scholarly journals A Transcriptomic Variation Map Provides Insights into The Genetic Basis of Pinus massoniana Evolution and Association of Oleoresin Yield

2020 ◽  
Author(s):  
Qinghua Liu ◽  
Yini Xie ◽  
Bin Liu ◽  
Huanhuan Yin New ◽  
Zhichun Zhou ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Transcriptome Sequencing ◽  
Distinct Group ◽  
Pinus Massoniana ◽  
Snp Markers ◽  
Sequencing Data ◽  
Masson Pine ◽  
Pinus Massoniana Lamb ◽  
Wild Accessions ◽  
Germplasm Analysis

Abstract Background: Masson pine (Pinus massoniana Lamb.), the dominant native coniferous species in South China, is commercially important for timber and oleoresin. However, knowledge of the genetic variability of the masson pine germplasm is still scarce. Here, the genetic diversity and population structure of masson pine germplasm were assessed using 204 wild accessions from 10 main distribution regions by 94,194 core SNPs obtained from transcriptome sequencing data. Results: The average expected heterozygosity was 0.2724, implying abundant genetic diversity within masson pine germplasm. Analysis of molecular variance (AMOVA) revealed that 3.29% variation sourced from the genetic differentiation. Structure analysis identified two geographically distinct groups. Discriminant analysis of principal components (DAPC) showed one geographically distinct group was divided two clusters furtherly. Sichuan and Chongqing provenance is the geographical origin, and diffuses outward along two lines. Oleoresin yield might be reflected by the evolution, and exhibits two different changing trends between two diffusing line. It may be associated with the genes of chitinase, CYP720B, Cytochrome P450, ABC transporter and AP2/ERF based on SNPs and expression. Conclusions: SNP markers by transcriptome sequencing have a strong power in evaluating genetic diversity within species and the genetic control of objective trait. The function of these genes will be verified and the strong associated genes with oleoresin yield will be used in the improvement of oleoresin yield by early genotype selection or genetic engineering.

scholarly journals Identification, classification, and characterization of AP2/ERF superfamily genes in Masson pine (Pinus massoniana Lamb.)

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Peihuang Zhu ◽  
Yu Chen ◽  
Jinfeng Zhang ◽  
Fan Wu ◽  
Xiaofeng Wang ◽  
...  
Keyword(s):  
Target Genes ◽  
Southern China ◽  
Pinus Massoniana ◽  
Sequencing Data ◽  
Masson Pine ◽  
Treatment Conditions ◽  
Pinus Massoniana Lamb ◽  
Systematic Identification

AbstractTranscription factors (TFs) play crucial regulatory roles in controlling the expression of the target genes in plants. APETALA2/Ethylene-responsive factors (AP2/ERF) are part of a large superfamily of plant-specific TFs whose members are involved in the control of plant metabolism, development and responses to various biotic and abiotic stresses. However, the AP2/ERF superfamily has not been identified systematically in Masson pine (Pinus massoniana), which is one of the most important conifer in southern China. Therefore, we performed systematic identification of the AP2/ERF superfamily using transcriptome sequencing data from Masson pine. In the current study, we obtained 88 members of the AP2/ERF superfamily. All PmAP2/ERF members could be classified into 3 main families, AP2 (7 members), RAV (7 members), ERF (73 members) families, and a soloist protein. Subcellular localization assays suggested that two members of PmAP2/ERF were nuclear proteins. Based on pine wood nematode (PWN) inoculated transcriptome and qPCR analysis, we found that many members of PmAP2/ERF could respond to PWN inoculation and PWN related treatment conditions in vitro. In general, members of the AP2/ERF superfamily play an important role in the response of Masson pine responds to PWN. Furthermore, the roles of the AP2/ERF superfamily in other physiological activities of Masson pine remain to be further studied.

Thinning effects on forest evolution in Masson pine (Pinus massoniana Lamb.) conversion from pure plantations into mixed forests

2020 ◽  
Vol 477 ◽  
pp. 118503
Author(s):  
Cheng Deng ◽  
Shougong Zhang ◽  
Yuanchang Lu ◽  
Robert E. Froese ◽  
Xiaojun Xu ◽  
...  
Keyword(s):  
Pinus Massoniana ◽  
Mixed Forests ◽  
Masson Pine ◽  
Pinus Massoniana Lamb

scholarly journals Core set construction and association analysis of Pinus massoniana from Guangdong province in southern China using SLAF-seq

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Qingsong Bai ◽  
Yanling Cai ◽  
Boxiang He ◽  
Wanchuan Liu ◽  
Qingyou Pan ◽  
...  
Keyword(s):  
Resource Selection ◽  
Southern China ◽  
Significant Snps ◽  
Pinus Massoniana ◽  
Snp Markers ◽  
Masson Pine ◽  
Sequencing Technologies ◽  
Population Structure Analysis ◽  
Resource Collection ◽  
Specific Locus

Abstract Germplasm resource collection and utilization are important in forestry species breeding. High-through sequencing technologies have been playing increasing roles in forestry breeding. In this study, specific-locus amplified fragment sequencing (SLAF-seq) was employed to analyze 149 masson pine (Pinus massoniana) accessions collected from Guangdong in China. A large number of 471,660 SNPs in the total collection were identified from 599,164 polymorphic SLAF tags. Population structure analysis showed that 149 masson pines could not be obviously divided into subpopulations. Two core sets, containing 29 masson pine accessions for increasing resin and wood yield respectively, were obtained from the total collection. Phenotypic analyses of five traits showed abundant variations, 25 suggestive and 9 significant SNPs were associated with the resin-yielding capacity (RYC’) and volume of wood (VW) using EMMAX and FaST-LMM; 22 suggestive and 11 significant SNPs were associated with RYC’ and VW using mrMLM and FASTmrMLM. Moreover, a large number of associated SNPs were detected in trait HT, DBH, RW and RYC using mrMLM, FASTmrMLM, FASTmrEMMA and ISIS EM-BLASSO. The core germplasm sets would be a valuable resource for masson pine improvement and breeding. In addition, the associated SNP markers would be meaningful for masson pine resource selection.

scholarly journals Development and Application of Novel Indel Markers in Flax (Linum Usitatissimum L.) Through Whole-genome Re-sequencing

2021 ◽  
Author(s):  
Hui Jiang ◽  
Gen Pan ◽  
Touming Liu ◽  
Li Chang ◽  
Siqi Huang ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Principal Component ◽  
Snp Markers ◽  
Diversity Analysis ◽  
Whole Genome ◽  
Chromosome 2 ◽  
Sequencing Data ◽  
Single Nucleotide ◽  
Genetic Diversity Analysis ◽  
Indel Markers

Abstract Flax is an important oil and fibre crop grown in Northern Europe, Canada, India, and China. The development of molecular markers has accelerated the process of flax molecular breeding and has improved yield and quality. Presently, simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers in the whole genome have been developed for flax. However, the development of flax insertion/deletion (InDel) markers has not been reported. A total of 17,110 InDel markers were identified by comparing whole-genome re-sequencing data of two accessions (87-3 and 84-3) with the flax reference genome. The length of InDels ranged from 1–277 bp, with 1–15 bp accounting for the highest rate (95.55%). The most common InDels were in the form of single nucleotide (8840), dinucleotide (3700), and trinucleotide (1349), and chromosome 2 (1505) showed the highest number of InDels among flax chromosomes, while chromosome 10 (913) presented with the lowest number. From 17,110 InDel markers, 90 primers that were evenly distributed in the flax genome were selected. Thirty-two pairs of polymorphic primers were detected in two flax accessions, and the polymorphism rate was 40.70%. Furthermore, genetic diversity analysis, population structure and principal component analyse (PCA) divided 69 flax accessions into two categories, namely oilseed flax and fibre flax using 32 pairs of polymorphic primers. Additionally, correlation analysis showed that InDel-26 and InDel-81 were associated with oil content traits, and two candidate genes (lus10031535 and lus10025284) tightly linked to InDel-26 or InDel-81, might be involved in flax lipid biosynthesis and lipid metabolism. This study is the first to develop InDel markers based on re-sequencing in flax and clustered the markers into two well-separated groups for oil and fibre. The results demonstrated that InDel markers developed herein could be used for flax germplasm identification, genetic diversity analysis, and molecular marker-assisted breeding.

scholarly journals Combined Transcriptome and Proteome Analysis of Masson Pine (Pinus massoniana Lamb.) Seedling Root in Response to Nitrate and Ammonium Supplementations

2020 ◽  
Vol 21 (20) ◽  
pp. 7548
Author(s):  
Qifei Ren ◽  
Yunchao Zhou ◽  
Xinwei Zhou
Keyword(s):  
Transcription Factors ◽  
Lateral Roots ◽  
Pinus Massoniana ◽  
Malate Synthase ◽  
Root Tips ◽  
Masson Pine ◽  
Pine Seedlings ◽  
N Assimilation ◽  
Pinus Massoniana Lamb ◽  
Glutathione Cycle

Nitrogen (N) is an essential nutrient for plant growth and development. Plant species respond to N fluctuations and N sources, i.e., ammonium or nitrate, differently. Masson pine (Pinus massoniana Lamb.) is one of the pioneer plants in the southern forests of China. It shows better growth when grown in medium containing ammonium as compared to nitrate. In this study, we had grown masson pine seedlings in medium containing ammonium, nitrate, and a mixture of both, and performed comparative transcriptome and proteome analyses to observe the differential signatures. Our transcriptome and proteome resulted in the identification of 1593 and 71 differentially expressed genes and proteins, respectively. Overall, the masson pine roots had better performance when fed with a mixture of ammonium and nitrate. The transcriptomic and proteomics results combined with the root morphological responses suggest that when ammonium is supplied as a sole N-source to masson pine seedlings, the expression of ammonium transporters and other non-specific NH4+-channels increased, resulting in higher NH4+ concentrations. This stimulates lateral roots branching as evidenced from increased number of root tips. We discussed the root performance in association with ethylene responsive transcription factors, WRKYs, and MADS-box transcription factors. The differential analysis data suggest that the adaptability of roots to ammonium is possibly through the promotion of TCA cycle, owing to the higher expression of malate synthase and malate dehydrogenase. Masson pine seedlings managed the increased NH4+ influx by rerouting N resources to asparagine production. Additionally, flavonoid biosynthesis and flavone and flavonol biosynthesis pathways were differentially regulated in response to increased ammonium influx. Finally, changes in the glutathione s-transferase genes suggested the role of glutathione cycle in scavenging the possible stress induced by excess NH4+. These results demonstrate that masson pine shows increased growth when grown under ammonium by increased N assimilation. Furthermore, it can tolerate high NH4+ content by involving asparagine biosynthesis and glutathione cycle.

scholarly journals Multi-Scale Evaluation of the Effect of Phenol Formaldehyde Resin Impregnation on the Dimensional Stability and Mechanical Properties of Pinus Massoniana Lamb.

Forests ◽  
2019 ◽  
Vol 10 (8) ◽  
pp. 646 ◽  
Author(s):  
Wang ◽  
Chen ◽  
Xie ◽  
Cai ◽  
Yuan ◽  
...  
Keyword(s):  
Mechanical Properties ◽  
Cell Wall ◽  
Dimensional Stability ◽  
Cell Walls ◽  
Phenol Formaldehyde ◽  
Pinus Massoniana ◽  
Swelling Properties ◽  
Masson Pine ◽  
Pine Wood ◽  
Pinus Massoniana Lamb

The local chemistry and mechanics of the control and phenol formaldehyde (PF) resin modified wood cell walls were analyzed to illustrate the modification mechanism of wood. Masson pine (Pinus massoniana Lamb.) is most widely distributed in the subtropical regions of China. However, the dimensional instability and low strength of the wood limits its use. Thus, the wood was modified by PF resin at concentrations of 15%, 20%, 25%, and 30%, respectively. The density, surface morphology, chemical structure, cell wall mechanics, shrinking and swelling properties, and macro-mechanical properties of Masson pine wood were analyzed to evaluate the modification effectiveness. The morphology and Raman spectra changes indicated that PF resin not only filled in the cell lumens, but also penetrated into cell walls and interacted with cell wall polymers. The filling and diffusing of resin in wood resulted in improved dimensional stability, such as lower swelling and shrinking coefficients, an increase in the elastic modulus (Er) and hardness (H) of wood cell walls, the hardness of the transverse section and compressive strength of the wood. Both the dimensional stability and mechanical properties improved as the PF concentration increased to 20%; that is, a PF concentration of 20% may be preferred to modify Masson pine wood.

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