Genetic Map Construction and Functional Characterization of Genes within the Segregation Distortion Regions (SDRs) in the F2:3 Populations Derived from Wild Cotton Species of the D Genome

Abstract Background: Segregation distortion (SD) is a phenomenon common among stable or segregating populations, and the principle behind it still puzzles many researchers. The F2:3 progenies developed from the wild cotton species of the D genomes were used to investigate the possible plant transcription factors within the segregation distortion regions (SDRs). A consensus map was developed between two maps from the four D genome, map A derived from F2:3 progenies of Gossypium klotzschianum and G. davidsonii while Map B from G. thurberi and G. trilobum F2:3 generations. In each map, 188 individual plants were used. Results: The consensus linkage map had 1 492 markers across the 13 linkage groups; with a map size of 1467.445 cM and an average marker distance of 1.037 0 cM. Chromosome D502 had the highest percentage of SD with 58.621%, followed by Chromosome D507 with 47.887%. Six thousand and thirty- eight genes were mined within the SDRs on chromosome D502 and D507 of the consensus map. Within chromosome D502 and D507, 2,308 and 3 730 genes were mined, respectively, and were found to belong to 1 117 domains out of which 622 domains were common across the two chromosomes. Moreover, the first 9 domains were members of the plant resistance genes (R genes), while Pkinase; Protein kinase domain (PF00069) was the dominant group with 188 genes. Further analysis on the dominant domains revealed that 287 miRNAs were found to target various genes, such as the gr-miR398, gra-miR5207, miR164a, miR164b, miR164c among others, which have been found to target top-ranked stress-responsive transcription factors such as NAC genes. Moreover, some of the stress- responsive cis-regulatory elements were also detected. Furthermore, RNA profiling of the genes from the dominant family showed that higher numbers of genes were highly upregulated under salt and osmotic stress conditions, and also they were highly expressed at different stages of fiber development. Conclusion: The results indicated the critical role of the SDRs in the evolution of significant genes in plants.

Download Full-text

Genetic map construction and functional characterization of genes within the segregation distortion regions (SDRs) in the F2:3 populations derived from wild cotton species of the D genome

Journal of Cotton Research ◽

10.1186/s42397-020-00072-2 ◽

2020 ◽

Vol 3 (1) ◽

Author(s):

Joy Nyangasi KIRUNGU ◽

Richard Odongo MAGWANGA ◽

Margaret Linyerera SHIRAKU ◽

Pu LU ◽

Teame Gereziher MEHARI ◽

...

Keyword(s):

Transcription Factors ◽

Segregation Distortion ◽

Critical Role ◽

Functional Characterization ◽

Dominant Gene ◽

Regulatory Elements ◽

Consensus Map ◽

D Genome ◽

Cotton Species ◽

Wild Cotton

Abstract Background Segregation distortion (SD) is a common phenomenon among stable or segregating populations, and the principle behind it still puzzles many researchers. The F2:3 progenies developed from the wild cotton species of the D genomes were used to investigate the possible plant transcription factors within the segregation distortion regions (SDRs). A consensus map was developed between two maps from the four D genomes, map A derived from F2:3 progenies of Gossypium klotzschianum and G. davidsonii while Map B from G. thurberi and G. trilobum F2:3 generations. In each map, 188 individual plants were used. Results The consensus linkage map had 1 492 markers across the 13 linkage groups with a map size of 1 467.445 cM and an average marker distance of 1.037 0 cM. Chromosome D502 had the highest percentage of SD with 58.6%, followed by Chromosome D507 with 47.9%. Six thousand and thirty-eight genes were mined within the SDRs on chromosome D502 and D507 of the consensus map. Within chromosome D502 and D507, 2 308 and 3 730 genes were mined, respectively, and were found to belong to 1 117 gourp out of which 622 groups were common across the two chromosomes. Moreover, genes within the top 9 groups related to plant resistance genes (R genes), whereas 188 genes encoding protein kinase domain (PF00069) comprised the largest group. Further analysis of the dominant gene group revealed that 287 miRNAs were found to target various genes, such as the gra-miR398, gra-miR5207, miR164a, miR164b, miR164c among others, which have been found to target top-ranked stress-responsive transcription factors such as NAC genes. Moreover, some of the stress- responsive cis-regulatory elements were also detected. Furthermore, RNA profiling of the genes from the dominant family showed that higher numbers of genes were highly upregulated under salt and osmotic stress conditions, and also they were highly expressed at different stages of fiber development. Conclusion The results indicated the critical role of the SDRs in the evolution of the key regulatory genes in plants.

Download Full-text

Genetic Map Construction and Functional Characterization of Genes within the Segregation Distortion Regions (SDRs) in the F2:3 Populations Derived from Wild Cotton Species of the D Genome

10.21203/rs.3.rs-30612/v1 ◽

2020 ◽

Author(s):

Joy Nyangasi KIRUNGU ◽

Richard Odongo MAGWANGA ◽

Margaret Linyerera SHIRAKU ◽

LU Pu ◽

Teame Gereziher MEHARI ◽

...

Keyword(s):

Transcription Factors ◽

Segregation Distortion ◽

Functional Characterization ◽

Regulatory Elements ◽

Kinase Domain ◽

Consensus Map ◽

Dominant Group ◽

D Genome ◽

Cotton Species ◽

Wild Cotton

Abstract Background Segregation distortion (SD) is a phenomenon common among stable or segregating populations, and the principle behind it still puzzles many researchers. The F2:3 progenies developed from the wild cotton species of the D genomes were used to investigate the possible plant transcription factors within the segregation distortion regions (SDRs). A consensus map was developed between two maps from the four D genome, map A derived from an F2:3 progenies of Gossypium klotzschianum and G. davidsonii while Map B from G. thurberi and G. trilobum F2:3 generations. In each map 188 individual plants were used. Results The consensus linkage map had 1,492 markers across the 13 linkage groups; with a map size of 1,467.445 cM and average marker distance of 1.0370 cM. Chromosome D502 had the highest percentage of SD with 58.621% followed by Chromosome D507 with 47.887%. Six thousand and thirty eight genes were mined within the SDRs on chromosome D502 and D507 of the consensus map. Within chromosome D502 and D507, 2,308 and 3,730 genes were mined, respectively and were found to belong to 1,117 domains out of which 622 domains were common across the two chromosomes. Moreover, the first 9 domains were members of the plant resistance genes (R genes), while Pkinase; Protein kinase domain (PF00069) was the dominant group with 188 genes. Further analysis on the dominant domains revealed that 287 miRNAs were found to target various genes, such as the gr-miR398, gra-miR5207, miR164a, miR164b, miR164c among others, which have been found to target top-ranked stress-responsive transcription factors such as NAC genes. Moreover, some of the stress responsive cis-regulatory elements were also detected. Furthermore, RNA profiling of the genes from the dominant family showed that higher numbers of genes were highly upregulated under salt and osmotic stress conditions in addition their higher expression at different stages fiber development. Conclusion The result obtained provided an indication of the important role of the SDRs in the evolution of significant genes in plants.

Download Full-text

Genetic Map Construction and Functional Characterization of Genes within the Segregation Distortion Regions (SDRs) in the F2:3 Populations Derived from Wild Cotton Species of the D Genome

10.21203/rs.3.rs-30612/v2 ◽

2020 ◽

Author(s):

Joy Nyangasi KIRUNGU ◽

Richard Odongo MAGWANGA ◽

Margaret Linyerera SHIRAKU ◽

LU Pu ◽

Teame Gereziher MEHARI ◽

...

Keyword(s):

Transcription Factors ◽

Segregation Distortion ◽

Functional Characterization ◽

Regulatory Elements ◽

Kinase Domain ◽

Consensus Map ◽

Dominant Group ◽

D Genome ◽

Cotton Species ◽

Wild Cotton

Abstract Background: Segregation distortion (SD) is a phenomenon common among stable or segregating populations, and the principle behind it still puzzles many researchers. The F2:3 progenies developed from the wild cotton species of the D genomes were used to investigate the possible plant transcription factors within the segregation distortion regions (SDRs). A consensus map was developed between two maps from the four D genome, map A derived from an F2:3 progenies of Gossypium klotzschianum and G. davidsonii while Map B from G. thurberi and G. trilobum F2:3 generations. In each map 188 individual plants were used. Results: The consensus linkage map had 1492 markers across the 13 linkage groups; with a map size of 1467.445 cM and average marker distance of 1.037 0 cM. Chromosome D502 had the highest percentage of SD with 58.621% followed by Chromosome D507 with 47.887%. Six thousand and thirty eight genes were mined within the SDRs on chromosome D502 and D507 of the consensus map. Within chromosome D502 and D507, 2,308 and 3 730 genes were mined, respectively, and were found to belong to 1 117 domains out of which 622 domains were common across the two chromosomes. Moreover, the first 9 domains were members of the plant resistance genes (R genes), while Pkinase; Protein kinase domain (PF00069) was the dominant group with 188 genes. Further analysis on the dominant domains revealed that 287 miRNAs were found to target various genes, such as the gr-miR398, gra-miR5207, miR164a, miR164b, miR164c among others, which have been found to target top-ranked stress-responsive transcription factors such as NAC genes. Moreover, some of the stress responsive cis-regulatory elements were also detected. Furthermore, RNA profiling of the genes from the dominant family showed that higher numbers of genes were highly upregulated under salt and osmotic stress conditions, and in addition they were highly expressed at different stages of fiber development. Conclusion: The result obtained provided an indication of the important role of the SDRs in the evolution of significant genes in plants.

Download Full-text

Genetic map construction and functional characterization of genes within the segregation distortion regions (SDRs) in the F2:3 generation derived from wild cotton species of the D genome

10.7287/peerj.preprints.27845 ◽

2019 ◽

Author(s):

Joy Nyangasi Kirungu ◽

Richard Odongo Magwanga ◽

Margaret Linyerera Shiraku ◽

Pu Lu ◽

Teame Gereziher Mehari ◽

...

Keyword(s):

Transcription Factors ◽

Segregation Distortion ◽

Functional Characterization ◽

Regulatory Elements ◽

D Genome ◽

Rna Profiling ◽

Cotton Species ◽

Wild Cotton ◽

Gossypium Thurberi ◽

Marker Distance

Segregation distortion (SD) is a phenomenon common among stable or segregating populations, and the principle behind it is still an issue that puzzles many researchers. An F2:3 generations developed from the wild cotton species of the D genomes was applied to investigate the possible plant transcription factors within the segregation distortion regions (SDRs). We constructed a consensus map between two maps in the D genome, map A; Gossypium klotzschianum and Gossypium davidsonii and Map B; Gossypium thurberi and Gossypium trilobum. The two maps were developed from 188 F2:3 populations for each map, a total of 1492 markers, were linked to the 13 linkage groups. The consensus linkage map size was 1467.445 cM with an average marker distance of 1.0370cM. Chr02 had the highest percentage of segregation distortion with 58.621% followed by Chr07 with 47.887%. A total of 6,038 genes were mined within the segregation distortion regions (SDR region) of Chr02 and Chr07 with 2,308 gene in Chr02 and 3,730 genes in Chr07, we obtained a total of 1,117 domains within the SDR with a total of 622 domains shared between the two chromosomes, the first 9 domains all belonged to the plant resistance genes (R genes), the largest domain was PF00069 with a total of 188 genes. A total of 287 miRNAs were found to target the various genes, such as gr-miR398, gra-miR5207, miR164a, miR164b, miR164c among others which have been found to target top-ranked stress-responsive transcription factors such as NAC genes. Moreover, the genes were found to be regulated by various stress responsive cis-regulatory elements. RNA profiling showed that higher numbers of genes were highly upregulated in abiotic and different fiber development stages. The result shows that the SDR regions could be playing an important role in the evolution of significant genes in plants.

Download Full-text

Genetic map construction and functional characterization of genes within the segregation distortion regions (SDRs) in the F2:3 generation derived from wild cotton species of the D genome

10.7287/peerj.preprints.27845v1 ◽

2019 ◽

Author(s):

Joy Nyangasi Kirungu ◽

Richard Odongo Magwanga ◽

Margaret Linyerera Shiraku ◽

Pu Lu ◽

Teame Gereziher Mehari ◽

...

Keyword(s):

Transcription Factors ◽

Segregation Distortion ◽

Functional Characterization ◽

Regulatory Elements ◽

D Genome ◽

Rna Profiling ◽

Cotton Species ◽

Wild Cotton ◽

Gossypium Thurberi ◽

Marker Distance

Download Full-text

Genome-wide identification and expression analysis of bZIP gene family in Carthamus tinctorius L.

Scientific Reports ◽

10.1038/s41598-020-72390-z ◽

2020 ◽

Vol 10 (1) ◽

Author(s):

Haoyang Li ◽

Lixia Li ◽

Guodong ShangGuan ◽

Chang Jia ◽

Sinan Deng ◽

...

Keyword(s):

Transcription Factors ◽

Functional Characterization ◽

Draft Genome ◽

Functional Differentiation ◽

Regulatory Elements ◽

Carthamus Tinctorius ◽

Specific Pattern ◽

Basic Leucine Zipper ◽

Protein Motifs ◽

Genome Wide

Abstract The basic leucine zipper (bZIP) is a widely known transcription factors family in eukaryotes. In plants, the role of bZIP proteins are crucial in various biological functions such as plant growth and development, seed maturation, response to light signal and environmental stress. To date, bZIP protein family has been comprehensively identified in Arabidopsis, castor, rice, ramie, soybean and other plant species, however, the complete genome-wide investigation of Carthamus tinctorius-bZIP family still remains unexplained. Here, we identified 52 putative bZIP genes from Carthamus tinctorius using a draft genome assembly and further analyzed their evolutionary classification, physicochemical properties, Conserved domain analysis, functional differentiation and the investigation of expression level in different tissues. Based on the common bZIP domain, CtbZIP family were clustered into 12 subfamilies renamed as (A–J, S, X), of which the X is a unique subfamily to Carthamus tinctorius. A total of 20 conserved protein motifs were found in CtbZIP proteins. The expression profiling of CtbZIP genes deciphered their tissue-specific pattern. Furthermore, the changes in CtbZIP transcript abundance suggested that their transcription regulation could be highly influenced by light intensity and hormones. Collectively, this study highlights all functional and regulatory elements of bZIP transcription factors family in Carthamus tinctorius which may serve as potential candidates for functional characterization in future.

Download Full-text

Critical role for Ets, AP-1 and GATA-like transcription factors in regulating mouse Toll-like receptor 4 (Tlr4) gene expression

Biochemical Journal ◽

10.1042/bj20041243 ◽

2005 ◽

Vol 387 (2) ◽

pp. 355-365 ◽

Cited By ~ 57

Author(s):

Thierry ROGER ◽

Isabelle MICONNET ◽

Anne-Laure SCHIESSER ◽

Hirofumi KAI ◽

Kensuke MIYAKE ◽

...

Keyword(s):

Transcription Factors ◽

Promoter Activity ◽

Critical Role ◽

Regulatory Elements ◽

Mrna Levels ◽

Toll Like Receptor ◽

Toll Like Receptor 4 ◽

Gram Negative ◽

Inflammatory Stimuli ◽

Tlr4 Gene

TLR4 (Toll-like receptor 4) is essential for sensing the endotoxin of Gram-negative bacteria. Mutations or deletion of the TLR4 gene in humans or mice have been associated with altered predisposition to or outcome of Gram-negative sepsis. In the present work, we studied the expression and regulation of the Tlr4 gene of mouse. In vivo, TLR4 levels were higher in macrophages compared with B, T or natural killer cells. High basal TLR4 promoter activity was observed in RAW 264.7, J774 and P388D1 macrophages transfected with a TLR4 promoter reporter vector. Analysis of truncated and mutated promoter constructs identified several positive [two Ets (E twenty-six) and one AP-1 (activator protein-1) sites] and negative (a GATA-like site and an octamer site) regulatory elements within 350 bp upstream of the transcriptional start site. The myeloid and B-cell-specific transcription factor PU.1 bound to the proximal Ets site. In contrast, none among PU.1, Ets-1, Ets-2 and Elk-1, but possibly one member of the ESE (epithelium-specific Ets) subfamily of Ets transcription factors, bound to the distal Ets site, which was indispensable for Tlr4 gene transcription. Endotoxin did not affect macrophage TLR4 promoter activity, but it decreased TLR4 steady-state mRNA levels by increasing the turnover of TLR4 transcripts. TLR4 expression was modestly altered by other pro- and anti-inflammatory stimuli, except for PMA plus ionomycin which strongly increased promoter activity and TLR4 mRNA levels. The mouse and human TLR4 genes were highly conserved. Yet, notable differences exist with respect to the elements implicated in gene regulation, which may account for species differences in terms of tissue expression and modulation by microbial and inflammatory stimuli.

Download Full-text

Genome-Wide Identification and Functional Characterization of GATA Transcription Factor Gene Family in Alternaria alternata

Journal of Fungi ◽

10.3390/jof7121013 ◽

2021 ◽

Vol 7 (12) ◽

pp. 1013

Author(s):

Yanan Chen ◽

Yingzi Cao ◽

Yunpeng Gai ◽

Haijie Ma ◽

Zengrong Zhu ◽

...

Keyword(s):

Transcription Factors ◽

Environmental Stress ◽

Alternaria Alternata ◽

Gene Knockout ◽

Critical Role ◽

Functional Characterization ◽

Oxidoreductase Activity ◽

Fungal Virulence ◽

Gata Transcription Factors ◽

Citrus Leaves

In the present study, we identified six GATA transcription factors (AaAreA, AaAreB, AaLreA, AaLreB, AaNsdD, and AaSreA) and characterized their functions in response to environmental stress and virulence in the tangerine pathotype of Alternaria alternata. The targeted gene knockout of each of the GATA-coding genes decreased the growth to varying degrees. The mutation of AaAreA, AaAreB, AaLreB, or AaNsdD decreased the conidiation. All the GATA transcription factors were found to be required for tolerance to cumyl hydroperoxide and tert-butyl-hydroperoxide (oxidants) and Congo red (a cell-wall-destructing agent). Pathogenicity assays assessed on detached citrus leaves revealed that mutations of AaAreA, AaLreA, AaLreB, or AaNsdD significantly decreased the fungal virulence. A comparative transcriptome analysis between the ∆AreA mutant and the wild-type strain revealed that the inactivation of AaAreA led to alterations in the expression of genes involved in a number of biological processes, including oxidoreductase activity, amino acid metabolism, and secondary metabolite biogenesis. Taken together, our findings revealed that GATA-coding genes play diverse roles in response to environmental stress and are important regulators involved in fungal development, conidiation, ROS detoxification, as well as pathogenesis. This study, for the first time, systemically underlines the critical role of GATA transcription factors in response to environmental stress and virulence in A. alternata.

Download Full-text

Identification and characterization of genes related to salt stress tolerance within segregation distortion regions of genetic map in F2 population of upland cotton

PLoS ONE ◽

10.1371/journal.pone.0247593 ◽

2021 ◽

Vol 16 (3) ◽

pp. e0247593

Author(s):

Muhammad Shehzad ◽

Zhongli Zhou ◽

Allah Ditta ◽

Majid Khan ◽

Xiaoyan Cai ◽

...

Keyword(s):

Transcription Factors ◽

Gene Family ◽

Segregation Distortion ◽

Sequence Data ◽

Expression Profiles ◽

Gene Families ◽

Regulatory Elements ◽

Salt Tolerant ◽

F2 Population ◽

Upregulated Genes

Segregation distortion (SD) is a genetic mechanism commonly found in segregating or stable populations. The principle behind this puzzles many researchers. The F2 generation developed from wild Gossypium darwinii and G. hirsutum CCRI12 species was used to investigate the possible transcription factors within the segregation distortion regions (SDRs). The 384 out of 2763 markers were distorted in 29 SDRs on 18 chromosomes. Good collinearity was observed among genetic and physical maps of G. hirsutum and G. barbadense syntenic blocks. Total 568 genes were identified from SDRs of 18 chromosomes. Out of these genes, 128 belonged to three top-ranked salt-tolerant gene families. The DUF597 contained 8 uncharacterized genes linked to Pkinase (PF00069) gene family in the phylogenetic tree, while 15 uncharacterized genes clustered with the zinc finger gene family. Two hundred thirty four miRNAs targeted numerous genes, including ghr-miR156, ghr-miR399 and ghr-miR482, while others targeted top-ranked stress-responsive transcription factors. Moreover, these genes were involved in the regulation of numerous stress-responsive cis-regulatory elements. The RNA sequence data of fifteen upregulated genes were verified through the RT-qPCR. The expression profiles of two highly upregulated genes (Gh_D01G2015 and Gh_A01G1773) in salt-tolerant G. darwinii showed antagonistic expression in G. hirsutum. The results indicated that salt-tolerant genes have been possibly transferred from the wild G. darwinii species. A detailed functional analysis of these genes can be carried out which might be helpful in the future for gene cloning, transformation, gene editing and the development of salt-resistant cotton varieties.

Download Full-text

A cis-regulatory element promoting increased transcription at low temperature in cultured ectothermic Drosophila cells

BMC Genomics ◽

10.1186/s12864-021-08057-4 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Yu Bai ◽

Emmanuel Caussinus ◽

Stefano Leo ◽

Fritz Bosshardt ◽

Faina Myachina ◽

...

Keyword(s):

Transcription Factors ◽

Low Temperature ◽

Functional Characterization ◽

Regulatory Elements ◽

Transcriptional Level ◽

Cool Temperature ◽

Reporter Assay ◽

Transcriptional Responses ◽

General Response

Abstract Background Temperature change affects the myriad of concurrent cellular processes in a non-uniform, disruptive manner. While endothermic organisms minimize the challenge of ambient temperature variation by keeping the core body temperature constant, cells of many ectothermic species maintain homeostatic function within a considerable temperature range. The cellular mechanisms enabling temperature acclimation in ectotherms are still poorly understood. At the transcriptional level, the heat shock response has been analyzed extensively. The opposite, the response to sub-optimal temperature, has received lesser attention in particular in animal species. The tissue specificity of transcriptional responses to cool temperature has not been addressed and it is not clear whether a prominent general response occurs. Cis-regulatory elements (CREs), which mediate increased transcription at cool temperature, and responsible transcription factors are largely unknown. Results The ectotherm Drosophila melanogaster with a presumed temperature optimum around 25 °C was used for transcriptomic analyses of effects of temperatures at the lower end of the readily tolerated range (14–29 °C). Comparative analyses with adult flies and cell culture lines indicated a striking degree of cell-type specificity in the transcriptional response to cool. To identify potential cis-regulatory elements (CREs) for transcriptional upregulation at cool temperature, we analyzed temperature effects on DNA accessibility in chromatin of S2R+ cells. Candidate cis-regulatory elements (CREs) were evaluated with a novel reporter assay for accurate assessment of their temperature-dependency. Robust transcriptional upregulation at low temperature could be demonstrated for a fragment from the pastrel gene, which expresses more transcript and protein at reduced temperatures. This CRE is controlled by the JAK/STAT signaling pathway and antagonizing activities of the transcription factors Pointed and Ets97D. Conclusion Beyond a rich data resource for future analyses of transcriptional control within the readily tolerated range of an ectothermic animal, a novel reporter assay permitting quantitative characterization of CRE temperature dependence was developed. Our identification and functional dissection of the pst_E1 enhancer demonstrate the utility of resources and assay. The functional characterization of this CoolUp enhancer provides initial mechanistic insights into transcriptional upregulation induced by a shift to temperatures at the lower end of the readily tolerated range.

Download Full-text