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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]

12-Oxophytodienoate reductase (OPR) enzymes in dicots are categorized as flavin mononucleotide (FMN)–dependent oxidoreductases and are divided into two subgroups. Although subgroup II OPRs have been identified as being involved in a critical step in the production of jasmonic acid (JA), the functions of subgroup I OPRs are uncertain. In this study, we cloned a potential subgroup I OPR gene, EpOPR1, from Echium plantagineum using comparative transcriptome analysis. EpOPR1 expression was found to be significantly increased in root samples containing secondary metabolites such as shikonin and its derivatives. Using a transgenic hairy root system, we further explored the role of EpOPR1 in the production of these secondary metabolites. The results indicated that although the chemical profile of EpOPR1 overexpressing hairy roots (OPRO) is similar to that of the empty vector hairy roots (EV), the EpOPR1 overexpressing line considerably increased the yield of acetylshikonin by around two-fold. Our findings shed light on the potential role of subgroup I OPRs in E. plantagineum secondary metabolism regulation. [ABSTRACT FROM AUTHOR]

Plagiodera versicolora Laicharting is a highly damaging leaf beetle foraging on willow leaves. In willow germplasm collections, observation has shown that Salix suchowensis Cheng was severely foraged by this leaf beetle while Salix triandra L. was damage free or only slightly damaged. Results of olfactometer bioassays show that the headspace volatiles from leaves of S. triandra significantly repelled adult beetles, suggesting that this species produces volatile repellents against P. versicolora. S. suchowensis had no effect on the beetles. Gas chromatography-mass spectrometry was carried out to profile the headspace volatile organic compounds and 23 compounds from leaves of the alternate species in significantly different concentrations were detected. The effects of 20 chemical analogs on host discrimination were examined. Olfactory response to these chemicals showed that o-cymene, a S. suchowensis specific constituent, significantly attracted adult P. versicolora. In contrast, cis-3-hexenyl acetate, a constituent concentrated more in S. triandra than in S. suchowensis, significantly repelled beetles. Mixing o-cymene and cis-3-hexenyl acetate in comparable concentrations as in the volatiles of S. suchowensis demonstrated that the latter could mask the attracting effect of the former, causing a neutral response by adult beetles to leaves of S. suchowensis against clean air. In addition, chemical analogs have the same effect as plants when resembling volatile organic compounds in real samples. Two volatile metabolites were detected triggering host discrimination by one of the most damaging insect pests to host and non-host willows. The two metabolites are of considerable potential for use as olfactory signs in managing the beetles. [ABSTRACT FROM AUTHOR]

Genetically engineered (GE) maize has been thoroughly studied regarding its agro-environmental impact; however, its concerns for the soil environment remain. This work was aimed to decode rhizosphere microbe interactions and potential ecological hazards associated with GE maize. Rhizobacterial communities of field grown transgenic insect-resistant 2A5 maize carrying mcry1Ab and mcry2Ab genes were compared with control Z58 using PacBio sequencing platform. Also full-length 16S rDNA gene sequencing was used to verify the partial (V3–V4) sequencing results obtained in 2017. Measures of α-diversity displayed transgenic 2A5 to be significantly lower in species richness at the flowering stage; however, diversity remained undisturbed. β-diversity was least affected by genetic modifications where similar community profiles were shared by transgenic 2A5 and control Z58. In addition, root exudation patterns were found to drive variations in bacterial assemblages based on developmental stages. For example, genus Massilia successfully colonized the rhizosphere at jointing stage, while Mucilaginobacter showed higher relative abundance in flowering stages of both 2A5 and Z58. These members are known to possess attributes related to plant growth. The impact of dual-transgene insertion on nifH gene abundance was also analyzed where no apparent significant difference in nifH gene copy number was observed. Our results confirmed that full-length 16S rDNA sequencing was sufficient to provide higher taxonomic resolution. Also, results of our 2-year field trials confirmed that there is no significant impact of mcry gene integration on belowground biomasses. Therefore, GE insect-resistant 2A5 maize carrying mcry1Ab and mcry2Ab genes can continue to benefit human populations by increasing crop productivity. In future, further research needs to be catalyzed to analyze the impact of Bt-insertion on microbial community structure across the years for ecosystem sustainability. [ABSTRACT FROM AUTHOR]

Shikonin and its derivatives are the main components of traditional Chinese medicine, Zicao. The pharmacological potential of shikonin and its derivatives have been extensively studied. Yet, less is known about the microbial assemblages associated with shikonin producing Borage plants. We studied microbial profiles of two Borage species, Echium plantagineum (EP) and Lithospermum erythrorhizon (LE), to identify the dynamics of microbial colonization pattern within three rhizo-compatments and two distinct soil types. Results of α and β-diversity via PacBio sequencing revealed significantly higher microbial richness and diversity in the natural soil along with a decreasing microbial gradient across rhizosphere to endosphere. Our results displayed genotype and soil type–dependent fine-tuning of microbial profiles. The host plant was found to exert effects on the physical and chemical properties of soil, resulting in reproducibly different micro-biota. Analysis of differentially abundant microbial OTUs displayed Planctomycetes and Bacteroidetes to be specifically enriched in EP and LE rhizosphere while endosphere was mostly prevailed by Cyanobacteria. Network analysis to unfold co-existing microbial species displayed different types of positive and negative interactions within different communities. The data provided here will help to identify microbes associated with different rhizo-compartments of potential host plants. In the future, this might be helpful for manipulating the keystone microbes for ecosystem functioning. [ABSTRACT FROM AUTHOR]

Shikonins are the main naphthoquinones in the root periderm of Echium plantagineum, as well as the hypocotyl and root hairs of young seedlings. These red pigments can be used as dyes or for medicinal uses since ancient times. Geranylhydroquinone 3″-hydroxylase (GHQH) has recently been identified to catalyze the C-3″ site of geranylhydroquinone to form 3″-hydroxy-geranyl-hydroquinone in shikonin biosynthetic pathway. In this study, we cloned a geranylhydroquinone 3″-hydroxylase candidate gene (EpGHQH1) from E. plantagineum, and further characterized its function in shikonin biosynthesis using the hairy root system by overexpression and RNA interference strategies. The obtained results showed that overexpression of EpGHQH1 increased the accumulation of shikonins, showing 2.1-fold higher in acetylshikonin yield than that of control lines. On the contrary, down-regulation of EpGHQH1 resulted in a decline in shikonin production. Furthermore, the EpGHQH1 expression levels in germinated seedlings showed a high positive relation with shikonin accumulation. These findings demonstrated the function of EpGHQH1 in enhancing shikonin biosynthesis of E. plantagineum, and provided the first example of transgenic hairy root system from E. plantagineum for functional analysis of genes in metabolite biosynthesis. Key message: We reported a possible GHQH gene (EpGHQH1), and demonstrated its positive role in shikonin biosynthesis of E. plantagineum with the transgenic hairy root system by overexpression and RNAi strategies. [ABSTRACT FROM AUTHOR]

Gene expression analysis is crucial for uncovering components underlying important biological processes for a focal organism. Large-scale gene co-expression networks generally exhibit small-world, scale-free properties; and the degree distributions of these networks follow power-law forms. Topology properties are often informative for determining the key components of the biological systems and their genetic mechanisms. Some basic topology properties display dissimilarity in different tissues, which helps to elucidate the different genetic mechanisms underlying important biological processes among tissues from the top to bottom of trees. In this study, the topology properties of gene co-expression networks were compared in leaf, shoot, wood, and root tissues of poplar. The comparison results demonstrated that the differences of topology properties exist among tissues and the root tissue displays larger average degree and network density, indicating that genes in root tissue are more highly co-expressed than those in the other three tissues. The nodes with a large degree, also known as hub genes, were annotated by the NetAffx Analysis Center and the agriGO tool, with annotation results that these highly interconnected genes are involved in the key biological processes in each tissue. This study also revealed the topology properties' differences between gene co-expression networks and random network, suggesting the existence of hierarchically organized module and small-world organizations in networks of poplar. The approach described in this research offers an effective strategy for identifying key genes involved in the important biological processes in poplar. [ABSTRACT FROM AUTHOR]

Members of the WUSCHEL-related homeobox (WOX) transcription factor family are essential for determining cell fate and regulating diverse developmental processes in plants. Many WOX genes have been systematically investigated in woody plants such as Populus trichocarpa, but not in Salix suchowensis. Whole-genome sequence data for S. suchowensis is now available for comprehensive study of WOX genes in S. suchowensis. We thus surveyed the genome of S. suchowensis and demonstrated active expression of 15 WOX genes. In a phylogenetic analysis of WOX genes, the 15 SsWOX genes clustered among the modern/WUS, intermediate and ancient clades similar to the WOX genes of Arabidopsis thaliana. Based on the conserved intron/exon structure, SsWOX genes in the same subgroup had similar conserved exon–intron structures and motif domains. Furthermore, among several SsWOX subgroups, WUS (Wuschel)-box and EAR (the ERF-associated amphiphilic repression)-like motifs were conserved. Expression profiles of WOX genes in roots, stems and leaves indicate that SsWOX genes have various conserved roles in the tissues. Comparative analysis of the expression patterns in Salix suchowensis with that of Arabidopsis suggests that different shoot regeneration abilities are controlled by different WOX genes in plants. The analysis provide an overview of differentially expressed SsWOX genes during shoot regeneration, but also contribute to understanding the evolution of WOX genes in Salicaceae and the interrelations of WOX genes and other transcription factors, providing targets for further study. [ABSTRACT FROM AUTHOR]

The SnRK (sucrose non-fermenting-1 related protein kinase) families respond to salt tolerance, nutritional stress, disease stress, and carbon metabolic regulation. In this study, the SnRK2.8 gene was cloned from Arabidopsis thaliana and nominated AtSnRK2.8. Bioinformatics characterization of AtSnRK2.8 showed that it contained an ATP binding site and a serine/threonine protein kinase binding site at the N-terminal catalytic domain. In addition, the AtSnRK2.8 protein contained special domain I at the C-terminal catalytic domain. Real-time polymerase chain reaction (PCR) results showed that the AtSnRK2.8 gene was expressed in all tested tissues and was highly expressed in seeds. Our analyses proved that the AtSnRK2.8 gene expression was upregulated by salt and drought stresses. The recombinant AtSnRK2.8 protein was expressed using a pET-28a system and purified with HisTrap HP affinity columns. The recombinant AtSnRK2.8 protein has the properties of a protein kinase. The results of overexpressing AtSnRK2.8 in Nanlin895 poplar showed that the transgenic poplar plants had a better ability to resist drought and salt stress compared to the wild type, and adapted well to drought and a high-salt environment. [ABSTRACT FROM AUTHOR]

Key message: Two large-effect QTLs and 14 candidate genes conferring resistance to Marssonina leaf spot disease were identified in an F1Populus deltoides pedigree, which provided valuable information for cloning the particular underlying genes in future. Marssonina leaf spot disease (MLSD), which is caused by Marssonina brunnea, is a devastating threat to poplar plantations. To map quantitative trait loci (QTLs) underlying resistance to MLSD, an F1P. deltoides pedigree has been established and genetic maps were constructed for the mapping parents according to the two-way pseudo-testcross mapping strategy. The female map contained 913 markers spanning a total genetic distance of 3132 cM, with linkage groups (LGs) corresponding to the 19 haploid chromosomes in poplar, whereas the paternal map contained 252 markers distributed on 22 LGs and covered a genetic length of 1809 cM. The established maps were further aligned to the poplar consensus genetic map based on the integrated SSR markers. The resistance to MLSD was recorded as a complex binary trait based on the black spot symptom on leaves. Analyses of QTLs revealed two large-effect QTLs in LGs VI and XVI, namely qMLSD-VI-1 and qMLSD-XVI-2, which explained 50.3% and 34.5% of the total phenotypic variance, respectively. A significant interaction between these two QTLs was detected based on a two-way ANOVA. In this mapping pedigree, the female parent contributed all of the QTL alleles conferring resistance to M. brunnea. Genome sequences in the target regions were obtained by aligning the QTL intervals to the poplar genome sequence with the mapped SSR markers. The importance and utility of the 14 candidate genes associated with disease resistance identified in the QTL intervals should be more thoroughly characterized in future studies. [ABSTRACT FROM AUTHOR]

Gene knockdown and gene-silencing pathways in eukaryotic organisms are associated with small RNAs 20 to 25 nucleotides in length, which include microRNAs (miRNAs) and small interfering RNAs (siRNAs). These small RNAs are recruited to repress gene expression upstream or downstream of the transcription pathway. RNA interference (RNAi) is a biological inhibitor of gene expression that results in the destruction of messenger RNAs (mRNAs), leading to the inhibition of protein production. Indeed, RNA silencing plays a key role in plant development in terms of the plant’s response to both biotic and abiotic stresses. Conversely, Viral Suppressors of RNA silencing (VSRs) are proteins that hamper antiviral RNAi activation in plants, lead to suppress plant RNA-silencing. These VSR proteins prevent the induction of the plant antiviral RNAi immune response. This review focuses on small RNAs in plants and their roles in the responses of plants to biotic and abiotic stresses. [ABSTRACT FROM AUTHOR]

The prior knowledge plays an important role in increasing the performance of the support vector machines (SVMs). Traditional SVMs do not consider any prior knowledge of the training set. In this paper, the neighbors' distribution knowledge is incorporated into SVMs. The neighbors' distribution can be measured by the sum of the cosine value of the angle, which is between the difference between the sample and its corresponding neighbor, and the difference between the sample and the mean of corresponding neighbors. The neighbors' distribution knowledge reflects the sample's importance in the training processing. It can be explained as the relative margin or instance weight. In this paper, the neighbors' distribution knowledge is regarded as the relative margin and incorporated into the framework of density-induced margin support vector machines whose relative margin is measured by relative density degree. The results of the experiments, performed on both artificial synthetic datasets and real-world benchmark datasets, demonstrate that SVMs performs better after incorporating neighbors' distribution. Furthermore, experimental results also show that neighbors' distribution are more suitable than relative density degree to represent the relative margin. [ABSTRACT FROM AUTHOR]

Unlike two-class (multi-class) support vector machines, massive targets and few outliers are available in one-class support vector machine. The strategies to select useful data for two-class (multi-class) support vector machines are not suitable for one-class support vector machine. In this paper, relative density degree is introduced to select useful data for one-class support vector machine. These data would become support vectors after training and locate near the boundary of the data distribution. The relative density degree of the data near the boundary of the training set is smaller than that of the data in the interior of the training set. Thus, the data near the boundary of training set can be preserved and the others can be disposed through relative density degree. Experimental results show that merely preserving about 20 % of the training set, the performance will not decrease and be better than previous related method. But the model is simpler and the training process is faster. [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]

In plants, many small interfering RNAs (siRNAs) direct de novo methylation by DNA methyltransferase. DNA methylation typically occurs by RNA-directed DNA methylation (RdDM), which directs transcriptional gene silencing of transposons and endogenous transgenes. RdDM is driven by non-coding RNAs (ncRNAs) produced by DNA-dependent RNA polymerases IV and V (PolIV and PolV). The production of siRNAs is initiated by PolIV and ncRNAs produced by PolIV are precursors of 24-nucleotide siRNAs. In contrast, ncRNAs produced by PolV are involved in scaffolding RNAs. In this review, we summarize recent studies of RdDM. In particular, we focus on the mechanisms involved in chromatin remodeling by PolIV and PolV. [ABSTRACT FROM AUTHOR]

Abiotic stresses such as drought and high salinity inhibit plant growth and productivity. NAC transcription factors play a variety of important roles in plant development and abiotic stress responses. To date, the transformation of NAC genes into poplar plants has not been reported. In this study, we introduced the CarNAC3 and CarNAC6 salinity and drought tolerant genes from Cicer arietinum (chickpea) into Populus deltoides × Populus euramericana 'Nanlin895' (poplar) plants using Agrobacterium tumefaciens-mediated transformation . We verified the integration of the two genes into the poplar genome using polymerase chain reaction (PCR) and their stable expression was confirmed at the transcript level using real-time (RT)-PCR. The growth rates of roots and shoots and the clawed root rate increased in transformed plants grown in agar medium or in soil and increased in response to drought and salt stress conditions. Proline and photoprotectant pigment accumulation and antioxidant enzyme activities increased in response to abiotic stress, but the accumulation of photosynthetic pigments and malondialdehyde (MDA) decreased in transgenic lines relative to wild-type control plants. The CarNAC3 transgene was expressed at higher levels than the CarNAC6 transgene. Our results showed that the CarNAC3 and CarNAC6 genes enhanced the capacity for osmotic adjustment and increased antioxidant enzyme activity and suggest that these genes could play a significant role in improving drought and salt tolerance when expressed in poplar plants. [ABSTRACT FROM AUTHOR]

The uredinial stage in the life cycle of Melampsora larici- populina on poplar leaves is the most important pathogenic phase. We captured partial phases of uredinial infection in the wild, aiming to reconstruct the process of uredinial ontogeny by using scanning and transmission electron microscope. At the initial infection stage, germ tubes germinated from the echinulate urediniospores. Germ tubes were frequently seen to merge with the leaf surface and cuticle breakage was observed, indicating direct hyphal penetration. Stomata penetration occurred commonly, sometimes with more than one germ tube penetrating the same stoma. Melampsora larici- populina did not form appressoria in the infection process, implying that infectious behavior of this pathogen may differ from the other rust pathogens. In general, germ tubes branched randomly, and no distinct evidence indicated that stoma could induce or orient germ tube branches. However, oriented germ tube growth has been occasionally observed in other studies. The urediniospores collapsed and finally wizened when they became nutrient stressed. At the last stage of infection, the uredinia erupted from the leaf epidermis and appeared as orange pustules on the leaf surface. [ABSTRACT FROM AUTHOR]

CarNAC3 contains 285 amino acids and a conserved NAC domain. NAC genes, including NAM, ATAF1, ATAF2, and CUC2, are members of one of the largest transcription factor families in plants. CarNAC3, a member of the NAP group, plays an important role in plant development and responses to abiotic stresses. In this study, CarNAC3 was transformed into hybrid poplar plants ( Populus deltoides × P. euramericana 'Nanlin895') using Agrobacterium tumefaciens. PCR analysis confirmed integration of the introduced T-DNA into the target genome. Reverse transcription PCR confirmed the transformation, and Southern and northern blotting verified the transgene copy number and gene expression, respectively. Fourteen lines of positive transformants were transplanted into a greenhouse to verify their drought and salt tolerances. Under normal conditions, transgenic poplar plants were shorter than the wild-type, but under drought and salt stresses, they maintained their normal rooting and stem growth rates, while those of the wild-type plants were suppressed. Under stress conditions, CarNAC3 expression caused increases in proline and photosynthetic pigment levels and in antioxidant enzyme activities. Furthermore, the expression of CarNAC3 lowered malondialdehyde concentrations compared with the wild-type control. Overall, our results indicated that the CarNAC3 transgene enhanced drought and salt tolerance in transgenic poplar plants. [ABSTRACT FROM AUTHOR]

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

In this study, single-nucleotide polymorphisms (SNPs) and insertions/deletions (InDels) in the genome of Ziziphus jujuba were identified using sequences generated by the Roche 454 GS-FLX sequencer. A total of, 573,141 reads were produced with an average read length of 360 bp. After quality control, 258,754 of the filtered reads were assembled into 23,864 contigs, and 293,458 remained as singletons. Using the contig assemblies as a reference, 17,160 SNPs and 478 InDels were identified. Among the SNPs, transitions occurred three times more frequently than transversions. In transitions, the number of C/T and G/A transitions was similar. Among the transversions, A/T was the most abundant, and C/G was much rarer than any of the other types of transversions, accounting for only about half the numbers of A/C, A/T and G/T transversions. For the InDels, mononucleotide changes amounted to 64.4 % of the total number of InDels. In general, the frequency of detected InDels decreased as the length of the InDels increased. This study provides valuable marker resources for future genetic studies of Ziziphus spp. [ABSTRACT FROM AUTHOR]

Polyploid breeding is an important means for creating elite varieties for the development of poplar plantations. However, polyploid poplars are rare in natural stands. In this study, we established an analytical toolkit to perform marker-aided selection of polyploid poplars. This toolkit contains 12 SSR primer pairs with sites located in the exonic DNA regions and resulting amplified microsatellites in the intronic/intergenic regions. Highly conserved primer pairs were selected by testing in eight species from four poplar sections. The amplified loci's variability was examined using trees from a germplasm collection of Populus deltoides. Subsequently, copy numbers amplified by the highly variable primers were experimentally determined using progeny of a full-sib diploid pedigree. Based on the above tests, a subset of primers were finally selected and used for marker-aided selection of polyploid poplars from a set of natural Populus tomentosa stands. The reliability of the established analytical toolkit was further verified using a flow cytometer. We established a fast and reliable technique to screen polyploid poplars from natural stands. [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]

Epidemic outbreaks of rust disease have been observed in most of the black cottonwood ( Populus trichocarpa) plantations in the south of China in recent years. However, the exact pathogens that cause rust disease in this area remain largely unknown. In this study we collected rust fungi from black cottonwood plantations at four different places in the south of China. Examination of these fungi by scanning electron microscope (SEM) and light microscopy (LM) revealed that the morphological characteristics of urediniospores for all the collected fungi were very close to that of Melampsora larici-populina. Using species-specific primers, these pathogens were confirmed to be M. larici-populina. In a survey on the resistance to rust disease for 88 genotypes of black cottonwood, nine potential candidate genotypes were detected that may be free from infection of rust pathogen. The results of this study provide essential information for breeding new rust-resistant black cottonwood cultivars. [ABSTRACT FROM AUTHOR]

Marker transmission ratio distortion (TRD) revealed in genetic mapping studies on distant crosses can be used to infer the genetic basis relating to reproductive barriers between species. Unlike measuring the degree of TRD by the overall number of segregation distorted markers in the affected genome regions, mapping the segregation distorting loci (SDL) provides reliable statistic parameters that help to confine the target genomic regions for further characterization at molecular level. Using the linkage map constructed for a natural hybrid of Pinus hwangshanensis and Pinus massoniana, we perform SDL analyses and align the established map to the loblolly pine consensus map. Altogether, six SDLs with relatively strong LOD supports are detected on four linkage groups of the established map. Since gametes inheriting different alternate chromatid blocks from the SDL affecting genome regions have uneven chance to descend to the offspring, the corresponding genome regions are supposed to play more significant roles in rendering the reproductive isolations between P. hwangshanensis and P. massoniana. This paper presents a case study on a crucial step for uncovering the hidden genetic factors that trigger the uneven descending of gametes in a natural hybrid pine. [ABSTRACT FROM AUTHOR]

Genetic determination of gender is a fundamental developmental and evolutionary process in plants. Although it appears that dioecy in Populus is genetically controlled, the precise gender-determining systems remain unclear. The recently released second draft assembly and annotated gene set of the Populus genome provided an opportunity to revisit this topic. We hypothesized that over evolutionary time, selective pressure has reformed the genome structure and gene composition in the peritelomeric region of the chromosome XIX, which has resulted in a distinctive genome structure and cluster of genes contributing to gender determination in Populus trichocarpa. Multiple lines of evidence support this working hypothesis. First, the peritelomeric region of the chromosome XIX contains significantly fewer single nucleotide polymorphisms than the rest of Populus genome and has a distinct evolutionary history. Second, the peritelomeric end of chromosome XIX contains the largest cluster of the nucleotide-binding site-leucine-rich repeat (NBS-LRR) class of disease resistance genes in the entire Populus genome. Third, there is a high occurrence of small microRNAs on chromosome XIX, which is coincident to the region containing the putative gender-determining locus and the major cluster of NBS-LRR genes. Further, by analyzing the metabolomic profiles of floral bud in male and female Populus trees using a gas chromatography-mass spectrometry, we found that there are gender-specific accumulations of phenolic glycosides. Taken together, these findings led to the hypothesis that resistance to and regulation of a floral pathogen and gender determination coevolved, and that these events triggered the emergence of a nascent sex chromosome. Further studies of chromosome XIX will provide new insights into the genetic control of gender determination in Populus. [ABSTRACT FROM AUTHOR]

With the development of high-throughput sequencing techniques, transcriptome sequencing projects which provide valuable resources for designing simple sequence repeat (SSR) primers have been carried out for many plants. However, the utility of SSRs for molecular breeding depends on genome-wide distribution and coverage, as well as moderately high allelic variability, in the available SSR library. In this study, we characterized the exonic SSRs developed from the publicly available Populus genome as a case study to determine their value for molecular breeding. As expected, our results confirmed that microsatellites occurred approximately three times less often in coding regions than in non-coding regions. Mutability test also showed that exonic SSRs contained less allelic variability than intronic SSRs. More importantly, exonic SSRs were unevenly distributed both among and within chromosomes. Large exonic SSRs deserts were observed on several chromosomes. Differential selection between paralogous chromosomes, at the gene level, appears to be responsible for these SSR deserts, though the mechanisms that cause chromosome-specific SSR deserts are not known. This work provides ample evidence that the candidate gene approach based on unigenes identified from transcribed sequences may not be the best strategy to identify highly polymorphic SSRs. [ABSTRACT FROM AUTHOR]

The capacity to root from cuttings is a key factor for the mass deployment of superior genotypes in clonal forestry. We studied the genetic basis of rooting capacity by mapping quantitative trait loci (QTLs) that control growth rate and form of root traits in a full-sib family of 93 hybrids derived from an interspecific cross between two Populus species, P. deltoides and P. euramericana. The hybrid family was typed for different marker systems (including SSRs, AFLPs, RAPDs, ISSRs, and SNPs), leading to the construction of two linkage maps based on the female P. deltoides (D map) and male P. euramericana (E map) with a pseudotestcross mapping strategy. The two maps were scanned by functional mapping to detect QTLs that control early growth trajectories of two rooting traits, maximal single-root length and the total number of roots per cutting, measured at five time points in water culture. Of the six QTLs detected for these two growth traits, only one is segregating in P. deltoides with poor rooting capacity, while the other five are segregating in P. euramericana showing good rooting capacity. Tests with functional mapping suggest different developmental patterns of the genetic effects of these root QTLs in time course. Five QTLs were detected to change their effects on root growth trajectories with time, whereas one detected to affect root growth consistently in time course. Knowledge about the genetic and developmental control mechanisms of root QTLs will have important implications for the genetic improvement of vegetative propagation traits in Populus. [ABSTRACT FROM AUTHOR]

We mapped and analyzed the microsatellites throughout 284295605 base pairs of the unambiguously assembled sequence scaffolds along 19 chromosomes of the haploid poplar genome. Totally, we found 150985 SSRs with repeat unit lengths between 2 and 5 bp. The established microsatellite physical map demonstrated that SSRs were distributed relatively evenly across the genome of Populus. On average, These SSRs occurred every 1883 bp within the poplar genome and the SSR densities in intergenic regions, introns, exons and UTRs were 85.4%, 10.7%, 2.7% and 1.2%, respectively. We took di-, tri-, tetra-and pentamers as the four classes of repeat units and found that the density of each class of SSRs decreased with the repeat unit lengths except for the tetranucleotide repeats. It was noteworthy that the length diversification of microsatellite sequences was negatively correlated with their repeat unit length and the SSRs with shorter repeat units gained repeats faster than the SSRs with longer repeat units. We also found that the GC content of poplar sequence significantly correlated with densities of SSRs with uneven repeat unit lengths (tri-and penta-), but had no significant correlation with densities of SSRs with even repeat unit lengths (di-and tetra-). In poplar genome, there were evidences that the occurrence of different microsatellites was under selection and the GC content in SSR sequences was found to significantly relate to the functional importance of microsatellites. [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]

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]

Polyploid breeding is an important means for creating elite willow cultivars, and therefore provokes an active demand for discriminating the ploidy levels of natural willow stands. In this study, we established an analytical toolkit for polyploid willow identification by combining molecular markers and flow cytometry (FCM). A total of 10 single-copy fully informative SSRs were chosen for marker-aided selection based on a segregation test with a full-sib willow pedigree and a mutability test with a collection of natural willow stands. Aided by these molecular markers, we performed polyploid selection in two tree species and two shrub species of the genus Salix. The ploidy levels of the investigated samples were further examined using a flow cytometer. It was previously shown that results from marker-aided selection were consistent with those from FCM measurements. Based on ploidy level assessment in different willow species, it was found that tree willows were dominantly tetraploid, whereas shrub willows were most frequently diploid. With this analytical toolkit, polyploids can be rapidly screened from a large number of natural stands; thereafter, the exact ploidy levels of the polyploid candidates can be efficiently confirmed by FCM. This analytical toolkit will greatly enhance polyploid breeding programs for 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]