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Shrub willows are widely planted for landscaping, soil remediation, and biomass production, due to their rapid growth rates. Identification of regulatory genes in wood formation would provide clues for genetic engineering of willows for improved growth traits on marginal lands. Here, we conducted an expression quantitative trait locus (eQTL) analysis, using a full sibling F1 population of Salix suchowensis, to explore the genetic mechanisms underlying wood formation. Based on variants identified from simplified genome sequencing and gene expression data from RNA sequencing, 16,487 eQTL blocks controlling 5505 genes were identified, including 2148 cis-eQTLs and 16,480 trans-eQTLs. eQTL hotspots were identified, based on eQTL frequency in genomic windows, revealing one hotspot controlling genes involved in wood formation regulation. Regulatory networks were further constructed, resulting in the identification of key regulatory genes, including three transcription factors (JAZ1, HAT22, MYB36) and CLV1, BAM1, CYCB2;4, CDKB2;1, associated with the proliferation and differentiation activity of cambium cells. The enrichment of genes in plant hormone pathways indicates their critical roles in the regulation of wood formation. Our analyses provide a significant groundwork for a comprehensive understanding of the regulatory network of wood formation in S. suchowensis. [ABSTRACT FROM AUTHOR]

Willows, in the genus Salix, are widespread on the earth with significant ecological and economic values for humans. Although about 500 Salix species have been estimated, the genomic foundation of their adaptations to environments with diverse stresses has been underexplored. Here, we applied a pan-transcriptome approach to investigate the phylogenetic relationships and genetic variations among 16 willow species. A pan-transcriptome of 29,668 gene families was assembled, 69% of which exhibited presence/absence variation across the analyzed species. In comparison to core genes present in all species, shell gene families absent in at least one species were enriched with genes in pathways of signaling transduction and response to stimuli, suggesting their functions in the interaction with diverse environmental factors. A phylogenetic tree of 16 willow species was constructed with high confidence based on 870 single-copy orthologous genes, providing detailed evolutionary relationships of willow sections. The willow species were further assigned into four species clusters using the gene numbers in each family. The diversity of gene family size and gene expression levels among the willow species are closely associated with their geographical distributions. The gene family members involved in DNA repair and cellular response to DNA damage stimuli were expanded in willow species from high-altitude regions in southwestern China, which may contribute to their tolerance to ultraviolet radiation stress. Our study generates a comprehensive pan-transcriptome resource for a large set of Salix species and provides insights into the adaptations of willows to diverse environments, which will be valuable for comparative analysis with other related woody and herbaceous plants. [ABSTRACT FROM AUTHOR]

Many willow species, especially the short-rotation coppice willows, are suitable for development into renewable bioenergy crops. In this study, we conducted high-throughput transcriptome sequencing of a shrub willow, S. suchowensis, to generate expressed sequence tags ( ESTs) for gene discovery and molecular marker development. Totally, 136.1 million clean reads were generated from five different tissues of S. suchowensis using Illumina RNA-seq technology. De novo sequence assembly produced 90 269 unigenes, among which 64 127 unigenes were annotated in one or more of the NR, Swiss-Prot, GO, COG and KEGG databases. A total of 21 052 simple sequence repeats were identified in the expressed sequence assemblies, and a primer database containing 36 912 EST- SSR markers were developed for 12 304 SSR loci. Subsequently, 25 primers were randomly selected for experimental test. Among which, 24 primers succeeded in PCR amplification and 21 produced amplicons in expected sizes, suggesting that the sequence assemblies were of high quality. The established sequence database and marker resource are useful for different aspects of genetic studies on Salix spp., and particularly valuable for marker-assisted breeding of willows. [ABSTRACT FROM AUTHOR]

A letter to the editor is presented on a study conducted on common genome duplication in willow genome and poplar genome.

Willow (Salix spp.), a woody plant in forms of tree, sub-tree, or shrub, has long been cultivated as an important fiber resource and for environmental protection. To manage commercial willow plantations, there is an increasing demand for the genetic discrimination of willow cultivars based on molecular markers. In this study, based on the genomic sequences of Salix suchowensis, a core set of 16 highly polymorphic simple sequence repeat (SSR) primer pairs were selected for the molecular discrimination of different willow cultivars. Using these primer pairs, DNA fingerprints of a collection of 25 elite willow cultivars were generated and their genetic identities were analyzed based on the SSR genotyping profiles and the UPGMA clustering. Subsequently, we examined the ploidy levels of these cultivars by combining SSR marker genotyping with flow cytometry measurements. It was found that, in this collection, the shrub cultivars were mainly presented as diploids, while cultivars in tree form mainly existed as polyploids. This study established a reference DNA fingerprinting database for managing the commercial willow cultivars, and the determination of their ploidy levels provided critical information for aiding the polyploid breeding programs in willows. [ABSTRACT FROM AUTHOR]