scholarly journals Relationship between the Phenylpropanoid Pathway and Dwarfism of Paspalum seashore Based on RNA-Seq and iTRAQ

2021 ◽  
Vol 22 (17) ◽  
pp. 9568
Author(s):  
Yong Zhang ◽  
Jun Liu ◽  
Jingjin Yu ◽  
Huangwei Zhang ◽  
Zhimin Yang
Keyword(s):  
Molecular Mechanism ◽  
Lignin Content ◽  
Warm Season ◽  
Phenylpropanoid Pathway ◽  
Rna Seq ◽  
Flavonoid Content ◽  
Dwarf Phenotype ◽  
Seashore Paspalum ◽  
Differential Expression Pattern ◽  
Key Genes

Seashore paspalum is a major warm-season turfgrass requiring frequent mowing. The use of dwarf cultivars with slow growth is a promising method to decrease mowing frequency. The present study was conducted to provide an in-depth understanding of the molecular mechanism of T51 dwarfing in the phenylpropane pathway and to screen the key genes related to dwarfing. For this purpose, we obtained transcriptomic information based on RNA-Seq and proteomic information based on iTRAQ for the dwarf mutant T51 of seashore paspalum. The combined results of transcriptomic and proteomic analysis were used to identify the differential expression pattern of genes at the translational and transcriptional levels. A total of 8311 DEGs were detected at the transcription level, of which 2540 were upregulated and 5771 were downregulated. Based on the transcripts, 2910 proteins were identified using iTRAQ, of which 392 (155 upregulated and 237 downregulated) were DEPs. The phenylpropane pathway was found to be significantly enriched at both the transcriptional and translational levels. Combined with the decrease in lignin content and the increase in flavonoid content in T51, we found that the dwarf phenotype of T51 is closely related to the abnormal synthesis of lignin and flavonoids in the phenylpropane pathway. CCR and HCT may be the key genes for T51 dwarf. This study provides the basis for further study on the dwarfing mechanism of seashore paspalum. The screening of key genes lays a foundation for further studies on the molecular mechanism of seashore paspalum dwarfing.

scholarly journals PpNAC187 Enhances Lignin Synthesis in ‘Whangkeumbae’ Pear (Pyrus pyrifolia) ‘Hard-End’ Fruit

Molecules ◽  
2019 ◽  
Vol 24 (23) ◽  
pp. 4338
Author(s):  
Mingtong Li ◽  
Chenxia Cheng ◽  
Xinfu Zhang ◽  
Suping Zhou ◽  
Caihong Wang ◽  
...  
Keyword(s):  
Transgenic Tobacco ◽  
Lignin Content ◽  
Lignin Biosynthesis ◽  
Phenylpropanoid Pathway ◽  
Pyrus Pyrifolia ◽  
Rna Seq ◽  
Pear Fruit ◽  
Nac Transcription Factors ◽  
Vessel Elements ◽  
Leaf Tissues

A disorder in pears that is known as ‘hard-end’ fruit affects the appearance, edible quality, and market value of pear fruit. RNA-Seq was carried out on the calyx end of ‘Whangkeumbae’ pear fruit with and without the hard-end symptom to explore the mechanism underlying the formation of hard-end. The results indicated that the genes in the phenylpropanoid pathway affecting lignification were up-regulated in hard-end fruit. An analysis of differentially expressed genes (DEGs) identified three NAC transcription factors, and RT-qPCR analysis of PpNAC138, PpNAC186, and PpNAC187 confirmed that PpNAC187 gene expression was correlated with the hard-end disorder in pear fruit. A transient increase in PpNAC187 was observed in the calyx end of ‘Whangkeumbae’ fruit when they began to exhibit hard-end symptom. Concomitantly, the higher level of PpCCR and PpCOMT transcripts was observed, which are the key genes in lignin biosynthesis. Notably, lignin content in the stem and leaf tissues of transgenic tobacco overexpressing PpNAC187 was significantly higher than in the control plants that were transformed with an empty vector. Furthermore, transgenic tobacco overexpressing PpNAC187 had a larger number of xylem vessel elements. The results of this study confirmed that PpNAC187 functions in inducing lignification in pear fruit during the development of the hard-end disorder.

scholarly journals Correlation Analysis of Lignin Accumulation and Expression of Key Genes Involved in Lignin Biosynthesis of Ramie (Boehmeria nivea)

Genes ◽  
2019 ◽  
Vol 10 (5) ◽  
pp. 389 ◽  
Author(s):  
Yinghong Tang ◽  
Fang Liu ◽  
Hucheng Xing ◽  
Kaiquan Mao ◽  
Guo Chen ◽  
...  
Keyword(s):  
Natural Fiber ◽  
Lignin Content ◽  
Phenylpropanoid Pathway ◽  
Maturation Period ◽  
Expression Levels ◽  
Relative Expression ◽  
Lignin Synthesis ◽  
Boehmeria Nivea ◽  
Expression Of Genes ◽  
Key Genes

The phloem of the stem of ramie (Boehmeria nivea) is an important source of natural fiber for the textile industry. However, the lignin content in the phloem affects the quality of ramie phloem fiber. In this study, the lignin content and related key gene expression levels were analyzed in the phloem and xylem at different developmental periods. The results showed that the relative expression levels of lignin synthesis-related key genes in the xylem and phloem of the stem gradually decreased from the fast-growing period to the late maturation period, but the corresponding lignin content increased significantly. However, the relative expression levels of a few genes were the highest during the maturation period. During all three periods, the lignin content in ramie stems was positively correlated with the expression of genes, including PAL, C4H and 4CL1 in the phenylpropanoid pathway, F5H and CCoAOMT in the lignin-specific synthetic pathway, and CAD in the downstream pathway of lignin synthesis, but the lignin content was negatively correlated with the expression of genes including 4CL3 in the phenylpropanoid pathway and UDP-GT in the shunt pathway of lignin monomer synthesis. The ramie 4CL3 recombinant protein prefers cinnamic acid as a substrate during catalysis, and it negatively regulates lignin synthesis. It is speculated that ramie 4CL3 is mainly involved in the synthesis of ramie flavonoid compounds, and that 4CL1 is mainly involved in lignin synthesis.

PpNAC187 enhances lignin synthesis in ‘Whangkeumbae’ pear (Pyrus pyrifolia) ‘hard-end’ fruit

2019 ◽  
Author(s):  
Mingtong Li ◽  
Chenxia Cheng ◽  
Xinfu Zhang ◽  
Suping Zhou ◽  
Caihong Wang ◽  
...  
Keyword(s):  
Transgenic Tobacco ◽  
Lignin Content ◽  
Lignin Biosynthesis ◽  
Phenylpropanoid Pathway ◽  
Pyrus Pyrifolia ◽  
Rna Seq ◽  
Pear Fruit ◽  
Nac Transcription Factors ◽  
Vessel Elements ◽  
Leaf Tissues

Abstract Background: A disorder in pears known as ‘hard-end’ fruit affects the appearance, edible quality, and market value of pear fruit. To explore the mechanism underlying the formation of hard-end, RNA-Seq was carried out on the calyx end of ‘Whangkeumbae’ pear fruit with and without the hard-end symptom. Result: Results indicated that genes in the phenylpropanoid pathway affecting lignification were up-regulated in hard-end fruit. An analysis of differentially expressed genes (DEGs) identified three NAC transcription factors, and RT-qPCR analysis of PpNAC138, PpNAC186 and PpNAC187 confirmed that PpNAC187 gene expression was correlated with the hard-end disorder in pear fruit. A transient increase in PpNAC187 was observed in the calyx end of ‘Whangkeumbae’ fruit when they began to exhibit hard-end symptom. Concomitantly, the higher level of PpCCR, Pp4CL and PpCOMT transcripts was observed; which are the key genes in lignin biosynthesis. Notably, lignin content in the stem and leaf tissues of transgenic tobacco overexpressing PpNAC187 was significantly higher than in control plants transformed with an empty vector. Furthermore, transgenic tobacco overexpressing PpNAC187 had a larger number of xylem vessel elements. Conclusion: The results of this study confirmed that PpNAC187 functions in inducing lignification in pear fruit during the development of the hard-end disorder.

scholarly journals A mutation in LacDWARF1 results in a GA-deficient dwarf phenotype in sponge gourd (Luffa acutangula)

2021 ◽  
Author(s):  
Gangjun Zhao ◽  
Caixia Luo ◽  
Jianning Luo ◽  
Junxing Li ◽  
Hao Gong ◽  
...  
Keyword(s):  
Gene Annotation ◽  
Recessive Gene ◽  
Genomic Region ◽  
Dwarf Mutant ◽  
Rna Seq ◽  
Dwarf Phenotype ◽  
Sponge Gourd ◽  
Response To Stress ◽  
Luffa Acutangula ◽  
Generation Sequencing

Abstract Key message A dwarfism gene LacDWARF1 was mapped by combined BSA-Seq and comparative genomics analyses to a 65.4 kb physical genomic region on chromosome 05. Abstract Dwarf architecture is one of the most important traits utilized in Cucurbitaceae breeding because it saves labor and increases the harvest index. To our knowledge, there has been no prior research about dwarfism in the sponge gourd. This study reports the first dwarf mutant WJ209 with a decrease in cell size and internodes. A genetic analysis revealed that the mutant phenotype was controlled by a single recessive gene, which is designated Lacdwarf1 (Lacd1). Combined with bulked segregate analysis and next-generation sequencing, we quickly mapped a 65.4 kb region on chromosome 5 using F2 segregation population with InDel and SNP polymorphism markers. Gene annotation revealed that Lac05g019500 encodes a gibberellin 3β-hydroxylase (GA3ox) that functions as the most likely candidate gene for Lacd1. DNA sequence analysis showed that there is an approximately 4 kb insertion in the first intron of Lac05g019500 in WJ209. Lac05g019500 is transcribed incorrectly in the dwarf mutant owing to the presence of the insertion. Moreover, the bioactive GAs decreased significantly in WJ209, and the dwarf phenotype could be restored by exogenous GA3 treatment, indicating that WJ209 is a GA-deficient mutant. All these results support the conclusion that Lac05g019500 is the Lacd1 gene. In addition, RNA-Seq revealed that many genes, including those related to plant hormones, cellular process, cell wall, membrane and response to stress, were significantly altered in WJ209 compared with the wild type. This study will aid in the use of molecular marker-assisted breeding in the dwarf sponge gourd.

scholarly journals Bioinformatics-based Screening of Key Genes for Saponin Metabolism in Quinoa

2021 ◽  
Author(s):  
Chengang Guo ◽  
Zhimin wei ◽  
Wei Lyu ◽  
Yanlou Geng
Keyword(s):  
Differentially Expressed Genes ◽  
Principal Component ◽  
Enrichment Analysis ◽  
Hierarchical Cluster ◽  
Gene Set Enrichment Analysis ◽  
Differentially Expressed ◽  
Differential Analysis ◽  
Rna Seq ◽  
Protein Coding ◽  
Key Genes

Abstract Quinoa saponins have complex, diverse and evident physiologic activities. However, the key regulatory genes for quinoa saponin metabolism are not yet well studied. The purpose of this study was to explore genes closely related to quinoa saponin metabolism. In this study, the significantly differentially expressed genes in yellow quinoa were firstly screened based on RNA-seq technology. Then, the key genes for saponin metabolism were selected by gene set enrichment analysis (GSEA) and principal component analysis (PCA) statistical methods. Finally, the specificity of the key genes was verified by hierarchical clustering. The results of differential analysis showed that 1654 differentially expressed genes were achieved after pseudogenes deletion. Therein, there were 142 long non-coding genes and 1512 protein-coding genes. Based on GSEA analysis, 116 key candidate genes were found to be significantly correlated with quinoa saponin metabolism. Through PCA dimension reduction analysis, 57 key genes were finally obtained. Hierarchical cluster analysis further demonstrated that these key genes can clearly separate the four groups of samples. The present results could provide references for the breeding of sweet quinoa and would be helpful for the rational utilization of quinoa saponins.

scholarly journals Identification of Key Genes Affecting Porcine Fat Deposition Based on Co-Expression Network Analysis of Weighted Genes

2021 ◽  
Author(s):  
Kai Xing ◽  
Huatao Liu ◽  
Fengxia Zhang ◽  
Yibing Liu ◽  
Yong Shi ◽  
...  
Keyword(s):  
Network Analysis ◽  
Production Efficiency ◽  
Fat Deposition ◽  
Rna Seq ◽  
Genetic Studies ◽  
Gene Expression Matrix ◽  
Differential Gene ◽  
Key Genes ◽  
Strong Candidate ◽  
Molecular Regulatory Mechanisms

Abstract Background: Fat deposition is an important economic consideration for pig production. The amount of fat deposition in pigs seriously affects production efficiency, quality, and reproductive performance, while also affecting consumers' choice of pork. Weighted gene co-expression network analysis (WGCNA) has been shown to be effective in pig genetic studies. Therefore, this study aimed to identify modules that co-express genes associated with fat deposition in pigs (Songliao black and Landrace breeds) with extreme levels of backfat (high and low), and to identify the central genes in each of these modules. Results: We used RNA-seq of different pig tissues to construct a gene expression matrix consisting of 12 862 genes from 36 samples. Eleven co-expression modules were identified using WGCNA; the number of genes in these modules ranged from 39 to 3363. We found four co-expression modules were significantly correlated with backfat thickness. A total of 14 genes ( RAD9A , IGF2R , SCAP , TCAP , DGAT1 , GPS2 , IGF1 , MAPK8 , FABP , FABP5 , LEPR , UCP3 , APOF , and FASN ) were found to be related to fat deposition. Conclusions: RAD9A , TCAP , GPS2 , and APOF were found to be the key genes in the four modules according to the degree of gene connectivity. Combining the results of differential gene analysis, APOF was proposed as a strong candidate gene for body size traits. This study explores the key genes that regulate porcine fat deposition and lays the foundation for further research into the molecular regulatory mechanisms behind porcine fat deposition.

scholarly journals Salinity Tolerance of Selected Seashore Paspalums and Bermudagrasses: Root and Verdure Responses and Criteria

HortScience ◽  
2004 ◽  
Vol 39 (5) ◽  
pp. 1143-1147 ◽  
Author(s):  
Geungjoo Lee ◽  
Robert N. Carrow ◽  
Ronny R. Duncan
Keyword(s):  
Salinity Tolerance ◽  
Cynodon Dactylon ◽  
Sand Dunes ◽  
Total Yield ◽  
Warm Season ◽  
Sand Culture ◽  
Root Characteristics ◽  
Seashore Paspalum ◽  
Absolute Growth ◽  
Total Growth

Seashore paspalum (Paspalum vaginatum Swartz) is a warm season turfgrass that survives in sand dunes along coastal sites and around brackish ponds or estuaries. The first exposure to salt stress normally occurs in the rhizosphere for persistent turfgrass. Information on diversity in salinity tolerance of seashore paspalums is limited. From Apr. to Oct. 1997, eight seashore paspalum ecotypes (SI 94-1, SI 92, SI 94-2, `Sea Isle 1', `Excalibur', `Sea Isle 2000', `Salam', `Adalayd') and four bermudagrass (Cynodon dactylon × C. transvaalensis Butt-Davy) cultivars (`Tifgreen', `Tifway', `TifSport', `TifEagle') were investigated for levels of salinity tolerance based on root and verdure responses in nutrient/sand culture under greenhouse conditions. Different salt levels (1.1 to 41.1 dS·m-1) were created with sea salt. Measurements were taken for absolute growth at 1.1 (ECw0; electrical conductivity of water), 24.8 (ECw24), 33.1 (ECw 32), and 41.1 dS·m-1 (ECw40), threshold ECw, and ECw for 25% growth reduction from ECw0 growth (ECw25%). Varying levels of salinity tolerance among the 12 entries were observed based on root, verdure, and total plant yield. Ranges of root characteristics were inherent growth (ECw0) = 0.20 to 0.61 g dry weight (DW); growth at ECw24 = 0.11 to 0.47 g; growth at ECw32 = 0.13 to 0.50 g; growth at ECw40 = 0.13 to 0.50 g; threshold ECw = 3.1 to 9.9 dS·m-1; and ECw25% = 23 to 39 dS·m-1. For verdure, ranges were inherent growth at ECw0 = 0.40 to 1.07 g DW; growth at ECw40 = 0.31 to 0.84 g; and ratio of yields at ECw40 to ECw0 = 0.54 to 1.03. Ranges for total growth were inherent growth at ECw0 = 0.72 to 2.66 g DW; growth at ECw24 = 0.55 to 2.23 g; growth at ECw32 = 0.54 to 2.08 g; growth at ECw40 = 0.52 to 1.66 g; threshold ECw = 2.3 to 12.8 dS·m-1; and ECw25% = 16 to 38 dS·m-1. Significant salinity tolerance differences existed among seashore paspalums and bermudagrasses as demonstrated by root, verdure, and total growth measurements. When grasses were ranked across all criteria exhibiting a significant F test based on root, verdure, and total growth, the most tolerant ecotypes were SI 94-1 and SI 92. Salinity tolerance of bermudagrass cultivars was relatively lower than SI 94-1 and SI 92. For assessing salinity tolerance, minimum evaluation criteria must include absolute growth at ECw0 and ECw 40 dS·m-1 for halophytes, but using all significant parameters of root and total yield is recommended for comprehensive evaluation.

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