Molecular Characterization Revealed the Role of Thaumatin-Like Proteins of Bread Wheat in Stress Response

Thaumatin-like proteins (TLPs) are related to pathogenesis-related-5 (PR-5) family and involved in stress response. Herein, a total of 93 TLP genes were identified in the genome of Triticum aestivum. Further, we identified 26, 27, 39, and 37 TLP genes in the Brachypodium distachyon, Oryza sativa, Sorghum bicolor, and Zea mays genomes for comparative characterization, respectively. They could be grouped into small and long TLPs with conserved thaumatin signature motif. Tightly clustered genes exhibited conserved gene and protein structure. The physicochemical analyses suggested significant differences between small and long TLPs. Evolutionary analyses suggested the role of duplication events and purifying selection in the expansion of the TLP gene family. Expression analyses revealed the possible roles of TLPs in plant development and abiotic and fungal stress response. Recombinant expression of TaTLP2-B in Saccharomyces cerevisiae provided significant tolerance against cold, heat, osmotic, and salt stresses. The results depicted the importance of TLPs in cereal crops that would be highly useful in future crop improvement programs.

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Genome Wide Identification and Comparative Analysis of the Serpin Gene Family in Brachypodium and Barley

Plants ◽

10.3390/plants9111439 ◽

2020 ◽

Vol 9 (11) ◽

pp. 1439

Author(s):

Shazia Rehman ◽

Bodil Jørgensen ◽

Ejaz Aziz ◽

Riffat Batool ◽

Samar Naseer ◽

...

Keyword(s):

Gene Family ◽

Protease Inhibitors ◽

Brachypodium Distachyon ◽

In Silico Analysis ◽

Purifying Selection ◽

Serpin Gene ◽

Bioinformatic Tools ◽

Duplication Events ◽

Genome Level

Serpins (serine protease inhibitors) constitute one of the largest and most widely distributed superfamilies of protease inhibitors and have been identified in nearly all organisms. To gain significant insights, a comprehensive in silico analysis of the serpin gene family was carried out in the model plant for temperate grasses Brachypodium distachyon and barley Hordeum vulgare using bioinformatic tools at the genome level for the first time. We identified a total of 27 BdSRPs and 25 HvSRP genes in Brachypodium and barley, respectively, showing an unexpectedly high gene number in these model plants. Gene structure, conserved motifs and phylogenetic comparisons of serpin genes supported the role of duplication events in the expansion and evolution of serpin gene family. Further, purifying selection pressure was found to be a main driving force in the evolution of serpin genes. Genome synteny analysis indicated that BdSRP genes were present in syntenic regions of barley, rice, sorghum and maize, suggesting that they evolved before the divergence of these species from common ancestor. The distinct expression pattern in specific tissues further suggested a specialization of functions during development and in plant defense. These results suggest that the LR serpins (serpins with Leu-Arg residues at P2–P1′) identified here can be utilized as candidates for exploitation in disease resistance, pest control and preventing stress-induced cell death. Additionally, serpins were identified that could lead to further research aimed at validating and functionally characterizing the role of potential serpin genes from other plants.

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Identification of Raf-Like Kinases B Subfamily Genes in Gossypium Species Revealed GhRAF42 Enhanced Salt Tolerance in Cotton

International Journal of Molecular Sciences ◽

10.3390/ijms222312649 ◽

2021 ◽

Vol 22 (23) ◽

pp. 12649

Author(s):

Zhen Peng ◽

Xuran Jiang ◽

Zhenzhen Wang ◽

Xiaoyang Wang ◽

Hongge Li ◽

...

Keyword(s):

Salt Tolerance ◽

Gene Family ◽

Purifying Selection ◽

Integrated Analysis ◽

Abiotic Factor ◽

Virus Induced Gene Silencing ◽

Salt Stress Response ◽

Suitable Candidate ◽

Duplication Events

Salinity is a critical abiotic factor that significantly reduces agricultural production. Cotton is an important fiber crop and a pioneer on saline soil, hence genetic architecture that underpins salt tolerance should be thoroughly investigated. The Raf-like kinase B-subfamily (RAF) genes were discovered to regulate the salt stress response in cotton plants. However, understanding the RAFs in cotton, such as Enhanced Disease Resistance 1 and Constitutive Triple Response 1 kinase, remains a mystery. This study obtained 29, 28, 56, and 54 RAF genes from G. arboreum, G. raimondii, G. hirsutum, and G. barbadense, respectively. The RAF gene family described allopolyploidy and hybridization events in allotetraploid cotton evolutionary connections. Ka/Ks analysis advocates that cotton evolution was subjected to an intense purifying selection of the RAF gene family. Interestingly, integrated analysis of synteny and gene collinearity suggested dispersed and segmental duplication events involved in the extension of RAFs in cotton. Transcriptome studies, functional validation, and virus-induced gene silencing on salt treatments revealed that GhRAF42 is engaged in salt tolerance in upland cotton. This research might lead to a better understanding of the role of RAFs in plants and the identification of suitable candidate salt-tolerant genes for cotton breeding.

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Quantitative Epigenetics: A New Avenue for Crop Improvement

Epigenomes ◽

10.3390/epigenomes4040025 ◽

2020 ◽

Vol 4 (4) ◽

pp. 25 ◽

Cited By ~ 1

Author(s):

Vijay Gahlaut ◽

Gaurav Zinta ◽

Vandana Jaiswal ◽

Sanjay Kumar

Keyword(s):

Molecular Breeding ◽

Recombinant Inbred Lines ◽

Crop Improvement ◽

Genotyping By Sequencing ◽

Phenotypic Traits ◽

Epigenetic Variation ◽

Epigenome Editing ◽

Epigenetic Diversity ◽

Improvement Programs

Plant breeding conventionally depends on genetic variability available in a species to improve a particular trait in the crop. However, epigenetic diversity may provide an additional tier of variation. The recent advent of epigenome technologies has elucidated the role of epigenetic variation in shaping phenotype. Furthermore, the development of epigenetic recombinant inbred lines (epi-RILs) in model species such as Arabidopsis has enabled accurate genetic analysis of epigenetic variation. Subsequently, mapping of epigenetic quantitative trait loci (epiQTL) allowed association between epialleles and phenotypic traits. Likewise, epigenome-wide association study (EWAS) and epi-genotyping by sequencing (epi-GBS) have revolutionized the field of epigenetics research in plants. Thus, quantitative epigenetics provides ample opportunities to dissect the role of epigenetic variation in trait regulation, which can be eventually utilized in crop improvement programs. Moreover, locus-specific manipulation of DNA methylation by epigenome-editing tools such as clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9 (CRISPR/Cas9) can potentially facilitate epigenetic based molecular breeding of important crop plants.

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Genome-Wide Identification, Evolution, and Expression Analysis of TPS and TPP Gene Families in Brachypodium distachyon

Plants ◽

10.3390/plants8100362 ◽

2019 ◽

Vol 8 (10) ◽

pp. 362 ◽

Cited By ~ 3

Author(s):

Song Wang ◽

Kai Ouyang ◽

Kai Wang

Keyword(s):

Stress Responses ◽

Brachypodium Distachyon ◽

Interaction Network ◽

Purifying Selection ◽

Gene Interaction ◽

Gene Families ◽

Gene Interaction Network ◽

Genome Wide ◽

Duplication Events ◽

Gene Structures

Trehalose biosynthesis enzyme homologues in plants contain two families, trehalose-6-phosphate synthases (TPSs) and trehalose-6-phosphate phosphatases (TPPs). Both families participate in trehalose synthesis and a variety of stress-resistance processes. Here, nine BdTPS and ten BdTPP genes were identified based on the Brachypodium distachyon genome, and all genes were classified into three classes. The Class I and Class II members differed substantially in gene structures, conserved motifs, and protein sequence identities, implying varied gene functions. Gene duplication analysis showed that one BdTPS gene pair and four BdTPP gene pairs are formed by duplication events. The value of Ka/Ks (non-synonymous/synonymous) was less than 1, suggesting purifying selection in these gene families. The cis-elements and gene interaction network prediction showed that many family members may be involved in stress responses. The quantitative real-time reverse transcription (qRT-PCR) results further supported that most BdTPSs responded to at least one stress or abscisic acid (ABA) treatment, whereas over half of BdTPPs were downregulated after stress treatment, implying that BdTPSs play a more important role in stress responses than BdTPPs. This work provides a foundation for the genome-wide identification of the B. distachyon TPS–TPP gene families and a frame for further studies of these gene families in abiotic stress responses.

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The Arabidopsis SENESCENCE-ASSOCIATED GENE 13 Regulates Dark-Induced Senescence and Plays Contrasting Roles in Defense Against Bacterial and Fungal Pathogens

Molecular Plant-Microbe Interactions ◽

10.1094/mpmi-11-19-0329-r ◽

2020 ◽

Vol 33 (5) ◽

pp. 754-766 ◽

Cited By ~ 7

Author(s):

Nikhilesh Dhar ◽

Julie Caruana ◽

Irmak Erdem ◽

Krishna V. Subbarao ◽

Steven J. Klosterman ◽

...

Keyword(s):

Oxidative Stress ◽

Cell Death ◽

Seed Germination ◽

Stress Responses ◽

Fungal Pathogens ◽

Crop Improvement ◽

Anthocyanin Accumulation ◽

Normal Seed ◽

Conserved Gene

SENESCENCE-ASSOCIATED GENE 13 (SAG13) of Arabidopsis is a widely conserved gene of unknown function that has been extensively used as a marker of plant senescence. SAG13 induction occurs during plant cell death processes, including senescence and hypersensitive response, a type of programmed cell death that occurs in response to pathogens. This implies that SAG13 expression is regulated through at least two different signaling pathways affecting these two different processes. Our work highlights a contrasting role for SAG13 in regulating resistance against disease-causing biotrophic bacterial and necrotrophic fungal pathogens with contrasting infection strategies. We provide further evidence that SAG13 is not only induced during oxidative stress but also plays a role in protecting the plant against other stresses. SAG13 is also required for normal seed germination, seedling growth, and anthocyanin accumulation. The work presented here provides evidence for the role of SAG13 in regulating multiple plant processes including senescence, defense, seed germination, and abiotic stress responses. SAG13 is a valuable molecular marker for these processes and is conserved in multiple plant species, and this knowledge has important implications for crop improvement.

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Thaumatin-like proteins: Molecular characterization, evolutionary analysis and expression profiling in major cereal crops

10.1101/2020.09.24.311928 ◽

2020 ◽

Author(s):

Alok Sharma ◽

Himanshu Sharma ◽

Santosh Kumar Upadhyay

Keyword(s):

Stress Responses ◽

Defense Mechanism ◽

Brachypodium Distachyon ◽

Crop Improvement ◽

Regulatory Elements ◽

Evolutionary Analysis ◽

Specific Expression ◽

Extracellular Region ◽

Improvement Programs

AbstractBackgroundPR superfamily, pathogenesis related (PR) proteins divided into P1-PR17 subfamilies, is involved in the defense mechanism of plants. Thaumatin-like proteins (TLPs) are part of PR-5 family that facilitates resistance against abiotic and biotic stress responses.ResultsIn the present study, a total of 26, 27, 39, 93 and 37 TLPs with conserved signature-motif were identified in Brachypodium distachyon, Oryza sativa, Sorghum bicolor, Triticum aestivum and Zea mays, respectively. They were phylogenetically divided into 10 different clades. Majority of genes possessed one to three exons. Physicochemical analysis suggested significant differences between small and long TLPs. Majority consisted of signal peptide and localized in extracellular region. Evolutionary analyses suggested the role of duplication events in the expansion of this gene family. Tissue-specific expression of certain genes suggested their role in development, while differential expression revealed their putative roles in stress-response. The occurrence of assorted set of cis-regulatory elements further suggested their diverse functions. Co-expression analysis depicted their interaction with several stress responsive genes.ConclusionsThe detailed characterization of TLP proteins in cereals depicted their importance in combating various biotic and abiotic challenges. This study would be useful in further characterization of individual TLP genes in each plant, and various crop improvement programs in future studies.

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The Female-Specific W Chromosomes of Birds Have Conserved Gene Contents but Are Not Feminized

Genes ◽

10.3390/genes11101126 ◽

2020 ◽

Vol 11 (10) ◽

pp. 1126 ◽

Cited By ~ 1

Author(s):

Luohao Xu ◽

Qi Zhou

Keyword(s):

Sex Chromosomes ◽

Expression Patterns ◽

Purifying Selection ◽

Gene Content ◽

Recombination Suppression ◽

Evolutionary Patterns ◽

Conserved Gene ◽

Heterogametic Sex ◽

Female Specific

Sex chromosomes are unique genomic regions with sex-specific or sex-biased inherent patterns and are expected to be more frequently subject to sex-specific selection. Substantial knowledge on the evolutionary patterns of sex-linked genes have been gained from the studies on the male heterogametic systems (XY male, XX female), but the understanding of the role of sex-specific selection in the evolution of female-heterogametic sex chromosomes (ZW female, ZZ male) is limited. Here we collect the W-linked genes of 27 birds, covering the three major avian clades: Neoaves (songbirds), Galloanserae (chicken), and Palaeognathae (ratites and tinamous). We find that the avian W chromosomes exhibit very conserved gene content despite their independent evolution of recombination suppression. The retained W-linked genes have higher dosage-sensitive and higher expression level than the lost genes, suggesting the role of purifying selection in their retention. Moreover, they are not enriched in ancestrally female-biased genes, and have not acquired new ovary-biased expression patterns after becoming W-linked. They are broadly expressed across female tissues, and the expression profile of the W-linked genes in females is not deviated from that of the homologous Z-linked genes. Together, our new analyses suggest that female-specific positive selection on the avian W chromosomes is limited, and the gene content of the W chromosomes is mainly shaped by purifying selection.

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Genome-Wide Investigation of the Role of MicroRNAs in Desiccation Tolerance in the Resurrection Grass Tripogon loliiformis

Plants ◽

10.3390/plants7030068 ◽

2018 ◽

Vol 7 (3) ◽

pp. 68 ◽

Cited By ~ 5

Author(s):

Isaac Njaci ◽

Brett Williams ◽

Claudia Castillo-González ◽

Martin Dickman ◽

Xiuren Zhang ◽

...

Keyword(s):

Stress Response ◽

Water Use Efficiency ◽

Water Use ◽

Desiccation Tolerance ◽

Molecular Mechanisms ◽

Crop Improvement ◽

Resurrection Plant ◽

Small Rna Sequencing ◽

Use Efficiency

Drought causes approximately two-thirds of crop and yield loss worldwide. To sustain future generations, there is a need to develop robust crops with enhanced water use efficiency. Resurrection plants are naturally resilient and tolerate up to 95% water loss with the ability to revive upon watering. Stress is genetically encoded and resilient species may garner tolerance by tightly regulating the expression of stress-related genes. MicroRNAs (miRNAs) post-transcriptionally regulate development and other stress response processes in eukaryotes. However, their role in resurrection plant desiccation tolerance is poorly understood. In this study, small RNA sequencing and miRNA expression profiling was conducted using Tripogon loliiformis plants subjected to extreme water deficit conditions. Differentially expressed miRNA profiles, target mRNAs, and their regulatory processes were elucidated. Gene ontology enrichment analysis revealed that development, stress response, and regulation of programmed cell death biological processes; Oxidoreductase and hydrolyase molecular activities; and SPL, MYB, and WRKY transcription factors were targeted by miRNAs during dehydration stress, indicating the indispensable regulatory role of miRNAs in desiccation tolerance. This study provides insights into the molecular mechanisms of desiccation tolerance in the resurrection plant T. loliiformis. This information will be useful in devising strategies for crop improvement on enhanced drought tolerance and water use efficiency.

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Fab Advances in Fabaceae for Abiotic Stress Resilience: From ‘Omics’ to Artificial Intelligence

International Journal of Molecular Sciences ◽

10.3390/ijms221910535 ◽

2021 ◽

Vol 22 (19) ◽

pp. 10535

Author(s):

Dharmendra Singh ◽

Priya Chaudhary ◽

Jyoti Taunk ◽

Chandan Kumar Singh ◽

Deepti Singh ◽

...

Keyword(s):

Artificial Intelligence ◽

Abiotic Stress ◽

Stress Response ◽

Abiotic Stress Tolerance ◽

Crop Improvement ◽

Genetic Determinants ◽

Diverse Range ◽

Food Legume ◽

Legume Crops ◽

Improvement Programs

Legumes are a better source of proteins and are richer in diverse micronutrients over the nutritional profile of widely consumed cereals. However, when exposed to a diverse range of abiotic stresses, their overall productivity and quality are hugely impacted. Our limited understanding of genetic determinants and novel variants associated with the abiotic stress response in food legume crops restricts its amelioration. Therefore, it is imperative to understand different molecular approaches in food legume crops that can be utilized in crop improvement programs to minimize the economic loss. ‘Omics’-based molecular breeding provides better opportunities over conventional breeding for diversifying the natural germplasm together with improving yield and quality parameters. Due to molecular advancements, the technique is now equipped with novel ‘omics’ approaches such as ionomics, epigenomics, fluxomics, RNomics, glycomics, glycoproteomics, phosphoproteomics, lipidomics, regulomics, and secretomics. Pan-omics—which utilizes the molecular bases of the stress response to identify genes (genomics), mRNAs (transcriptomics), proteins (proteomics), and biomolecules (metabolomics) associated with stress regulation—has been widely used for abiotic stress amelioration in food legume crops. Integration of pan-omics with novel omics approaches will fast-track legume breeding programs. Moreover, artificial intelligence (AI)-based algorithms can be utilized for simulating crop yield under changing environments, which can help in predicting the genetic gain beforehand. Application of machine learning (ML) in quantitative trait loci (QTL) mining will further help in determining the genetic determinants of abiotic stress tolerance in pulses.

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Quantitative Epigenetics: A New Avenue for Crop Improvement

10.20944/preprints202009.0348.v1 ◽

2020 ◽

Author(s):

Vijay Gahlaut ◽

Gaurav Zinta ◽

Vandana Jaiswal

Keyword(s):

Molecular Breeding ◽

Recombinant Inbred Lines ◽

Crop Improvement ◽

Phenotypic Traits ◽

Epigenetic Variation ◽

Model Species ◽

Epigenome Editing ◽

Epigenetic Diversity ◽

Improvement Programs

Plant breeding conventionally depends on genetic variability available in a species to improve a particular trait in the crop. However, epigenetic diversity may provide an additional tier of variation. The recent advent of epigenome technologies has elucidated the role of epigenetic variation in shaping phenotype. Further, the development of epigenetic recombinant inbred lines (epi-RILs) in the model species such as Arabidopsis has enabled accurate genetic analysis of epigenetic variation. Subsequently, mapping of epigenetic quantitative trait loci (epiQTL) allowed association between epialleles and phenotypic traits. Thus, quantitative epigenetics provides ample opportunities to dissect the role of epigenetic variation in trait regulation, which can be eventually utilized in crop improvement programs. Moreover, locus-specific manipulation of DNA methylation by epigenome-editing tools such as clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9 (CRISPR/Cas9) can facilitate epigenetic based molecular breeding of important crop plants.

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