Comparative genomic profiling of CBFs pan-gene family in five yellowhorn cultivars and functional identification of Xg11_CBF11 DOI Creative Commons
Juan Wang,

Xizhen Liang,

Weiyang Zhang

et al.

Frontiers in Plant Science, Journal Year: 2024, Volume and Issue: 15

Published: Nov. 19, 2024

C-repeat binding factor (

Language: Английский

The role of pangenomics in orphan crop improvement DOI Creative Commons
Haifei Hu, Junliang Zhao, William J. W. Thomas

et al.

Nature Communications, Journal Year: 2025, Volume and Issue: 16(1)

Published: Jan. 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.

Language: Английский

Citations

2
Pear genomes display significant genetic diversity and provide novel insights into the fruit quality traits differentiation DOI Creative Commons
Baopeng Ding, Haifei Hu, Yunpeng Cao

et al.

Horticultural Plant Journal, Journal Year: 2024, Volume and Issue: 10(6), P. 1274 - 1290

Published: Aug. 14, 2024

The pear (Pyrus spp.) is well known for diverse flavors, textures, and global horticultural importance. However, the genetic diversity responsible its extensive phenotypic variations remains largely unexplored. Here, we de novo assembled annotated genomes of maternal (PsbM) paternal (PsbF) lines hybrid 'Yuluxiang' constructed pangenome 1.15 Gb by combining these two with five previously published representing cultivated wild germplasm. Using pangenome, identified 21 224 gene PAVs (Presence-absence variation) 1 158 812 SNPs (Single Nucleotide Polymorphism) in non-reference genome that were absent PsbM reference genome. Compared SNP markers, PAV-based analysis provides additional insights into population structure. In addition, some genes associated fruit quality traits have differential occurrence frequencies expression between Asian European populations. Moreover, our revealed a mutated an insertion promoter region PsbMGH3.1 potentially enhance sepal shedding 'Xuehuali' which vital quality. may play role IAA pathway, contributing to distinct low-auxin phenotype observed plants heterologously overexpressing this gene. This research helps capture populations genomic resources accelerating breeding.

Language: Английский

Citations

8
The power of small signaling peptides in crop and horticultural plants DOI Creative Commons

Chao Ji,

Hui Li,

Zilin Zhang

et al.

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

Published: Jan. 1, 2025

Language: Английский

Citations

1
Graphical pangenomics-enabled characterization of structural variant impact on gene expression in Brassica napus DOI Creative Commons
Gözde Yildiz, Silvia Zanini, Sven E. Weber

et al.

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

Published: April 1, 2025

Language: Английский

Citations

0
Brassica Panache: A multi‐species graph pangenome representing presence absence variation across forty‐one Brassica genomes DOI Creative Commons
Tessa R. MacNish, Hawlader Abdullah Al-Mamun, Philipp E. Bayer

et al.

The Plant Genome, Journal Year: 2024, Volume and Issue: unknown

Published: Dec. 8, 2024

Abstract Brassicas are an economically important crop species that provide a source of healthy oil and vegetables. With the rising population impact climate change on agriculture, there is increasing need to improve agronomically traits crops such as Brassica . The genomes plant have significant sequence presence absence variation (PAV), which genetic can be used for improvement, this captured through construction pangenomes. Graph pangenomes recent reference format represent genomic with or alternate paths in graph. contain information alignment, PAV, annotation. Here we present first multi‐species graph pangenome visualized analyzer chromosomal exploration (Panache).

Language: Английский

Citations

2
A stepwise guide for pangenome development in crop plants: an alfalfa (Medicago sativa) case study DOI Creative Commons
Harpreet Kaur, Laura M. Shannon, Deborah A. Samac

et al.

BMC Genomics, Journal Year: 2024, Volume and Issue: 25(1)

Published: Oct. 31, 2024

The concept of pangenomics and the importance structural variants is gaining recognition within plant genomics community. Due to advancements in sequencing computational technology, it has become feasible sequence entire genome numerous individuals a single species at reasonable cost. Pangenomes have been constructed for many major diploid crops, including rice, maize, soybean, sorghum, pearl millet, peas, sunflower, grapes, mustards. However, pangenomes polyploid are relatively scarce available only few crops wheat, cotton, rapeseed, potatoes.

Language: Английский

Citations

0
Unlocking diversity from wild relatives of perennial fruit crops in the pan-genomics era DOI
Jean Sabety, Anže Švara,

Richard Tegtmeier

et al.

Current Opinion in Plant Biology, Journal Year: 2024, Volume and Issue: 82, P. 102652 - 102652

Published: Oct. 31, 2024

Language: Английский

Citations

0
Comparative genomic profiling of CBFs pan-gene family in five yellowhorn cultivars and functional identification of Xg11_CBF11 DOI Creative Commons
Juan Wang,

Xizhen Liang,

Weiyang Zhang

et al.

Frontiers in Plant Science, Journal Year: 2024, Volume and Issue: 15

Published: Nov. 19, 2024

C-repeat binding factor (

Language: Английский

Citations

0