Genome-wide identification and expression profiling of DREB genes in Saccharum spontaneum

Abstract Background The dehydration-responsive element-binding proteins (DREBs) are important transcription factors that interact with a DRE/CRT (C-repeat) sequence and involve in response to multiple abiotic stresses in plants. Modern sugarcane are hybrids from the cross between Saccharum spontaneum and Saccharum officinarum, and the high sugar content is considered to the attribution of S. officinaurm, while the stress tolerance is attributed to S. spontaneum. To understand the molecular and evolutionary characterization and gene functions of the DREBs in sugarcane, based on the recent availability of the whole genome information, the present study performed a genome-wide in silico analysis of DREB genes and transcriptome analysis in the polyploidy S. spontaneum. Results Twelve DREB1 genes and six DREB2 genes were identified in S. spontaneum genome and all proteins contained a conserved AP2/ERF domain. Eleven SsDREB1 allele genes were assumed to be originated from tandem duplications, and two of them may be derived after the split of S. spontaneum and the proximal diploid species sorghum, suggesting tandem duplication contributed to the expansion of DREB1-type genes in sugarcane. Phylogenetic analysis revealed that one DREB2 gene was lost during the evolution of sugarcane. Expression profiling showed different SsDREB genes with variable expression levels in the different tissues, indicating seven SsDREB genes were likely involved in the development and photosynthesis of S. spontaneum. Furthermore, SsDREB1F, SsDREB1L, SsDREB2D, and SsDREB2F were up-regulated under drought and cold condition, suggesting that these four genes may be involved in both dehydration and cold response in sugarcane. Conclusions These findings demonstrated the important role of DREBs not only in the stress response, but also in the development and photosynthesis of S. spontaneum.

Download Full-text

SNP discovery by amplicon sequencing and multiplex SNP genotyping in the allopolyploid species Brassica napusThis article is one of a selection of papers from the conference “Exploiting Genome-wide Association in Oilseed Brassicas: a model for genetic improvement of major OECD crops for sustainable farming”.

Genome ◽

10.1139/g10-079 ◽

2010 ◽

Vol 53 (11) ◽

pp. 948-956 ◽

Cited By ~ 35

Author(s):

G. Durstewitz ◽

A. Polley ◽

J. Plieske ◽

H. Luerssen ◽

E. M. Graner ◽

...

Keyword(s):

Genetic Analysis ◽

Oilseed Rape ◽

Expressed Sequence Tag ◽

Diploid Species ◽

Amplicon Sequencing ◽

Snp Markers ◽

Snp Analysis ◽

Genome Wide ◽

A Genome ◽

Illumina Goldengate

Oilseed rape ( Brassica napus ) is an allotetraploid species consisting of two genomes, derived from B. rapa (A genome) and B. oleracea (C genome). The presence of these two genomes makes single nucleotide polymorphism (SNP) marker identification and SNP analysis more challenging than in diploid species, as for a given locus usually two versions of a DNA sequence (based on the two ancestral genomes) have to be analyzed simultaneously during SNP identification and analysis. One hundred amplicons derived from expressed sequence tag (ESTs) were analyzed to identify SNPs in a panel of oilseed rape varieties and within two sister species representing the ancestral genomes. A total of 604 SNPs were identified, averaging one SNP in every 42 bp. It was possible to clearly discriminate SNPs that are polymorphic between different plant varieties from SNPs differentiating the two ancestral genomes. To validate the identified SNPs for their use in genetic analysis, we have developed Illumina GoldenGate assays for some of the identified SNPs. Through the analysis of a number of oilseed rape varieties and mapping populations with GoldenGate assays, we were able to identify a number of different segregation patterns in allotetraploid oilseed rape. The majority of the identified SNP markers can be readily used for genetic mapping, showing that amplicon sequencing and Illumina GoldenGate assays can be used to reliably identify SNP markers in tetraploid oilseed rape and to convert them into successful SNP assays that can be used for genetic analysis.

Download Full-text

Comprehensive Genome-Wide Analysis of The Catalase Enzyme Toolbox In Potato (Solanum Tuberosum L.)

10.21203/rs.3.rs-1020759/v1 ◽

2021 ◽

Author(s):

Rania Jbir Koubaa ◽

Mariem Ayadi ◽

Mohamed Najib Saidi ◽

Safa Charfeddine ◽

Radhia Gargouri Bouzid ◽

...

Keyword(s):

Stress Responses ◽

Expression Profiling ◽

Phylogenetic Trees ◽

Solanum Tuberosum L ◽

Potato Cultivar ◽

Promoter Sequence ◽

3D Protein Structure ◽

Genome Wide Analysis ◽

Genome Wide ◽

A Genome

Abstract As antioxidant enzymes, catalase (CAT) protects organisms from oxidative stress via the production of reactive oxygen species (ROS). These enzymes play important roles in diverse biological processes. However, little is known about the CAT genes in potato plants despite its important economical rank of this crop in the world. Yet, abiotic and biotic stresses severely hinder growth and development of the plants which affects the production and quality of the crop. To define the possible roles of CAT genes under various stresses, a genome-wide analysis of CAT gene family has been performed in potato plant.In this study, the StCAT gene’s structure, secondary and 3D protein structure, physicochemical properties, synteny analysis, phylogenetic tree and also expression profiling under various developmental and environmental cues were predicted using bioinformatics tools. The expression analysis by RT-PCR was performed using commercial potato cultivar. Three genes encoding StCAT that code for three proteins each of size 492 aa, interrupted by seven introns have been identified in potatoes. StCAT proteins were found to be localized in the peroxisome which is judged as the main H2O2 cell production site during different processes. Many regulating cis-elements related to stress responses and plant hormones signaling were found in the promoter sequence of each gene. The analysis of motifs and phylogenetic trees showed that StCAT are closer to their homologous in S. lycopersicum and share a 41% – 95% identity with other plants’ CATs. Expression profiling revealed that StCAT1 is the constitutively expressive member; while StCAT2 and StCAT3 are the stress-responsive members.

Download Full-text

hsa-MiR-19a-3p and hsa-MiR-19b-3p Are Associated with Spinal Cord Injury-Induced Neuropathic Pain: Findings from a Genome-Wide MicroRNA Expression Profiling Screen

Neurotrauma Reports ◽

10.1089/neur.2021.0011 ◽

2021 ◽

Vol 2 (1) ◽

pp. 424-439

Author(s):

Liang Ye ◽

Leslie R. Morse ◽

Scott P. Falci ◽

Julie K. Olson ◽

Mayank Shrivastava ◽

...

Keyword(s):

Spinal Cord ◽

Spinal Cord Injury ◽

Neuropathic Pain ◽

Expression Profiling ◽

Microrna Expression ◽

Genome Wide ◽

A Genome ◽

Cord Injury

Download Full-text

Detection and application of genome-wide variations in peach for association and genetic relationship analysis

BMC Genetics ◽

10.1186/s12863-019-0799-8 ◽

2019 ◽

Vol 20 (1) ◽

Cited By ~ 2

Author(s):

Liping Guan ◽

Ke Cao ◽

Yong Li ◽

Jian Guo ◽

Qiang Xu ◽

...

Keyword(s):

Genetic Relationship ◽

Dna Markers ◽

High Throughput Sequencing ◽

Prunus Persica ◽

Genetic Research ◽

Diploid Species ◽

Sequencing Data ◽

Relationship Analysis ◽

Genome Wide ◽

A Genome

Abstract Background Peach (Prunus persica L.) is a diploid species and model plant of the Rosaceae family. In the past decade, significant progress has been made in peach genetic research via DNA markers, but the number of these markers remains limited. Results In this study, we performed a genome-wide DNA markers detection based on sequencing data of six distantly related peach accessions. A total of 650,693~1,053,547 single nucleotide polymorphisms (SNPs), 114,227~178,968 small insertion/deletions (InDels), 8386~12,298 structure variants (SVs), 2111~2581 copy number variants (CNVs) and 229,357~346,940 simple sequence repeats (SSRs) were detected and annotated. To demonstrate the application of DNA markers, 944 SNPs were filtered for association study of fruit ripening time and 15 highly polymorphic SSRs were selected to analyze the genetic relationship among 221 accessions. Conclusions The results showed that the use of high-throughput sequencing to develop DNA markers is fast and effective. Comprehensive identification of DNA markers, including SVs and SSRs, would be of benefit to genetic diversity evaluation, genetic mapping, and molecular breeding of peach.

Download Full-text

A Ten-MicroRNA Signature Identified from a Genome-Wide MicroRNA Expression Profiling in Human Epithelial Ovarian Cancer

PLoS ONE ◽

10.1371/journal.pone.0096472 ◽

2014 ◽

Vol 9 (5) ◽

pp. e96472 ◽

Cited By ~ 56

Author(s):

Lin Wang ◽

Miao-Jun Zhu ◽

Ai-Min Ren ◽

Hong-Fei Wu ◽

Wu-Mei Han ◽

...

Keyword(s):

Ovarian Cancer ◽

Epithelial Ovarian Cancer ◽

Expression Profiling ◽

Microrna Expression ◽

Genome Wide ◽

A Genome

Download Full-text

Genome-Wide Analysis of R2R3-MYB Transcription Factors Family in The Autopolyploid Saccharum Spontaneum: An Exploration of Dominance Expression and Stress Response

10.21203/rs.3.rs-199103/v1 ◽

2021 ◽

Author(s):

Yuan Yuan ◽

Xiping Yang ◽

Mengfang Feng ◽

Hongyan Ding ◽

Khan Muhammad Tahir ◽

...

Keyword(s):

Transcription Factors ◽

Stress Response ◽

Gene Family ◽

Expression Analysis ◽

Expression Profiling ◽

Saccharum Spontaneum ◽

Myb Gene ◽

Genome Wide ◽

Myb Genes ◽

R2r3 Myb

Abstract Background: Sugarcane (Saccharum) is the most important sugar crop in the world. As one of the most enriched transcription factor families in plants, MYB genes display a great potential to contribute to sugarcane improvement by trait modification. We have identified the sugarcane MYB gene family at a whole-genome level through systematic evolution analyses and expression profiling. R2R3-MYB is a large subfamily involved in many plant-specific processes. Results: A total of 202 R2R3-MYB genes (356 alleles) were identified in the polyploid Saccharum spontaneum genome and classified into 15 subgroups by phylogenetic analysis. The sugarcane MYB family had more members by a comparative analysis in sorghum and significant advantages among most plants, especially grasses. Collinearity analysis revealed that 70% of the SsR2R3-MYB genes had experienced duplication events, logically suggesting the contributors to the MYB gene family expansion. Functional characterization was performed to identify 56 SsR2R3-MYB genes involved in various plant bioprocesses with expression profiling analysis on 60 RNA-seq databases. We identified 22 MYB genes specifically expressed in the stem, of which MYB43, MYB53, MYB65, MYB78, and MYB99 were validated by qPCR. Allelic expression dominance in the stem was more significant than that in the leaf, implying the differential expression of alleles may be responsible for the high expression of MYB in the stem. MYB169, MYB181, MYB192 were identified as candidate C4 photosynthetic regulators by C4 expression pattern and robust circadian oscillations. Furthermore, stress expression analysis showed that MYB36, MYB48, MYB54, MYB61 actively responded to drought treatment; 19 and 10 MYB genes were involved in response to the sugarcane pokkah boeng and mosaic disease, respectively. Conclusions: A Genome-wide expression analysis demonstrated that SsMYB genes were involved in stem development and stress response. This study largely contributed to understanding the extent to which MYB transcription factors investigate regulatory mechanisms and functional divergence in sugarcane.

Download Full-text

Development of an SNP Marker Set for Marker-Assisted Backcrossing Using Genotyping-By-Sequencing in Tetraploid Perilla

10.21203/rs.3.rs-1177284/v1 ◽

2021 ◽

Author(s):

Yun-Joo Kang ◽

Bo-Mi Lee ◽

Jangmi Kim ◽

Moon Nam ◽

Myoung-Hee Lee ◽

...

Keyword(s):

Recurrent Selection ◽

Diploid Species ◽

Genotyping By Sequencing ◽

Snp Markers ◽

Genetic Maps ◽

Linkage Maps ◽

Linkage Groups ◽

Genome Wide ◽

A Genome ◽

Marker Assisted Backcrossing

Abstract High-quality molecular markers are essential for marker-assisted selection to accelerate breeding progress. Compared with diploid species, recently diverged polyploid crop species tend to have highly similar homeologous subgenomes, which is expected to limit the development of broadly applicable locus-specific single-nucleotide polymorphism (SNP) assays. Furthermore, it is particularly challenging to make genome-wide marker sets for species that lack a reference genome. Here, we report the development of a genome-wide set of kompetitive allele specific PCR (KASP) markers for marker-assisted recurrent selection (MARS) in the tetraploid minor crop perilla. To find locus-specific SNP markers across the perilla genome, we used genotyping-by-sequencing (GBS) to construct linkage maps of two F2 populations. The two resulting high-resolution linkage maps comprised 2,326 and 2,454 SNP markers that spanned a total genetic distance of 2,133 cM across 16 linkage groups and 2,169 cM across 21 linkage groups, respectively. We then obtained a final genetic map consisting of 22 linkage groups with 1,123 common markers from the two genetic maps. We selected 96 genome-wide markers for MARS and confirmed the accuracy of markers in the two F2 populations using a high-throughput Fluidigm system. We confirmed that 91.8% of the SNP genotyping results from the Fluidigm assay were the same as the results obtained through GBS. These results provide a foundation for marker-assisted backcrossing and the development of new varieties of perilla.

Download Full-text

Detection and application of genome-wide variations in peach for association and genetic relationship analysis

10.21203/rs.2.10634/v3 ◽

2019 ◽

Author(s):

Liping Guan ◽

ke Cao ◽

yong Li ◽

jian guo ◽

qiang xu ◽

...

Keyword(s):

Genetic Relationship ◽

Dna Markers ◽

High Throughput Sequencing ◽

Prunus Persica ◽

Genetic Research ◽

Diploid Species ◽

Sequencing Data ◽

Relationship Analysis ◽

Genome Wide ◽

A Genome

Abstract Background: Peach (Prunus persica L.) is a diploid species and model plant of the Rosaceae family. In the past decade, significant progress has been made in peach genetic research via DNA markers, but the number of these markers remains limited. Results: In this study, we performed a genome-wide DNA markers detection based on sequencing data of six distantly related peach accessions. A total of 650,693~1,053,547 single nucleotide polymorphisms (SNPs), 114,227~178,968 small insertion/deletions (InDels), 8,386~12,298 structure variants (SVs), 2,111~2,581 copy number variants (CNVs) and 229,357~346,940 simple sequence repeats (SSRs) were detected and annotated. To demonstrate the application of DNA markers, 944 SNPs were filtered for association study of fruit ripening time and 15 highly polymorphic SSRs were selected to analyze the genetic relationship among 221 accessions. Conclusions: The results showed that the use of high-throughput sequencing to develop DNA markers is fast and effective. Comprehensive identification of DNA markers, including SVs and SSRs, would be of benefit to genetic diversity evaluation, genetic mapping, and molecular breeding of peach.

Download Full-text

Detection and application of genome-wide variations in peach for association and genetic relationship analysis

10.21203/rs.2.10634/v2 ◽

2019 ◽

Author(s):

Liping Guan ◽

ke Cao ◽

yong Li ◽

jian guo ◽

qiang xu ◽

...

Keyword(s):

Genetic Relationship ◽

Dna Markers ◽

High Throughput Sequencing ◽

Prunus Persica ◽

Genetic Research ◽

Diploid Species ◽

Sequencing Data ◽

Relationship Analysis ◽

Genome Wide ◽

A Genome

Abstract Abstract Background: Peach (Prunus persica L.) is a diploid species and model plant of the Rosaceae family. In the past decade, significant progress has been made in peach genetic research via DNA markers, but the number of these markers remains limited. Results: In this study, we performed a genome-wide DNA markers detection based on sequencing data of six distantly related peach accessions. A total of 650,693~1,053,547 single nucleotide polymorphisms (SNPs), 114,227~178,968 small insertion/deletions (InDels), 8,386~12,298 structure variants (SVs), 2,111~2,581 copy number variants (CNVs) and 229,357~346,940 simple sequence repeats (SSRs) were detected and annotated. To demonstrate the application of DNA markers, 944 SNPs were filtered for association study of fruit ripening time and 15 highly polymorphic SSRs were selected to analyze the genetic relationship among 221 accessions. Conclusions: The results showed that the use of high-throughput sequencing to develop DNA markers is fast and effective. Comprehensive identification of DNA markers, including SVs and SSRs, would be of benefit to genetic diversity evaluation, genetic mapping, and molecular breeding of peach.

Download Full-text