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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]

Sex has a significant effect on various traits among dioecious plants. In this analysis of the sex effect on the radial growth and wood density of numerous 20-year-old trees of Populus deltoides growing in a common garden, male trees performed better than the females in radial growth, but sex did not significantly affect wood density. Growth rate and wood density were weakly negatively correlated. Sex selection is also critical for controlling seed-hair pollution from P. deltoides plantations. However, because the juvenile period of P. deltoides lasts for years, a reliable technique to determine the sex of juveniles has been needed. Here we developed a marker-aided technique to discriminate the sexes of P. deltoides seedlings. This study provides essential information on target traits and a highly desirable genetic toolkit for accelerate breeding programs for this important tree species. [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]

By screening sequence reads from the Salix suchowensis chloroplast (cp) genome that were generated by next-generation sequencing platforms, we assembled a complete circular pseudomolecule for the cp genome. This pseudomolecule is 155,508 bp long and has a typical quadripartite structure that contains two single copy regions, a large single copy region (LSC, 84,385 bp), and a small single copy region (SSC, 16,209 bp) separated by inverted repeat regions (IRs, 27,457 bp). Gene annotation revealed that the S. suchowensis cp genome encoded 119 unique genes, including four ribosome RNA genes, 30 transfer RNA genes, 82 protein-coding genes, and three pseudogenes. Analysis of the repetitive sequences revealed 31 tandem repeats, 16 forward repeats, and five palindromic repeats. In addition, a total of 148 perfect microsatellites, which were characterized as A/T dominant in nucleotide composition, were detected. Significant shifting of the IR/SSC boundaries was revealed by comparing this cp genome with those of other rosid plants. We also constructed phylogenetic trees to demonstrate the phylogenetic position of S. suchowensis in Rosidae based on 66 orthologous protein-coding genes present in the cp genomes of 32 species. Sequencing 30 amplicons based on the pseudomolecule for experimental verification revealed 99.88% accuracy for the S. suchowensis cp genome assembly. Therefore, we assembled a high-quality pseudomolecule of the S. suchowensis cp genome, which is a useful resource for facilitating development of this shrub willow into a more productive bioenergy crop. [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]

The complete nucleotide sequences of the mitochondrial (mt) genome of an extremophile species Thellungiella parvula (T. parvula) have been determined with the lengths of 255,773 bp. T. parvula mt genome is a circular sequence and contains 32 protein-coding genes, 19 tRNA genes, and three ribosomal RNA genes with a 11.5% coding sequence. The base composition of 27.5% A, 27.5% T, 22.7% C, and 22.3% G in descending order shows a slight bias of 55% AT. Fifty-three repeats were identified in the mitochondrial genome of T. parvula, including 24 direct repeats, 28 tandem repeats (TRs), and one palindromic repeat. Furthermore, a total of 199 perfect microsatellites have been mined with a high A/T content (83.1%) through simple sequence repeat (SSR) analysis and they were distributed unevenly within this mitochondrial genome. We also analyzed other plant mitochondrial genomes’ evolution in general, providing clues for the understanding of the evolution of organelles genomes in plants. Comparing with other Brassicaceae species, T. parvula is related to Arabidopsis thaliana whose characters of low temperature resistance have been well documented. This study will provide important genetic tools for other Brassicaceae species research and improve yields of economically important plants. [ABSTRACT FROM AUTHOR]

Oil camellia (Camellia oleifera Abel.) is a widely cultivated economically important plant. In China, more than 100 elite cultivars have been authorized for commercial plantations, representing the developmental base for the oil camellia industry. Since oil camellia seedlings are frequently traded and introduced to new places, there is an active demand to develop a rapid and reliable identification toolkit to protect and ensure the effective use of these resources. In this study, ten highly polymorphic simple sequence repeat (SSR) primer pairs were screened from the SSR primer database of oil camellia, and DNA fingerprints of 128 elite oil camellia cultivars were constructed with these primer pairs. By analyzing the fingerprinting profiles, all of these cultivars were found to have unique DNA fingerprints, except 'Changlin 40' and 'Fuyang 40', which shared a complete similarity across all of the fingerprints generated by these ten SSR primer pairs, indicating that they were either synonyms or vegetative mutants. Synonyms are a major source of confusion in protecting and managing new varieties of plants. Although the synonymy of these two cultivars needs to be further confirmed, our data indicated a high possibility of synonyms among the authorized oil camellia cultivars. This study provides a desirable genetic toolkit for the identification and management of the elite oil camellia cultivars, and also for the intellectual property right protection of breeders. [ABSTRACT FROM AUTHOR]

The huge amount of gene expression data generated by microarray and next-generation sequencing technologies present challenges to exploit their biological meanings. When searching for the coexpression genes, the data mining process is largely affected by selection of algorithms. Thus, it is highly desirable to provide multiple options of algorithms in the user-friendly analytical toolkit to explore the gene expression signatures. For this purpose, we developed GESearch, an interactive graphical user interface (GUI) toolkit, which is written in MATLAB and supports a variety of gene expression data files. This analytical toolkit provides four models, including the mean, the regression, the delegate, and the ensemble models, to identify the coexpression genes, and enables the users to filter data and to select gene expression patterns by browsing the display window or by importing knowledge-based genes. Subsequently, the utility of this analytical toolkit is demonstrated by analyzing two sets of real-life microarray datasets from cell-cycle experiments. Overall, we have developed an interactive GUI toolkit that allows for choosing multiple algorithms for analyzing the gene expression signatures. [ABSTRACT FROM AUTHOR]

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

Gene introgression and hybrid barriers have long been a major focus of studies of geographically overlapping species. Two pine species, Pinus massoniana and P. hwangshanensis, are frequently observed growing adjacent to each other, where they overlap in a narrow hybrid zone. As a consequence, these species constitute an ideal system for studying genetic introgression and reproductive barriers between naturally hybridizing, adjacently distributed species. In this study, we sampled 270 pine trees along an elevation gradient in Anhui Province, China and analyzed these samples using EST-SSR markers. The molecular data revealed that direct gene flow between the two species was fairly low, and that the majority of gene introgression was intermediated by backcrossing. On the basis of empirical observation, the on-site distribution of pines was divided into a P. massoniana zone, a hybrid zone, and a P. hwangshanensis zone. STRUCTURE analysis revealed the existence of a distinct species boundary between the two pine species. The genetic boundary of the hybrid zone, on the other hand, was indistinct owing to intensive backcrossing with parental species. Compared with P. massoniana, P. hwangshanensis was found to backcross with the hybrids more intensively, consistent with the observation that morphological and anatomical characteristics of trees in the contact zone were biased towards P. hwangshanensis. The introgression ability of amplified alleles varied across species, with some being completely blocked from interspecific introgression. Our study has provided a living example to help explain the persistence of adjacently distributed species coexisting with their interfertile hybrids. [ABSTRACT FROM AUTHOR]

Oil camellia trees are important woody plants for the production of high-quality cooking oil. On the contrary to their economic importance, their genetic and genomic resources are very limited, which greatly hamper the genetic studies on oil camellia trees. Microsatellites or simple sequence repeats (SSRs) have great value in many aspects of genetic analyses due to their high polymorphism and codominant inheritance. In this study, we report the large-scale development and characterization of SSR markers derived from genomic sequences of Camellia chekiangoleosa by high-throughput pyrosequencing technology. A total of 1,091,393 genomic shotgun reads were generated using Roche 454 FLX sequencer, the average read length was 319 bp, and the total sequence throughput was 347.9 Mb. These sequences were assembled into 35,315 contigs with total length of 14.8 Mb and the N50 contig size of 770 bp. By analyzing with microsatellite (MISA), a total of 5,844 perfect microsatellites were detected from the assembled sequences. Among them, tetranucleotide repeats were found to be the most frequent microsatellites in the genome of C. chekiangoleosa, and all the dominant repeat motifs for different types of SSRs were detected to be rich in A/T. Experimental analysis with 900 SSR primer pairs revealed that 66 % of them succeeded in PCR amplification. Further investigation with 345 SSR primer pairs showed that a relatively high percentage of primers amplified polymorphic loci (31.9 %). Experimental data also revealed that, overall, long microsatellite repeats (>20 bp) were more variable than the short ones (<20 bp) in the genome of oil camellia tree. [ABSTRACT FROM AUTHOR]

Almost all plants in the genus Populus are dioecious (i.e. trees are either male or female), but it is unknown whether dioecy evolved in a common ancestor or independently in different subgenera. Here, we sequence the small peritelomeric X- and Y-linked regions of P. deltoides chromosome XIX. Two genes are present only in the Y-linked region. One is a duplication of a non-Y-linked, female-specifically expressed response regulator, which produces siRNAs that block this gene's expression, repressing femaleness. The other is an LTR/Gypsy transposable element family member, which generates long non-coding RNAs. Overexpression of this gene in A. thaliana promotes androecium development. We also find both genes in the sex-determining region of P. simonii, a different poplar subgenus, which suggests that they are both stable components of poplar sex-determining systems. By contrast, only the duplicated response regulator gene is present in the sex-linked regions of P. davidiana and P. tremula. Therefore, findings in our study suggest dioecy may have evolved independently in different poplar subgenera. Dioecy has evolved independently from hermaphroditic ancestors in different plant lineages. Here, the authors assemble Populus deltoides male and female genomes, and show the putative roles of a femaleness gene and a maleness gene in sex determination, which suggests independent evolution in different poplar species. [ABSTRACT FROM AUTHOR]

The complete mitochondrial genome ofMedicago truncatula(M. truncatula) was reported in this study. The mitochondrial genome (mitogenome) was assembled to 271 618 nt. The mitogenome contains 31 protein-coding genes, three rRNA genes and 16 tRNAs. The overall base composition of the mitogenome in descending order is A: 27.21%, C: 22.61%, G: 22.78% and T: 27.40%, and the G + C content is 45.39%. Additionally, 30 exons and 17 introns were identified in eight genes and nine tandem repeats were identified with the period size from 10 nt to 33 nt. Phylogenetic analysis shows that theM. truncatulagenome is evolutionarily closest to that of Lotus japonicas. With the complete mitogenome ofM. truncatula, it is beneficial to the further research of mitogenome of seed plants, and especially helpful for elucidating vital activities of legumes. [ABSTRACT FROM PUBLISHER]

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]

Willows (Salix) and poplars (Populus) are dioecious plants in Salicaceae family. Sex chromosome in poplar genome was consistently reported to be associated with chromosome XIX. In contrast to poplar, this study revealed that chromosome XV was sex chromosome in willow. Previous studies revealed that both ZZ/ZW and XX/XY sex-determining systems could be present in some species of Populus. In this study, sex of S. suchowensis was found to be determined by the ZW system in which the female was the heterogametic gender. Gene syntenic and collinear comparisons revealed macrosynteny between sex chromosomes and the corresponding autosomes between these two lineages. By contrast, no syntenic segments were found to be shared between poplar's and willow's sex chromosomes. Syntenic analysis also revealed substantial chromosome rearrangements between willow's alternate sex chromatids. Since willow and poplar originate from a common ancestor, we proposed that evolution of autosomes into sex chromosomes in these two lineages occurred after their divergence. Results of this study indicate that sex chromosomes in Salicaceae are still at the early stage of evolutionary divergence. Additionally, this study provided valuable information for better understanding the genetics and evolution of sex chromosome in dioecious plants. [ABSTRACT FROM AUTHOR]