Plant graph-based pangenomics: techniques, applications, and challenges

aBIOTECH, Journal Year: 2025, Volume and Issue: unknown

Published: March 28, 2025

Abstract Innovations in DNA sequencing technologies have greatly boosted population-level genomic studies plants, facilitating the identification of key genetic variations for investigating population diversity and accelerating molecular breeding crops. Conventional methods analysis typically rely on small variants, such as SNPs indels, use single linear reference genomes, which introduces biases reduces performance highly divergent regions. By integrating level sequences, pangenomes, particularly graph offer a promising solution to these challenges. To date, numerous algorithms been developed constructing pangenome graphs, aligning reads performing variant genotyping based graphs. As demonstrated various plant pangenomic studies, advancements allow detection previously hidden especially structural thereby enhancing applications mapping agronomically important genes. However, noteworthy challenges remain be overcome applying approaches plants. Addressing issues will require development more sophisticated tailored specifically Such improvements contribute scalability this approach, production super-pangenomes, hundreds or even thousands de novo–assembled genomes from one species genus can integrated. This, turn, promote broader pan-omic further advancing our understanding driving innovations crop breeding.

Language: Английский

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Graphical pangenomics-enabled characterization of structural variant impact on gene expression in Brassica napus

Theoretical and Applied Genetics, Journal Year: 2025, Volume and Issue: 138(4)

Published: April 1, 2025

Language: Английский

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Genome-Wide Association Analysis of Seedling Traits in Upland Cotton Under Low Temperature Stress

Published: Jan. 1, 2025

Language: Английский

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Gossypium latifolium genome reveals the genetic basis of domestication of upland cotton from semi-wild races to cultivars

The Crop Journal, Journal Year: 2025, Volume and Issue: unknown

Published: April 1, 2025

Language: Английский

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Disease Resistance at the Molecular Level: Omics-Based Approaches for Tomato Defense

Published: Jan. 1, 2025

Language: Английский

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Insights into spinach domestication from genome sequences of two wild spinach progenitors, Spinacia turkestanica and Spinacia tetrandra

New Phytologist, Journal Year: 2024, Volume and Issue: 243(1), P. 477 - 494

Published: May 7, 2024

Cultivated spinach (Spinacia oleracea) is a dioecious species. We report high-quality genome sequences for its two closest wild relatives, Spinacia turkestanica and tetrandra, which are also dioecious, used to study the genetics of domestication. Using combination genomic approaches, we assembled genomes both these species analyzed them in comparison with previously S. oleracea genome. These diverged c. 6.3 million years ago (Ma), while cultivated split from 0.8 Ma. In all three species, six chromosomes include very large gene-poor, repeat-rich regions, which, oleracea, pericentromeric regions low recombination rates male female genetic maps. describe population evidence that similar recombine rarely. characterized 282 structural variants (SVs) have been selected during genes associated leaf margin type flowering time. downy mildew resistance loci derived introgression Collectively, this reveals architecture assemblies highlights importance SVs domestication spinach.

Language: Английский

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k-mer-Based Genome-Wide Association Studies in Plants: Advances, Challenges, and Perspectives

Genes, Journal Year: 2023, Volume and Issue: 14(7), P. 1439 - 1439

Published: July 13, 2023

Genome-wide association studies (GWAS) have allowed the discovery of marker-trait associations in crops over recent decades. However, their power is hampered by a number limitations, with key one among them being an overreliance on single-nucleotide polymorphisms (SNPs) as molecular markers. Indeed, SNPs represent only type genetic variation and are usually derived from alignment to single genome assembly that may be poorly representative population under study. To overcome this,

Language: Английский

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Back to wild relatives for future breeding through super-pangenome

Molecular Plant, Journal Year: 2023, Volume and Issue: 16(9), P. 1363 - 1365

Published: Aug. 11, 2023

Language: Английский

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Combined genome and transcriptome analysis of elite fiber quality in Gossypium barbadense

PLANT PHYSIOLOGY, Journal Year: 2024, Volume and Issue: 195(3), P. 2158 - 2175

Published: March 21, 2024

Abstract Gossypium barbadense, which is one of several species cotton, well known for its superior fiber quality. However, the genetic basis high-quality remains largely unexplored. Here, we resequenced 269 G. barbadense accessions. Phylogenetic structure analysis showed that set accessions was clustered into 3 groups: G1 and G2 mainly included modern cultivars from Xinjiang, China, G3 related to widely introduced in different regions worldwide. A genome-wide association study 5 quality traits across multiple field environments identified a total 512 qtls (main-effect QTLs) 94 qtlEs (QTL-by-environment interactions) quality, 292 57 colocated with previous studies. We extracted genes located these loci performed expression comparison, local analysis, introgression segment identification. The results high hormone-related during development, introgressions hirsutum, recombination domesticated elite allelic variation were major contributors improve barbadense. In total, 839 candidate encoding region variations associated mined. confirmed haplotype GB_D03G0092H traced hirsutum introgression, 1-bp deletion leading frameshift mutation compared GB_D03G0092B, significantly improved localized plasma membrane, while GB_D03G0092B both nucleus membrane. Overexpression Arabidopsis (Arabidopsis thaliana) elongation longitudinal cells. Our systematically reveals provides segments gene resources breeding cotton cultivars.

Language: Английский

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The Detection of a Functional 168 bp Deletion of the HOXB13 Gene Determining Short Tail and Its Association with Senior Growth Traits in Sheep Breeds Worldwide

Animals, Journal Year: 2024, Volume and Issue: 14(11), P. 1617 - 1617

Published: May 29, 2024

In recent years, genome-wide association studies (GWAS) have uncovered that the HOXB13 gene is a key regulatory factor for tail length trait of sheep. Further research has found there functional 168 bp SINE element insertion upstream gene, which leads to occurrence long tails in However, frequency mutations among different sheep breeds around world and its relationship with growth traits are still unclear. This study used whole-genome sequencing (WGS) data, including 588 samples from 33 world, evaluate globally. At same time, this also selected 3392 six breeds. The genetic variation InDel locus was determined through genotyping, Luxi black-headed analyzed. results indicate polymorphism significantly correlated hip width adult ewes breed (p < 0.05) DD genotype larger than ID 0.05). indicates consistency between on traits, may contribute promotion improvement.

Language: Английский

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