Genomic selection (GS) facilitates the rapid selection of superior genotypes and accelerates the breeding cycle. In this review, we discuss the history, principles, and basis of GS and genomic-enabled prediction (GP) as well as the genetics and statistical complexities of GP models, including genomic genotype×environment (G×E) interactions. We also examine the accuracy of GP models and methods for two cereal crops and two legume crops based on random cross-validation. GS applied to maize breeding has shown tangible genetic gains. Based on GP results, we speculate how GS in germplasm enhancement (i.e., prebreeding) programs could accelerate the flow of genes from gene bank accessions to elite lines. Recent advances in hyperspectral image technology could be combined with GS and pedigree-assisted breeding.
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http://dx.doi.org/10.1016/j.tplants.2017.08.011 | DOI Listing |
Brief Bioinform
November 2024
Department of Biology, University of Padova, Via U.Bassi 58/ B, 35131, Italy.
Shallow whole-genome sequencing (sWGS) offers a cost-effective approach to detect copy number alterations (CNAs). However, there remains a gap for a standardized workflow specifically designed for sWGS analysis. To address this need, in this work we present SAMURAI, a bioinformatics pipeline specifically designed for analyzing CNAs from sWGS data in a standardized and reproducible manner.
View Article and Find Full Text PDFProc Natl Acad Sci U S A
February 2025
Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada.
ClpXP is a two-component mitochondrial matrix protease. The caseinolytic mitochondrial matrix peptidase chaperone subunit X (ClpX) recognizes and translocates protein substrates into the degradation chamber of the caseinolytic protease P (ClpP) for proteolysis. ClpXP degrades damaged respiratory chain proteins and is necessary for cancer cell survival.
View Article and Find Full Text PDFAppl Microbiol Biotechnol
January 2025
Chair of Microbiology, Technical University of Munich, TUM School of Life Science, Emil-Ramann-Str. 4, 85354, Freising, Germany.
The anaerobic bacterium Clostridium cellulovorans is a promising candidate for the sustainable production of biofuels and platform chemicals due to its cellulolytic properties. However, the genomic engineering of the species is hampered because of its poor genetic accessibility and the lack of genetic tools. To overcome this limitation, a protocol for triparental conjugation was established that enables the reliable transfer of vectors for markerless chromosomal modification into C.
View Article and Find Full Text PDFInfect Immun
January 2025
Department of Microbiology and Immunology, University of Western Ontario, London, Ontario, Canada.
is a predominant cause of post-operative surgical site infections and persistent bacteremia. Here, we describe a patient who experienced three episodes of infection over a period of 4 months following a total knee arthroplasty. The initial bloodstream isolate (SAB-0429) was a clonal complex 5 (CC5) and methicillin-resistant (MRSA), whereas two subsequent isolates (SAB-0485 and SAB-0495) were CC5 isolates but methicillin-sensitive .
View Article and Find Full Text PDFEvolution
January 2025
Department of Biological Sciences, Duquesne University, Pittsburgh, PA, 15282, United States.
Male reproductive proteins frequently evolve rapidly in animals, potentially due to adaptive evolution driven by sperm competition, polyspermy avoidance, or pathogen defense. Alternatively, elevated rates of protein change may be due to relaxed constraint. The prostate-specific protease KLK3 has experienced dynamic evolution since its origin stemming from a gene duplication in the ancestor of all Old World primates, with instances of rapid evolution, stasis, and pseudogenization.
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