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 Role of Suillus placidus in Improving the Drought Tolerance of Masson Pine (Pinus massoniana Lamb.) Seedlings

Forests ◽  
2021 ◽  
Vol 12 (3) ◽  
pp. 332
Author(s):  
Min Li ◽  
Haoyun Wang ◽  
Xizhou Zhao ◽  
Zhongke Lu ◽  
Xueguang Sun ◽  
...  
Keyword(s):  
Drought Stress ◽  
Defense Mechanism ◽  
Southern China ◽  
Dry Weight ◽  
Pinus Massoniana ◽  
Photosynthetic Performance ◽  
Ectomycorrhizal Fungus ◽  
Severe Drought ◽  
Masson Pine ◽  
Pine Seedlings

Masson pine is an important afforestation species in southern China, where seasonal drought is common. The present study focused on the effects of Suillus placidus, an ectomycorrhizal fungus, inoculation on the growth and physiological and biochemical performance of masson pine seedlings under four different watering treatments (well-watered, mild drought, moderate drought, and severe drought) to evaluate the symbiotic relationship between S. placidus and masson pine seedlings. Ectomycorrhizal-inoculated (ECM) and non-inoculated (NM) seedlings were grown in pots and maintained for 60 days using the weighing method. Results showed that seedlings’ growth, dry weight, RWC, chlorophyll content, PSII efficiency, and photosynthesis decreased as drought stress intensified in both ECM and NM plants. This suggests that drought stress significantly limits the growth and photosynthetic performance of masson pine seedlings. Nevertheless, increased An/gs and proline contents in both NM and ECM prevented oxidative damage caused by drought stress. In addition, increased peroxidase (POD) activity is an essential defense mechanism of ECM seedling under drought stress. Compared with NM, ECM seedlings showed faster growth, higher RWC, and photosynthetic performance, and lower lipid peroxidation in cell membranes under drought stress, as indicated by higher POD activity and lower proline and malondialdehyde (MDA). Our experiment found that S. placidus inoculation can enhance the drought resistance of masson pine seedlings by increasing antioxidant enzyme activity, water use efficiency, and proline content, thereby enhancing growth under water-deficiency conditions. S. placidus can be used to cultivate high-quality seedlings and improve their survival in regions that experience seasonal droughts.

scholarly journals Identification and Validation of Marketing Weight-Related SNP Markers Using SLAF Sequencing in Male Yangzhou Geese

Genes ◽  
2021 ◽  
Vol 12 (8) ◽  
pp. 1203
Author(s):  
Sherif Melak ◽  
Qin Wang ◽  
Ye Tian ◽  
Wei Wei ◽  
Lifan Zhang ◽  
...  
Keyword(s):  
Growth Performance ◽  
Performance Studies ◽  
Bulked Segregant Analysis ◽  
Significant Snps ◽  
Phenotypic Selection ◽  
Snp Markers ◽  
Nucleotide Polymorphisms ◽  
Economic Trait ◽  
Significant Difference ◽  
Specific Locus

Growth performance is a complex economic trait for avian production. The swan goose (Anser cygnoides) has never been exploited genetically like chickens or other waterfowl species such as ducks. Traditional phenotypic selection is still the main method for genetic improvement of geese body weight. In this study, specific locus amplified fragment sequencing (SLAF-seq) with bulked segregant analysis (BSA) was conducted for discovering and genotyping single nucleotide polymorphisms (SNPs) associated with marketing weight trait in male geese. A total of 149,045 SNPs were obtained from 427,093 SLAF tags with an average sequencing depth of 44.97-fold and a Q30 value of 93.26%. After SNPs’ filtering, a total of 12,917 SNPs were included in the study. The 31 highest significant SNPs—which had different allelic frequencies—were further validated by individual-based AS-PCR genotyping in two populations. The association between 10 novel SNPs and the marketing weight of male geese was confirmed. The 10 significant SNPs were involved in linear regression model analysis, which confirmed single-SNP associations and revealed three types of SNP networks for marketing weight. The 10 significant SNPs were located within or close to 10 novel genes, which were identified. The qPCR analysis showed significant difference between genotypes of each SNP in seven genes. Developed SLAF-seq and identified genes will enrich growth performance studies, promoting molecular breeding applications to boost the marketing weight of Chinese geese.

scholarly journals 1. A genetic linkage map of Pinus massoniana based on SRAP, SSR and ESTP markers

2014 ◽  
Vol 63 (1-6) ◽  
pp. 1-8 ◽  
Author(s):  
Wenxia Chen ◽  
Mu Cao ◽  
Yuanxiu Wang ◽  
Zhichun Zhou ◽  
Li-An Xu
Keyword(s):  
Linkage Map ◽  
Genetic Linkage ◽  
Genetic Linkage Map ◽  
Mapping Population ◽  
Southern China ◽  
Pinus Massoniana ◽  
Genetic Maps ◽  
Masson Pine ◽  
F1 Progeny ◽  
Genomic Studies

Abstract Pinus massoniana (masson pine) is the most important native pine in southern China. High-density genetic maps have not been constructed for the species. In this study, a genetic linkage map with 251 markers (47 SSRs, 23 ESTPs and 181 SRAPs) was constructed using a F1 progeny mapping population derived from controlled pollination of two parents of different provenances. At LOD 7.0, a total of 17 linkage groups were constructed with twelve groups having nine or more markers and five other groups of two to four markers each. The total map length was 1,956 cM with an average of 8.4 cM among individual loci. The current linkage map represented 93% of the estimated genome length of 2,114 cM for masson pine. Such linkage map are useful for future genomic studies of masson pine including comparative mapping in Pinaceae and quantitative trait loci (QTL) mapping for economically important traits.

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.

Using the dummy variable model approach to construct compatible single-tree biomass equations at different scales — a case study for Masson pine (Pinus massoniana) in southern China

2011 ◽  
Vol 41 (7) ◽  
pp. 1547-1554 ◽  
Author(s):  
Wei Sheng Zeng ◽  
Hui Ru Zhang ◽  
Shou Zheng Tang
Keyword(s):  
Southern China ◽  
Forest Biomass ◽  
Pinus Massoniana ◽  
Biomass Estimation ◽  
Tree Biomass ◽  
Variable Model ◽  
Masson Pine ◽  
Dummy Variable ◽  
Single Tree ◽  
Biomass Equations

It is fundamental for monitoring and assessment of national forest biomass to develop generalized single-tree biomass models suitable for large-scale forest biomass estimation. However, the compatibility of forest biomass estimates among different scales is a real problem. Based on the aboveground biomass data of Masson pine (Pinus massoniana Lamb.) in southern China, generalized single-tree biomass equations applying to national and regional forest biomass estimation were constructed using the dummy variable model method, which provided an effective approach to solving the compatibility of forest biomass estimates among different scales. The results show that aboveground biomass estimates of individual trees with the same diameter are different to some extent among the forest origins and geographic regions and that a dummy model with specific (local) parameters is better than a population-average model. The dummy variable model can be applied to develop other generalized compatible models such as tree volume equations.

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.

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