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Keywords = genome–phenome bridges

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24 pages, 1653 KiB  
Review
Advanced High-Throughput Phenotyping Techniques for Managing Abiotic Stress in Agricultural Crops—A Comprehensive Review
by Srushtideep Angidi, Kartik Madankar, Muhammad Massub Tehseen and Anshika Bhatla
Crops 2025, 5(2), 8; https://doi.org/10.3390/crops5020008 - 28 Feb 2025
Cited by 3 | Viewed by 1630
Abstract
Abiotic stresses, such as drought, salinity, and heat, exacerbated by climate change, pose significant challenges to global agriculture. These stresses negatively impact crop physiology, leading to yield losses and complicating efforts to breed resilient varieties. While advancements in molecular biology and genomics have [...] Read more.
Abiotic stresses, such as drought, salinity, and heat, exacerbated by climate change, pose significant challenges to global agriculture. These stresses negatively impact crop physiology, leading to yield losses and complicating efforts to breed resilient varieties. While advancements in molecular biology and genomics have identified stress-resistance genes, their effective utilization in breeding programs depends on precise phenotypic evaluation under diverse stress conditions. High-throughput phenotyping (HTP) technologies have emerged as indispensable tools, enabling non-destructive, rapid assessment of critical traits like root architecture, chlorophyll content, and canopy temperature in controlled and field environments. Unlike existing reviews, this manuscript critically addresses technological barriers such as cost scalability, field adaptability, and the integration of artificial intelligence for real-time data analysis. Additionally, it provides a fresh perspective on multi-omics integration in phenomics to bridge the genotype–phenotype gap, ensuring a more holistic approach to precision agriculture. This review bridges gaps in crop improvement by identifying practical solutions to enhance the adoption of HTP in breeding programs. It ensures food security amidst the escalating impacts of climate change. Full article
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28 pages, 2930 KiB  
Review
Alternative Transcripts Diversify Genome Function for Phenome Relevance to Health and Diseases
by Shane A. Carrion, Jennifer J. Michal and Zhihua Jiang
Genes 2023, 14(11), 2051; https://doi.org/10.3390/genes14112051 - 8 Nov 2023
Cited by 4 | Viewed by 3564
Abstract
Manipulation using alternative exon splicing (AES), alternative transcription start (ATS), and alternative polyadenylation (APA) sites are key to transcript diversity underlying health and disease. All three are pervasive in organisms, present in at least 50% of human protein-coding genes. In fact, ATS and [...] Read more.
Manipulation using alternative exon splicing (AES), alternative transcription start (ATS), and alternative polyadenylation (APA) sites are key to transcript diversity underlying health and disease. All three are pervasive in organisms, present in at least 50% of human protein-coding genes. In fact, ATS and APA site use has the highest impact on protein identity, with their ability to alter which first and last exons are utilized as well as impacting stability and translation efficiency. These RNA variants have been shown to be highly specific, both in tissue type and stage, with demonstrated importance to cell proliferation, differentiation and the transition from fetal to adult cells. While alternative exon splicing has a limited effect on protein identity, its ubiquity highlights the importance of these minor alterations, which can alter other features such as localization. The three processes are also highly interwoven, with overlapping, complementary, and competing factors, RNA polymerase II and its CTD (C-terminal domain) chief among them. Their role in development means dysregulation leads to a wide variety of disorders and cancers, with some forms of disease disproportionately affected by specific mechanisms (AES, ATS, or APA). Challenges associated with the genome-wide profiling of RNA variants and their potential solutions are also discussed in this review. Full article
(This article belongs to the Special Issue Advances in Human Genetics and Multi-omics)
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