Transcriptomic analysis of salt tolerance-associated genes and diversity analysis using indel markers in yardlong bean (Vigna unguiculata ssp. sesquipedialis)

Abstract Background High salinity is a devastating abiotic stresses for crops. To understand the molecular basis of salinity stress in yardlong bean (Vigna unguiculata ssp. sesquipedalis), and to develop robust markers for improving this trait in germplasm, whole transcriptome RNA sequencing (RNA-seq) was conducted to compare the salt-tolerant variety Suzi 41 and salt-sensitive variety Sujiang 1419 under normal and salt stress conditions. Results Compared with controls, 417 differentially expressed genes (DEGs) were identified under exposure to high salinity, including 42 up- and 11 down-regulated DEGs in salt-tolerant Suzi 41 and 186 up- and 197 down-regulated genes in salt-sensitive Sujiang 1419, validated by qRT-PCR. DEGs were enriched in “Glycolysis/Gluconeogenesis” (ko00010), “Cutin, suberine and wax biosynthesis” (ko00073), and “phenylpropanoid biosynthesis” (ko00940) in Sujiang 1419, although “cysteine/methionine metabolism” (ko00270) was the only pathway significantly enriched in salt-tolerant Suzi 41. Notably, AP2/ERF, LR48, WRKY, and bHLH family transcription factors (TFs) were up-regulated under high salt conditions. Genetic diversity analysis of 84 yardlong bean accessions using 26 InDel markers developed here could distinguish salt-tolerant and salt-sensitive varieties. Conclusions These findings show a limited set of DEGs, primarily TFs, respond to salinity stress in V. unguiculata, and that these InDels associated with salt-inducible loci are reliable for diversity analysis.

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Transcriptome analysis of bread wheat leaves in response to salt stress

PLoS ONE ◽

10.1371/journal.pone.0254189 ◽

2021 ◽

Vol 16 (7) ◽

pp. e0254189

Author(s):

Nazanin Amirbakhtiar ◽

Ahmad Ismaili ◽

Mohammad-Reza Ghaffari ◽

Raheleh Mirdar Mansuri ◽

Sepideh Sanjari ◽

...

Keyword(s):

Salt Tolerance ◽

Salinity Stress ◽

Expression Patterns ◽

Transcript Abundance ◽

Crop Productivity ◽

Mapk Signaling ◽

Salt Tolerant ◽

Illumina Hiseq ◽

Phenylpropanoid Biosynthesis ◽

Wheat Leaves

Salinity is one of the main abiotic stresses limiting crop productivity. In the current study, the transcriptome of wheat leaves in an Iranian salt-tolerant cultivar (Arg) was investigated in response to salinity stress to identify salinity stress-responsive genes and mechanisms. More than 114 million reads were generated from leaf tissues by the Illumina HiSeq 2500 platform. An amount of 81.9% to 85.7% of reads could be mapped to the wheat reference genome for different samples. The data analysis led to the identification of 98819 genes, including 26700 novel transcripts. A total of 4290 differentially expressed genes (DEGs) were recognized, comprising 2346 up-regulated genes and 1944 down-regulated genes. Clustering of the DEGs utilizing Kyoto Encyclopedia of Genes and Genomes (KEGG) indicated that transcripts associated with phenylpropanoid biosynthesis, transporters, transcription factors, hormone signal transduction, glycosyltransferases, exosome, and MAPK signaling might be involved in salt tolerance. The expression patterns of nine DEGs were investigated by quantitative real-time PCR in Arg and Moghan3 as the salt-tolerant and susceptible cultivars, respectively. The obtained results were consistent with changes in transcript abundance found by RNA-sequencing in the tolerant cultivar. The results presented here could be utilized for salt tolerance enhancement in wheat through genetic engineering or molecular breeding.

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Advanced Breeding Strategies and Future Perspectives of Salinity Tolerance in Rice

Agronomy ◽

10.3390/agronomy11081631 ◽

2021 ◽

Vol 11 (8) ◽

pp. 1631

Author(s):

Md Azadul Haque ◽

Mohd Y. Rafii ◽

Martini Mohammad Yusoff ◽

Nusaibah Syd Ali ◽

Oladosu Yusuff ◽

...

Keyword(s):

Genome Editing ◽

Salinity Stress ◽

Salinity Tolerance ◽

High Salinity ◽

Abiotic Factors ◽

Rice Production ◽

Salt Tolerant ◽

Rice Varieties ◽

Rice Plants ◽

Breeding Techniques

Rice, generally classified as a typical glycophyte, often faces abiotic stresses such as excessive drought, high salinity, prolonged submergence, cold, and temperature, which significantly affects growth, development, and ultimately, grain yield. Among these negative impacts of abiotic factors in rice production, salinity stress is a major constraint, followed by drought. There is considerable research on the use of marker-assisted selection (MAS), genome editing techniques, and transgenic studies that have profoundly improved the present-day rice breeders’ toolboxes for developing salt-tolerant varieties. Salinity stresses significantly affect rice plants during seedling and reproductive stages. Hence, greater understanding and manipulation of genetic architecture in developing salt-tolerant rice varieties will significantly impact sustainable rice production. Rice plants’ susceptibility or tolerance to high salinity has been reported to be the result of coordinated actions of multiple stress-responsive quantitative trait loci (QTLs)/genes. This paper reviews recent literature, updating the effects of salinity stress on rice plants and germplasm collections and screening for salinity tolerance by different breeding techniques. Mapping and identification of QTLs salt tolerance genes are illuminated. The present review updates recent breeding for improvement in rice tolerance to salinity stress and how state-of-the-art tools such as MAS or genetic engineering and genome editing techniques, including mutagenesis and conventional breeding techniques, can assist in transferring salt-tolerant QTLs genes into elite rice genotypes, accelerating breeding of salt-resistant rice cultivars.

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SALT TOLERANCE IN TEN CULTIVARS OF EGGPLANT (Solanum melongena L.)

HortScience ◽

10.21273/hortsci.25.9.1149d ◽

1990 ◽

Vol 25 (9) ◽

pp. 1149d-1149

Author(s):

Mahdi S. Abdal ◽

Jagan N. Sharma

Keyword(s):

Salt Tolerance ◽

Salinity Stress ◽

High Salinity ◽

Solanum Melongena ◽

Quantitative Information ◽

Salt Tolerant ◽

Vegetable Crop ◽

Leaf Necrosis ◽

Final Survival ◽

Ongoing Project

Eggplant is an important vegetable crop in Kuwait. Eggplant is considered to have moderately sensitive salt-tolerance, though no quantitative information is available on its salt sensitivity. Selecting salt-tolerant genotypes in eggplant is an ongoing project at Kuwait Institute for Scientific Research. Towards the goal of selecting salt-tolerant genotypes in eggplant a completely randomized experiment using 10 cultivars, replicated 3 times were tested against 2 levels of high salinity stress (EC MS.cm-1 at 25°C, 15.0 and 18.0) along with the control (EC MS.cm-1 at 25°C, 3.0). The experiment was conducted on 15 days old seedlings inside a greenhouse. Data on shoot length and visual observations on leaf necrosis, leaf collapse and root color was also recorded. There was a clear degree of variability as well as significant differences in growth and final survival, between cultivars at 2 levels of salinity stress. Those genotypes that showed significant higher growth rates and survival without any signs on leaf necrosis and root collapse formed the basis salt-tolerant genotypes.

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Genetic diversity analysis of yardlong bean genotypes (Vigna unguiculata subsp. sesquipedalis) based on IRAP marker

Biodiversitas Journal of Biological Diversity ◽

10.13057/biodiv/d210333 ◽

2020 ◽

Vol 21 (3) ◽

Author(s):

Muhammad Habib Widyawan ◽

Sri Wulandary ◽

Taryono

Keyword(s):

Genetic Diversity ◽

Cluster Analysis ◽

Vigna Unguiculata ◽

Genetic Similarity ◽

Polymorphic Information Content ◽

Resolving Power ◽

Diversity Analysis ◽

Genetic Diversity Analysis ◽

Irap Marker ◽

Yardlong Bean

Abstract. Widyawan MH, Wulandary S, Taryono. 2020. Genetic diversity analysis of yardlong bean genotypes (Vigna unguiculata subsp. sesquipedalis) based on IRAP marker. Biodiversitas 21: 1101-1107. Inter-Retrotransposon Amplified Polymorphism (IRAP) marker is a PCR-based molecular marker that detects polymorphism between retrotransposon sites. This marker has been utilized and successfully assessed genetic diversity in many crop species. Yardlong bean (Vigna unguiculata subsp. sesquipedalis) was an important vegetable legume crop that grown mainly for its fresh pod that rich in nutritional benefits for humans, ultimately dietary fiber and protein. Trends of people awareness to nutritional content of food are increasing, therefore breeding for quality traits is important. Genetic diversity analysis is an important and elementary step in breeding programs in order to determine the breeding strategy. The aims of this research are to perform an optimization of IRAP marker and applied it for genetic diversity analysis in 16 yardlong bean genotypes. Seven primers were used as marker in a pair or single combination and resulted in 11 optimized markers that able to be used for genetic diversity analysis. Sixteen yardlong bean genotypes consisting of commercial cultivars and local genotypes from Indonesia were genotyped using eleven IRAP markers. Marker polymorphism and diversity parameters from each marker i.e. Percentage of Polymorphic Loci (PPL), Expected Heterozygosity (He), Polymorphic Information Content (PIC), Effective Multiplex Ratio (EMR), Marker Index (MI), Discriminating Power (D), and Resolving Power (RP) were calculated. Based on those values, several markers used in this study were considered as informative and efficient in terms of analyzing genetic diversity in yardlong bean. Jaccard's method was used to measure genetic similarity and it is revealed that there is high level of similarity between yardlong bean genotypes used in this study. Thus, it is implied that there is a narrow genetic diversity of yardlong bean genotypes used in this study. Cluster analysis was performed to construct dendrogram based on genetic similarity and classified 16 yardlong genotypes into 4 clusters. Interestingly, majority of the clusters formed were not able to classified genotypes based on their origin. The result of cluster analysis then confirmed by Principal Coordinate Analysis (PCoA) that able to explain 47.76 % of total variation. The results of this study provide a foundation for the genetic diversity analysis based on IRAP marker and genetic improvement in yardlong bean.

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Comprehensive Analysis of Transcriptomics and Metabolomics between the Heads and Tails of Angelica Sinensis: Genes Related to Phenylpropanoid Biosynthesis Pathway

Combinatorial Chemistry & High Throughput Screening ◽

10.2174/1386207323999201103221952 ◽

2020 ◽

Vol 23 ◽

Author(s):

Jie Yang ◽

Chi Zhang ◽

Wei-Hong Li ◽

Tian-Er Zhang ◽

Guang-Zhong Fan ◽

...

Keyword(s):

Ferulic Acid ◽

Metabolic Regulation ◽

Comprehensive Analysis ◽

Angelica Sinensis ◽

Rna Seq ◽

Targeted Metabolomics ◽

Kegg Pathways ◽

Qrt Pcr ◽

Phenylpropanoid Biosynthesis ◽

Combined Strategy

Background:: In Traditional Chinese Medicine (TCM), the heads and tails of Angelica sinensis (Oliv.) Diels (AS) is used in treating different diseases due to their different pharmaceutical efficacies. The underline mechanisms, however, have not been fully explored. Objective:: Novel mechanisms responsible for the discrepant activities between AS heads and tails were explored by a combined strategy of transcriptomes and metabolomics. Method:: Six pairs of the heads and tails of AS roots were collected in Min County, China. Total RNA and metabolites, which were used for RNA-seq and untargeted metabolomics analysis, were respectively isolated from each AS sample (0.1 g) by Trizol and methanol reagent. Subsequently, differentially expressed genes (DEGs) and discrepant pharmaceutical metabolites were identified for comparing AS heads and tails. Key DEGs and metabolites were quantified by qRT-PCR and targeted metabolomics experiment. Results:: Comprehensive analysis of transcriptomes and metabolomics results suggested that five KEGG pathways with significant differences included 57 DEGs. Especially, fourteen DEGs and six key metabolites were relation to the metabolic regulation of Phenylpropanoid biosynthesis (PB) pathway. Results of qRT-PCR and targeted metabolomics indicated that higher levels of expression of crucial genes in PB pathway, such as PAL, CAD, COMT and peroxidase in the tail of AS were positively correlated with levels of ferulic acid-related metabolites. The average content of ferulic acid in tails (569.58162.39 nmol/g) was higher than those in the heads (168.73  67.30 nmol/g) (P˂0.01); Caffeic acid in tails (3.82  0.88 nmol/g) vs heads (1.37  0.41 nmol/g) (P˂0.01), and Cinnamic acid in tails (0.24  0.09 nmol/g) vs heads (0.14  0.02 nmol/g) (P˂0.05). Conclusion:: Our work demonstrated that overexpressed genes and accumulated metabolites derived from PB pathway might be responsible for the discrepant pharmaceutical efficacies between AS heads and tails.

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Biostimulation of Vigna unguiculata subsp. sesquipedalis—Cultivar Sesquipedalis (Yardlong Bean)—by Brevibacillus sp. B65 in Organoponic Conditions

Current Microbiology ◽

10.1007/s00284-021-02453-5 ◽

2021 ◽

Vol 78 (5) ◽

pp. 1882-1891

Author(s):

Teresa M. Orberá Ratón ◽

Iraida Bayard Vedey ◽

Ann Cuypers

Keyword(s):

Vigna Unguiculata ◽

Yardlong Bean

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RcTGA1 and glucosinolate biosynthesis pathway involvement in the defence of rose against the necrotrophic fungus Botrytis cinerea

BMC Plant Biology ◽

10.1186/s12870-021-02973-z ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Penghua Gao ◽

Hao Zhang ◽

Huijun Yan ◽

Qigang Wang ◽

Bo Yan ◽

...

Keyword(s):

Disease Resistance ◽

Gene Annotation ◽

Infected Plant ◽

Grey Mould ◽

Cascade Reactions ◽

Postharvest Quality ◽

Rna Seq ◽

Protein Activity ◽

Phenylpropanoid Biosynthesis ◽

And Cluster Analysis

Abstract Background Rose is an important economic crop in horticulture. However, its field growth and postharvest quality are negatively affected by grey mould disease caused by Botrytis c. However, it is unclear how rose plants defend themselves against this fungal pathogen. Here, we used transcriptomic, metabolomic and VIGS analyses to explore the mechanism of resistance to Botrytis c. Result In this study, a protein activity analysis revealed a significant increase in defence enzyme activities in infected plants. RNA-Seq of plants infected for 0 h, 36 h, 60 h and 72 h produced a total of 54 GB of clean reads. Among these reads, 3990, 5995 and 8683 differentially expressed genes (DEGs) were found in CK vs. T36, CK vs. T60 and CK vs. T72, respectively. Gene annotation and cluster analysis of the DEGs revealed a variety of defence responses to Botrytis c. infection, including resistance (R) proteins, MAPK cascade reactions, plant hormone signal transduction pathways, plant-pathogen interaction pathways, Ca2+ and disease resistance-related genes. qPCR verification showed the reliability of the transcriptome data. The PTRV2-RcTGA1-infected plant material showed improved susceptibility of rose to Botrytis c. A total of 635 metabolites were detected in all samples, which could be divided into 29 groups. Metabonomic data showed that a total of 59, 78 and 74 DEMs were obtained for T36, T60 and T72 (T36: Botrytis c. inoculated rose flowers at 36 h; T60: Botrytis c. inoculated rose flowers at 60 h; T72: Botrytis c. inoculated rose flowers at 72 h) compared to CK, respectively. A variety of secondary metabolites are related to biological disease resistance, including tannins, amino acids and derivatives, and alkaloids, among others; they were significantly increased and enriched in phenylpropanoid biosynthesis, glucosinolates and other disease resistance pathways. This study provides a theoretical basis for breeding new cultivars that are resistant to Botrytis c. Conclusion Fifty-four GB of clean reads were generated through RNA-Seq. R proteins, ROS signalling, Ca2+ signalling, MAPK signalling, and SA signalling were activated in the Old Blush response to Botrytis c. RcTGA1 positively regulates rose resistance to Botrytis c. A total of 635 metabolites were detected in all samples. DEMs were enriched in phenylpropanoid biosynthesis, glucosinolates and other disease resistance pathways.

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