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How the pan-genome is changing crop genomics and improvement.
Della Coletta, R, Qiu, Y, Ou, S, Hufford, MB, Hirsch, CN
Genome biology. 2021;(1):3
Abstract
Crop genomics has seen dramatic advances in recent years due to improvements in sequencing technology, assembly methods, and computational resources. These advances have led to the development of new tools to facilitate crop improvement. The study of structural variation within species and the characterization of the pan-genome has revealed extensive genome content variation among individuals within a species that is paradigm shifting to crop genomics and improvement. Here, we review advances in crop genomics and how utilization of these tools is shifting in light of pan-genomes that are becoming available for many crop species.
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Through 40,000 years of human presence in Southern Europe: the Italian case study.
Aneli, S, Caldon, M, Saupe, T, Montinaro, F, Pagani, L
Human genetics. 2021;(10):1417-1431
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The Italian Peninsula, a natural pier across the Mediterranean Sea, witnessed intricate population events since the very beginning of the human occupation in Europe. In the last few years, an increasing number of modern and ancient genomes from the area have been published by the international research community. This genomic perspective started unveiling the relevance of Italy to understand the post-Last Glacial Maximum (LGM) re-peopling of Europe, the earlier phase of the Neolithic westward migrations, and its linking role between Eastern and Western Mediterranean areas after the Iron Age. However, many open questions are still waiting for more data to be addressed in full. With this review, we summarize the current knowledge emerging from the available ancient Italian individuals and, by re-analysing them all at once, we try to shed light on the avenues future research in the area should cover. In particular, open questions concern (1) the fate of pre-Villabruna Europeans and to what extent their genomic components were absorbed by the post-LGM hunter-gatherers; (2) the role of Sicily and Sardinia before LGM; (3) to what degree the documented genetic structure within the Early Neolithic settlers can be described as two separate migrations; (4) what are the population events behind the marked presence of an Iranian Neolithic-like component in Bronze Age and Iron Age Italian and Southern European samples.
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Machine learning approaches for crop improvement: Leveraging phenotypic and genotypic big data.
Tong, H, Nikoloski, Z
Journal of plant physiology. 2021;:153354
Abstract
Highly efficient and accurate selection of elite genotypes can lead to dramatic shortening of the breeding cycle in major crops relevant for sustaining present demands for food, feed, and fuel. In contrast to classical approaches that emphasize the need for resource-intensive phenotyping at all stages of artificial selection, genomic selection dramatically reduces the need for phenotyping. Genomic selection relies on advances in machine learning and the availability of genotyping data to predict agronomically relevant phenotypic traits. Here we provide a systematic review of machine learning approaches applied for genomic selection of single and multiple traits in major crops in the past decade. We emphasize the need to gather data on intermediate phenotypes, e.g. metabolite, protein, and gene expression levels, along with developments of modeling techniques that can lead to further improvements of genomic selection. In addition, we provide a critical view of factors that affect genomic selection, with attention to transferability of models between different environments. Finally, we highlight the future aspects of integrating high-throughput molecular phenotypic data from omics technologies with biological networks for crop improvement.
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Hyperbolic rules of the cooperative organization of eukaryotic and prokaryotic genomes.
Petoukhov, SV
Bio Systems. 2020;:104273
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Abstract
The author's method of oligomer sums for analysis of oligomer compositions of eukaryotic and prokaryotic genomes is described. The use of this method revealed the existence of general rules for the cooperative oligomeric organization of a wide list of genomes. These rules are called hyperbolic because they are associated with hyperbolic sequences including the harmonic progression 1, 1/2, 1/3, .., 1/n. These rules are demonstrated by examples of quantitative analysis of many genomes from the human genome to the genomes of archaea and bacteria. The hyperbolic (harmonic) rules, speaking about the existence of algebraic invariants in full genomic sequences, are considered as candidates for the role of universal rules for the cooperative organization of genomes. The results concerns additionally the problem of the origin of life. The described phenomenological results were obtained as consequences of the previously published author's quantum-information model of long DNA sequences. The oligomer sums method was also applied to the analysis of long genes and viruses including the COVID-19 virus; this revealed, in characteristics of many of them, the phenomenon of such rhythmically repeating deviations from model hyperbolic sequences, which are associated with DNA triplets. In addition, an application of the oligomer sums method is shown to the analysis of amino acid sequences in long proteins like the protein Titin. The topics of the algebraic harmony in living bodies and of the quantum-information approach in biology are discussed.
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CRISPR FokI Dead Cas9 System: Principles and Applications in Genome Engineering.
Saifaldeen, M, Al-Ansari, DE, Ramotar, D, Aouida, M
Cells. 2020;(11)
Abstract
The identification of the robust clustered regularly interspersed short palindromic repeats (CRISPR) associated endonuclease (Cas9) system gene-editing tool has opened up a wide range of potential therapeutic applications that were restricted by more complex tools, including zinc finger nucleases (ZFNs) and transcription activator-like effector nucleases (TALENs). Nevertheless, the high frequency of CRISPR system off-target activity still limits its applications, and, thus, advanced strategies for highly specific CRISPR/Cas9-mediated genome editing are continuously under development including CRISPR-FokI dead Cas9 (fdCas9). fdCas9 system is derived from linking a FokI endonuclease catalytic domain to an inactive Cas9 protein and requires a pair of guide sgRNAs that bind to the sense and antisense strands of the DNA in a protospacer adjacent motif (PAM)-out orientation, with a defined spacer sequence range around the target site. The dimerization of FokI domains generates DNA double-strand breaks, which activates the DNA repair machinery and results in genomic edit. So far, all the engineered fdCas9 variants have shown promising gene-editing activities in human cells when compared to other platforms. Herein, we review the advantages of all published variants of fdCas9 and their current applications in genome engineering.
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Development of a Cardiac Sarcomere Functional Genomics Platform to Enable Scalable Interrogation of Human TNNT2 Variants.
Pettinato, AM, Ladha, FA, Mellert, DJ, Legere, N, Cohn, R, Romano, R, Thakar, K, Chen, YS, Hinson, JT
Circulation. 2020;(23):2262-2275
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Abstract
BACKGROUND Pathogenic TNNT2 variants are a cause of hypertrophic and dilated cardiomyopathies, which promote heart failure by incompletely understood mechanisms. The precise functional significance for 87% of TNNT2 variants remains undetermined, in part, because of a lack of functional genomics studies. The knowledge of which and how TNNT2 variants cause hypertrophic and dilated cardiomyopathies could improve heart failure risk determination, treatment efficacy, and therapeutic discovery, and provide new insights into cardiomyopathy pathogenesis, as well. METHODS We created a toolkit of human induced pluripotent stem cell models and functional assays using CRISPR/Cas9 to study TNNT2 variant pathogenicity and pathophysiology. Using human induced pluripotent stem cell-derived cardiomyocytes in cardiac microtissue and single-cell assays, we functionally interrogated 51 TNNT2 variants, including 30 pathogenic/likely pathogenic variants and 21 variants of uncertain significance. We used RNA sequencing to determine the transcriptomic consequences of pathogenic TNNT2 variants and adapted CRISPR/Cas9 to engineer a transcriptional reporter assay to assist prediction of TNNT2 variant pathogenicity. We also studied variant-specific pathophysiology using a thin filament-directed calcium reporter to monitor changes in myofilament calcium affinity. RESULTS Hypertrophic cardiomyopathy-associated TNNT2 variants caused increased cardiac microtissue contraction, whereas dilated cardiomyopathy-associated variants decreased contraction. TNNT2 variant-dependent changes in sarcomere contractile function induced graded regulation of 101 gene transcripts, including MAPK (mitogen-activated protein kinase) signaling targets, HOPX, and NPPB. We distinguished pathogenic TNNT2 variants from wildtype controls using a sarcomere functional reporter engineered by inserting tdTomato into the endogenous NPPB locus. On the basis of a combination of NPPB reporter activity and cardiac microtissue contraction, our study provides experimental support for the reclassification of 2 pathogenic/likely pathogenic variants and 2 variants of uncertain significance. CONCLUSIONS Our study found that hypertrophic cardiomyopathy-associated TNNT2 variants increased cardiac microtissue contraction, whereas dilated cardiomyopathy-associated variants decreased contraction, both of which paralleled changes in myofilament calcium affinity. Transcriptomic changes, including NPPB levels, directly correlated with sarcomere function and can be used to predict TNNT2 variant pathogenicity.
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The Past, Present, and Future of Maize Improvement: Domestication, Genomics, and Functional Genomic Routes toward Crop Enhancement.
Liu, J, Fernie, AR, Yan, J
Plant communications. 2020;(1):100010
Abstract
After being domesticated from teosinte, cultivated maize (Zea mays ssp. mays) spread worldwide and now is one of the most important staple crops. Due to its tremendous phenotypic and genotypic diversity, maize also becomes to be one of the most widely used model plant species for fundamental research, with many important discoveries reported by maize researchers. Here, we provide an overview of the history of maize domestication and key genes controlling major domestication-related traits, review the currently available resources for functional genomics studies in maize, and discuss the functions of most of the maize genes that have been positionally cloned and can be used for crop improvement. Finally, we provide some perspectives on future directions regarding functional genomics research and the breeding of maize and other crops.
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Highlights on Genomics Applications for Lysosomal Storage Diseases.
La Cognata, V, Guarnaccia, M, Polizzi, A, Ruggieri, M, Cavallaro, S
Cells. 2020;(8)
Abstract
Lysosomal storage diseases (LSDs) are a heterogeneous group of rare multisystem genetic disorders occurring mostly in infancy and childhood, characterized by a gradual accumulation of non-degraded substrates inside the lysosome. Although the cellular pathogenesis of LSDs is complex and still not fully understood, the approval of disease-specific therapies and the rapid emergence of novel diagnostic methods led to the implementation of extensive national newborn screening (NBS) programs in several countries. In the near future, this will help the development of standardized workflows aimed to more timely diagnose these conditions. Hereby, we report an overview of LSD diagnostic process and treatment strategies, provide an update on the worldwide NBS programs, and discuss the opportunities and challenges arising from genomics applications in screening, diagnosis, and research.
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Plant phenomics: High-throughput technology for accelerating genomics.
Pasala, R, Pandey, BB
Journal of biosciences. 2020
Abstract
Plant phenomics is a high-throughput path-breaking area that meets all the requirements for the collection of accurate, rapid and multi-faceted phenotypic data. Plant phenomics is an approach to envisage complex traits that are appropriate for selection, and provides relevant information as to why particular genotype can stand out in particular environmental conditions. The technique of plant phenotyping can be operated in various dimensions, from the gene to the whole-plant level under a specific environment, and management practices. Through this review, we discuss the recent advances in plant phenomics, highlighting different field and confined high-throughput technologies for utilization in forward and reverse genetics. These plant phenomics technique are very relevant in stress identification, study physiological processes, rapid and efficient screening, dissection and confirmation for understanding the genetic basis of different traits, genes and aspects. Highthroughput phenomics technologies are essential to avoid human error and to reduce time consumption while phenotyping large germplasm populations, or for confirmation of gene or trait functional analysis.
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Genomics-Assisted Breeding for Quantitative Disease Resistances in Small-Grain Cereals and Maize.
Miedaner, T, Boeven, ALG, Gaikpa, DS, Kistner, MB, Grote, CP
International journal of molecular sciences. 2020;(24)
Abstract
Generating genomics-driven knowledge opens a way to accelerate the resistance breeding process by family or population mapping and genomic selection. Important prerequisites are large populations that are genomically analyzed by medium- to high-density marker arrays and extensive phenotyping across locations and years of the same populations. The latter is important to train a genomic model that is used to predict genomic estimated breeding values of phenotypically untested genotypes. After reviewing the specific features of quantitative resistances and the basic genomic techniques, the possibilities for genomics-assisted breeding are evaluated for six pathosystems with hemi-biotrophic fungi: Small-grain cereals/Fusarium head blight (FHB), wheat/Septoria tritici blotch (STB) and Septoria nodorum blotch (SNB), maize/Gibberella ear rot (GER) and Fusarium ear rot (FER), maize/Northern corn leaf blight (NCLB). Typically, all quantitative disease resistances are caused by hundreds of QTL scattered across the whole genome, but often available in hotspots as exemplified for NCLB resistance in maize. Because all crops are suffering from many diseases, multi-disease resistance (MDR) is an attractive aim that can be selected by specific MDR QTL. Finally, the integration of genomic data in the breeding process for introgression of genetic resources and for the improvement within elite materials is discussed.