Publications by authors named "Xiangyang Kang"

26 Publications

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Integrated transcriptome and miRNA sequencing approaches provide insights into salt tolerance in allotriploid Populus cathayana.

Planta 2021 Jul 5;254(2):25. Epub 2021 Jul 5.

Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China.

Main Conclusion: Some salt-stress responsive DEGs, mainly involved in ion transmembrane transport, hormone regulation, antioxidant system, osmotic regulation, and some miRNA jointly regulated the salt response process in allotriploid Populus cathayana. The molecular mechanism of plant polyploid stress resistance has been a hot topic in biological research. In this study, Populus diploids and first division restitution (FDR) and second division restitution (SDR) triploids were selected as research materials. All materials were treated with 70 mM NaCl solutions for 30 days in the same pot environment. We observed the growth state of triploids and diploids and determined the ratio of potassium and sodium ions, peroxidase (POD) activity, proline content, and ABA and jasmonic acid (JA) hormone content in leaves in the same culture environment with the same concentration of NaCl solution treatment. In addition, RNA-seq technology was used to study the differential expression of mRNA and miRNA. The results showed that triploid Populus grew well and the K content and the K/Na ratio in the salt treatment were significantly lower than those in the control. The contents of ABA, JA, POD, and proline were increased compared with contents in diploid under salt stress. The salt-stress responsive DEGs were mainly involved in ion transport, cell homeostasis, the MAPK signaling pathway, peroxisome, citric acid cycle, and other salt response and growth pathways. The transcription factors mainly included NAC, MYB, MYB_related and AP2/ERF. Moreover, the differentially expressed miRNAs involved 32 families, including 743 miRNAs related to predicted target genes, among which 22 miRNAs were significantly correlated with salt-stress response genes and related to the regulation of hormones, ion transport, reactive oxygen species (ROS) and other biological processes. Our results provided insights into the physiological and molecular aspects for further research into the response mechanisms of allotriploid Populus cathayana to salt stress. This study provided valuable information for the salt tolerance mechanism of allopolyploids.
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http://dx.doi.org/10.1007/s00425-021-03600-9DOI Listing
July 2021

The diverse roles of cytokinins in regulating leaf development.

Hortic Res 2021 Jun 1;8(1):118. Epub 2021 Jun 1.

College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI, USA.

Leaves provide energy for plants, and consequently for animals, through photosynthesis. Despite their important functions, plant leaf developmental processes and their underlying mechanisms have not been well characterized. Here, we provide a holistic description of leaf developmental processes that is centered on cytokinins and their signaling functions. Cytokinins maintain the growth potential (pluripotency) of shoot apical meristems, which provide stem cells for the generation of leaf primordia during the initial stage of leaf formation; cytokinins and auxins, as well as their interaction, determine the phyllotaxis pattern. The activities of cytokinins in various regions of the leaf, especially at the margins, collectively determine the final leaf morphology (e.g., simple or compound). The area of a leaf is generally determined by the number and size of the cells in the leaf. Cytokinins promote cell division and increase cell expansion during the proliferation and expansion stages of leaf cell development, respectively. During leaf senescence, cytokinins reduce sugar accumulation, increase chlorophyll synthesis, and prolong the leaf photosynthetic period. We also briefly describe the roles of other hormones, including auxin and ethylene, during the whole leaf developmental process. In this study, we review the regulatory roles of cytokinins in various leaf developmental stages, with a focus on cytokinin metabolism and signal transduction processes, in order to shed light on the molecular mechanisms underlying leaf development.
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http://dx.doi.org/10.1038/s41438-021-00558-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8167137PMC
June 2021

Transcriptome comparison of different ploidy reveals the mechanism of photosynthetic efficiency superiority of triploid poplar.

Genomics 2021 Jul 19;113(4):2211-2220. Epub 2021 May 19.

Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, PR China; National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing 100083, PR China; Key Laboratory for Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, PR China. Electronic address:

Triploid poplars have obvious growth advantages, especially in leaf development and photosynthetic characteristics, but the molecular mechanism has not been revealed yet. In order to better understand the regulation mechanisms of leaf and chlorophyll development in the triploid poplars, we combined the leaf phenotypic data with the transcriptomic data of the 5th, 10th, and 25th leaves from triploid and diploid poplars, using weighted gene co-expression network analysis (WGCNA), and revealed that PpnGRF5-1 had a strong correlation with leaf development and net photosynthetic rate (Pn). PpnGRF5-1 overexpression transgenic plants showed that the leaf area, Pn, and chlorophyll concentration were significantly increased. Transcriptomic data analysis of the third leaf from PpnGRF5-1 overexpression transgenic plants showed that PpnGRF5-1 could up-regulate the expression levels of chlorophyll synthesis genes and down-regulate the transcription of chlorophyll degradation enzymes. Overall, our studies have greatly expanded our understanding of the molecular mechanisms regulating triploid growth dominance.
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http://dx.doi.org/10.1016/j.ygeno.2021.05.009DOI Listing
July 2021

Variation of homologous recombination in Populus tomentosa with different genotypes.

Yi Chuan 2021 Feb;43(2):182-193

Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China;National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing 100083, China;Beijing Laboratory of Urban and Rural Ecological Environment, Beijing Forestry University, Beijing 100083, China.

Homologous recombination is an important source of biological genetic variation. Limited by detection methods, there are only a few reports on the homologous recombination in high plants and its product - heteroduplex DNA (hDNA). In the present study, applying the strategy of detecting hDNA by constructing populations from inhibited post-meiotic segregation, two hybrid triploid populations were constructed from two maternal parents inPopulus tomentosa by inhibiting post-meiotic segregation. One hundred and ten simple sequence repeat (SSR) markers were used to study the occurrence and variation of hDNA on nine chromosomes inP. tomentosa with different genotypes. The results showed that the frequencies of hDNA between two female parents inP. tomentosa ranged from 8.5% to 87.2%. The hDNA frequency was positively correlated to the distance from the centromere, but the average hDNA frequency on a chromosome had no correlation with the chromosome length. One to 3 times recombination events were detected on most chromosomes, and only a few four- or five-times recombination events were detected. The overall frequencies of hDNA on the same chromosome in two genotypic individuals were roughly similar, while the hDNA frequencies varied greatly at specific SSR loci. Compared withTacamahaca poplar hybrid,P. pseudo-simonii × P. nigra 'Zheyin3#', detection of homologous recombination times and the frequency and location of hDNA were largely different. This study is the first to describe the characteristics and variations of homologous recombination inP. tomentosa with two different genotypes, which will provide valuable insights for exploring the characteristics and variations of homologous recombination among interspecies and intraspecies in higher plant.
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http://dx.doi.org/10.16288/j.yczz.20-205DOI Listing
February 2021

Comparative proteomic analysis provides insight into the molecular mechanism of vegetative growth advantage in allotriploid Populus.

Genomics 2021 May 5;113(3):1180-1192. Epub 2021 Mar 5.

Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, PR China; National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing 100083, PR China; College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, PR China. Electronic address:

Though allotriploid poplar shows a salient vegetative growth advantage that impacts biomass and lumber yield, the proteomic data of Populus allotriploids have not been scrutinized for identifying the underlying molecular mechanisms. We conducted a large-scale label-free proteomics profiling of the 5th, 10th, and 25th leaves of allotriploids and diploids, and identified 4587 protein groups. Among 932 differentially expressed proteins (DEPs), 22 are transcription factors (TFs) that could regulate vegetative growth advantage in allotriploids. The DEPs involved in light reaction, Calvin cycle, and photorespiration, protein synthesis, sucrose synthesis, starch synthesis, and starch decomposition displayed elevated expression in Populus allotriploids. However, the DEPs functioning in sucrose decomposition, tricarboxylic acid (TCA) cycle, and protein degradation exhibited significantly downregulated expression. The alternations of these DEPs augmented efficiency of photosynthesis, carbon fixation, sucrose and starch accumulation, and decreased capacity of carbohydrate consumption, leading to larger volume of biomass and vigorous growth in Populus allotriploids.
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http://dx.doi.org/10.1016/j.ygeno.2021.03.002DOI Listing
May 2021

Growth-regulating factor 5 (GRF5)-mediated gene regulatory network promotes leaf growth and expansion in poplar.

New Phytol 2021 04 14;230(2):612-628. Epub 2021 Feb 14.

College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI, 49931, USA.

Although polyploid plants have larger leaves than their diploid counterparts, the molecular mechanisms underlying this difference (or trait) remain elusive. Differentially expressed genes (DEGs) between triploid and full-sib diploid poplar trees were identified from two transcriptomic data sets followed by a gene association study among DEGs to identify key leaf growth regulators. Yeast one-hybrid system, electrophoretic mobility shift assay, and dual-luciferase assay were employed to substantiate that PpnGRF5-1 directly regulated PpnCKX1. The interactions between PpnGRF5-1 and growth-regulating factor (GRF)-interacting factors (GIFs) were experimentally validated and a multilayered hierarchical regulatory network (ML-hGRN)-mediated by PpnGRF5-1 was constructed with top-down graphic Gaussian model (GGM) algorithm by combining RNA-sequencing data from its overexpression lines and DAP-sequencing data. PpnGRF5-1 is a negative regulator of PpnCKX1. Overexpression of PpnGRF5-1 in diploid transgenic lines resulted in larger leaves resembling those of triploids, and significantly increased zeatin and isopentenyladenine in the apical buds and third leaves. PpnGRF5-1 also interacted with GIFs to increase its regulatory diversity and capacity. An ML-hGRN-mediated by PpnGRF5-1 was obtained and could largely elucidate larger leaves. PpnGRF5-1 and the ML-hGRN-mediated by PpnGRF5-1 were underlying the leaf growth and development.
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http://dx.doi.org/10.1111/nph.17179DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8048564PMC
April 2021

High-quality de novo assembly of the Eucommia ulmoides haploid genome provides new insights into evolution and rubber biosynthesis.

Hortic Res 2020 Nov 1;7(1):183. Epub 2020 Nov 1.

Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, 100083, Beijing, People's Republic of China.

We report the acquisition of a high-quality haploid chromosome-scale genome assembly for the first time in a tree species, Eucommia ulmoides, which is known for its rubber biosynthesis and medicinal applications. The assembly was obtained by applying PacBio and Hi-C technologies to a haploid that we specifically generated. Compared to the initial genome release, this one has significantly improved assembly quality. The scaffold N50 (53.15 MB) increased 28-fold, and the repetitive sequence content (520 Mb) increased by 158.24 Mb, whereas the number of gaps decreased from 104,772 to 128. A total of 92.87% of the 26,001 predicted protein-coding genes identified with multiple strategies were anchored to the 17 chromosomes. A new whole-genome duplication event was superimposed on the earlier γ paleohexaploidization event, and the expansion of long terminal repeats contributed greatly to the evolution of the genome. The more primitive rubber biosynthesis of this species, as opposed to that in Hevea brasiliensis, relies on the methylerythritol-phosphate pathway rather than the mevalonate pathway to synthesize isoprenyl diphosphate, as the MEP pathway operates predominantly in trans-polyisoprene-containing leaves and central peels. Chlorogenic acid biosynthesis pathway enzymes were preferentially expressed in leaves rather than in bark. This assembly with higher sequence contiguity can foster not only studies on genome structure and evolution, gene mapping, epigenetic analysis and functional genomics but also efforts to improve E. ulmoides for industrial and medical uses through genetic engineering.
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http://dx.doi.org/10.1038/s41438-020-00406-wDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7603500PMC
November 2020

Molecular Mechanism of Slow Vegetative Growth in Tetraploid.

Genes (Basel) 2020 11 27;11(12). Epub 2020 Nov 27.

Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China.

Tetraploid plants often have altered rates of vegetative growth relative to their diploid progenitors. However, the molecular basis for altered growth rates remains a mystery. This study reports microRNA (miRNA) and gene expression differences in tetraploids and counterpart diploids using RNA and miRNA sequencing. The results showed that there was no significant difference between young leaves in the expression of vegetative growth-related miRNAs. However, as leaves aged, the expression of auxin- and gibberellin-related miRNAs was significantly upregulated, while the expression of senescence-related miRNAs was significantly downregulated. The dose effect enhanced the negative regulation of the target genes with , , , and being downregulated, and and being upregulated. As a result, the chloroplast degradation of tetraploid leaves was accelerated, the photosynthetic rate was decreased, and the synthesis and decomposition ability of carbohydrate was decreased.
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http://dx.doi.org/10.3390/genes11121417DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7761321PMC
November 2020

Construction of a breeding parent population of Populus tomentosa based on SSR genetic distance analysis.

Sci Rep 2020 10 29;10(1):18573. Epub 2020 Oct 29.

Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, 100083, China.

Parent selection is the core of hybrid breeding. The breeding strategy involving the parental identification of superior open-pollinated progeny of Populous tomentosa germplasm resources can significantly improve the efficiency of parental matching. However, due to some factors such as loose powdering time and pollen competitiveness, the offspring derived from open-pollination families which do not undergo completely random mating. Although hybrid combinations based on the male identification method have a high combining ability, this method cannot easily cover the mating combinations of all male and female specimens in the germplasm bank. In addition, the performance of superior plants in open-pollinated families also affects the selection result. If the trait performance value is higher than the population average, then the special combining ability of the reconstructed hybrid combination may be overestimated. Obtaining a solution to the above problems is of great significance for improving the efficiency and accuracy of selecting hybrid parents of P. tomentosa. In this study, 24 pairs of SSR (Simple Sequence Repeats) molecular markers were used to analyze the genetic differentiation of P. tomentosa germplasm resources. The results showed that the genetic variation of the P. tomentosa population was derived from individuals within the provenance, indicating that high genetic diversity is preserved in provenances. The correlation analysis showed that there was a significant positive correlation between the special combining ability of planting height and diameter at breast height (dbh) of the 34 full-sib progeny population and the genetic distance between the parents. Then, the genetic distance between 18 female plants with high fertility and 68 male plants with large pollen quantity was analyzed using this correlation. Fifteen female parents and 12 male parents were screened out, and 52 hybrid combinations with high specific combining ability for growth traits were predicted. Furthermore, for the male parent identification of superior individual plants, we constructed the breeding parent population including 10 female parents and 5 male parents, generating 14 hybrid combinations with potentially high combining ability. The results of the hybridization test showed that the specific combining ability of plant height and dbh was significantly higher than the controlled pollination. Moreover, genetic distance and paternal identification can be used to rapidly and efficiently construct hybrid parent combinations and breeding parent populations.
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http://dx.doi.org/10.1038/s41598-020-74941-wDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7596703PMC
October 2020

Molecular Mechanism of Vegetative Growth Advantage in Allotriploid .

Int J Mol Sci 2020 Jan 10;21(2). Epub 2020 Jan 10.

Beijing Advanced Innovation Center for Breeding by Molecular Design, Beijing Forestry University, No. 35, Qinghua East Road, Haidian District, Beijing 100083, China.

Allotriploid poplar has a prominent vegetative growth advantage that impacts dramatically on lumber yield. The growth regulation is complex which involves abundant genes, metabolic and signaling pathways, while the information about the functional control process is very little. We used high-throughput sequencing and physiological index measurement to obtain a global overview of differences between allotriploid and diploid . The genes related to plant growth advantage show a higher expression compared to diploid, and most of them are revolved around hormones, photosynthesis and product accumulation. Thus, allotriploid showed more efficient photosynthesis, carbon fixation, sucrose and starch synthesis, and metabolism as well as augmented biosynthesis of auxin, cytokinin, and gibberellin. These data enable the connection of metabolic processes, signaling pathways, and specific gene activity, which will underpin the development of network models to elucidate the process of triploid advantage growth.
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http://dx.doi.org/10.3390/ijms21020441DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7014019PMC
January 2020

Induction, identification and characterization of tetraploidy in .

Breed Sci 2019 Mar 7;69(1):160-168. Epub 2019 Mar 7.

College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China.

of Solanaceae was widely used as healthy vegetables and natural medicine foods for containing numerous functional components in leaves, roots and fruits. In the present study, tetraploid plants of were obtained efficiently by treating their leaves with colchicine . The highest induction frequency of the tetraploids was 31.4%, which was obtained by preculturing the leaves for 10 days and then treating them with 100 mg/L of colchicine concentration for 48 h. The ploidy levels of the regenerated plants were determined by flow cytometry and chromosome counting methods. Cytological, morphological, and histological characterization validated the results of flow cytometry, revealing the differences between the two kinds of ploidy plants in their tissue culture stage and field production stages. Morphological indexes also provide a simple and intuitionistic method for distinguishing tetraploid from diploid plants. As the chromosome number increased, the stomatal size and number of the chloroplasts in the stomata also increased, but the stomatal density decreased. The results indicate that the chromosome number is correlated with the stomatal index. The generated tetraploid is a potentially useful cultivated variety and will be beneficial for producing triploid progeny in the future.
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http://dx.doi.org/10.1270/jsbbs.18144DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6507718PMC
March 2019

Genetic analysis of admixture and hybrid patterns of Populus hopeiensis and P. tomentosa.

Sci Rep 2019 03 18;9(1):4821. Epub 2019 Mar 18.

State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Silviculture of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China.

Hybridization and introgression have resulted in reticulate evolution within the genus Populus. Consequently, the origin and evolutionary history of some hybrids has become blurred. P. hopeiensis and P. tomentosa are endemic to China, and there is still controversy about their origin. We employ phylogeny, Bayesian estimation of admixture, and approximate Bayesian computation to investigate their origin with 10 nuclear DNA and 6 cpDNA regions. The combined evidences firmly support the hypothesis that they are hybrids and dominated by Fs. P. hopeiensis was generated via hybridization between the paternal species P. alba and maternal species P. davidiana. Surprisingly, P. tomentosa was divided into two genetic types with different maternal parents. P. adenopoda hybridized with P. alba directly to generate the first genetic type (mb1) and hybridized with P. davidiana followed by P. alba to generate the second (mb2). In both genetic types, P. alba acted as the male parent. The maternal parent was P. adenopoda and P. davidiana for mb1 and mb2, respectively. Hybridization not only generated these hybrids but also resulted in a unidirectional gene flow from P. davidiana to P. adenopoda. The Populus species have maintained a delicate balance between their genetic integrity and gene exchange.
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http://dx.doi.org/10.1038/s41598-019-41320-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6423230PMC
March 2019

Analysis of genetic composition and transmitted parental heterozygosity of natural 2n gametes in Populus tomentosa based on SSR markers.

Planta 2018 Jun 9;247(6):1407-1421. Epub 2018 Mar 9.

Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, 100083, China.

Main Conclusion: Natural 2n female gametes and transmission of parental heterozygosity by natural 2n gametes in Populus tomentosa are reported for the first time, which provides a new approach to polyploid breeding. Naturally occurring 2n pollen is widespread in Populus tomentosa and plays an important role in polyploid breeding. However, the competitiveness of 2n pollen is lower than that of haploid pollen during pollination and fertilization, so 2n pollen is less efficient at fertilizing haploid female gametes to produce polyploids. In theory, polyploids can also be obtained when 2n female gametes are fertilized by haploid pollen. Thus, the question becomes whether natural 2n female gametes exist in P. tomentosa, which can be answered by examining the genetic composition of natural 2n gametes. In this study, the origin of 87 triploids from the hybrid combination "X-2 × Z-5" was identified by SSR markers and 21% of natural 2n gametes were found to originate from female parents. Four SSR loci with low recombination rates were used to identify the genetic composition of natural 2n gametes. The results showed that the genetic composition of 2n female gametes was mainly characterized by SDR, while 2n male gametes were mainly produced by FDR. Moreover, the transmission of parental heterozygosity by natural 2n gametes, which is significantly different between female and male parents in FDR and SDR types, was analysed using 42 SSR primers. Here, we report naturally occurring 2n female gametes for the first time in P. tomentosa and reveal the genetic constitution and transmitted parental heterozygosity of these gametes. Our results provide a foundation for theoretical research into 2n gametes and their application in new polyploid breeding strategies.
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http://dx.doi.org/10.1007/s00425-018-2871-4DOI Listing
June 2018

High temperature exposure did not affect induced 2n pollen viability in Populus.

Plant Cell Environ 2018 06 20;41(6):1383-1393. Epub 2018 Apr 20.

National Engineering Laboratory for Tree Breeding, No.35, Qinghua East Road, Haidian District, 100083, Beijing, People's Republic of China.

High temperature exposure is widely used as a physical mutagenic agent to induce 2n gametes in Populus. However, whether high temperature exposure affects induced 2n pollen viability remains unknown. To clarify whether high temperature exposure affected the induced 2n pollen viability, 2n pollen induced by 38 and 41 °C temperatures, pollen morphology, 2n pollen germination in vitro, and crossing induced 2n pollen with normal gametes to produce a triploid was, based on observations of meiosis, conducted in Populus canescens. We found that the dominant meiotic stages (F = 56.6, p < .001) and the treatment duration (F = 21.4, p < .001) significantly affected the occurrence rate of induced 2n pollen. A significant decrease in pollen production and an increase in aborted pollen were observed (p < .001). High temperature sometimes affected in ectexine deposition and some narrow furrows were also analysed via details of ectexine structure. However, no significant difference in 2n pollen germination rate was observed between natural 2n pollen (26.7%) and high-temperature-induced 2n pollen (26.2%), and 42 triploids were created by crossing high-temperature-induced 2n pollen, suggesting that 38 and 41 °C temperatures exposure will not result in dysfunctional induced 2n pollen.
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http://dx.doi.org/10.1111/pce.13165DOI Listing
June 2018

Proteomic Changes Between Allotriploids and Diploids Revealed Using an iTRAQ-based Quantitative Approach.

Curr Proteomics 2017 Sep;14(3):166-174

National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing100083, China.

Background: Polyploid breeding is a powerful approach for Populus genetic improve-ment because polyploid trees have valuable characteristics, including better timber quality and a higher degree of stress resistance compared with their full-sib diploids. However, the genetic mech-anism underlying this phenomenon remains unknown.

Objective: To better understand the proteomic changes between Populus allotriploids and diploids, we examined the proteomic profiles of allotriploid and diploid Populus by iTRAQ labeling coupled with two-dimensional liquid chromatography and MALDI-TOF/TOF mass spectrometry (MS).

Method: iTRAQ labeling coupled with two-dimensional liquid chromatography and MALDI-TOF/TOF mass spectrometry (MS).

Results: Between the Populus allotriploid and the full-sib diploid, 932 differentially expressed proteins (DEPs) were identified. These DEPs were primarily involved in stress, defense, transportation, transcriptional and/or translational modification, and energy production. The pathway analysis indi-cated that most of the DEPs were implicated in carbohydrate transport and metabolism, nitrogen me-tabolism and glycolysis, and the ribosome assembly pathway. These data suggest high protein di-vergence between Populus allotriploids and diploids, and rapid changes during hybridization.

Conclusion: The results provide new data for further understanding of the mechanisms of polyploid trees that generally display increased height growth compared with their full-sib diploids.
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http://dx.doi.org/10.2174/1570164614666170310142405DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5676023PMC
September 2017

MicroRNA expression changes following synthesis of three full-sib Populus triploid populations with different heterozygosities.

Plant Mol Biol 2017 Oct 7;95(3):215-225. Epub 2017 Sep 7.

National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, People's Republic of China.

Key Message: Through high-throughput sequencing, we compared the relative expression levels of miRNA in three full-sib Populus triploid populations with that in their parents and one diploid hybrid population. We found similar numbers of miRNAs differentially expressed between the parents and the four progeny hybrid populations. In addition, unbalanced parental expression level dominance of miRNAs were found in the three allotriploid and interspecific hybrid populations, which may reprogram gene expression networks and contribute to the growth of Populus hybrids. These results indicated that hybridization has a great impact on the miRNA expression variation in the newly synthesized Populus triploid and diploid hybrid populations. However, we also found no significant differences in miRNA expression among one diploid and three triploid hybrid populations, hinting that miRNA abundances do not increase with the genome content. No dosage effect of miRNA expression could lead to dosage-dependent negative effects on target genes and their downstream pathway in polyploids. We speculate that polyploids may gain advantages from the slight decrease in miRNA regulation, suggesting an important molecular mechanism of polyploid advantage. Hybridization with three types of induced 2n gametes transmitted different parental heterozygosities has been proven as an efficient method for Populus triploid production. Several researches have shown that miRNA could be non-additively expressed in allopolyploids. However, it is still unclear whether the non-additively expressed miRNAs result from the effect of hybridization or polyploidization, and whether a dose response to the additional genomic content exists for the expression of miRNA. Toward this end, through high-throughput sequencing, we compared the expression levels of miRNA in three full-sib Populus triploid populations with that in their parents and one interspecific hybrid population. We found similar numbers of miRNAs differentially expressed between the parents and the four progeny hybrid populations. Unbalanced parental expression level dominance of miRNAs were found in the three triploid and diploid hybrid populations, which may reprogram gene expression networks and affect the growth of Populus hybrids. These results indicated that hybridization has a great impact on the miRNA expression variation in the newly synthesized Populus triploid and diploid hybrid populations. However, we also found no significant differences in miRNA expression among the three triploid populations and the diploid hybrid population. No dosage effect of miRNA expression could lead to dosage-dependent negative effects on target genes and their downstream pathway in polyploids. We speculate that polyploids may gain advantages from the decrease in miRNA negative regulation, suggesting an important molecular mechanism of polyploid advantage.
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http://dx.doi.org/10.1007/s11103-017-0627-3DOI Listing
October 2017

High temperature-induced production of unreduced pollen and its cytological effects in Populus.

Sci Rep 2017 07 13;7(1):5281. Epub 2017 Jul 13.

Beijing Advanced Innovation Centre for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, 100083, People's Republic of China.

Temperature change is of potential to trigger the formation of unreduced gametes. In this study, we showed that short periods of high temperature treatment can induce the production of 2n pollen in Populus pseudo-simonii Kitag. The meiotic stage, duration of treatment, and temperature have significant effects on the induction of 2n pollen. Heat stress resulted in meiotic abnormalities, including failure of chromosome separation, chromosome stickiness, laggards and micronuclei. Spindle disorientations in the second meiotic division, such as parallel, fused, and tripolar spindles, either increased in frequency or were induced de novo by high temperature treatment. We found that the high temperature treatment induced depolymerisation of meiotic microtubular cytoskeleton, resulting in the failure of chromosome segregation. New microtubular cytoskeletons were able to repolymerise in some heat-treated cells after transferring them to normal conditions. However, aberrant cytokinesis occurred owing to defects of new radial microtubule systems, leading to production of monads, dyads, triads, and polyads. This suggested that depolymerisation and incomplete restoration of microtubules may be important for high temperature-induction of unreduced gametes. These findings might help us understand how polyploidisation is induced by temperature-related stress and support the potential effects of global climate change on reproductive development of plants.
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http://dx.doi.org/10.1038/s41598-017-05661-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5509662PMC
July 2017

Transcriptomic changes following synthesis of a Populus full-sib diploid and allotriploid population with different heterozygosities driven by three types of 2n female gamete.

Plant Mol Biol 2015 Nov 29;89(4-5):493-510. Epub 2015 Sep 29.

National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, People's Republic of China.

Diploid gametes are usually applied to produce triploids of Populus [originating from first-division restitution (FDR), second-division restitution (SDR), and postmeiotic restitution (PMR) 2n eggs]. Three types of 2n gametes transmitted different parental heterozygosities in Populus. Failed spindle formation and no chromosomal separation to opposite poles during meiosis I mean that FDR 2n gametes carry nonsister chromatids that are potentially heterozygous. By contrast, SDR 2n gametes result from failed sister chromatid separation in meiosis II, and therefore, they carry sister chromatid that are potentially homozygous. Completely homozygous 2n gametes can arise from the PMR mechanism. The alteration of gene expression resulting from allopolyploidization is a prominent feature in plants. We compared gene expression in the full-sib progeny of three allotriploid Populus populations (triploid-F, triploid-S, and triploid-P) with that in its parent species, and their full-sib diploid F1 hybrid. Genome-wide expression level dominance was biased toward the maternal in the diploid F1 hybrid and three allotriploid populations, whereas our data indicated important, but different, effects of the transmission of different heterozygosity by 2n female gametes in the expression patterns of allopolyploids. Because of the higher level of heterozygosity, the triploids had higher rates of non-additive and transgressive expression patterns in the triploid-F than in triploid-S and triploid-P. Compared with diploid F1, about 30-fold more genes (251) were differently expressed in the triploid-F than in the triploid-S (9) and triploid-P (8), respectively. These findings indicate that hybridization and polyploidization have immediate and distinct effects on the large-scale patterns of gene expression, and different effects on the transmission of heterozygosity by three 2n female gametes.
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http://dx.doi.org/10.1007/s11103-015-0384-0DOI Listing
November 2015

Microsporogenesis and flower development in Eucalyptus urophylla × E. tereticornis.

Breed Sci 2015 Mar 1;65(2):138-44. Epub 2015 Mar 1.

National Engineering Laboratory for Tree Breeding, Beijing Forestry University , Beijing 100083 , P R China ; Key Laboratory for Genetics and Breeding of Forest Trees and Ornamental Plants, Ministry of Education, Beijing Forestry University , Beijing 100083 , P R China.

We compared microsporogenesis and flower development in Eucalyptus urophylla × E. tereticornis. In this study, although microsporogenesis and cytokinesis occurred simultaneously during meiosis of pollen mother cells, we observed a strong asynchronism in different anthers from a flower bud. The developmental period of microsporogenesis in anthers originated from the long thrum before the short thrum. Flower development was also asynchronous at different locations on a branch. The flower buds grew on the lower side of the branch and showed greater increases in diameter. In addition, we observed a relationship between microsporogenesis development and flower bud diameter growth. Generally, when the pachytene stage was first observed in a small single flower bud growing on top of a flowering branch, the remaining microsporogenesis stages (from diplotene to tetrad) in the whole branch occurred over the next 5-9 days. Thus, the start of microsporogenesis in E. urophylla × E. tereticornis could be determined, which may be applicable to future breeding studies.
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http://dx.doi.org/10.1270/jsbbs.65.138DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4430506PMC
March 2015

Inheritance and variation of Cytosine methylation in three populus allotriploid populations with different heterozygosity.

PLoS One 2015 22;10(4):e0126491. Epub 2015 Apr 22.

National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, Peoples' Republic of China; Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, Peoples' Republic of China.

DNA methylation is an epigenetic mechanism with the potential to regulate gene expression and affect plant phenotypes. Both hybridization and genome doubling may affect the DNA methylation status of newly formed allopolyploid plants. Previous studies demonstrated that changes in cytosine methylation levels and patterns were different among individual hybrid plant, therefore, studies investigating the characteristics of variation in cytosine methylation status must be conducted at the population level to avoid sampling error. In the present study, an F1 hybrid diploid population and three allotriploid populations with different heterozygosity [originating from first-division restitution (FDR), second-division restitution (SDR), and post-meiotic restitution (PMR) 2n eggs of the same female parent] were used to investigate cytosine methylation inheritance and variation relative to their common parents using methylation-sensitive amplification polymorphism (MSAP). The variation in cytosine methylation in individuals in each population exhibited substantial differences, confirming the necessity of population epigenetics. The total methylation levels of the diploid population were significantly higher than in the parents, but those of the three allotriploid populations were significantly lower than in the parents, indicating that both hybridization and polyploidization contributed to cytosine methylation variation. The vast majority of methylated status could be inherited from the parents, and the average percentages of non-additive variation were 6.29, 3.27, 5.49 and 5.07% in the diploid, FDR, SDR and PMR progeny populations, respectively. This study lays a foundation for further research on population epigenetics in allopolyploids.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0126491PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4406749PMC
April 2016

Differential transcriptome analysis between Populus and its synthesized allotriploids driven by second-division restitution.

J Integr Plant Biol 2015 Dec 3;57(12):1031-45. Epub 2015 Apr 3.

National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China.

In this report, we compared transcriptomic differences between a synthetic Populus section Tacamahaca triploid driven by second-division restitution and its parents using a high-throughput RNA-seq method. A total of 4,080 genes were differentially expressed between the high-growth vigor allotriploids (SDR-H) and their parents, and 719 genes were non-additively expressed in SDR-H. Differences in gene expression between the allotriploid and male parent were more significant than those between the allotriploid and female parent, which may be caused by maternal effects. We observed 3,559 differentially expressed genes (DEGs) between the SDR-H and male parent. Notably, the genes were mainly involved in metabolic process, cell proliferation, DNA methylation, cell division, and meristem and developmental growth. Among the 1,056 DEGs between SDR-H and female parent, many genes were associated with metabolic process and carbon utilization. In addition, 1,789 DEGs between high- and low-growth vigor allotriploid were mainly associated with metabolic process, auxin poplar transport, and regulation of meristem growth. Our results indicated that the higher poplar ploidy level can generate extensive transcriptomic diversity compared with its parents. Overall, these results increased our understanding of the driving force for phenotypic variation and adaptation in allopolyploids driven by second-division restitution.
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http://dx.doi.org/10.1111/jipb.12328DOI Listing
December 2015

Differential profiling analysis of miRNAs reveals a regulatory role in low N stress response of Populus.

Funct Integr Genomics 2015 Jan 16;15(1):93-105. Epub 2014 Nov 16.

National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing, 100083, People's Republic of China,

Nitrogen (N) is an essential mineral element for plant growth processes, and its availability severely affects the productivity of plants, especially trees. MicroRNAs (miRNAs) are a class of non-coding RNAs approximately 21 nucleotides in length that play important roles in plant growth, development and stress responses. To identify Populus miRNAs and their functions in response to nutrition stress, high-throughput sequencing was performed using Populus tomentosa plantlets treated with or without low concentrations of N. We identified 160 conserved miRNAs, 15 known but non-conserved miRNAs, 2 candidate novel miRNAs and 71 corresponding miRNA*s. Differential expression analysis showed that expression of the 21 conserved miRNA families was significantly altered. Real-time quantitative PCR (qPCR) was used to further validate and analyze the dynamic expression of the identified miRNAs. A total of 218 target genes from the low-N-responsive miRNAs were predicted, and their functions were further annotated in combination with Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses. These results suggest that miRNAs play important roles in the response of Populus to low N stress. Furthermore, this study provides the first identification and profiles of N stress-responsive miRNAs from trees.
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http://dx.doi.org/10.1007/s10142-014-0408-xDOI Listing
January 2015

Induction of 2n female gametes in Populus adenopoda Maxim by high temperature exposure during female gametophyte development.

Breed Sci 2013 Mar 1;63(1):96-103. Epub 2013 Mar 1.

National Engineering Laboratory for Tree Breeding, Beijing Forestry University , Beijing 100083, P. R. China ; Key Laboratory for Genetics and Breeding of Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Biotechnology, Beijing Forestry University , Beijing 100083, P. R. China.

In order to produce triploid plants, 2n female gametes were induced by treating female buds and developing embryo sacs of Populus adenopoda Maxim with high temperature exposure. During megasporogenesis, tests were conducted on the relationship between female gametophyte development and morphological changes of female catkins. In the resulting progeny, 12 triploids were produced, and the highest rate of triploid production was 40%. Cytological observation revealed that the pachytene to diakinesis phase of meiotic stages may be a suitable period for inducing megaspore chromosome doubling through high temperature exposure. On the other hand, catkins of 6-72 h after pollination were treated for inducing embryo sac chromosome doubling. In the offspring seedlings, 51 triploids were detected and the highest efficiency of triploid production was 83.33%. Correlation analysis between the proportion of each embryo sac's developmental stage and the percentage of triploid production indicated that the second mitotic division may be the most effective stage for 2n female gamete induction. Our findings showed that high temperature exposure is an ideal method for 2n female gamete induction. Heterozygous offspring are valuable for breeding programs of P. adenopoda.
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http://dx.doi.org/10.1270/jsbbs.63.96DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3621450PMC
March 2013

Identification and characterization of salt-responsive microRNAs in Populus tomentosa by high-throughput sequencing.

Biochimie 2013 Apr 6;95(4):743-50. Epub 2012 Nov 6.

National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Biotechnology, Beijing Forestry University, 100083 Beijing, People's Republic of China.

Salt is one of the main environmental factors limiting plant growth and a better understanding of mechanisms of salt stress would aid efforts to bolster plant salt tolerance. MicroRNAs are well known for their important regulatory roles in response to abiotic stress in plants. In this study, high-throughput sequencing was employed to identify miRNAs in Populus tomentosa plantlets treated or not with salt (200 mM for 10 h). We found 141 conserved miRNAs belonging to 31 families, 29 non-conserved but previously-known miRNAs belonging to 26 families, and 17 novel miRNAs. Under salt stress, 19 miRNAs belonging to seven conserved miRNA families were significantly downregulated, and two miRNAs belonging to two conserved miRNA families were upregulated. Of seven non-conserved miRNAs with significantly altered expression, five were downregulated and two were upregulated. Furthermore, eight miRNAs were validated by qRT-PCR and their dynamic differential expressions were analyzed. In addition, 269 target genes of identified miRNAs were predicted and categorized by function. These results provide new insights into salt-responsive miRNAs in Populus.
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http://dx.doi.org/10.1016/j.biochi.2012.10.025DOI Listing
April 2013

Identification of novel and conserved Populus tomentosa microRNA as components of a response to water stress.

Funct Integr Genomics 2012 Jun 14;12(2):327-39. Epub 2012 Mar 14.

National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Biotechnology, Beijing Forestry University, 100083 Beijing, People's Republic of China.

MicroRNAs (miRNAs) are a class of small, non-coding RNAs that play important downregulation roles in plants growth, development, and stress responses. To better identify Populus tomentosa miRNAs and understand the functions of miRNAs in response to water stress (drought and flooding), 152 conserved miRNAs belonging to 36 miRNA families, 8 known but non-conserved miRNAs and 64 candidate novel miRNAs belonging to 54 miRNA families were identified and analyzed from three small RNA (sRNA) libraries (drought treatment, flooding treatment, and control) by high-throughput sequencing combined with qRT-PCR. Significant changes in the expression of 17 conserved miRNA families and nine novel miRNAs were observed in response to drought stress, and in seven conserved miRNA families and five novel miRNAs in response to flooding stress. Both miRNA and miRNA*s were involved in the regulation of plant stress responses. The annotation of the potential targets of miRNAs with differential expression indicate that many types of genes encoding transcription factors, enzymes, and signal transduction components are implicated in the abiotic stress response..
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http://dx.doi.org/10.1007/s10142-012-0271-6DOI Listing
June 2012

[Potential ecological risks of transgenic trees].

Ying Yong Sheng Tai Xue Bao 2004 Jul;15(7):1281-4

Key Laboratory for Genetics & Breeding of Forest Trees and Ornamental Plants, MOE, Beijing Forestry University, Beijing 100083, China.

A new approach to genetic improvement of trees has been introduced with the birth of gene engineering technique. Compared to that in crops, gene introduction in trees has bigger potential ecological risk in environmental release and extension, because trees, most of which are wind-dispersed, grow on various habitats, have longer life span, and subject to relatively more extensive management. Extensive plantation of transgenic trees may reduce the genetic diversity of the trees concerned. Co-evolution of pests and pathogens is likely to be caused under the pressure of long-term and continuous selection of the trees derived from gene transferring. Escaping of exogenous gene may have a certain kind of influence on fitness of plants naturally generated, and as a result, have influence on species diversity in the natural world. It is not reasonable for China, a developing country, to reject gene introduction as an approach to promote forestry development. It is also important, on the other hand, to take future ecological safety into consideration because it is unwise to get present profit at the cost of future profit. To strengthen basic study on gene transferring, adopting safe management of varieties generated from gene transferring and increasing funds on research and management of transgenic trees are believed to be measures to decrease, to the greatest extent, ecological risks brought about by gene transferring of trees, and to quicken transformation of products of trees derived from gene-transferring into merchandises.
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July 2004