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Articles by James Simmonds
Homoeolog expression in polyploid wheat mutants shows limited transcriptional compensation
Introduction Whole-genome duplications (WGDs), hybridisations, and small-scale duplications have resulted in an abundance of gene duplicates in plant genomes – on average, 65% of genes in plant genomes have a paralog (Panchy et al., 2016). These duplications can provide opportunities for genetic innovation when mutations cause one of the copies to adopt a novel function (neo-functionalisation; Birchler & Yang, 2022).
De novo annotation reveals transcriptomic complexity across the hexaploid wheat pan-genome - Nature Communications
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Abstract Wheat is the most widely cultivated crop in the world, with over 215 million hectares grown annually. The 10+ Wheat Genomes Project recently sequenced and assembled to chromosome-level the genomes of nine wheat cultivars, uncovering genetic diversity and selection within the pan-genome of wheat. Here, we provide a wheat pan-transcriptome with de novo annotation and differential expression analysis for these wheat cultivars across multiple tissues.
By Thomas Lux, Rachel Rusholme-Pilcher, Angéla Juhász, Gemy Kaithakottil, Susan Duncan, James Simmonds, Jonathan Wright, Benedict Coombes, Karim Gharbi, Moeko Okada, Hirokazu Handa, Kentaro Shimizu, Heidrun Gundlach, Daniel Lang, Michelle L. Colgrave, Wilfried Haerty, Cristobal Uauy, David Swarbreck, Philippa Borrill, Jesse Poland, Simon G. Krattinger, Nils Stein, Curtis Pozniak, Benjamen White
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Nature
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Autoactive CNGC15 enhances root endosymbiosis in legume and wheat - Nature
Abstract Nutrient acquisition is crucial for sustaining life. Plants develop beneficial intracellular partnerships with arbuscular mycorrhiza (AM) and nitrogen-fixing bacteria to surmount the scarcity of soil nutrients and tap into atmospheric dinitrogen, respectively1,2. Initiation of these root endosymbioses requires symbiont-induced oscillations in nuclear calcium (Ca2+) concentrations in root cells3.
Stigma longevity is not a major limiting factor in hybrid wheat seed production
Abstract Hybrids offer a promising approach to improve crop performance because the progeny are often superior to their parent lines and they outyield inbred varieties. A major challenge in producing hybrid progeny in wheat, however, lies in the low outcrossing rates of the maternal parent. This is often attributed to suboptimal synchronisation of male and female flowering as delayed pollination can result in reproductive failure due to female stigma deterioration.
FIGL1 prevents aberrant chromosome associations and fragmentation and limits crossovers in polyploid wheat meiosis
Introduction Meiosis is a specialised form of cell division in which DNA replication is followed by two sequential rounds of cell division to halve the chromosome number during gamete formation.
Delayed development of basal spikelets in wheat explains their increased floret abortion and rudimentary nature
New Results doi: https://doi.org/10.1101/2023.02.17.528935 Abstract Wheat (Triticum aestivum L.) breeding efforts have increased grain yield predominantly by raising grain numbers per spikelet, rather than grain weight or spikelet number. However, across a single spike large differences exist in the number of grains per spikelet. The central spikelets produce the highest number of grains in any given genotype while apical and basal spikelets are less productive.
FANCM promotes class I interfering crossovers and suppresses class II non-interfering crossovers in wheat meiosis - Nature Communications
Abstract FANCM suppresses crossovers in plants by unwinding recombination intermediates. In wheat, crossovers are skewed toward the chromosome ends, thus limiting generation of novel allelic combinations. Here, we observe that FANCM maintains the obligate crossover in tetraploid and hexaploid wheat, thus ensuring that every chromosome pair exhibits at least one crossover, by localizing class I crossover protein HEI10 at pachytene.
Identification of transcription factors regulating senescence in wheat through gene regulatory network modelling
Identification of transcription factors regulating senescence in wheat through gene regulatory network modelling Philippa Borrill, Sophie A Harrington, James Simmonds, Cristobal Uauy bioRxiv 456749; doi: https://doi.org/10.1101/456749
Gene editing and mutagenesis reveal inter-cultivar differences and additivity in the contribution of TaGW2 homoeologues to grain size and weight in wheat | SpringerLink
Using the wheat TILLING populations and the CRISPR-Cas9-based genome editing technology, we showed that the KO of each of the three homoeologues of the TaGW2 gene, which are all functional in Bobwhite (Zhang et al. 2018), and the A and B genome copies of the TaGW2 gene in Paragon increase GS and TGW. Our results are consistent with the previous studies (Simmonds et al. 2016; Zhang et al. 2018) demonstrating that the functional copies of the TaGW2 gene are negative regulators of GS and TGW.
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