Mapping Regulatory Determinants in Plants

Galli, Mary; Feng, Fan; Gallavotti, Andrea

doi:10.3389/fgene.2020.591194

Cited by 20 publications

(15 citation statements)

References 111 publications

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“…Our data leveraging interspecies gene transfer and chimeric transgene expression suggest that cis -encoded regulation of RA1 expression is a key factor in modulating meristem determinacy that ultimately impacts grass inflorescence architecture. With the ability to map hundreds of regulatory regions and transcription factor binding sites across diverse plant genomes (Lu et al, 2019; Galli et al, 2020), it will be important to understand the regulatory context of the conserved cis sequences that reside in RA1 promoters.…”

Section: Resultsmentioning

confidence: 99%

Interspecies transfer of syntenic RAMOSA1 orthologs and promoter cis sequences impacts maize inflorescence architecture

Strable

Unger-Wallace

Aragón-Raygoza

et al. 2022

Preprint

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Grass inflorescences support floral structures that each bear a single grain, where variation in branch architecture directly impacts yield. The maize RAMOSA1 (ZmRA1) transcription factor acts as a key regulator of inflorescence development by imposing branch meristem determinacy. Here, we show RA1 transcripts accumulate in boundary domains adjacent to spikelet meristems in Sorghum bicolor (Sb) and Setaria viridis (Sv) inflorescences similar as in the developing maize tassel and ear. To evaluate functional conservation of syntenic RA1 orthologs and promoter cis sequences in maize, sorghum and setaria, we utilized interspecies gene transfer and assayed genetic complementation in a common inbred background by quantifying recovery of normal branching in highly ramified ra1-R mutants. A ZmRA1 transgene that includes endogenous upstream and downstream flanking sequences recovered normal tassel and ear branching in ra1-R. Interspecies expression of two transgene variants of the SbRA1 locus, modeled as the entire endogenous tandem duplication or just the non-frameshifted downstream copy, complemented ra1-R branching defects and induced novel fasciation and branch patterns. The SvRA1 locus lacks conserved, upstream noncoding cis sequences found in maize and sorghum; interspecies expression of an SvRA1 transgene did not or only partially recovered normal inflorescence forms. Driving expression of the SvRA1 coding region by the ZmRA1 upstream region, however, recovered normal inflorescence morphology in ra1-R. These data leveraging interspecies gene transfer suggest that cis-encoded temporal regulation of RA1 expression is a key factor in modulating branch meristem determinacy that ultimately impacts grass inflorescence architecture.

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Section: Resultsmentioning

confidence: 99%

Interspecies transfer of syntenic RAMOSA1 orthologs and promoter cis sequences impacts maize inflorescence architecture

Strable

Unger-Wallace

Aragón-Raygoza

et al. 2022

Preprint

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“…Sequencing the genomes of each individual line in the panel would allow identification of structural variations, SNPs, and small insertions/deletions. A physical map of all CRM and DR gene locations within each line in the panel could then be created using known CRMs and DR gene databases (Kong et al ., 2018; Qi et al ., 2018; Tonnessen et al ., 2019; Galli et al ., 2020). If no databases are available for a particular crop, an available database for a closely related species can be used to search for homologous CREs and CRMs.…”

Section: The Futurementioning

confidence: 99%

“…One example shows a group of TF binding sites to be co‐localized within promoters of multiple genes involved in hormonal signaling, an important subset of DR gene functionality (Tu et al ., 2020). Different biotic stressors elicit different combinations of TF activity, leading to specialized DR gene expression caused by their shared TF binding site profile (Spitz & Furlong, 2012; Galli et al ., 2020). Co‐localization of different TF binding sites brings adaptability to a DR gene promoter, allowing flexibility in the activation, timing and amplitude of expression.…”

Section: Introductionmentioning

confidence: 99%

“…The concept of specific organizations of CREs led to the term cis ‐regulatory module (CRM) (Hardison & Taylor, 2012). The combination of DNA sequence motifs in a fixed region relative to a downstream gene are conserved patterns that show up across species in both plants and animals (Hardison & Taylor, 2012; Tonnessen et al ., 2019; Galli et al ., 2020). Recent studies uncovered CRMs associated with plant DR genes and resistant host phenotypes.…”

Section: Introductionmentioning

confidence: 99%

“…Genomic data mining of the genotypes responsible for diversity in DR gene regulation across crop varieties has led to identification of polymorphisms within intergenic regions, and more specifically, the regulatory regions of DR genes. These regulatory regions include: (1) the proximal promoter (1-2 Kb from transcription start site); (2) untranslated regions (UTR) of a gene; and (3) the distal accessible chromatin regions up to 100 Kb from a protein-coding gene (Galli et al, 2020) (Fig. 1a).…”

Section: Introductionmentioning

confidence: 99%

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Intergenic spaces: a new frontier to improving plant health

et al. 2021

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To more sustainably mitigate the impact of crop diseases on plant health and productivity, there is a need for broader spectrum, long-lasting resistance traits. Defense Response (DR) genes, located throughout the genome, participate in cellular and system-wide defense mechanisms to stave off infection by diverse pathogens. This multigenic resistance avoids rapid evolution of a pathogen to overcome host resistance. DR genes reside within resistance-associated Quantitative Trait Loci (QTL), and alleles of DR genes in resistant varieties are more active during pathogen attack relative to susceptible haplotypes. Differential expression of DR genes results from polymorphisms in their regulatory regions, which include cis-regulatory elements such as transcription factor binding sites as well as features that influence epigenetic structural changes to modulate chromatin accessibility during infection. Many of these elements are found in clusters, known as cis-Regulatory Modules (CRMs), which are distributed throughout the host genome. Regulatory regions involved in plantpathogen interactions may also contain pathogen effector binding elements that regulate DR gene expression, and that, when mutated, result in a change in the plants' response. We posit that CRMs Accepted ArticleThis article is protected by copyright. All rights reserved and the multiple regulatory elements that comprise them are potential targets for marker-assisted breeding for broad-spectrum, durable disease resistance.

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Differential gene expression during floral transition in pineapple

Paull,

Ksouri,

Kantar

et al. 2023

Plant Direct

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Pineapple (Ananas comosus var. comosus) and ornamental bromeliads are commercially induced to flower by treatment with ethylene or its analogs. The apex is transformed from a vegetative to a floral meristem and shows morphological changes in 8 to 10 days, with flowers developing 8 to 10 weeks later. During eight sampling stages ranging from 6 h to 8 days after treatment, 7961 genes were found to exhibit differential expression (DE) after the application of ethylene. In the first 3 days after treatment, there was little change in ethylene synthesis or in the early stages of the ethylene response. Subsequently, three ethylene response transcription factors (ERTF) were up‐regulated and the potential gene targets were predicted to be the positive flowering regulator CONSTANS‐like 3 (CO), a WUSCHEL gene, two APETALA1/FRUITFULL (AP1/FUL) genes, an epidermal patterning gene, and a jasmonic acid synthesis gene. We confirm that pineapple has lost the flowering repressor FLOWERING LOCUS C. At the initial stages, the SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1 (SOC1) was not significantly involved in this transition. Another WUSCHEL gene and a PHD homeobox transcription factor, though not apparent direct targets of ERTF, were up‐regulated within a day of treatment, their predicted targets being the up‐regulated CO, auxin response factors, SQUAMOSA, and histone H3 genes with suppression of abscisic acid response genes. The FLOWERING LOCUS T (FT), TERMINAL FLOWER (TFL), AGAMOUS‐like APETELAR (AP2), and SEPETALA (SEP) increased rapidly within 2 to 3 days after ethylene treatment. Two FT genes were up‐regulated at the apex and not at the leaf bases after treatment, suggesting that transport did not occur. These results indicated that the ethylene response in pineapple and possibly most bromeliads act directly to promote the vegetative to flower transition via APETALA1/FRUITFULL (AP1/FUL) and its interaction with SPL, FT, TFL, SEP, and AP2. A model based on AP2/ERTF DE and predicted DE target genes was developed to give focus to future research. The identified candidate genes are potential targets for genetic manipulation to determine their molecular role in flower transition.

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Mapping Regulatory Determinants in Plants

Cited by 20 publications

References 111 publications

Interspecies transfer of syntenic RAMOSA1 orthologs and promoter cis sequences impacts maize inflorescence architecture

Interspecies transfer of syntenic RAMOSA1 orthologs and promoter cis sequences impacts maize inflorescence architecture

Intergenic spaces: a new frontier to improving plant health

Differential gene expression during floral transition in pineapple

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