater susceptibility to fungal infection by Melampsora spp in the F2 family. There were also consistent female-biased sex ratios in both the F1 and F2 families. ConclusionsThese results provide the first evidence of sexual dimorphism in S. purpurea and also confirm the prevalence of female-biased sex ratios previously found in other Salix species.

plant biology↗