Unravelling inversions: Technological advances, challenges, and potential impact on crop breeding DOI Creative Commons
Haifei Hu, Armin Scheben, Jian Wang

et al.

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

ODGI: understanding pangenome graphs DOI Creative Commons
Andrea Guarracino, Simon Heumos, Sven Nahnsen

et al.

Bioinformatics, Journal Year: 2022, Volume and Issue: 38(13), P. 3319 - 3326

Published: May 10, 2022

Pangenome graphs provide a complete representation of the mutual alignment collections genomes. These models offer opportunity to study entire genomic diversity population, including structurally complex regions. Nevertheless, analyzing hundreds gigabase-scale genomes using pangenome is difficult as it not well-supported by existing tools. Hence, fast and versatile software required ask advanced questions such data in an efficient way.

Language: Английский

Citations

97
Plant pan-genomics and its applications DOI Creative Commons
Junpeng Shi, Zhixi Tian, Jinsheng Lai

et al.

Molecular Plant, Journal Year: 2022, Volume and Issue: 16(1), P. 168 - 186

Published: Dec. 15, 2022

Language: Английский

Citations

72
A review of the pangenome: how it affects our understanding of genomic variation, selection and breeding in domestic animals? DOI Creative Commons
Ying Gong, Yefang Li, Xuexue Liu

et al.

Journal of Animal Science and Biotechnology/Journal of animal science and biotechnology, Journal Year: 2023, Volume and Issue: 14(1)

Published: May 5, 2023

Abstract As large-scale genomic studies have progressed, it has been revealed that a single reference genome pattern cannot represent genetic diversity at the species level. While domestic animals tend to complex routes of origin and migration, suggesting possible omission some population-specific sequences in current genome. Conversely, pangenome is collection all DNA contains shared by individuals (core genome) also able display sequence information unique each individual (variable genome). The progress research humans, plants proved missing components identification large structural variants (SVs) can be explored through pangenomic studies. Many specific shown related biological adaptability, phenotype important economic traits. maturity technologies methods such as third-generation sequencing, Telomere-to-telomere genomes, graphic reference-free assembly will further promote development pangenome. In future, combined with long-read data multi-omics help resolve SVs their relationship main traits interest domesticated animals, providing better insights into animal domestication, evolution breeding. this review, we mainly discuss how analysis reveals variations (sheep, cattle, pigs, chickens) impacts on phenotypes contribute understanding diversity. Additionally, go potential issues future perspectives livestock poultry.

Language: Английский

Citations

46
Technology-enabled great leap in deciphering plant genomes DOI
Lingjuan Xie, Xiaojiao Gong, Kun Yang

et al.

Nature Plants, Journal Year: 2024, Volume and Issue: 10(4), P. 551 - 566

Published: March 20, 2024

Language: Английский

Citations

34
Plant pangenomes for crop improvement, biodiversity and evolution DOI
Mona Schreiber, Murukarthick Jayakodi, Nils Stein

et al.

Nature Reviews Genetics, Journal Year: 2024, Volume and Issue: 25(8), P. 563 - 577

Published: Feb. 20, 2024

Language: Английский

Citations

32
The super-pangenome of Populus unveils genomic facets for its adaptation and diversification in widespread forest trees DOI Creative Commons
Tingting Shi, Xinxin Zhang,

Yukang Hou

et al.

Molecular Plant, Journal Year: 2024, Volume and Issue: 17(5), P. 725 - 746

Published: March 13, 2024

Understanding the underlying mechanisms and links between genome evolution adaptive innovations stands as a key goal in evolutionary studies. Poplars, among world's most widely distributed cultivated trees, exhibit extensive phenotypic diversity environmental adaptability. In this study, we present genus-level super-pangenome comprising 19 Populus genomes, revealing likely pivotal role of private genes facilitating local climate adaptation. Through integration pangenomes with transcriptomes, methylomes, chromatin accessibility mapping, unveil that trajectories pangenes duplicated are closely linked to genomic landscapes regulatory epigenetic architectures, notably CG methylation gene-body regions. Further comparative analyses have enabled identification 142 202 structural variants across species intersect significant number contribute substantially both divergence. We experimentally validated ∼180-bp presence/absence variant affecting expression CUC2 gene, crucial for leaf serration formation. Finally, developed user-friendly web-based tool encompassing multi-omics resources associated (http://www.populus-superpangenome.com). Together, pioneering resource forest trees not only aids advancement breeding efforts globally important tree genus but also offers valuable insights into potential avenues comprehending biology.

Language: Английский

Citations

25
The Marchantia polymorpha pangenome reveals ancient mechanisms of plant adaptation to the environment DOI Creative Commons
Chloé Beaulieu, Cyril Libourel,

Duchesse Lacourt Mbadinga Zamar

et al.

Nature Genetics, Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 17, 2025

Language: Английский

Citations

3
Plant pan-genomics: recent advances, new challenges, and roads ahead DOI Creative Commons
Wei Li, Jianan Liu, Hongyu Zhang

et al.

Journal of genetics and genomics/Journal of Genetics and Genomics, Journal Year: 2022, Volume and Issue: 49(9), P. 833 - 846

Published: June 21, 2022

Pan-genomics can encompass most of the genetic diversity a species or population and has proved to be powerful tool for studying genomic evolution origin domestication species, providing information plant improvement. Plant genomics greatly progressed because improvements in sequencing technologies rapid reduction costs. Nevertheless, pan-genomics still presents many challenges, including computationally intensive assembly methods, high costs with large numbers samples, ineffective integration big data, difficulty applying it downstream multi-omics analysis breeding research. In this review, we summarize definition recent achievements pan-genomics, computational used pan-genome construction, applications pan-genomes molecular breeding. We also discuss challenges perspectives future studies provide detailed pipeline sample selection, genome annotation, structural variation identification, construction application graph-based pan-genomes. The aim is important guidance research better understanding basis evolution, crop domestication, phenotypic studies.

Language: Английский

Citations

62
Multi-omics revolution to promote plant breeding efficiency DOI Creative Commons
Umer Mahmood, Xiaodong Li, Yonghai Fan

et al.

Frontiers in Plant Science, Journal Year: 2022, Volume and Issue: 13

Published: Dec. 8, 2022

Crop production is the primary goal of agricultural activities, which always taken into consideration. However, global systems are coming under increasing pressure from rising food demand rapidly growing world population and changing climate. To address these issues, improving high-yield climate-resilient related-traits in crop breeding an effective strategy. In recent years, advances omics techniques, including genomics, transcriptomics, proteomics, metabolomics, paved way for accelerating plant/crop to cope with climate enhance production. Optimized phenotypic plasticity platform integration, exploited by evolving machine learning algorithms will aid development biological interpretations complex traits. The precise progressive assembly desire alleles using genome editing approaches enhanced strategies would enable future crops excel combating climates. Furthermore, plant genetic engineering ensures exclusive approach developing nutrient sufficient crops, productivity can sustainably adequately meet world's food, nutrition, energy needs. This review provides overview how integration could be select varieties desired

Language: Английский

Citations

56
Genomics of plant speciation DOI Creative Commons
Dan G. Bock,

Zhe Cai,

Cassandra Elphinstone

et al.

Plant Communications, Journal Year: 2023, Volume and Issue: 4(5), P. 100599 - 100599

Published: April 12, 2023

Studies of plants have been instrumental for revealing how new species originate. For several decades, botanical research has complemented and, in some cases, challenged concepts on speciation developed via the study other organisms while also additional ways which can form. Now, ability to sequence genomes at an unprecedented pace and scale allowed biologists settle decades-long debates tackle emerging challenges research. Here, we review these recent genome-enabled developments plant speciation. We discuss complications related identification reproductive isolation (RI) loci using analyses landscape genomic divergence highlight important role that structural variants speciation, as increasingly revealed by sequencing technologies. Further, genomics advanced what know routes formation, like hybridization or whole-genome duplication, casting doubt others, population bottlenecks genetic drift. While fast-track genes mutations confer RI, emphasize follow-up molecular field experiments remain critical. Nonetheless, clarified outsized ancient rather than mutations, particularly early during conclude highlighting promising avenues future study. These include expanding so far about epigenetic changes broadening scope taxonomic breadth studies, synthesizing information from extensive data already generated community.

Language: Английский

Citations

39