Genome-wide transcription factor binding in leaves from C<sub>3</sub>and C<sub>4</sub>grasses

Burgess, Steven J.; Reyna-Llorens, Ivan; Stevenson, Sean Ross; Singh, Pallavi; Jaeger, Katja E.; Hibberd, Julian M.

doi:10.1101/165787

Cited by 19 publications

(28 citation statements)

References 88 publications

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“…Similarly, none of the 9 core C 4 genes showed a domestication signal at the gene level. The absence of large sequence variation at the gene level is also consistent with previous evolutionary studies suggesting that relatively minor changes to pre-existing regulatory networks and the use of pre-existing cis-elements were often sufficient to recruit genes into the C 4 pathway [43][44][45]. The C 4 isoform of the NADP-ME gene found in maize and sorghum is one such gene that has been found to be activated for C 4 photosynthesis via subtle changes to its promoter, while the rest of the gene is highly conserved [32].…”

Section: Discussionsupporting

confidence: 88%

Genetic diversity of C4 photosynthesis pathway genes in Sorghum bicolor (L.)

Tao

George‐Jaeggli

Bouteille-Pallas

et al. 2019

Preprint

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Background C4 photosynthesis has evolved in over 60 different plant taxa and is an excellent example of convergent evolution. Plants using the C4 photosynthetic pathway have an efficiency advantage, particularly in hot and dry environments. They account for 23% of global primary production and include some of our most productive cereals. While previous genetic studies comparing phylogenetically related C3 and C4 species have elucidated the genetic diversity underpinning the C4 photosynthetic pathway, no previous studies have described the genetic diversity of the genes involved in this pathway within a C4 crop species. Enhanced understanding of the allelic diversity and selection signatures of genes in this pathway may present opportunities to improve photosynthetic efficiency, and ultimately yield, by exploiting natural variation. Results Here, we present the first genetic diversity survey of 8 known C4 gene families in an important C4 crop, Sorghum bicolor (L.) Moench using sequence data of 48 genotypes covering wild and domesticated sorghum accessions. Average nucleotide diversity of C4 gene families varied more than 20-fold from the NADP-MDH gene family (θπ =0.2×10-3) to the PPDK gene family (θπ = 5.21×10-3). Genetic diversity of C4 genes was reduced by 22.43% in cultivated sorghum compared to wild and weedy sorghum, indicating that the group of wild and weedy sorghum may constitute an untapped reservoir for alleles related to the C4 photosynthetic pathway. A SNP-level analysis identified purifying selection signals on C4 PPDK and CA genes, and balancing selection signals on C4 PPDK-RP and PEPC genes. Allelic distribution of these C4 genes was consistent with selection signals detected.Conclusions Domestication of sorghum has reshaped diversity of C4 pathway. A better understanding of the genetic diversity of this pathway in sorghum paves the way for mining the natural allelic variation for the improvement of photosynthesis.

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Section: Discussionsupporting

confidence: 88%

Genetic diversity of C4 photosynthesis pathway genes in Sorghum bicolor (L.)

Tao

George‐Jaeggli

Bouteille-Pallas

et al. 2019

Preprint

View full text Add to dashboard Cite

show abstract

“…Similarly, none of the 9 core C 4 genes showed a domestication signal at the gene 10 level. The absence of large sequence variation at the gene level is also consistent with previous evolutionary studies suggesting that relatively minor changes to pre-existing regulatory networks and the use of pre-existing cis-elements were often sufficient to recruit genes into the C 4 pathway [43][44][45].…”

Section: Discussionsupporting

confidence: 86%

Genetic diversity of C4 photosynthesis pathway genes in Sorghum bicolor (L.)

Tao

George‐Jaeggli

Bouteille-Pallas

et al. 2019

Preprint

View full text Add to dashboard Cite

Background C 4 photosynthesis has evolved in over 60 different plant taxa and is an excellent example of convergent evolution. Plants using the C 4 photosynthetic pathway have an efficiency advantage, particularly in hot and dry environments. They account for 23% of global primary production and include some of our most productive cereals. While previous genetic studies comparing phylogenetically related C 3 and C 4 species have elucidated the genetic diversity underpinning the C 4 photosynthetic pathway, no previous studies have described the genetic diversity of the genes involved in this pathway within a C 4 crop species. Enhanced understanding of the allelic diversity and selection signatures of genes in this pathway may present opportunities to improve photosynthetic efficiency, and ultimately yield, by exploiting natural variation. Results Here, we present the first genetic diversity survey of 8 known C 4 gene families in an important C 4 crop, Sorghum bicolor (L.) Moench using sequence data of 48 genotypes covering wild and domesticated sorghum accessions. Average nucleotide diversity of C 4 gene families varied more than 20-fold from the NADP-MDH gene family (θπ =0.2×10 -3 ) to the PPDK gene family (θπ = 5.21×10 -3 ). Genetic diversity of C 4 genes was reduced by 22.43% in cultivated sorghum compared to wild and weedy sorghum, indicating that the group of wild and weedy sorghum may constitute an untapped reservoir for alleles related to the C 4 photosynthetic pathway. A SNP-level analysis identified purifying selection signals on C 4 PPDK and CA genes, and balancing selection signals on C 4 PPDK-RP and PEPC genes. Allelic distribution of these C 4 genes was consistent with selection signals detected. Conclusions Domestication of sorghum has reshaped diversity of C 4 pathway. A better understanding of the genetic diversity of this pathway in sorghum paves the way for mining the natural allelic variation for the improvement of photosynthesis.

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“…A complete understanding of the potential CREs within a particular species would require profiling of chromatin accessibility and/or chromatin interactions in a wide variety of tissues, cell types and conditions. Although chromatin accessibility, histone modifications and chromatin interactions often show substantial variation in different tissues (12,14,21) the majority of DNA methylation patterns are quite stable in plant species especially during vegetative development (22)(23)(24) and in the face of environmental stress (25)(26)(27)(28) . There are well-characterized examples of specific changes in DNA methylation in endosperm tissues (29,30) as well as in specific cell types in plant gametophytes (31)(32)(33)(34)(35) .…”

Section: Introductionmentioning

confidence: 99%

Stable unmethylated DNA demarcates expressed genes and their cis-regulatory space in plant genomes

Crisp

Marand

Noshay

et al. 2020

Preprint

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The genomic sequences of crops continue to be produced at a frenetic pace. However, it remains challenging to develop complete annotations of functional genes and regulatory elements in these genomes. Here, we explore the potential to use DNA methylation profiles to develop more complete annotations. Using leaf tissue in maize, we define ∼100,000 unmethylated regions (UMRs) that account for 5.8% of the genome; 33,375 UMRs are found greater than 2 kilobase pairs from genes. UMRs are highly stable in multiple vegetative tissues and they capture the vast majority of accessible chromatin regions from leaf tissue. However, many UMRs are not accessible in leaf (leaf-iUMRs) and these represent a set of genomic regions with potential to become accessible in specific cell types or developmental stages. Leaf-iUMRs often occur near genes that are expressed in other tissues and are enriched for transcription factor (TF) binding sites of TFs that are also not expressed in leaf tissue. The leaf-iUMRs exhibit unique chromatin modification patterns and are enriched for chromatin interactions with nearby genes. The total UMRs space in four additional monocots ranges from 80-120 megabases, which is remarkably similar considering the range in genome size of 271 megabases to 4.8 gigabases. In summary, based on the profile from a single tissue, DNA methylation signatures pinpoint both accessible regions and regions poised to become accessible or expressed in other tissues. UMRs provide powerful filters to distill large genomes down to the small fraction of putative functional genes and regulatory elements.Significance StatementCrop genomes can be very large with many repetitive elements and pseudogenes. Distilling a genome down to the relatively small fraction of regions that are functionally valuable for trait variation can be like looking for needles in a haystack. The unmethylated regions in a genome are highly stable during vegetative development and can reveal the locations of potentially expressed genes or cis-regulatory elements. This approach provides a framework towards complete annotation of genes and discovery of cis-regulatory elements using methylation profiles from only a single tissue.

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Genome-wide transcription factor binding in leaves from C₃and C₄grasses

Cited by 19 publications

References 88 publications

Genetic diversity of C4 photosynthesis pathway genes in Sorghum bicolor (L.)

Genetic diversity of C4 photosynthesis pathway genes in Sorghum bicolor (L.)

Genetic diversity of C4 photosynthesis pathway genes in Sorghum bicolor (L.)

Stable unmethylated DNA demarcates expressed genes and their cis-regulatory space in plant genomes

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Genome-wide transcription factor binding in leaves from C3and C4grasses

Cited by 19 publications

References 88 publications

Genetic diversity of C4 photosynthesis pathway genes in Sorghum bicolor (L.)

Genetic diversity of C4 photosynthesis pathway genes in Sorghum bicolor (L.)

Genetic diversity of C4 photosynthesis pathway genes in Sorghum bicolor (L.)

Stable unmethylated DNA demarcates expressed genes and their cis-regulatory space in plant genomes

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Genome-wide transcription factor binding in leaves from C₃and C₄grasses