The role of pangenomics in orphan crop improvement

Nature Communications, Год журнала: 2025, Номер 16(1)

Опубликована: Янв. 2, 2025

Global food security depends heavily on a few staple crops, while orphan despite being less studied, offer the potential benefits of environmental adaptation and enhanced nutritional traits, especially in changing climate. Major crops have benefited from genomics-based breeding, initially using single genomes later pangenomes. Recent advances DNA sequencing enabled pangenome construction for several offering more comprehensive understanding genetic diversity. Orphan crop research has now entered pangenomics era applying these pangenomes with advanced selection methods genome editing technologies can transform neglected species into broader agricultural significance. A reference is not enough to harness full variation species. Here, authors review principles, applications improvement, discuss possible ways support pangenomics-driven molecular breeding.

Язык: Английский

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Gap-free genome assembly and metabolomics analysis of common bean provide insights into genomic characteristics and metabolic determinants of seed coat pigmentation

Journal of genetics and genomics/Journal of Genetics and Genomics, Год журнала: 2025, Номер unknown

Опубликована: Март 1, 2025

Язык: Английский

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Recent Advances in Molecular Tools and Pre-Breeding Activities in White Lupin (Lupinus albus)

Plants, Год журнала: 2025, Номер 14(6), С. 914 - 914

Опубликована: Март 14, 2025

The higher adaptation of landraces to local agroclimatic conditions resulting from natural and moderate artificial selection by farmers within specific environments makes them a crucial source alleles genotypes for cultivation breeding programs. Unlike modern cultivars, which have been developed under more intense selective pressures, exhibit broader genetic base that has documented in landrace collections many crops. This review provides an overview the importance resource valorisation legume species, focusing on cultivated species Lupinus genus, particularly white lupin (Lupinus albus). On one hand, legumes, including Lupins, are considered alternative protein framework sustainable agriculture. other they often neglected terms efforts, despite receiving increasing attention recent years. Here, we also report latest advances development genomic tools, such as novel pangenome identification markers loci target traits, tolerance alkaline soils, can effectively support albus, especially introgression desirable locally adapted varieties.

Язык: Английский

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The evolutionary history of the common bean (Phaseolus vulgaris) revealed by chloroplast and nuclear genomes analysis

Theoretical and Applied Genetics, Год журнала: 2025, Номер 138(2)

Опубликована: Фев. 1, 2025

The origin of common bean was investigated throughout chloroplast and nuclear WGS data considering recombination events. Our results support the Mesoamerican bean. remarkable evolutionary history (Phaseolus vulgaris L.) has led to emergence three wild main gene pools corresponding different eco-geographical areas: Mesoamerica, Andes northern Peru/Ecuador. Recent works proposed novel scenarios, Peru/Ecuador population been described as a new species called P. debouckii, rekindling debate about vulgaris. Here we shed light on by analyzing genomes large varietal collection representing entire geographical distribution forms including Andean individuals. We assembled 37 de novo used them construct time frame for divergence genotypes under investigation, revealing that separation occurred ~ 0.15 Mya. clearly reject recent deboukii hypothesis. These also imply two independent migratory events from Mesoamerica North South Andes, probably facilitated birds. work represents paradigmatic example importance taking into account genetic rearrangements produced when investigating phylogeny analysis studying crop species.

Язык: Английский

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Genomic research and genetic improvement of orphan crops: novel strategies for addressing global food security challenges

Опубликована: Янв. 1, 2025

Язык: Английский

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The unexplored diversity of rough-seeded lupins provides rich genomic resources and insights into lupin evolution

Nature Communications, Год журнала: 2025, Номер 16(1)

Опубликована: Май 10, 2025

Язык: Английский

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Telomere-to-telomere genome of common bean (Phaseolus vulgaris L., YP4)

GigaScience, Год журнала: 2025, Номер 14

Опубликована: Янв. 1, 2025

Abstract Background Common bean is a significant grain legume in human diets. However, the lack of complete reference genome for common beans has hindered efforts to improve agronomic cultivars. Findings Herein, we present first telomere-to-telomere (T2T) assembly (Phaseolus vulgaris L., YP4) using PacBio High-Fidelity reads, ONT ultra-long sequencing, and Hi-C technologies. The resulted size 560.30 Mb with an N50 55.11 Mb, exhibiting high completeness accuracy (BUSCO score: 99.5%, quality value (QV): 54.86). sequences were anchored into 11 chromosomes, 20 22 telomeres identified, leading formation 9 T2T pseudomolecules. Furthermore, identified repetitive elements accounting 61.20% predicted 29,925 protein-coding genes. Phylogenetic analysis suggested estimated divergence time approximately 11.6 million years ago between P. Vigna angularis. Comparative revealed expanded gene families variations YP4 G19833 associated defense response. Conclusions genomic insights presented here are crucial future genetic studies not only but also other legumes.

Язык: Английский

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Marker-Assisted Breeding in Common Bean for Drought Tolerance

Опубликована: Янв. 1, 2025

Язык: Английский

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