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1
Artykuł dostępny w postaci pełnego tekstu - kliknij by otworzyć plik
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Detection of SNPs based on DNA specific-locus amplified fragment sequencing in Chinese fir (Cunninghamia lanceolata (Lamb.) Hook)

100%
Su Y., Hu D., Zheng H.
Dendrobiology
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2016
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tom 76
Compared to angiosperms, conifers represent more complex genomes with larger giga-genome size. To detect large-scale single nucleotide polymorphisms (SNPs), whole genome sequencing of a conifer population is still unaffordable. In this work, we report the use of DNA specific-locus amplified fragment sequencing (SLAF-seq) for large-scale SNP detection in Chinese fir (Cunninghamia lanceolata (Lamb.) Hook), an ecological and economic important conifer in China. SLAF libraries of 18 parent clones of a Chinese fir 2.5 generation seed orchard were sequenced and a total of 117,924 SLAFs were developed. We detected 147,376 SNPs from these SLAFs; 146,231 of them represented simple nucleotide change in A/G, C/T, A/C, A/T, C/G or G/T. The most frequent SNPs occurred in C/T (34.3%), while the majority of SNPs (68.2%) belonged to transition events (A/G and C/T). Notably, all the sequenced samples had high portion (78.2–80.9%) of common SNPs indicating that the Chinese fir genomes tended to change its nucleotides at common loci. 48,406 informative SNPs were then successfully utilized to genotype the tested samples (n = 18) followed by a phylogenetic tree to clarify their genetic relationship. Furthermore, a set of very high linkage disequilibrium (0.51–1.00) were identified from these informative SNPs. In brief, our work demonstrated that SLAF-seq is an alternative and cost-effectively high-throughput approach for large-scale SNP exploitation in Chinese fir. While the obtained SNPs offer useful marker resource for further genetic and genomic studies and will be helpful for Chinese fir breeding programs.
2

Exploring the response of net primary productivity variations to land use/land cover change: a case study in Anhui, China

100%
Yang H., Hu D., Peng F., Wang Y.
Polish Journal of Environmental Studies
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2019
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tom 28
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nr 5
Land use and land cover change (LUCC) has a significant influence on regional net primary productivity (NPP) in territorial ecosystems. Evaluating the driving factors of LUCC and the influences of LUCC on NPP is significant for understanding the driving mechanisms deeply and improve land management. NPP as estimated by the Carnegie–Ames–Stanford Approach (CASA) model was employed as an important indicator to evaluate the influences of LUCC on regional NPP and decouple interactive effects of LUCC and climate change on NPP in Anhui from 2001 to 2010. The results demonstrated that 34.25% of the whole area had occurred in LUCC. The most dominant transformation of LUCC was the conversion from grassland and crop/natural vegetation mosaic to forest and cropland. The area of cropland and forest had the most increments compared to other land use types, with an increase of 30.52% and 35.29% of that in 2001. Socio-economic development, economic interests and government policies took an important role in driving the LUCC. The total NPP increased mainly due to the contributions of the area expansion of cropland and forest. Climate change resulted in the decreased NPP of 449.84 GgC, whereas LUCC facilitated the NPP in the increase of 1816.05 GgC. This result indicates that the increased NPP induced by LUCC could offset the NPP decrease from climate change during the study periods. This paper also demonstrated that reforestation and forest protection were indeed effective in promoting ecosystem productivity.
3
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Genotypic variation of Cunninghamia lanceolata revealed by phenotypic traits and SRAP markers

88%
Zheng H., Duan H., Hu D., Li Y., Hao Y.
Dendrobiology
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2015
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tom 74
The success of a tree breeding program largely depended on the available genetic variability of the germplasms. Our present study aimed to assess the phenotypic variation and DNA variability using sequence-related amplified polymorphism (SRAP) markers among 50 Cunninghamia lanceolata (Chinese fir) genotypes. Extensive phenotypic variations (p < 0.05 or 0.01) were found for all the growth and wood property traits (height, diameter at breast height, stem volume, and wood basic density, hygroscopicity, heart-wood ratio, tracheid length, tracheid diameter and tracheid length-diameter ratio) with coefficients of variation spanning from 6.8 to 31.3%. At the DNA level, thirty-five SRAP primer combinations produced 498 bands with 89.4% polymorphism across genotypes; moreover, the Nei’s gene diversity was detected to be ranged between 0.204 and 0.373 (mean = 0.279), while the Shannon’s Information Index stretched from 0.324 to 0.555 with an average value of 0.427. Significance (p < 0.01) of the variability of SRAP polymorphism among genotypes was further demonstrated by AMOVA. These results indicated a relatively high level of genetic diversity in genotypes. The SRAP’ dendrogram additionally revealed that these genotypes could be split into 7 clusters with higher discriminating capacity over that of phenotype. Notably, a total of 99 statistically significant (p < 0.05) marker-trait associations related to the growth and wood property traits were identified. These marker-trait associations corresponded to 77 different SRAP markers with R2 (percentage of the phenotypic variation explained by marker) ranging from 8.3 to 26.4%.
4

Subcellular distribution and physiological responses of Potamogeton crispus to yttrium

76%
Xu Q., Zhang W., Sha S., Yang Y., Su C., Hu D.
Acta Physiologiae Plantarum
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2019
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tom 41
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nr 06
Potamogeton crispus was exposed to a range of external yttrium (Y) concentrations (0–30 μM) for 20 days to investigate the effects of Y accumulation on the homeostasis of elements and the photochemistry of photosystem II (PS II). Yttrium accumulation increased in a concentration-dependent manner, with most Y being associated with polysaccharides. At all Y concentrations, significant declines in relative growth rates (fresh weight basis), photosynthetic pigments, and protein content were observed, as well as an increase in leaf area damage. Yttrium accumulation disrupted elemental homeostasis, with decrease observed for concentrations of micro- and macro-elements such as Cu, Zn, Mg, Mn, and K, and increases for S, Fe, and Ca. A significant reduction in PS II photochemistry occurred in Y-treated plants, as evidenced by decrease in Fv/Fm, Fv/Fo, Fv, ψo, φEo, φRo, φPo, and PIABS, and increases in Fo, Fo/Fv, and energy fluxes per reaction center (ABS/RC, ETo/RC, TRo/RC, and DIo/RC). In addition, Y treatment significantly reduced chloroplast ATPase activity and ATP level and induced changes in chloroplast ultrastructure including an increase in plastoglobule size and organelle shape. AsA and GSH content slightly increased at 10 µM Y and then declined and that of non-protein thiol was found to be enhanced at all the Y concentrations. The results suggest that Y exposure led to general disarray of cellular functions, similar to responses observed for other trace metals.
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Global transcriptome analysis reveals genes associated with seedling advance growth traits in a selfed family of Chinese fir (Cunninghamia lanceolata)

76%
Deng H., Hu D., Wei R., Yan S., Wang R., Zheng H.
Dendrobiology
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2022
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tom 87
6

Dissecting the distyly response to pollination using metabolite profiling in heteromorphic incompatibility system interactions of Plumbago auriculata Lam

64%
Hu D., Gao S., Li W., Lei T., Liu Y., Li Q., Li J., Jiang M.
Acta Physiologiae Plantarum
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2020
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tom 42
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nr 07
7

Cloning and identification of PK15 cells for enhanced replication of classical swine fever virus

64%
Yin M., Hu D., Li P., Kong L., Ning H., Yue F., Jiang J., Wang X.
Journal of Veterinary Research
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2020
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tom 64
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nr 1
8

Transcriptome profiling of Plumbago auriculata Lam. in response to cold stress

64%
Li W., Gao S., Li Q., Shen P., Li Y., Hu D., Lei T., Chen X., Li J.
Acta Physiologiae Plantarum
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2020
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tom 42
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nr 06
9

Overexpression of Rictor protein and Rictor-H. pylori interaction has impact on tumor progression and prognosis in patients with gastric cancer

52%
Wang F., Lou X., Zou Y., Hu D., Liu J., Ning J., Jiao Y., Zhang Z., Yang F., Fan L., Yu H., Wei W., Wang H., Sun G.
Folia Histochemica et Cytobiologica
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2020
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tom 58
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nr 2
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