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      Current research status and emerging trends in wheat: An integrated scientometric analysis based on ploidy uncovers hidden footprints in the scientific landscape

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          Abstract

          Wheat, a highly versatile staple crop cultivated extensively for its grains on a global scale, is poised to experience increased demand to sustain the burgeoning population, owing to its superior nutritional potential. Modern wheat, a hexaploid species, has evolved through the introgression of numerous preceding ploidies, including Einkorn, Emmer, Aegilops, and others, each possessing distinct qualitative and quantitative traits. Scientometric and topical analyses serve as effective tools to quantitatively evaluate scientific research by measuring the knowledge expressed in scientific publications and keywords. Thus, comprehending the research status regarding wheat domestication events within primary, secondary, and tertiary gene pools is paramount for enhancing wheat production. In this study, we analyze data retrieved from PubMed to elucidate the research status and identify bottlenecks across different ploidy of genomic pools of wheat. The publication trends on wheat have experienced exponential growth over the past three decades, with China emerging as a leading center for publications. In contrast to the publication frequency observed in hexaploid common wheat, scholarly output concerning Einkorn and Aegilops is approximately tenfold lesser, with emmer trailing behind at three times fewer publications. This discrepancy underscores the prioritization of expedited research initiatives targeting these species, aimed at elucidating latent biological characteristics and optimizing their breeding capabilities. Keywords such as “stress,” “GWAS,” and “gene” are prominent, reflecting the challenges posed by climatic factors on wheat production and their mitigation through molecular breeding and gene manipulation. Notably, the keyword “einkorn” highlights its potential as a donor for fine-tuning traits related to wheat adaptation processes and quality, crucial for modern wheat’s survivability under adverse climates. Conversely, higher publication rates on emmer are primarily associated with Italy, possibly due to its favorable Mediterranean climate for tetraploid wheat. Keywords like “Pasta” and “Ochratoxin, DON” are prevalent, with the former being derived from durum wheat and the latter being reported in higher amounts in durum compared to other wheat species, rendering it less suitable for consumption. Enriched keywords such as “genome” and “resistance” underscore the critical characteristics of Aegilops. Other significant keywords like “Aceria tosichella” possibly indicate multiple stages of resistance conferred by Aegilops, while the presence of the grain softness protein “puroindoline” enhances its acceptability for donation by Aegilops. Spelt, a close relative of common wheat, exhibits a research trend with thousands of annual publications and enriched keywords such as “stress” and “yield” reflect the current scientific emphasis on wheat research. Furthermore, hierarchical keywords like “bio-control” and “celiac disease” merit consideration for future research on hexaploid wheat.

          Graphical abstract

          The representation and visualization of key terms extracted from the scholarly landscape concerning various ploidy levels in wheat and their admixture, as unveiled through integrated scientometrics applied to archived literature within PubMed.

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          Most cited references52

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          PubTator central: automated concept annotation for biomedical full text articles

          PubTator Central (https://www.ncbi.nlm.nih.gov/research/pubtator/) is a web service for viewing and retrieving bioconcept annotations in full text biomedical articles. PubTator Central (PTC) provides automated annotations from state-of-the-art text mining systems for genes/proteins, genetic variants, diseases, chemicals, species and cell lines, all available for immediate download. PTC annotates PubMed (29 million abstracts) and the PMC Text Mining subset (3 million full text articles). The new PTC web interface allows users to build full text document collections and visualize concept annotations in each document. Annotations are downloadable in multiple formats (XML, JSON and tab delimited) via the online interface, a RESTful web service and bulk FTP. Improved concept identification systems and a new disambiguation module based on deep learning increase annotation accuracy, and the new server-side architecture is significantly faster. PTC is synchronized with PubMed and PubMed Central, with new articles added daily. The original PubTator service has served annotated abstracts for ∼300 million requests, enabling third-party research in use cases such as biocuration support, gene prioritization, genetic disease analysis, and literature-based knowledge discovery. We demonstrate the full text results in PTC significantly increase biomedical concept coverage and anticipate this expansion will both enhance existing downstream applications and enable new use cases.
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            Population genomic analysis of Aegilops tauschii identifies targets for bread wheat improvement

            Aegilops tauschii , the diploid wild progenitor of the D subgenome of bread wheat, is a reservoir of genetic diversity for improving bread wheat performance and environmental resilience. Here we sequenced 242 Ae. tauschii accessions and compared them to the wheat D subgenome to characterize genomic diversity. We found that a rare lineage of Ae. tauschii geographically restricted to present-day Georgia contributed to the wheat D subgenome in the independent hybridizations that gave rise to modern bread wheat. Through k -mer-based association mapping, we identified discrete genomic regions with candidate genes for disease and pest resistance and demonstrated their functional transfer into wheat by transgenesis and wide crossing, including the generation of a library of hexaploids incorporating diverse Ae. tauschii genomes. Exploiting the genomic diversity of the Ae. tauschii ancestral diploid genome permits rapid trait discovery and functional genetic validation in a hexaploid background amenable to breeding. Exploring the diversity of the wild progenitor of the wheat D subgenome allows for rapid trait discovery.
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              Genome evolution due to allopolyploidization in wheat.

              The wheat group has evolved through allopolyploidization, namely, through hybridization among species from the plant genera Aegilops and Triticum followed by genome doubling. This speciation process has been associated with ecogeographical expansion and with domestication. In the past few decades, we have searched for explanations for this impressive success. Our studies attempted to probe the bases for the wide genetic variation characterizing these species, which accounts for their great adaptability and colonizing ability. Central to our work was the investigation of how allopolyploidization alters genome structure and expression. We found in wheat that allopolyploidy accelerated genome evolution in two ways: (1) it triggered rapid genome alterations through the instantaneous generation of a variety of cardinal genetic and epigenetic changes (which we termed "revolutionary" changes), and (2) it facilitated sporadic genomic changes throughout the species' evolution (i.e., evolutionary changes), which are not attainable at the diploid level. Our major findings in natural and synthetic allopolyploid wheat indicate that these alterations have led to the cytological and genetic diploidization of the allopolyploids. These genetic and epigenetic changes reflect the dynamic structural and functional plasticity of the allopolyploid wheat genome. The significance of this plasticity for the successful establishment of wheat allopolyploids, in nature and under domestication, is discussed.
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                Author and article information

                Contributors
                Journal
                Heliyon
                Heliyon
                Heliyon
                Elsevier
                2405-8440
                15 August 2024
                30 August 2024
                15 August 2024
                : 10
                : 16
                : e36375
                Affiliations
                [1]Division for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, 110012, India
                Author notes
                [* ]Corresponding author. ma.iquebal@ 123456icar.gov.in
                [1]

                Equal contribution.

                Article
                S2405-8440(24)12406-1 e36375
                10.1016/j.heliyon.2024.e36375
                11381822
                39253144
                1651ea36-fbd5-4695-9e84-084176bc4acf
                © 2024 Published by Elsevier Ltd.

                This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).

                History
                : 22 May 2024
                : 9 August 2024
                : 14 August 2024
                Categories
                Research Article

                wheat,polyploidy,pubmed,scientometrics,china,natural language processing,topical analysis

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