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      The importance of genotyping within the climate-smart plant breeding value chain – integrative tools for genetic enhancement programs

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          Abstract

          The challenges faced by today’s agronomists, plant breeders, and their managers encompass adapting sustainably to climate variability while working with limited budgets. Besides, managers are dealing with a multitude of issues with different organizations working on similar initiatives and projects, leading to a lack of a sustainable impact on smallholder farmers. To transform the current food systems as a more sustainable and resilient model efficient solutions are needed to deliver and convey results. Challenges such as logistics, labour, infrastructure, and equity, must be addressed alongside adapting to increasingly unstable climate conditions which affect the life cycle of transboundary pathogens and pests. In this context, transforming food systems go far beyond just farmers and plant breeders and it requires substantial contributions from industry, global finances, transportation, energy, education, and country developmental sectors including legislators. As a result, a holistic approach is essential for achieving sustainable and resilient food systems to sustain a global population anticipated to reach 9.7 billion by 2050 and 11.2 billion by 2100. As of 2021, nearly 193 million individuals were affected by food insecurity, 40 million more than in 2020. Meanwhile, the digital world is rapidly advancing with the digital economy estimated at about 20% of the global gross domestic product, suggesting that digital technologies are increasingly accessible even in areas affected by food insecurity. Leveraging these technologies can facilitate the development of climate-smart cultivars that adapt effectively to climate variation, meet consumer preferences, and address human and livestock nutritional needs. Most economically important traits in crops are controlled by multiple loci often with recessive alleles. Considering particularly Africa, this continent has several agro-climatic zones, hence crops need to be adapted to these. Therefore, targeting specific loci using modern tools offers a precise and efficient approach. This review article aims to address how these new technologies can provide a better support to smallholder farmers.

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          Health Effects of Overweight and Obesity in 195 Countries over 25 Years.

          Background While the rising pandemic of obesity has received significant attention in many countries, the effect of this attention on trends and the disease burden of obesity remains uncertain. Methods We analyzed data from 67.8 million individuals to assess the trends in obesity and overweight prevalence among children and adults between 1980 and 2015. Using the Global Burden of Disease study data and methods, we also quantified the burden of disease related to high body mass index (BMI), by age, sex, cause, and BMI level in 195 countries between 1990 and 2015. Results In 2015, obesity affected 107.7 million (98.7-118.4) children and 603.7 million (588.2- 619.8) adults worldwide. Obesity prevalence has doubled since 1980 in more than 70 countries and continuously increased in most other countries. Although the prevalence of obesity among children has been lower than adults, the rate of increase in childhood obesity in many countries was greater than the rate of increase in adult obesity. High BMI accounted for 4.0 million (2.7- 5.3) deaths globally, nearly 40% of which occurred among non-obese. More than two-thirds of deaths related to high BMI were due to cardiovascular disease. The disease burden of high BMI has increased since 1990; however, the rate of this increase has been attenuated due to decreases in underlying cardiovascular disease death rates. Conclusions The rapid increase in prevalence and disease burden of elevated BMI highlights the need for continued focus on surveillance of BMI and identification, implementation, and evaluation of evidence-based interventions to address this problem.
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            Search-and-replace genome editing without double-strand breaks or donor DNA

            Summary Most genetic variants that contribute to disease 1 are challenging to correct efficiently and without excess byproducts 2–5 . Here we describe prime editing, a versatile and precise genome editing method that directly writes new genetic information into a specified DNA site using a catalytically impaired Cas9 fused to an engineered reverse transcriptase, programmed with a prime editing guide RNA (pegRNA) that both specifies the target site and encodes the desired edit. We performed >175 edits in human cells including targeted insertions, deletions, and all 12 types of point mutations without requiring double-strand breaks or donor DNA templates. We applied prime editing in human cells to correct efficiently and with few byproducts the primary genetic causes of sickle cell disease (requiring a transversion in HBB) and Tay-Sachs disease (requiring a deletion in HEXA), to install a protective transversion in PRNP, and to precisely insert various tags and epitopes into target loci. Four human cell lines and primary post-mitotic mouse cortical neurons support prime editing with varying efficiencies. Prime editing shows higher or similar efficiency and fewer byproducts than homology-directed repair, complementary strengths and weaknesses compared to base editing, and much lower off-target editing than Cas9 nuclease at known Cas9 off-target sites. Prime editing substantially expands the scope and capabilities of genome editing, and in principle can correct up to 89% of known genetic variants associated with human diseases.
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              Posttranscriptional regulation of the heterochronic gene lin-14 by lin-4 mediates temporal pattern formation in C. elegans.

              During C. elegans development, the temporal pattern of many cell lineages is specified by graded activity of the heterochronic gene Lin-14. Here we demonstrate that a temporal gradient in Lin-14 protein is generated posttranscriptionally by multiple elements in the lin-14 3'UTR that are regulated by the heterochronic gene Lin-4. The lin-14 3'UTR is both necessary and sufficient to confer lin-4-mediated posttranscriptional temporal regulation. The function of the lin-14 3'UTR is conserved between C. elegans and C. briggsae. Among the conserved sequences are seven elements that are each complementary to the lin-4 RNAs. A reporter gene bearing three of these elements shows partial temporal gradient activity. These data suggest a molecular mechanism for Lin-14p temporal gradient formation: the lin-4 RNAs base pair to sites in the lin-14 3'UTR to form multiple RNA duplexes that down-regulate lin-14 translation.
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                Author and article information

                Contributors
                URI : https://loop.frontiersin.org/people/444901Role: Role:
                URI : https://loop.frontiersin.org/people/202395Role:
                URI : https://loop.frontiersin.org/people/465873Role:
                URI : https://loop.frontiersin.org/people/27658Role:
                URI : https://loop.frontiersin.org/people/854635Role:
                URI : https://loop.frontiersin.org/people/265497Role:
                URI : https://loop.frontiersin.org/people/1908821Role:
                URI : https://loop.frontiersin.org/people/560617Role:
                Journal
                Front Plant Sci
                Front Plant Sci
                Front. Plant Sci.
                Frontiers in Plant Science
                Frontiers Media S.A.
                1664-462X
                06 February 2025
                2024
                : 15
                : 1518123
                Affiliations
                [1] 1 Genetic Resources Program, Alliance Bioversity International and International Center for Tropical Agriculture (CIAT) , Cali, Colombia
                [2] 2 Department of Plant Breeding, Swedish University of Agricultural Sciences , Alnarp, Sweden
                [3] 3 Plant Breeding and Genetics Section, Joint FAO/IAEA Center, International Atomic Energy Agency , Vienna, Austria
                [4] 4 Independent Researcher , Roskilde, Denmark
                [5] 5 Yam Breeding Unit, International Institute of Tropical Agriculture , Ibadan, Nigeria
                [6] 6 Genetics, Genomics, and Crop Improvement Division, International Potato Center , Lima, Peru
                [7] 7 Oilseeds Section, Department of Genetics & Plant Breeding, CCS Haryana Agricultural University , Hisar, India
                Author notes

                Edited by: Simardeep Kaur, The ICAR Research Complex for North Eastern Hill Region (ICAR RC NEH), India

                Reviewed by: Sonu Shekhawat, Indian Agricultural Research Institute (ICAR), India

                Deepesh Kumar, Indian Council of Agricultural Research, India

                *Correspondence: Ana Luísa Garcia-Oliveira, a.oliveira@ 123456cgiar.org

                †ORCID: Ana Luísa Garcia-Oliveira, orcid.org/0000-0001-8561-4172; Rodomiro Ortiz, orcid.org/0000-0002-1739-7206; Fatma Sarsu, orcid.org/0000-0003-2771-7418; Søren K. Rasmussen, orcid.org/0000-0001-6169-2504; Paterne Agre, orcid.org/0000-0003-1231-2530; Asrat Asfaw, orcid.org/0000-0002-4859-0631; Moctar Kante, orcid.org/0000-0003-4669-3132; Subhash Chander, orcid.org/0000-0001-5353-6317

                Article
                10.3389/fpls.2024.1518123
                11839310
                39980758
                2ff4ea84-9b18-45e3-b948-87bc056e5ffc
                Copyright © 2025 Garcia-Oliveira, Ortiz, Sarsu, Rasmussen, Agre, Asfaw, Kante and Chander

                This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

                History
                : 29 October 2024
                : 25 November 2024
                Page count
                Figures: 7, Tables: 3, Equations: 0, References: 225, Pages: 26, Words: 14285
                Funding
                Funded by: Bill and Melinda Gates Foundation , doi 10.13039/100000865;
                Award ID: INV-041105
                The author(s) declare financial support was received for the research, authorship, and/or publication of this article. Bill and Melinda Gates Foundation for their support through the RTB Breeding Investment Project (INV-041105).
                Categories
                Plant Science
                Review
                Custom metadata
                Plant Breeding

                Plant science & Botany
                agriculture,marker genotyping,mutation breeding,ngt,crispr,legislation,climate-smart cultivars

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