The genetic and epigenetic landscape of the Arabidopsis centromeres

Science, Год журнала: 2021, Номер 374(6569)

Опубликована: Ноя. 11, 2021

A closer look at centromeres Centromeres are key for anchoring chromosomes to the mitotic spindle, but they have been difficult sequence because can contain many repeating DNA elements. These repeats, however, carry regularly spaced, distinctive markers of heterogeneity between mostly, not completely, identical repeats. Such differences aid assembly. Naish et al . used ultra-long-read sequencing establish a reference assembly that resolves all five in small mustard plant Arabidopsis Their view into subtly homogenized world reveals retrotransposons interrupt centromere organization and repressive methylation excludes from meiotic crossover repair. Thus, evolve under opposing forces homogenization retrotransposon disruption. —PJH

Язык: Английский

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Addressing Research Bottlenecks to Crop Productivity

Trends in Plant Science, Год журнала: 2021, Номер 26(6), С. 607 - 630

Опубликована: Апрель 21, 2021

More symmetrical investment in crop research will create opportunities to improve models, combine new alleles through prebreeding, and suggest novel management practices.Consensus among public private sectors is that more needed understanding of hormone crosstalk, recombination rate, maintenance respiration, root structure function, source–sink balance.Greater these areas expected benefit a wide range crops across most environments.New phenomics, genomics, bioinformatics make it feasible explore the vast untapped collections genetic resources trait combinations.Filling knowledge gaps enable much integrated yield adaptation, improving breeding models. Asymmetry leads lost accelerate gain identifying sources combinations traits alleles. On basis consultation with scientists from major seed companies, we identified several three common features: (i) relatively underrepresented literature; (ii) high probability boosting productivity environments; (iii) could be researched 'precompetitive' space, leveraging previous knowledge, thereby models guide decisions. Areas included into hormones, recombination, roots, source–sink, which, along bioinformatics, strategies. Research growth adaptation under diverse cultivation scenarios has underpinned global food security, especially since Green Revolution, during which time population than doubled. During same time, area cultivated cereals, account for 70% total calories consumed by humans, barely changed while yields have tripled.i These two statistics alone clearly support impact on agronomy as well effective policy decisions agility farmers adopt technologies [1.Stewart B.A. Lal R. Increasing world average cereal crops: it's all about water.in: Sparks D.L. Advances Agronomy. Vol. 151. Elsevier, 2018: 1-44Google Scholar,2.Fischer T. et al.Crop Yields Global Food Security: Will Yield Increase Continue Feed World?. Australian Centre International Agricultural Research, 2014Google Scholar]. Nonetheless, challenges agriculture now faces are not just feed 10+ billion people within generation, but do so harsher less predictable climate, many cases water declining soil quality Clearly, research, breeding, must even effective. Crop integrates crossing strategies combined efficient selection progeny [3.Van Ginkel M. Ortiz Cross best best, select best: HELP selfing crops.Crop Sci. 2018; 58: 17-30Crossref Scopus (11) Google To date, impactful objectives been maintain resistance ever-evolving spectrum pests diseases (e.g., [4.Singh R.P. al.Emergence spread races wheat stem rust fungus: continued threat security prospects control.Phytopathology. 2015; 105: 872-884Crossref PubMed (173) Scholar,5.Donatelli al.Modelling impacts agricultural systems.Agric. Syst. 2017; 155: 213-224Crossref (91) Scholar]), an array consumer-driven characteristics, such storability, baking quality, forth [6.Guzmán C. al.Genetic improvement grain CIMMYT semi-dwarf spring bread varieties developed 1965–2015: 50 years breeding.Field Crops Res. 210: 192-196Crossref (24) Scholar]). However, or environments require specific filled context. The technology exists apply allelic phenotype genotype at scale. Due large numbers involved screening (from thousands single cross millions double haploids), evaluation represent target (TPE) (see Glossary) expedient, genomic [7.Juliana P. al.Integrating genomic-enabled prediction high-throughput phenotyping climate-resilient wheat.Theor. Appl. Genet. 2019; 132: 177-194Crossref (23) Scholar], phenomic [8.Araus J.L. al.Translating gain.Trends Plant 23: 451-466Abstract Full Text PDF (170) modeling tools [9.Cooper al.Predicting future plant breeding: complementing empirical prediction.Crop Pasture 2014; 65: 311-336Crossref (148) advanced stage commercial In short, practical discipline focused products. upstream tends favor cutting-edge challenges, some methodological nature. focusing near- medium-term gains typically strategic enough warrant funding, too risk funds allocated breeding. As result, translation pure science [10.Reynolds al.Translational climate resilient, higher yielding Breed. Genom. 1e190016Google Some notable exceptions include photosynthesis [11.Long S.P. al.Meeting demand engineering potential.Cell. 161: 56-66Abstract (381) application tomography capture roots images [12.Morris E.C. al.Shaping 3D system architecture.Curr. Biol. 27: PR919-R930Abstract (54) gene editing [13.Gao H. al.Superior field performance waxy corn engineered using CRISPR-Cas9.Nat. Biotechnol. 2020; 38: 579-581Crossref (0) novelty significant driving force academia, including technologies. does grow symmetrically, creating instead islands necessarily connected [14.Borrell A. Reynolds Integrating greater synergy efficiency research.Food Energy Secur. 6: 26-32Crossref (3) While this approach works pushing back frontiers requires systematic achieve harvestable products seeds, fruits, tubers). For example, order crop's photosynthetic potential boost yield, extra photo-assimilates also distributed way optimizes development edible organs. case cereals other crops, expressed harvest index (HI). expression HI in, modern cultivars, approximately 0.4 0.55, attendant negative correlation between biomass [15.Aisawi K.A.B. al.The physiological progress cultivars 1966 2009.Crop 55: 1749-1764Crossref (86) attest apparent underutilization current capacity. partitioning reproductive match if value effectively translate security. There conundrums point asymmetrical knowledge. definition considers only above-ground biomass. This quite arbitrary, there being no scientific reason exclude below-ground one, analysis can easily performed structures compared those soil. Since important improvement, source error trivial. study wheat, differed 7% 20%, depending genotype, when considering versus biomass, [16.Reynolds M.P. al.Drought-adaptive derived wild relatives landraces.J. Exp. Bot. 2007; 177-186Crossref Another example asymmetry crop-focused academic emphasis over despite variation respiration associated [17.Wilson D. Response dark rate mature leaves Lolium perenne its effects young plants simulated swards.Ann. 1982; 49: 303-312Crossref (66) Furthermore, number studies show express significantly stronger relationship night temperature day [18.Lobell D.B. Ortiz-Monasterio J.I. Impacts temperatures yields: comparison CERES model predictions locations.Agron. J. 99: 469-477Crossref (123) Scholar,19.Shi W. al.High day- night-time affect dynamics contrasting rice genotypes.J. 68: 5233-5245Crossref (38) Because affects processes, flowering response, response key gap. needs renewed focus how manipulation photorespiration influence yields, degree effort great respiration. Indeed, recent work highlighted transgenic use alternative photorespiratory pathways exhibit improvements net CO2 uptake, accumulation, [20.South P.F. al.Synthetic glycolate metabolism stimulate field.Science. 636eaat9077Crossref (165) Scholar,21.Shen B.-R. al.Engineering chloroplastic bypass increase rice.Mol. Plant. 12: 199-214Abstract (40) importance environment influencing arising modifications addressed [22.Hammer G.L. al.Biological reality parsimony – why need both improvement! silico.Plants. 1diz010Google Asymmetrical crop-related additional conundrums. A literature search keywords 'photosynthesis' 'drought' identifies studies. deficit certainly inhibits gas exchange severe stress damage machinery, primary determinants access [23.White J.W. Castillo J.A. Relative effect shoot genotypes bean drought stress.Crop 1989; 29: 360-362Crossref (50) Scholar] budgeting [24.Messina C.D. al.Limited-transpiration may maize tolerance US Corn Belt.Agronomy. 107: 1978-1986Crossref (79) Subtle cultivar-level differences sensitivity apparatus marginal best; mundane analogy would tuning carburetor motor overcome block fuel line. exist, objective review illustrate crop-oriented better leveraged filling gaps. exist varying degrees, our premise addressing species environments. Therefore, processes they improved tandem. factor influences agenda difficulty working realistic environments, partially controlled. Lack control hampers rigorous production scenarios, where fields growing seasons ever completely same. Galileo's guideline 'measure what measurable, measurable so' applied advances remote sensing geographical information services. addition, generation molecular permit real-time estimates DNA metabolic monitored tissue taken directly experiments. (CGMs) provide mathematical framework integrate conduct quantitative evaluations TPE Scholar,24.Messina Scholar,25.Messina science: foundation advancing predictive agriculture.Crop 60: 544-546Crossref (6) providing dynamic help researching basic biology. unprecedented fill join investments. No matter component problem, whether cropping whole, broad maximize impact. An illuminating was showing zinc deficiency exacerbates due essential role detoxifying reactive oxygen species, leading foliar applications Zn 4 million ha Turkey [26.Bagci S.A. al.Effects field-grown Central Anatolia.J. Agron. 193: 198-206Crossref Before breakthrough, per se seriously confounded achieved (Figure 1) [27.Cakmak I. al.Zinc critical problem Anatolia.Plant Soil. 1996; 180: 165-172Crossref Perhaps overcoming bottleneck opens up possibilities introduction semidwarf genes cereals. their widespread adoption, tallness limited structural failure. allele (Rht1) Norin 10, originally variety Daruma, Gonjiro Inazuka Japan 1935. took 10 introgression, pleiotropic Rht nitrogen [28.Reynolds Borlaug N.E. international collaborative improvement.J. Agric. 2006; 144: 3-17Crossref (109) spearheaded Revolution tripling saving estimated 1 lives famine aforementioned examples systematic, demand-driven shy away logistical challenges. Five challenging that, tackled systematically, likely open bottlenecks discussed herein, discussion used CGMs. exhaustive cannot presented here, nor bottlenecks, emerge improves. were broadly agreed authors colleagues sectors. complementary each existing 2). opinion colleagues, 'best bets' achieving step changes roles increasing sink strength carbon assimilation meiotic harness diversity. reviewed: exploration prebreeding Illuminating 'black boxes' simulation modelling. authorship represents stakeholders sectors, topics priorities 'precompetitive space' defined companies exercise; words, general neglected, potentially hold industry. aid foraging, responsive abiotic biotic signals local highly adaptable behavior, termed 'developmental plasticity', offers breeders 'customized' architecture (RSA) adapted forage heterogenous conditions [29.Hodge plastic plant: responses heterogeneous supplies nutrients.New Phytol. 2004; 162: 9-24Crossref (1052) (N) form nitrate (NO3–) particular challenge capture, mobile leaches deeper layers. N exploit steeper angle brace crown [30.Trachsel S. al.Maize angles become low conditions.Field 2013; 140: 18-31Crossref (56) elongation lateral seminal [31.Gioia al.Impact domestication phenotypic durum fertilization.J. 66: 5519-5530Crossref reduced length density near surface axial [32.Zhan Lynch J.P. Reduced frequency branching improves low-N soils maize.J. 2055-2065Crossref (81) serve layers abundant. contrast, phosphate (P) available inorganic immobile concentrated topsoil [33.Rubio G. al.Topsoil foraging competitiveness phosphorus bean.Crop 2003; 43: 598-607Crossref P increased lengths patches availability [34.Flavel R.J. al.Quantifying (Triticum aestivum L) Oxisol.Plant 385: 303-310Crossref (7) shallower hairs [35.Bates T.R. Root confer competitive advantage availability.Plant 2001; 236: 243-250Crossref (125) cluster formation [36.Shane M.W. Lambers Cluster roots: curiosity context.Plant 2005; 274: 101-125Crossref (255) sorghum, [37.Singh V. variability sorghum.Crop 2011; 51: 2011-2020Crossref (36) enables × Skip row systems expressing angles, past decade, remain, following:•Given change, urgent determine RSA controlled signals, often mediated aerial temperature. Whilst heat impairs any developmental stage, rooting depth appear reduce [38.Lopes M.S. Partitioning assimilates cooler canopies wheat.Funct. 2010; 37: 147Crossref Scholar].•How carbon/biomass should invest resource sustainability, yet minimize yield? Surprisingly, detailed CGM simulations (validated reference data) predict 'less more,' lower longer [39.Postma optimal depends Physiol. 166: 590-602Crossref (160) addition RSA, anatomical scale cortical aerenchyma 50% [40.Zhu al.Root (Zea mays L.).Plant Cell Environ. 33: 740-749PubMed enabling reinvest C organs.•Despite recognition microbiome vice versa [41.de la Fuente C.C. al.An extended phenotype: rhizosphere, fitness.Plant 103: 951-964Crossref (9) multibillion-dollar industry selling microbiome-based coatings mechanisms integrating signaling. Studying arguably relevant, poses Indirect approaches canopy measurements determining extraction profiles electrical electromagnetic inductance methods infer traits, currently coarse resolution [42.Whalley W.R. al.Methods estimate activity field.Plant 415: 407-422Crossref (22) Invasive coring 'shovelomics' greatly facilitated throughput [43.Trachsel al.Shovelomics: L.) 341: 75-87Crossref (338) destructive techniques result loss finer-scale features roots), give snapshot development. Nondestructive imaging techniques, agar plates, rhizotrons, paper-based hydro-/aeroponic systems, temporal observed throughout possible transparent gels [44.Clark R.T. al.Three-dimensional software platform.Plant 156: 455-465Crossref (274) non–soil-based helps decrease experimental reducing heterogeneity microbial populations, results difficult extrapolate conditions. experiments [45.Messina al.Reproductive resilience underpin L.).bioRxiv. (Published online October 1, 2020. https://doi.org/10.1101/2020.09.30.320937)Google Magnetic resonance X-ray computed successfully noninvasively [46.Mairhofer al.Extracting multiple interacting microcomputed tomography.Plant 84: 1034-1043Crossref (19) Scholar,47.van Dusschoten al.Quantitative magnetic imaging.Plant 2016; 170: 1176-1188Crossref Nevertheless, expensive, throughput, deployable field. Understanding stresses vital develop [48.Lynch phenotypes nutrient capture: underexploited opportunity agriculture.New 223: 548-564Crossref (72) dries, vertical gradient availability. Roots experiencing reach [49.Uga Y. al.Control DEEPER ROOTING increases conditions.Nat. 45: 1097-1102Crossref (619) Water upper suppresses different [50.Sebastian al.Grasses suppress shoot-borne conserve drought.Proc. Natl. Acad. U. 113: 8861-8866Crossref (43) Scholar,51.Gao Y.Z. acquisition L.).J. 67: 4545-4557Crossref (84) few long ideotype suggested stress, saved extend profiles. indeed tuned based fundamental [52.Cooper gap productivity.Crop 582-604Crossref (10) colonizing

Язык: Английский

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Structural variation and DNA methylation shape the centromere-proximal meiotic crossover landscape in Arabidopsis

Genome biology, Год журнала: 2024, Номер 25(1)

Опубликована: Янв. 22, 2024

Centromeres load kinetochore complexes onto chromosomes, which mediate spindle attachment and allow segregation during cell division. Although centromeres perform a conserved cellular function, their underlying DNA sequences are highly divergent within between species. Despite variability in sequence, also universally suppressed for meiotic crossover recombination, across eukaryotes. However, the genetic epigenetic factors responsible suppression of centromeric crossovers remain to be completely defined.

Язык: Английский

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Meiotic recombination dynamics in plants with repeat-based holocentromeres shed light on the primary drivers of crossover patterning

Nature Plants, Год журнала: 2024, Номер 10(3), С. 423 - 438

Опубликована: Фев. 9, 2024

Abstract Centromeres strongly affect (epi)genomic architecture and meiotic recombination dynamics, influencing the overall distribution frequency of crossovers. Here we show how is regulated distributed in holocentric plant Rhynchospora breviuscula , a species with diffused centromeres. Combining immunocytochemistry, chromatin analysis high-throughput single-pollen sequencing, discovered that crossover distally biased, sharp contrast to hundreds centromeric units features. Remarkably, found crossovers were abolished inside but not their proximity, indicating absence canonical centromere effect. We further propose telomere-led synapsis homologues feature best explains observed landscape. Our results hint at primary influence mechanistic features pairing rather than organization determining biased R. whereas centromeres (epi)genetic properties only positioning locally.

Язык: Английский

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Epigenetic activation of meiotic recombination near Arabidopsis thaliana centromeres via loss of H3K9me2 and non-CG DNA methylation

Genome Research, Год журнала: 2018, Номер 28(4), С. 519 - 531

Опубликована: Март 12, 2018

Eukaryotic centromeres contain the kinetochore, which connects chromosomes to spindle allowing segregation. During meiosis, are suppressed for inter-homolog crossover, as recombination in these regions can cause chromosome missegregation and aneuploidy. Plant surrounded by transposon-dense pericentromeric heterochromatin that is epigenetically silenced histone 3 lysine 9 dimethylation (H3K9me2), DNA methylation CG non-CG sequence contexts. However, role of chromatin modifications control meiotic pericentromeres not fully understood. Here, we show disruption Arabidopsis thaliana H3K9me2 pathways, example, via mutation H3K9 methyltransferase genes KYP/SUVH4 SUVH5 SUVH6, or CHG gene CMT3, increases proximity centromeres. Using immunocytological detection MLH1 foci genotyping sequencing recombinant plants, observe pathway mutants increased crossovers. Increased H3K9me2/non-CG occurs hybrid inbred backgrounds likely involves contributions from both interfering noninterfering crossover repair pathways. We also double-strand breaks (DSBs) increase within pericentromeres, purification SPO11-1-oligonucleotides. Therefore, exert a repressive effect on DSB formation plant heterochromatin. Our results may account selection enhancer trap Dissociation (Ds) transposons into CMT3 with proximal transposon launch-pads.

Язык: Английский

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DNA Methylation and Histone H1 Jointly Repress Transposable Elements and Aberrant Intragenic Transcripts

Molecular Cell, Год журнала: 2019, Номер 77(2), С. 310 - 323.e7

Опубликована: Ноя. 12, 2019

Язык: Английский

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An Ultra High-Density Arabidopsis thaliana Crossover Map That Refines the Influences of Structural Variation and Epigenetic Features

Genetics, Год журнала: 2019, Номер 213(3), С. 771 - 787

Опубликована: Сен. 16, 2019

Abstract Rowan et al. generated a dataset of over 17,000 meiotic crossovers (COs) from 2000 F2 individuals single Arabidopsis thaliana cross. The unprecedented density COs and the high-quality reference genomes two... Many environmental, genetic, epigenetic factors are known to affect frequency positioning (COs). Suppression by large, cytologically visible inversions translocations has long been recognized, but relatively little is about how smaller structural variants (SVs) COs. To examine fine-scale determinants CO landscape, including SVs, we used rapid, cost-effective method for high-throughput sequencing generate precise map >17,000 between Col-0 Ler-0 accessions thaliana. were generally suppressed in regions with this effect did not depend on size variant region, was only marginally affected type. suppression extend far beyond SV borders rates slightly elevated flanking regions. Disease resistance gene clusters, which often exist as exhibited high at some loci, there tendency toward depressed loci where large differences two parents. Our high-density also revealed fine detail relates genetic (DNA motifs) (chromatin structure) features genome. We conclude that occurs narrow region spanning large- small-scale representing an influence landscape addition sequence variation along chromosomes.

Язык: Английский

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Double-edged sword: The evolutionary consequences of the epigenetic silencing of transposable elements

PLoS Genetics, Год журнала: 2020, Номер 16(7), С. e1008872 - e1008872

Опубликована: Июль 16, 2020

Transposable elements (TEs) are genomic parasites that selfishly replicate at the expense of host fitness. Fifty years evolutionary studies TEs have concentrated on deleterious genetic effects TEs, such as their disrupting genes and regulatory sequences. However, a flurry recent work suggests there is another important source TEs’ harmful effects—epigenetic silencing. Host genomes typically silence by deposition repressive epigenetic marks. While this silencing reduces selfish replication should benefit hosts, picture emerging triggers inadvertent spreading marks to otherwise expressed neighboring genes, ultimately jeopardizing In Review, we provide long-overdue overview genome-wide evidence for presence prevalence effects, highlighting both similarities differences across mammals, insects, plants. We lay out current understanding functional fitness consequences propose possible influences evolution hosts themselves. These unique indicate effect not only crucial component TE biology but could also be significant contributor genome function evolution.

Язык: Английский

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LEAFY is a pioneer transcription factor and licenses cell reprogramming to floral fate

Nature Communications, Год журнала: 2021, Номер 12(1)

Опубликована: Янв. 27, 2021

Abstract Master transcription factors reprogram cell fate in multicellular eukaryotes. Pioneer have prominent roles this process because of their ability to contact cognate binding motifs closed chromatin. Reprogramming is pervasive plants, whose development plastic and tuned by the environment, yet little known about pioneer kingdom. Here, we show that master factor LEAFY (LFY), which promotes floral through upregulation commitment APETALA1 ( AP1 ), a factor. In vitro, LFY binds endogenous target locus DNA assembled into nucleosome. vivo, associates with nucleosome occupied sites at majority its loci, including . Upon binding, ‘unlocks’ chromatin locally displacing H1 linker histone recruiting SWI/SNF remodelers, but broad changes accessibility occur later. Our study provides mechanistic framework for patterning inflorescence architecture uncovers striking similarities between animal

Язык: Английский

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Epigenetics for Crop Improvement in Times of Global Change

Biology, Год журнала: 2021, Номер 10(8), С. 766 - 766

Опубликована: Авг. 11, 2021

Epigenetics has emerged as an important research field for crop improvement under the on-going climatic changes. Heritable epigenetic changes can arise independently of DNA sequence alterations and have been associated with altered gene expression transmitted phenotypic variation. By modulating plant development physiological responses to environmental conditions, diversity—naturally, genetically, chemically, or environmentally induced—can help optimise traits in era challenged by global climate change. Beyond variation, modifications may contribute breeding providing useful markers allowing use epigenome diversity predict performance increase final production. Given difficulties transferring knowledge mechanisms from model plants crops, various strategies emerged. Among those are modelling frameworks dedicated predicting epigenetically controlled-adaptive traits, epigenetics vitro regeneration accelerate breeding, specific marks that modulate interest. The key challenge agriculture faces 21st century is production speeding up resilient species. Therefore, provides fundamental molecular information potential direct applications enhancement, tolerance, adaptation within context

Язык: Английский

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