Genome biology, Journal Year: 2023, Volume and Issue: 24(1)
Published: Dec. 8, 2023
Many elite genes have been identified from the available cotton genomic data, providing various genetic resources for gene-driven breeding. However, backbone cultivar-driven breeding is most widely applied strategy. Revealing basis of strategy's restriction crucial transition
Language: Английский
Annual Review of Genomics and Human Genetics, Journal Year: 2024, Volume and Issue: 25(1), P. 77 - 104
Published: April 25, 2024
The Human Genome Project was an enormous accomplishment, providing a foundation for countless explorations into the genetics and genomics of human species. Yet many years, genome reference sequence remained incomplete lacked representation genetic diversity. Recently, two major advances have emerged to address these shortcomings: complete gap-free sequences, such as one developed by Telomere-to-Telomere Consortium, high-quality pangenomes, Pangenome Reference Consortium. Facilitated in long-read DNA sequencing assembly algorithms, sequences resolve regions that been historically difficult sequence, including centromeres, telomeres, segmental duplications. In parallel, pangenomes capture extensive diversity across populations worldwide. Together, usher new era research, enhancing accuracy genomic analysis, paving path precision medicine, contributing deeper insights biology.
Language: Английский
Citations
7
The Nucleus, Journal Year: 2024, Volume and Issue: 67(1), P. 181 - 203
Published: March 21, 2024
Language: Английский
Citations
6
Cell Reports, Journal Year: 2023, Volume and Issue: 42(9), P. 113039 - 113039
Published: Aug. 30, 2023
Functional cloning and manipulation of genes controlling various agronomic traits are important for boosting crop production. Although bulked segregant analysis (BSA) is an efficient method functional cloning, its low throughput cannot satisfy the current need breeding food security. Here, we review rationale development conventional BSA discuss strengths drawbacks. We then propose next-generation (NG-BSA) integrating multiple cutting-edge technologies, including high-throughput phenotyping, biological big data, use machine learning. NG-BSA increases resolution genetic mapping quantitative trait (QTGs) optimizes candidate gene selection while providing a means to elucidate interaction network QTGs. The ability efficiently batch-clone QTGs makes it tool dissecting molecular mechanisms underlying traits, as well improvement Breeding 4.0 strategy, especially in targeted population crops.
Language: Английский
Citations
14
Plant Biotechnology Journal, Journal Year: 2023, Volume and Issue: 22(3), P. 544 - 554
Published: Nov. 14, 2023
Summary Inversions, a type of chromosomal structural variation, significantly influence plant adaptation and gene functions by impacting expression recombination rates. However, compared with other variations, their roles in functional biology crop improvement remain largely unexplored. In this review, we highlight technological methodological advancements that have allowed comprehensive understanding inversion variants through the pangenome framework machine learning algorithms. Genome editing is an efficient method for inducing or reversing mutations plants, providing effective mechanism to modify local Given potential inversions breeding, anticipate increasing attention on from scientific community future research breeding applications.
Language: Английский
Citations
14
Research Square (Research Square), Journal Year: 2024, Volume and Issue: unknown
Published: Feb. 28, 2024
Abstract Biological invasions are a major threat to biodiversity. Therefore, monitoring genomic features of invasive species is crucial understand their population structure and adaptive processes. However, resources scarce, compromising the study success. Here, we present reference genome Styela plicata , one most widespread marine species, combined with data 24 individuals from 6 populations distributed worldwide. We characterized large inversions in four chromosomes, accounting for ~ 15% size. These polymorphic through species’ distribution area, enriched genes enhancing fitness estuary harbor environments. Nonetheless, mask detection S. structure. When these structural variants removed, successfully identify main oceanographic barriers accurately characterize differentiation between within ocean basins. Several located chromosome 3 showcased as drivers biogeographic regions. Moreover, recover three mitogenomic clades, involving rearrangements leading cyto-nuclear coevolution likely involved mitochondrion during cell division. Our results suggest that contribute structuring adaptation processes, potentially success when colonizing new habitats.
Language: Английский
Citations
5
Biomolecules, Journal Year: 2023, Volume and Issue: 13(9), P. 1403 - 1403
Published: Sept. 17, 2023
The availability of multiple sequenced genomes from a single species made it possible to explore intra- and inter-specific genomic comparisons at higher resolution build clade-specific pan-genomes several crops. crops constructed various cultivars, accessions, landraces, wild ancestral represent compendium genes structural variations allow researchers search for the novel alleles that were inadvertently lost in domesticated during historical process crop domestication or extensive plant breeding. Fortunately, many valuable associated with desirable traits like disease resistance, abiotic stress tolerance, architecture, nutrition qualities exist species, relatives. ancestors landraces can be introduced back high-yielding varieties modern by implementing classical breeding, selection, transgenic/gene editing approaches. Thus, pan-genomic represents great leap research offers new avenues targeted breeding mitigate impact global climate change. Here, we summarize tools used pan-genome assembly annotations, web-portals hosting pan-genomes, etc. Furthermore, highlight few discoveries using approach future potential this emerging field study.
Language: Английский
Citations
12
Agriculture Communications, Journal Year: 2024, Volume and Issue: 2(2), P. 100039 - 100039
Published: March 30, 2024
A pangenome encompasses the complete genetic diversity of a species, by assembling range representative individuals from various populations. This review describes advances in plant pangenomics, tracing its evolution since initial genome sequencing 2000, and provides comprehensive best-practice advice to build linear or graphical pangenome, delineating strengths limitations different construction methods. The also examines challenges data visualisation, graph-based pangenomes their utility investigating potential function variation. Furthermore, we examine application breeding, including identification for crop improvement, integration multi-omics into databases advance breeding.
Language: Английский
Citations
4
aBIOTECH, Journal Year: 2025, Volume and Issue: 6(1), P. 22 - 32
Published: Jan. 18, 2025
Abstract The embryo spot trait leads to a deep purple or reddish coloration at the base of cotyledons embryo, visible on both sides flat potato ( Solanum tuberosum ) seeds. This has long been used by researchers and breeders as morphological marker during dihaploid induction. formation spots reflects accumulation anthocyanins, but genetic basis this remains unclear. In study, we mapped 6.78-Mb region end chromosome 10 using an F 2 population derived from cross between spotted spotless plants. recombination rate in candidate is severely suppressed, posing challenges for map-based cloning underlying gene suggesting large-scale rearrangements region. A de novo genome assembly individual comparative genomic analysis reference revealed 6.49-Mb inversion present plant genome. left breakpoint occurred promoter R2R3 MYB transcription factor that highly expressed cotyledon embryos not embryos. study elucidated provides foundation future causative gene.
Language: Английский
Citations
0
Industrial Crops and Products, Journal Year: 2025, Volume and Issue: 226, P. 120639 - 120639
Published: Feb. 6, 2025
Language: Английский
Citations
0
Nature Communications, Journal Year: 2025, Volume and Issue: 16(1)
Published: March 11, 2025
Structural variations (SVs) are diverse forms of genetic alterations and drive a wide range human diseases. Accurately genotyping SVs, particularly occurring at repetitive genomic regions, from short-read sequencing data remains challenging. Here, we introduce SVLearn, machine-learning approach for bi-allelic SVs. It exploits dual-reference strategy to engineer curated set genomic, alignment, features based on reference genome in concert with an allele-based alternative genome. Using 38,613 human-derived show that SVLearn significantly outperforms four state-of-the-art tools, precision improvements up 15.61% insertions 13.75% deletions regions. On two additional sets 121,435 cattle SVs 113,042 sheep demonstrates strong generalizability cross-species genotype weighted concordance score 90%. Notably, enables accurate low coverage, which is comparable the accuracy 30× coverage. Our studies suggest can accelerate understanding associations between genome-scale, high-quality genotyped diseases across multiple species. structural authors precise demonstrating robust coverage levels.
Language: Английский
Citations
0