43565
2019
2019
eng
14
745
postprint
1
2019-10-02
2019-10-02
--
A high‑throughput amplicon‑based method for estimating outcrossing rates
Background: The outcrossing rate is a key determinant of the population-genetic structure of species and their long-term evolutionary trajectories. However, determining the outcrossing rate using current methods based on PCRgenotyping individual offspring of focal plants for multiple polymorphic markers is laborious and time-consuming.
Results: We have developed an amplicon-based, high-throughput enabled method for estimating the outcrossing rate and have applied this to an example of scented versus non-scented Capsella (Shepherd’s Purse) genotypes. Our results show that the method is able to robustly capture differences in outcrossing rates. They also highlight potential biases in the estimates resulting from differential haplotype sharing of the focal plants with the pollen-donor population at individual amplicons.
Conclusions: This novel method for estimating outcrossing rates will allow determining this key population-genetic parameter with high-throughput across many genotypes in a population, enabling studies into the genetic determinants of successful pollinator attraction and outcrossing.
Postprints der Universität Potsdam Mathematisch-Naturwissenschaftliche Reihe
10.25932/publishup-43565
urn:nbn:de:kobv:517-opus4-435657
1866-8372
Plant Methods 15 (2019) 47 DOI: 10.1186/s13007-019-0433-9
<a href="http://publishup.uni-potsdam.de/opus4-ubp/frontdoor/index/index/docId/43564">Bibliographieeintrag der Originalveröffentlichung/Quelle</a>
false
true
CC-BY - Namensnennung 4.0 International
Friederike Jantzen
Natalia Joanna Wozniak
Christian Kappel
Adrien Sicard
Michael Lenhard
Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe
745
eng
uncontrolled
Outcrossing
eng
uncontrolled
Mixed mating
eng
uncontrolled
Outcrossing rate
eng
uncontrolled
Capsella
eng
uncontrolled
Amplicon sequencing
Biowissenschaften; Biologie
Pflanzen (Botanik)
open_access
Institut für Biochemie und Biologie
Referiert
Open Access
Universität Potsdam
https://publishup.uni-potsdam.de/files/43565/pmnr745.pdf
43564
2019
2019
eng
14
47
15
article
BioMed Central
London
1
2019-05-18
2019-05-18
--
A high‑throughput amplicon‑based method for estimating outcrossing rates
Background: The outcrossing rate is a key determinant of the population-genetic structure of species and their long-term evolutionary trajectories. However, determining the outcrossing rate using current methods based on PCRgenotyping individual offspring of focal plants for multiple polymorphic markers is laborious and time-consuming.
Results: We have developed an amplicon-based, high-throughput enabled method for estimating the outcrossing rate and have applied this to an example of scented versus non-scented Capsella (Shepherd’s Purse) genotypes. Our results show that the method is able to robustly capture differences in outcrossing rates. They also highlight potential biases in the estimates resulting from differential haplotype sharing of the focal plants with the pollen-donor population at individual amplicons.
Conclusions: This novel method for estimating outcrossing rates will allow determining this key population-genetic parameter with high-throughput across many genotypes in a population, enabling studies into the genetic determinants of successful pollinator attraction and outcrossing.
Plant Methods
10.1186/s13007-019-0433-9
1746-4811
Universität Potsdam
PA 2019_44
1894.48
<a href="http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-435657">Zweitveröffentlichung in der Schriftenreihe Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe ; 745</a>
false
false
CC-BY - Namensnennung 4.0 International
Friederike Jantzen
Natalia Joanna Wozniak
Christian Kappel
Adrien Sicard
Michael Lenhard
eng
uncontrolled
Outcrossing
eng
uncontrolled
Mixed mating
eng
uncontrolled
Outcrossing rate
eng
uncontrolled
Capsella
eng
uncontrolled
Amplicon sequencing
Biowissenschaften; Biologie
Pflanzen (Botanik)
open_access
Institut für Biochemie und Biologie
Referiert
Publikationsfonds der Universität Potsdam
Open Access
45397
2016
2016
eng
344
358
15
171
article
American Society of Plant Physiologists
Rockville
1
--
--
--
A JUMONJI Protein with E3 Ligase and Histone H3 Binding Activities Affects Transposon Silencing in Arabidopsis
Transposable elements (TEs) make up a large proportion of eukaryotic genomes. As their mobilization creates genetic variation that threatens genome integrity, TEs are epigenetically silenced through several pathways, and this may spread to neighboring sequences. JUMONJI (JMJ) proteins can function as antisilencing factors and prevent silencing of genes next to TEs. Whether TE silencing is counterbalanced by the activity of antisilencing factors is still unclear. Here, we characterize JMJ24 as a regulator of TE silencing. We show that loss of JMJ24 results in increased silencing of the DNA transposon AtMu1c, while overexpression of JMJ24 reduces silencing. JMJ24 has a JumonjiC (JmjC) domain and two RING domains. JMJ24 autoubiquitinates in vitro, demonstrating E3 ligase activity of the RING domain(s). JMJ24-JmjC binds the N-terminal tail of histone H3, and full-length JMJ24 binds histone H3 in vivo. JMJ24 activity is anticorrelated with histone H3 Lys 9 dimethylation (H3K9me2) levels at AtMu1c. Double mutant analyses with epigenetic silencing mutants suggest that JMJ24 antagonizes histone H3K9me2 and requires H3K9 methyltransferases for its activity on AtMu1c. Genome-wide transcriptome analysis indicates that JMJ24 affects silencing at additional TEs. Our results suggest that the JmjC domain of JMJ24 has lost demethylase activity but has been retained as a binding domain for histone H3. This is in line with phylogenetic analyses indicating that JMJ24 (with the mutated JmjC domain) is widely conserved in angiosperms. Taken together, this study assigns a role in TE silencing to a conserved JmjC-domain protein with E3 ligase activity, but no demethylase activity.
Plant physiology : an international journal devoted to physiology, biochemistry, cellular and molecular biology, biophysics and environmental biology of plants
10.1104/pp.15.01688
26979329
0032-0889
1532-2548
wos2016:2019
WOS:000375431500026
Baurle, I (reprint author), Univ Potsdam, Inst Biochem & Biol, D-14476 Potsdam, Germany., isabel.baeurle@uni-potsdam.de
Sofja Kovalevskaja Award from the Alexander von Humboldt Foundation; Deutsche Forschungsgemeinschaft [SFB 973]
importub
2020-03-22T18:12:02+00:00
filename=package.tar
e9b7eac1aa334aec193d376b92ba2dfe
Tina Kabelitz
Krzysztof Brzezinka
Thomas Friedrich
Michal Gorka
Alexander Graf
Christian Kappel
Isabel Bäurle
Institut für Biochemie und Biologie
Referiert
Import
46097
2017
2017
eng
5719
5730
12
68
review
Oxford Univ. Press
Oxford
1
--
--
--
A short story gets longer: recent insights into the molecular basis of heterostyly
Heterostyly is a fascinating adaptation to promote outbreeding and a classical paradigm of botany. In the most common type of heterostyly, plants either form flowers with long styles and short stamens, or short styles and long stamens. This reciprocal organ positioning reduces pollen wastage and promotes cross-pollination, thus increasing male fitness. In addition, in many heterostylous species selfing and the generation of unfit progeny due to inbreeding depression is limited by a self-incompatibility system, thus promoting female fitness. The two floral forms are genetically determined by the S locus as a complex supergene, namely a chromosomal region containing several individual genes that control the different traits, such as style or stamen length, and are held together by very tight linkage due to suppressed recombination. Recent molecular-genetic studies in several systems, including Turnera, Fagopyrum, Linum, and Primula have begun to identify and characterize the causal heterostyly genes residing at the S locus. An emerging theme from several families is that the dominant S haplotype represents a hemizygous region not present on the recessive s haplotype. This provides an explanation for the suppressed recombination and suggests a scenario for the chromosomal evolution of the S locus. In this review, we discuss the results from recent molecular-genetic analyses in light of the classical models on the genetics and evolution of heterostyly.
Journal of experimental botany
10.1093/jxb/erx387
29099983
0022-0957
1460-2431
wos:2017
WOS:000418365600005
Lenhard, M (reprint author), Univ Potsdam, Inst Biochem & Biol, Karl Liebknecht Str 24-25,House 26, D-14476 Potsdam, Germany., michael.lenhard@uni-potsdam.de
importub
2020-04-19T22:38:01+00:00
filename=package.tar
3f9b23b12eddd2113927a3b7bb5ec1ad
Christian Kappel
Cuong Nguyen Huu
Michael Lenhard
eng
uncontrolled
CYP734A50
eng
uncontrolled
distyly
eng
uncontrolled
GLOBOSA2
eng
uncontrolled
hemizygosity
eng
uncontrolled
heterostyly
eng
uncontrolled
Primula
eng
uncontrolled
S locus
eng
uncontrolled
supergene
eng
uncontrolled
tristyly
Institut für Biochemie und Biologie
Referiert
Import
38032
2014
2014
eng
821
832
12
3
65
review
Oxford Univ. Press
Oxford
1
--
--
--
An update on sugar transport and signalling in grapevine
In addition to their role as a source of reduced carbon, sugars may directly or indirectly control a wide range of activities in plant cells, through transcriptional and post-translational regulation. This control has been studied in detail using Arabidopsis thaliana, where genetic analysis offers many possibilities. Much less is known about perennial woody species. For several years, various aspects of sugar sensing and signalling have been investigated in the grape (Vitis vinifera L.) berry, an organ that accumulates high concentrations of hexoses in the vacuoles of flesh cells. Here we review various aspects of this topic: the molecular basis of sugar transport and its regulation by sugars in grapevine; the functional analysis of several sugar-induced genes; the effects of some biotic and abiotic stresses on the sugar content of the berry; and finally the effects of exogenous sugar supply on the ripening process in field conditions. A picture of complex feedback and multiprocess regulation emerges from these data.
Journal of experimental botany
10.1093/jxb/ert394
24323501
0022-0957
1460-2431
wos:2014
WOS:000331815300007
Delrot, S (reprint author), Univ Bordeaux, ISVV, EGFV, UMR 1287, F-33140 Villenave Dornon, France., serge.delrot@bordeaux.inra.fr
ECOS Sud programme [C11B01]; INRA; University of Bordeaux, Bordeaux
Sciences Agro; Regional Council of Aquitaine; Conseil Interprofessionnel
du Vin de Bordeaux
Fatma Lecourieux
Christian Kappel
David Lecourieux
Alejandra Serrano
Elizabeth Torres
Patricio Arce-Johnson
Serge Delrot
eng
uncontrolled
Fruit biology
eng
uncontrolled
grapevine
eng
uncontrolled
signalling
eng
uncontrolled
stress
eng
uncontrolled
sugar
eng
uncontrolled
transport
Institut für Biochemie und Biologie
Referiert
44940
2016
2016
eng
23
5
article
eLife Sciences Publications
Cambridge
1
--
--
--
Arabidopsis FORGETTER1 mediates stress-induced chromatin memory through nucleosome remodeling
Plants as sessile organisms can adapt to environmental stress to mitigate its adverse effects. As part of such adaptation they maintain an active memory of heat stress for several days that promotes a more efficient response to recurring stress. We show that this heat stress memory requires the activity of the FORGETTER1 (FGT1) locus, with fgt1 mutants displaying reduced maintenance of heat-induced gene expression. FGT1 encodes the Arabidopsis thaliana orthologue of Strawberry notch (Sno), and the protein globally associates with the promoter regions of actively expressed genes in a heat-dependent fashion. FGT1 interacts with chromatin remodelers of the SWI/ SNF and ISWI families, which also display reduced heat stress memory. Genomic targets of the BRM remodeler overlap significantly with FGT1 targets. Accordingly, nucleosome dynamics at loci with altered maintenance of heat-induced expression are affected in fgt1. Together, our results suggest that by modulating nucleosome occupancy, FGT1 mediates stress-induced chromatin memory.
eLife
10.7554/eLife.17061
2050-084X
wos2016:2019
e17061
WOS:000385375300001
Baurle, I (reprint author), Univ Potsdam, Inst Biochem & Biol, Potsdam, Germany., isabel.baeurle@uni-potsdam.de
Alexandervon Humboldt-Stiftung; Deutsche Forschungsgemeinschaft [SFB973]; Royal Society University
importub
2020-03-22T14:22:01+00:00
filename=package.tar
3f8f0bbc25dac357966f851196d75b16
Krzysztof Brzezinka
Simone Altmann
Hjördis Czesnick
Philippe Nicolas
Michal Gorka
Eileen Benke
Tina Kabelitz
Felix Jähne
Alexander Graf
Christian Kappel
Isabel Bäurle
Institut für Biochemie und Biologie
Referiert
Import
38026
2014
2014
eng
688
699
12
5
77
article
Wiley-Blackwell
Hoboken
1
--
--
--
Arabidopsis poly(A) polymerase PAPS1 limits founder-cell recruitment to organ primordia and suppresses the salicylic acid-independent immune response downstream of EDS1/PAD4
Polyadenylation of pre-mRNAs by poly(A) polymerase (PAPS) is a critical process in eukaryotic gene expression. As found in vertebrates, plant genomes encode several isoforms of canonical nuclear PAPS enzymes. In Arabidopsis thaliana these isoforms are functionally specialized, with PAPS1 affecting both organ growth and immune response, at least in part by the preferential polyadenylation of subsets of pre-mRNAs. Here, we demonstrate that the opposite effects of PAPS1 on leaf and flower growth reflect the different identities of these organs, and identify a role for PAPS1 in the elusive connection between organ identity and growth patterns. The overgrowth of paps1 mutant petals is due to increased recruitment of founder cells into early organ primordia, and suggests that PAPS1 activity plays unique roles in influencing organ growth. By contrast, the leaf phenotype of paps1 mutants is dominated by a constitutive immune response that leads to increased resistance to the biotrophic oomycete Hyaloperonospora arabidopsidis and reflects activation of the salicylic acid-independent signalling pathway downstream of ENHANCED DISEASE SUSCEPTIBILITY1 (EDS1)/PHYTOALEXIN DEFICIENT4 (PAD4). These findings provide an insight into the developmental and physiological basis of the functional specialization amongst plant PAPS isoforms.
The plant journal
10.1111/tpj.12421
24372773
0960-7412
1365-313X
wos:2014
WOS:000331848700003
Lenhard, M (reprint author), Univ Potsdam, Inst Biochem & Biol, Karl Liebknecht Str 24-25, D-14476 Golm, Germany., mlenhard@uni-potsdam.de
Deutsche Forschungsgemeinschaft [Le1412/3-1]; Rotation Programme PhD
Fellowship from the John Innes Centre; Gatsby Charitable Foundation
Gerda Trost
Son Lang Vi
Hjördis Czesnick
Peggy Lange
Nick Holton
Patrick Giavalisco
Cyril Zipfel
Christian Kappel
Michael Lenhard
eng
uncontrolled
poly(A) polymerase
eng
uncontrolled
founder-cell recruitment
eng
uncontrolled
organ growth
eng
uncontrolled
polyadenylation
Institut für Biochemie und Biologie
Referiert
55456
2017
2017
eng
23
8
article
Frontiers Research Foundation
Lausanne
1
2017-01-31
2017-01-31
--
Dissecting the Biochemical and Transcriptomic Effects of a Locally Applied Heat Treatment on Developing Cabernet Sauvignon Grape Berries
Reproductive development of grapevine and berry composition are both strongly influenced by temperature. To date, the molecular mechanisms involved in grapevine berries response to high temperatures are poorly understood. Unlike recent data that addressed the effects on berry development of elevated temperatures applied at the whole plant level, the present work particularly focuses on the fruit responses triggered by direct exposure to heat treatment (HT). In the context of climate change, this work focusing on temperature effect at the microclimate level is of particular interest as it can help to better understand the consequences of leaf removal (a common viticultural practice) on berry development. HT (+8 degrees C) was locally applied to clusters from Cabernet Sauvignon fruiting cuttings at three different developmental stages (middle green, veraison and middle ripening). Samples were collected 1, 7, and 14 days after treatment and used for metabolic and transcriptomic analyses. The results showed dramatic and specific biochemical and transcriptomic changes in heat exposed berries, depending on the developmental stage and the stress duration. When applied at the herbaceous stage, HT delayed the onset of veraison. Heating also strongly altered the berry concentration of amino acids and organic acids (e.g., phenylalanine, raminobutyric acid and malate) and decreased the anthocyanin content at maturity. These physiological alterations could be partly explained by the deep remodeling of transcriptome in heated berries. More than 7000 genes were deregulated in at least one of the nine experimental conditions. The most affected processes belong to the categories "stress responses," protein metabolism" and "secondary metabolism," highlighting the intrinsic capacity of grape berries to perceive HT and to build adaptive responses. Additionally, important changes in processes related to "transport," "hormone" and "cell wall" might contribute to the postponing of veraison. Finally, opposite effects depending on heating duration were observed for genes encoding enzymes of the general phenylpropanoid pathway, suggesting that the HI induced decrease in anthocyanin content may result from a combination of transcript abundance and product degradation.
Frontiers in plant science
10.3389/fpls.2017.00053
28197155
1664-462X
wos:2017
53
WOS:000392863600001
Lecourieux, D (reprint author), Univ Bordeaux, Inst Sci Vigne & Vin, UMR Ecophysiol & Genom Fonct Vigne, Villenave Dornon, France., david.lecourieux@inra.fr
2022-07-04T14:28:37+00:00
sword
importub
filename=package.tar
0e9a109591205a58222cf120bb43f622
Lecourieux, David
false
true
CC-BY - Namensnennung 4.0 International
Fatma Lecourieux
Christian Kappel
Philippe Pieri
Justine Charon
Jeremy Pillet
Ghislaine Hilbert
Christel Renaud
Eric Gomes
Serge Delrot
David Lecourieux
eng
uncontrolled
grapevine
eng
uncontrolled
berry development
eng
uncontrolled
microclimate
eng
uncontrolled
high temperature
eng
uncontrolled
microarrays
eng
uncontrolled
metabolomics/metabolite profiling
eng
uncontrolled
climate change
Biowissenschaften; Biologie
Institut für Biochemie und Biologie
Referiert
Import
38711
2015
2015
eng
10
6
article
Nature Publ. Group
London
1
--
--
--
Divergent sorting of a balanced ancestral polymorphism underlies the establishment of gene-flow barriers in Capsella
In the Bateson-Dobzhansky-Muller model of genetic incompatibilities post-zygotic gene-flow barriers arise by fixation of novel alleles at interacting loci in separated populations. Many such incompatibilities are polymorphic in plants, implying an important role for genetic drift or balancing selection in their origin and evolution. Here we show that NPR1 and RPP5 loci cause a genetic incompatibility between the incipient species Capsella grandiflora and C. rubella, and the more distantly related C. rubella and C. orientalis. The incompatible RPP5 allele results from a mutation in C. rubella, while the incompatible NPR1 allele is frequent in the ancestral C. grandiflora. Compatible and incompatible NPR1 haplotypes are maintained by balancing selection in C. grandiflora, and were divergently sorted into the derived C. rubella and C. orientalis. Thus, by maintaining differentiated alleles at high frequencies, balancing selection on ancestral polymorphisms can facilitate establishing gene-flow barriers between derived populations through lineage sorting of the alternative alleles.
Nature Communications
10.1038/ncomms8960
26268845
2041-1723
wos:2015
7960
WOS:000360346900001
Lenhard, M (reprint author), Univ Potsdam, Inst Biochem & Biol, Karl Liebknecht Str 24-25, D-14476 Potsdam, Germany., michael.lenhard@uni-potsdam.de
Genome Canada; Genome Quebec Applied Bioproducts and Crops (ABC) grant;
Deutsche Forschungsgemeinschaft [SPP1529]; ERC
Adrien Sicard
Christian Kappel
Emily B. Josephs
Young Wha Lee
Cindy Marona
John R. Stinchcombe
Stephen I. Wright
Michael Lenhard
Institut für Biochemie und Biologie
Referiert
Open Access
9356
2015
2015
eng
postprint
1
--
--
--
Divergent sorting of a balanced ancestral polymorphism underlies the establishment of gene-flow barriers in Capsella
In the Bateson–Dobzhansky–Muller model of genetic incompatibilities post-zygotic gene-flow barriers arise by fixation of novel alleles at interacting loci in separated populations. Many such incompatibilities are polymorphic in plants, implying an important role for genetic drift or balancing selection in their origin and evolution. Here we show that NPR1 and RPP5 loci cause a genetic incompatibility between the incipient species Capsella grandiflora and C. rubella, and the more distantly related C. rubella and C. orientalis. The incompatible RPP5 allele results from a mutation in C. rubella, while the incompatible NPR1 allele is frequent in the ancestral C. grandiflora. Compatible and incompatible NPR1 haplotypes are maintained by balancing selection in C. grandiflora, and were divergently sorted into the derived C. rubella and C. orientalis. Thus, by maintaining differentiated alleles at high frequencies, balancing selection on ancestral polymorphisms can facilitate establishing gene-flow barriers between derived populations through lineage sorting of the alternative alleles.
urn:nbn:de:kobv:517-opus4-93568
online registration
Nature Communications. - DOI: 10.1038/ncomms8960
<a href="http://publishup.uni-potsdam.de/opus4-ubp/frontdoor/index/index/docId/9355">Bibliographieeintrag der Originalveröffentlichung/Quelle</a>
CC-BY - Namensnennung 4.0 International
Adrien Sicard
Christian Kappel
Emily B. Josephs
Young Wha Lee
Cindy Marona
John R. Stinchcombe
Stephen I. Wright
Michael Lenhard
Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe
231
Naturwissenschaften und Mathematik
open_access
Institut für Biochemie und Biologie
Referiert
Open Access
Universität Potsdam
https://publishup.uni-potsdam.de/files/9356/pmnr231_online.pdf