Segregation distortion and genome-wide digenic interactions affect transmission of introgressed chromatin from wild cotton species

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.

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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.

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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

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.

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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/v3 ◽

2020 ◽

Author(s):

Joy Nyangasi KIRUNGU ◽

Richard Odongo MAGWANGA ◽

Margaret Linyerera SHIRAKU ◽

LU Pu ◽

Teame Gereziher MEHARI ◽

...

Keyword(s):

Transcription Factors ◽

Segregation Distortion ◽

Critical Role ◽

Functional Characterization ◽

Regulatory Elements ◽

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 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.

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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.

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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.

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The Gossypium stocksii genome as a novel resource for cotton improvement

G3 Genes|Genome|Genetics ◽

10.1093/g3journal/jkab125 ◽

2021 ◽

Author(s):

Corrinne E Grover ◽

Daojun Yuan ◽

Mark A Arick ◽

Emma R Miller ◽

Guanjing Hu ◽

...

Keyword(s):

Genome Sequence ◽

De Novo ◽

Pest Resistance ◽

Cotton Leaf ◽

High Quality ◽

Cotton Leaf Curl Virus ◽

Cotton Species ◽

Wild Cotton ◽

Leaf Curl Virus ◽

Insight Into

Abstract Cotton is an important textile crop whose gains in production over the last century have been challenged by various diseases. Because many modern cultivars are susceptible to several pests and pathogens, breeding efforts have included attempts to introgress wild, naturally resistant germplasm into elite lines. Gossypium stocksii is a wild cotton species native to Africa, which is part of a clade of vastly understudied species. Most of what is known about this species comes from pest resistance surveys and/or breeding efforts, which suggests that G. stocksii could be a valuable reservoir of natural pest resistance. Here we present a high-quality de novo genome sequence for G. stocksii. We compare the G. stocksii genome with resequencing data from a closely related, understudied species (G. somalense) to generate insight into the relatedness of these cotton species. Finally, we discuss the utility of the G. stocksii genome for understanding pest resistance in cotton, particularly resistance to cotton leaf curl virus.

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Genome-wide identification, phylogenetic and expressional analysis of the UXS gene family in cotton

10.21203/rs.2.22104/v1 ◽

2020 ◽

Author(s):

Yuxin Pan ◽

Jinpeng Wang ◽

Zhenyi Wang ◽

Hengwei Liu ◽

Lan Zhang ◽

...

Keyword(s):

Positive Selection ◽

Gene Family ◽

Expression Profiles ◽

Expression Patterns ◽

Subcellular Location ◽

Pcr Analysis ◽

Genome Wide ◽

Cotton Species ◽

Expressional Analysis ◽

Significant Positive Selection

Abstract Background: UDP-glucuronate decarboxylase (UXS) is an enzyme in plants and participates in cell wall noncellulose. Previous research suggested that cotton GhUXS gene regulated the conversion of non-cellulosic polysaccharides and modulates their composition in plant cell walls, showing its possible cellular function determining the quality of cotton fibers. Here, we performed evolutionary, phylogenetic, and expressional analysis of UXS genes from cottons and other selected plants. Results: By exploring the sequenced cotton genomes, we identified 10, 10, 18, and 20 UXSs genes in Gossypium raimondii , Gossypium arboretum , Gossypium hirsutum and Gossypium barbadense , and retrieved their homologs from other representative plants, including 5 dicots, 1 monocot, 5 green alga, 1 moss, and 1 lycophyte. Phylogenetic analysis suggested that UXS genes could be divided into four subgroups and members within each subgroup shared similar exon-intron structures, motif and subcellular location. Notably, gene colinearity information indicates 100% constructed trees to have aberrant topology, and helps determine and use corrected phylogeny. In spite of conservative nature of UXS, during the evolution of Gossypium , UXS genes were subjected to significant positive selection on key evolutionary nodes. Expression profiles derived from RNA-seq data showed distinct expression patterns of GhUXS genes in various tissues and different development. Most of GhUXS gene expressed highly at 10, 20 and 25 DPA (day post anthesis) of fibers. Real-time quantitative PCR analysis GhUXS genes expressed highly at 20 DPA or 25 DPA. Conclusions: UXS is relatively conserved in plants and significant positive selection affects cotton UXS evolution. The comparative genome-wide identification and expression profiling would lay an important foundation to understanding the biological functions of UXS gene family in cotton species and other plants.

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