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Hybrid allele expression development

Sherry LeClere, Chenxi Wu, Philip Westra, R Douglas Sammons
The understanding and mitigation of the appearance of herbicide-resistant weeds have come to the forefront of study in the past decade, as the number of weed species that are resistant to one or more herbicide modes of action is on the increase. Historically, weed resistance to auxin herbicides has been rare, but examples, such as Kochia scoparia L. Schrad (kochia), have appeared, posing a challenge to conventional agricultural practices. Reports of dicamba-resistant kochia populations began in the early 1990s in areas where auxin herbicides were heavily utilized for weed control in corn and wheat cropping systems, and some biotypes are resistant to other auxin herbicides as well...
March 12, 2018: Proceedings of the National Academy of Sciences of the United States of America
Narayanan Raghupathy, Kwangbom Choi, Matthew J Vincent, Glen L Beane, Keith Sheppard, Steven C Munger, Ron Korstanje, Fernando Pardo-Manual de Villena, Gary A Churchill, Alfonso Valencia
Motivation: Allele-specific expression (ASE) refers to the differential abundance of the allelic copies of a transcript. RNA sequencing (RNA-Seq) can provide quantitative estimates of ASE for genes with transcribed polymorphisms. When short-read sequences are aligned to a diploid transcriptome, readmapping ambiguities confound our ability to directly count reads. Multi-mapping reads aligning equally well to multiple genomic locations, isoforms, or alleles can comprise the majority (>85%) of reads...
February 12, 2018: Bioinformatics
Claudio S Quilodrán, Frédéric Austerlitz, Mathias Currat, Juan I Montoya-Burgos
The dispersal of non-native genes due to hybridization is a form of cryptic invasion with growing concern in evolution and conservation. This includes the spread of transgenic genes and antibiotic resistance. To investigate how genes and phenotypes are transmitted, we developed a general model that, for the first time, considers concurrently: multiple loci, quantitative and qualitative gene expression, assortative mating, dominance/recessivity inheritance and density-dependent demographic effects. Selection acting on alleles or genotypes can also be incorporated...
February 5, 2018: Scientific Reports
Feng Mao, Camilla Holmlund, Mahmood Faraz, Wanzhong Wang, Tommy Bergenheim, Samuel Kvarnbrink, Mikael Johansson, Roger Henriksson, Håkan Hedman
Recently, a genome-wide association study showed that a single nucleotide polymorphism (SNP) -rs11706832-in intron 2 of the human LRIG1 (Leucine-rich repeats and immunoglobulin-like domains 1) gene is associated with susceptibility to glioma. However, the mechanism by which rs11706832 affects glioma risk remains unknown; additionally, it is unknown whether the expression levels of LRIG1 are a relevant determinant of gliomagenesis. Here, we investigated the role of Lrig1 in platelet-derived growth factor (PDGF)-induced experimental glioma in mice by introducing mono-allelic and bi-allelic deletions of Lrig1 followed by inducing gliomagenesis via intracranial retroviral transduction of PDGFB in neural progenitor cells...
February 2, 2018: Oncogenesis
Valerie Weitensteiner, Rong Zhang, Julia Bungenberg, Matthias Marks, Jan Gehlen, Damian J Ralser, Alina C Hilger, Amit Sharma, Johannes Schumacher, Ulrich Gembruch, Waltraut M Merz, Albert Becker, Janine Altmüller, Holger Thiele, Bernhard G Herrmann, Benjamin Odermatt, Michael Ludwig, Heiko Reutter
BACKGROUND: Syndromic brain malformations comprise a large group of anomalies with a birth prevalence of about 1 in 1,000 live births. Their etiological factors remain largely unknown. To identify causative mutations, we used whole-exome sequencing (WES) in aborted fetuses and children with syndromic brain malformations in which chromosomal microarray analysis was previously unremarkable. METHODS: WES analysis was applied in eight case-parent trios, six aborted fetuses, and two children...
February 1, 2018: Birth Defects Research
Jutta A Baldauf, Caroline Marcon, Andrew Lithio, Lucia Vedder, Lena Altrogge, Hans-Peter Piepho, Heiko Schoof, Dan Nettleton, Frank Hochholdinger
Maize (Zea mays L.) displays an exceptional degree of structural genomic diversity [1, 2]. In addition, variation in gene expression further contributes to the extraordinary phenotypic diversity and plasticity of maize. This study provides a systematic investigation on how distantly related homozygous maize inbred lines affect the transcriptomic plasticity of their highly heterozygous F1 hybrids. The classical dominance model of heterosis explains the superiority of hybrid plants by the complementation of deleterious parental alleles by superior alleles of the second parent at many loci [3]...
January 8, 2018: Current Biology: CB
Jinwoo Shin, Goowon Jeong, Jong-Yoon Park, Hoyeun Kim, Ilha Lee
Kinetochore, a protein super-complex on the centromere of chromosomes, mediates chromosome segregation during cell division by providing attachment sites for spindle microtubules. The NDC80 complex, composed of four proteins, NDC80, NUF2, SPC24, and SPC25, is localized at the outer kinetochore and connects spindle fibers to the kinetochore. Although it is conserved across species, functional studies of this complex are rare in Arabidopsis. Here, we characterize a recessive mutant, meristem unstructured-1 (mun-1), exhibiting an abnormal phenotype with unstructured shoot apical meristem caused by ectopic expression of the WUSCHEL gene in unexpected tissues...
January 21, 2018: Plant Journal: for Cell and Molecular Biology
Baoheng Gui, Jesse Slone, Taosheng Huang
Several factors have been proposed as contributors to interfamilial and intrafamilial phenotypic variability in autosomal dominant disorders, including allelic variation, modifier genes, environmental factors and complex genetic and environmental interactions. However, regardless of the similarity of genetic background and environmental factors, asymmetric limb or trunk anomalies in a single individual and variable manifestation between monozygotic twins have been observed, indicating other mechanisms possibly involved in expressivity of autosomal dominant diseases...
2017: Frontiers in Genetics
Hillery C Metz, Nicole L Bedford, Yangshu Linda Pan, Hopi E Hoekstra
A central challenge in biology is to understand how innate behaviors evolve between closely related species. One way to elucidate how differences arise is to compare the development of behavior in species with distinct adult traits [1]. Here, we report that Peromyscus polionotus is strikingly precocious with regard to burrowing behavior, but not other behaviors, compared to its sister species P. maniculatus. In P. polionotus, burrows were excavated as early as 17 days of age, whereas P. maniculatus did not build burrows until 10 days later...
December 18, 2017: Current Biology: CB
Dexuan Meng, Jianyu Zhao, Cheng Zhao, Haishan Luo, Mujiao Xie, Renyi Liu, Jinsheng Lai, Xiaolan Zhang, Weiwei Jin
Gene imprinting is a widely observed epigenetic phenomenon in maize endosperm; however, whether it also occurs in the maize embryo remains controversial. Here, we used high-throughput RNA sequencing on laser capture microdissected and manually dissected maize embryos from reciprocal crosses between inbred lines B73 and Mo17 at six time points (3-13 days after pollination, DAP) to analyze allelic gene expression patterns. Co-expression analysis revealed sequential gene activation during maize embryo development...
February 2018: Plant Journal: for Cell and Molecular Biology
Xiaojiao Hu, Hongwu Wang, Kun Li, Yujin Wu, Zhifang Liu, Changling Huang
Heterosis refers to the phenomenon in which hybrid progeny show superior performance relative to their parents. Early maize ear development shows strong heterosis in ear architecture traits and greatly affects grain yield. To explore the underlying molecular mechanisms, genome-wide proteomics of immature ears of maize hybrid ZD909 and its parents were analyzed using tandem mass tag (TMT) technology. A total of 9,713 proteins were identified in all three genotypes. Among them, 3,752 (38.6%) proteins were differentially expressed between ZD909 and its parents...
November 23, 2017: Scientific Reports
Yueting Dai, Wenying Su, Chentao Yang, Bing Song, Yu Li, Yongping Fu
Identification of monokaryons and their mating types and discrimination of hybrid offspring are key steps for the crossbreeding of Pleurotus tuoliensis (Bailinggu). However, conventional crossbreeding methods are troublesome and time consuming. Using RNA-seq technology, we developed new expressed sequence tag-simple sequence repeat (EST-SSR) markers for Bailinggu to easily and rapidly identify monokaryons and their mating types, genetic diversity and hybrid offspring. We identified 1110 potential EST-based SSR loci from a newly-sequenced Bailinggu transcriptome and then randomly selected 100 EST-SSRs for further validation...
November 17, 2017: Genes
Jadiel A Wasson, Onur Birol, David J Katz
Genomically imprinted loci are expressed mono-allelically dependent upon the parent of origin. Their regulation not only illuminates how chromatin regulates gene expression but also how chromatin can be reprogrammed every generation. Because of their distinct parent of origin regulation, analysis of imprinted loci can be difficult. Single nucleotide polymorphisms (SNPs) are required to accurately assess these elements allele-specifically. However, publicly available SNP databases lack robust verification, making analysis of imprinting difficult...
November 14, 2017: G3: Genes—Genomes—Genetics
Maud Borensztein, Ikuhiro Okamoto, Laurène Syx, Guillaume Guilbaud, Christel Picard, Katia Ancelin, Rafael Galupa, Patricia Diabangouaya, Nicolas Servant, Emmanuel Barillot, Azim Surani, Mitinori Saitou, Chong-Jian Chen, Konstantinos Anastassiadis, Edith Heard
X-chromosome inactivation is established during early development. In mice, transcriptional repression of the paternal X-chromosome (Xp) and enrichment in epigenetic marks such as H3K27me3 is achieved by the early blastocyst stage. X-chromosome inactivation is then reversed in the inner cell mass. The mechanisms underlying Xp reactivation remain enigmatic. Using in vivo single-cell approaches (allele-specific RNAseq, nascent RNA-fluorescent in situ hybridization and immunofluorescence), we show here that different genes are reactivated at different stages, with more slowly reactivated genes tending to be enriched in H3meK27...
November 3, 2017: Nature Communications
Shun Sakuma, Udda Lundqvist, Yusuke Kakei, Venkatasubbu Thirulogachandar, Takako Suzuki, Kiyosumi Hori, Jianzhong Wu, Akemi Tagiri, Twan Rutten, Ravi Koppolu, Yukihisa Shimada, Kelly Houston, William T B Thomas, Robbie Waugh, Thorsten Schnurbusch, Takao Komatsuda
Increasing grain yield is an endless challenge for cereal crop breeding. In barley ( Hordeum vulgare ), grain number is controlled mainly by Six-rowed spike 1 ( Vrs1 ), which encodes a homeodomain leucine zipper class I transcription factor. However, little is known about the genetic basis of grain size. Here, we show that extreme suppression of lateral florets contributes to enlarged grains in deficiens barley. Through a combination of fine-mapping and resequencing of deficiens mutants, we have identified that a single amino acid substitution at a putative phosphorylation site in VRS1 is responsible for the deficiens phenotype...
December 2017: Plant Physiology
Christopher Kraus, Philipp H Schiffer, Hiroshi Kagoshima, Hideaki Hiraki, Theresa Vogt, Michael Kroiher, Yuji Kohara, Einhard Schierenberg
BACKGROUND: The free-living nematode Diploscapter coronatus is the closest known relative of Caenorhabditis elegans with parthenogenetic reproduction. It shows several developmental idiosyncracies, for example concerning the mode of reproduction, embryonic axis formation and early cleavage pattern (Lahl et al. in Int J Dev Biol 50:393-397, 2006). Our recent genome analysis (Hiraki et al. in BMC Genomics 18:478, 2017) provides a solid foundation to better understand the molecular basis of developmental idiosyncrasies in this species in an evolutionary context by comparison with selected other nematodes...
2017: EvoDevo
Alba Marina Gimenez, Luciana Chagas Lima, Katia Sanches Françoso, Priscila M A Denapoli, Raquel Panatieri, Daniel Y Bargieri, Jean-Michel Thiberge, Chiara Andolina, Francois Nosten, Laurent Renia, Ruth S Nussenzweig, Victor Nussenzweig, Rogerio Amino, Mauricio M Rodrigues, Irene S Soares
Plasmodium vivax is the most common species that cause malaria outside of the African continent. The development of an efficacious vaccine would contribute greatly to control malaria. Recently, using bacterial and adenoviral recombinant proteins based on the P. vivax circumsporozoite protein (CSP), we demonstrated the possibility of eliciting strong antibody-mediated immune responses to each of the three allelic forms of P. vivax CSP (PvCSP). In the present study, recombinant proteins representing the PvCSP alleles (VK210, VK247, and P...
2017: Frontiers in Immunology
Etsuko Itabashi, Kenji Osabe, Ryo Fujimoto, Tomohiro Kakizaki
Epigenetic regulation, covalent modification of DNA and changes in histone proteins are closely linked to plant development and stress response through flexibly altering the chromatin structure to regulate gene expression. In this review, we will illustrate the importance of epigenetic influences by discussing three agriculturally important traits of Brassicaceae. (1) Vernalization, an acceleration of flowering by prolonged cold exposure regulated through epigenetic silencing of a central floral repressor, FLOWERING LOCUS C...
October 20, 2017: Plant Cell Reports
Olga Tšuiko, Maaike Catteeuw, Masoud Zamani Esteki, Aspasia Destouni, Osvaldo Bogado Pascottini, Urban Besenfelder, Vitezslav Havlicek, Katrien Smits, Ants Kurg, Andres Salumets, Thomas D'Hooghe, Thierry Voet, Ann Van Soom, Joris Robert Vermeesch
STUDY QUESTION: Is the rate and nature of chromosome instability (CIN) similar between bovine in vivo-derived and in vitro-cultured cleavage-stage embryos? SUMMARY ANSWER: There is a major difference regarding chromosome stability of in vivo-derived and in vitro-cultured embryos, as CIN is significantly lower in in vivo-derived cleavage-stage embryos compared to in vitro-cultured embryos. WHAT IS KNOWN ALREADY: CIN is common during in vitro embryogenesis and is associated with early embryonic loss in humans, but the stability of in vivo-conceived cleavage-stage embryos remains largely unknown...
November 1, 2017: Human Reproduction
Benjamin Dubois, Pierre Bertin, Yordan Muhovski, Emmanuelle Escarnot, Dominique Mingeot
BACKGROUND: Celiac disease (CD) is caused by specific sequences of gluten proteins found in cereals such as bread wheat (Triticum aestivum ssp. aestivum) and spelt (T. aestivum ssp. spelta). Among them, the α-gliadins display the highest immunogenicity, with four T-cell stimulatory epitopes. The toxicity of each epitope sequence can be reduced or even suppressed according to the allelic form of each sequence. One way to address the CD problem would be to make use of this allelic variability in breeding programs to develop safe varieties, but tools to track the presence of toxic epitopes are required...
2017: Plant Methods
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