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Structural variation at the maize WUSCHEL1 locus alters stem cell organization in inflorescences.

ABSTRACT: Structural variation in plant genomes is a significant driver of phenotypic variability in traits important for the domestication and productivity of crop species. Among these are traits that depend on functional meristems, populations of stem cells maintained by the CLAVATA-WUSCHEL (CLV-WUS) negative feedback-loop that controls the expression of the WUS homeobox transcription factor. WUS function and impact on maize development and yield remain largely unexplored. Here we show that the maize dominant Barren inflorescence3 (Bif3) mutant harbors a tandem duplicated copy of the ZmWUS1 gene, ZmWUS1-B, whose novel promoter enhances transcription in a ring-like pattern. Overexpression of ZmWUS1-B is due to multimerized binding sites for type-B RESPONSE REGULATORs (RRs), key transcription factors in cytokinin signaling. Hypersensitivity to cytokinin causes stem cell overproliferation and major rearrangements of Bif3 inflorescence meristems, leading to the formation of ball-shaped ears and severely affecting productivity. These findings establish ZmWUS1 as an essential meristem size regulator in maize and highlight the striking effect of cis-regulatory variation on a key developmental program.

SUBMITTER: Chen Z

PROVIDER: S-EPMC8062686 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Structural Variation at the Maize wuschel1 Locus Alters Stem Cell Organization in Inflorescences

Project description:Purpose: The goal of this study is to identify differentially expressed genes (DEGs) in immature ears between Barren inflorescence3 (Bif3) mutant and its wild-type siblings in maize. Methods: the 3-4 mm ear primordia of maize wild-type and Bif3 mutant were dissected from maize plant at the reproductive stage, and samples were snap freeze using liquid nitrogen. The total RNAs were prepared using RNeasy mini kit (Qiagen). All those RNA samples of wild-type and Bif3 mutant were submitted for RNA-Seq. Conclusions: Our RNA-seq experiments identified 1380 up- and 242 down-regulated genes (P < 0.05, FDR < 0.1, fold-change > 1.5).

2021-03-17 | GSE158330 | GEO

Structural Variation at the Maize wuschel1 Locus Alters Stem Cell Organization in Inflorescences

Project description:Structural Variation at the Maize wuschel1 Locus Alters Stem Cell Organization in Inflorescences

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Structural organization of photosynthetic apparatus in agranal chloroplasts of maize.

Project description:We investigated the organization of photosystem II (PSII) in agranal bundle sheath thylakoids from a C(4) plant maize. Using blue native/SDS-PAGE and single particle analysis, we show for the first time that PSII in the bundle sheath (BS) chloroplasts exists in a dimeric form and forms light-harvesting complex II (LHCII).PSII supercomplexes. We also demonstrate that a similar set of photosynthetic membrane complexes exists in mesophyll and agranal BS chloroplasts, including intact LHCI.PSI supercomplexes, PSI monomers, PSII core dimers, PSII monomers devoid of CP43, LHCII trimers, LHCII monomers, ATP synthase, and cytochrome b(6)f complex. Fluorescence functional measurements clearly indicate that BS chloroplasts contain PSII complexes that are capable of performing charge separation and are efficiently sensitized by the associated LHCII. We identified a fraction of LHCII present within BS thylakoids that is weakly energetically coupled to the PSII reaction center; however, the majority of BS LHCII is shown to be tightly connected to PSII. Overall, we demonstrate that organization of the photosynthetic apparatus in BS agranal chloroplasts of a model C(4) plant is clearly distinct from that of the stroma lamellae of the C(3) plants. In particular, supramolecular organization of the dimeric LHCII.PSII in the BS thylakoids strongly suggests that PSII in the BS agranal membranes may donate electrons to PSI. We propose that the residual PSII activity may supply electrons to poise cyclic electron flow around PSI and prevent PSI overoxidation, which is essential for the CO(2) fixation in BS cells, and hence, may optimize ATP production within this compartment.

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The vsp locus of Mycoplasma bovis: gene organization and structural features.

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Structural Variation Evolution at the 15q11-q13 Disease-Associated Locus.

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Dynamic interplay between structural variation and 3D chromosome organization in pancreatic cancer

Project description:We investigate the spectrum of SVs and three-dimensional (3D) chromatin architecture in human pancreatic ductal epithelial cell carcinogenesis by using the state of art long-read single molecular real time (SMRT) and high-throughput chromosome conformation capture (Hi-C) sequencing techniques. Systematic integration of matched SMRT, in situ Hi-C, and RNA-seq datasets revealed the complicated dynamic interplay of SVs and 3D chromosome organization and their impacts on gene expression. Our studies identify and focus remodeling of chromatin folding domains associated with cross boundary SVs enabling aberrant interactions between regulatory elements. Moreover, our data also demonstrate the existence of complex genomic rearrangements associated with two key driver genes CDKN2A and SMAD4, and characterize their influence on cancer related gene expression from linear view to 3D perspective.

2022-05-01 | GSE185069 | GEO

Remarkable variation in maize genome structure inferred from haplotype diversity at the bz locus.

Project description:Maize is probably the most diverse of all crop species. Unexpectedly large differences among haplotypes were first revealed in a comparison of the bz genomic regions of two different inbred lines, McC and B73. Retrotransposon clusters, which comprise most of the repetitive DNA in maize, varied markedly in makeup, and location relative to the genes in the region and genic sequences, later shown to be carried by two helitron transposons, also differed between the inbreds. Thus, the allelic bz regions of these Corn Belt inbreds shared only a minority of the total sequence. To investigate further the variation caused by retrotransposons, helitrons, and other insertions, we have analyzed the organization of the bz genomic region in five additional cultivars selected because of their geographic and genetic diversity: the inbreds A188, CML258, and I137TN, and the land races Coroico and NalTel. This vertical comparison has revealed the existence of several new helitrons, new retrotransposons, members of every superfamily of DNA transposons, numerous miniature elements, and novel insertions flanked at either end by TA repeats, which we call TAFTs (TA-flanked transposons). The extent of variation in the region is remarkable. In pairwise comparisons of eight bz haplotypes, the percentage of shared sequences ranges from 25% to 84%. Chimeric haplotypes were identified that combine retrotransposon clusters found in different haplotypes. We propose that recombination in the common gene space greatly amplifies the variability produced by the retrotransposition explosion in the maize ancestry, creating the heterogeneity in genome organization found in modern maize.

| S-EPMC1693800 | biostudies-literature

Comprehensive 3D phenotyping reveals continuous morphological variation across genetically diverse sorghum inflorescences.

Project description:?Inflorescence architecture in plants is often complex and challenging to quantify, particularly for inflorescences of cereal grasses. Methods for capturing inflorescence architecture and for analyzing the resulting data are limited to a few easily captured parameters that may miss the rich underlying diversity. ?Here, we apply X-ray computed tomography combined with detailed morphometrics, offering new imaging and computational tools to analyze three-dimensional inflorescence architecture. To show the power of this approach, we focus on the panicles of Sorghum bicolor, which vary extensively in numbers, lengths, and angles of primary branches, as well as the three-dimensional shape, size, and distribution of the seed. ?We imaged and comprehensively evaluated the panicle morphology of 55 sorghum accessions that represent the five botanical races in the most common classification system of the species, defined by genetic data. We used our data to determine the reliability of the morphological characters for assigning specimens to race and found that seed features were particularly informative. ?However, the extensive overlap between botanical races in multivariate trait space indicates that the phenotypic range of each group extends well beyond its overall genetic background, indicating unexpectedly weak correlation between morphology, genetic identity, and domestication history.

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Gender variation of sequential inflorescences in a monoecious plant Sagittaria trifolia (Alismataceae).

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Structural variation at the ZNF558 locus controls a gene regulatory network in human brain development

Project description:The human forebrain has expanded in size and complexitycompared to that of chimpanzeedespite limited changesinprotein-coding genes, suggesting that gene regulation is an importantdriver of brain evolution. Here we identify a KRAB-ZFPtranscription factor, ZNF558, that isexpressed in human but not chimpanzee forebrain neural progenitor cells. ZNF558 evolved asa suppressor of LINE-1 transposons but has been co-opted to regulate the mitophagy geneSPATA18, supporting a link between mitochondrial homeostasis andcorticalexpansion. Theunusual on-off switchforZNF558expression resides in a downstream variable number tandemrepeat (VNTR) that is contracted in humans relative to chimpanzee.Our data reveal the brain-specific co-option of a transposon-controllingKRAB-ZFPand how a human-specificregulatory network is established by acis-acting structural genome variation. Thisrepresentsapreviouslyundescribedgenetic mechanisminthe evolution of the human brain.

2021-09-19 | GSE182224 | GEO

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