Multiomics plasticity in seed traits of pan-genome wheat cultivars DOI Open Access
Utpal Bose, J. Barbro Winkler,

Elisa Sorg

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Dec. 21, 2024

Abstract The molecular basis of cultivar-level variations in polyploid wheat that enables environmental adaptation while maintaining yield and quality remains poorly understood. We conducted a detailed phenotypic assessment multiomics analysis nine pan-genome cultivars grown under control drought conditions. aimed to investigate the subgenome-level variations, cultivar differences biochemical mechanisms affecting plant fitness moderate stress. Intrinsic water use efficiency, grain yield, protein content differed among cultivars, supporting plasticity stress responses. Biased proteome metabolome abundance changes response during vegetative stage indicate different strategies for utilization homeologous isoforms assigned A, B, D subgenomes. Drought effects were detected at level, but significant observed central carbon pathway metabolites micronutrient profiles. subgenomic localization seed storage proteins highlight nutrient reservoir accumulation emphasizes enhanced role S-rich prolamins response. Subgenomic define phenotypes by producing molecules accumulate enable underlying trade-offs between yield- or quality-related traits. These can be used select crops with increased resistance without compromising yield.

Language: Английский

Unraveling Allelic Impacts on Pre-Harvest Sprouting Resistance in TaVP1-B of Chinese Wheat Accessions Using Pan-Genome DOI Creative Commons
Danfeng Wang,

Xie Jin-jin,

Jingwen Wang

et al.

Plants, Journal Year: 2025, Volume and Issue: 14(4), P. 504 - 504

Published: Feb. 7, 2025

The TaVP1-B gene, located on the 3B chromosome of wheat, is a homolog Viviparous-1 (VP-1) gene maize and was reported to confer resistance pre-harvest sprouting (PHS) in wheat. In this study, structure analyzed using wheat pan-genome consisting 20 released cultivars (19 are from China), 3 single nucleotide polymorphisms (SNPs), which were identified at 496 bp, 524 1548 bp CDS region, respectively. Haplotypes analysis showed that these SNPs complete linkage disequilibrium only two haplotypes designated as hap1 (TGG) hap2 (GAA) present. Association between PHS four experiment environments revealed average accessions with significantly better than hap2, infers effects resistance. To further investigate impacts alleles locus resistance, SNP region converted KASP marker, used for genotyping 304 Chinese cultivars, whose evaluated three environments. rates (SRs) 135 lower 169 validating present study provided breeding-friendly marker functional variants can be genetic improvement

Language: Английский

Citations

1
Integration of multi-omics data accelerates molecular analysis of common wheat traits DOI Creative Commons
Ning Zhang, Li Tang, Songgang Li

et al.

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

Published: March 5, 2025

Integration of multi-omics data can provide information on biomolecules from different layers to illustrate the complex biology systematically. Here, we build a atlas containing 132,570 transcripts, 44,473 proteins, 19,970 phosphoproteins, and 12,427 acetylproteins across wheat vegetative reproductive phases. Using this atlas, elucidate transcriptional regulation network, contributions post-translational modification (PTM) transcript level protein abundance, biased homoeolog expression PTM in wheat. The genes/proteins related development disease resistance are systematically analyzed, thus identifying phosphorylation and/or acetylation modifications for seed proteins controlling grain quality resistance-related genes. Lastly, unique module TaHDA9-TaP5CS1, specifying de-acetylation TaP5CS1 by TaHDA9, is discovered, which regulates Fusarium crown rot via increasing proline content. Our holds great promise fast-tracking molecular breeding studies crops.

Language: Английский

Citations

1
Genomics-guided landscape unlocks superior alleles and genes for yellow rust resistance in wheat DOI Creative Commons
Jianhui Wu, Shengwei Ma, Jianqing Niu

et al.

Research Square (Research Square), Journal Year: 2025, Volume and Issue: unknown

Published: March 11, 2025

Abstract Yellow rust (YR), caused by Puccinia striiformis f. sp. tritici (Pst), poses a significant threat to wheat production worldwide. Breeding resistant cultivar is crucial for managing this disease. However, understanding of the genetic mechanisms underlying YR resistance remains fragmented. To address this, we conducted comprehensive analysis with variome data from 2,191 accessions worldwide and over 47,000 response records across multiple environments pathogen races. Through genome-wide association studies, established landscape 431 loci, providing rich resource (R) gene deployment. Furthermore, cloned genes corresponding three namely Yr5x effective against Pst races, Yr6/Pm5 that conferred two species, YrKB (TaEDR2-B) conferring broad-spectrum without yield penalty. These findings offer valuable insights into basis in lay foundation engineering durable disease resistance.

Language: Английский

Citations

1
The location and genome origin of alien chromatin in wheat founder parent Xiaoyan 6 DOI
Qiaoling Luo, Qiaoling Luo,

Chunyan Tong

et al.

Theoretical and Applied Genetics, Journal Year: 2025, Volume and Issue: 138(2)

Published: Feb. 1, 2025

Language: Английский

Citations

0
Construction of the super pan-genome for the genus Actinidia reveals structural variations linked to phenotypic diversity DOI Creative Commons
Haolin Wu, Wenjie Yang,

Guanyong Dong

et al.

Horticulture Research, Journal Year: 2025, Volume and Issue: 12(6)

Published: March 3, 2025

Kiwifruits, belonging to the genus Actinidia, are acknowledged as one of most successfully domesticated fruits in twentieth century. Despite rich wild resources and diverse phenotypes within this genus, insights into genomic changes still limited. Here, we conducted whole-genome sequencing on seven representative materials from highly diversified sections leading assembly annotation 14 haplotype genomes with sizes spanning 602.0 699.6 Mb. By compiling these genomes, constructed a super pan-genome for genus. We identified numerous structural variations (SVs, including gene copy number) diverged regions genomes. Notably, significant SV variability was observed intronic MED25 TTG1 genes across different materials, suggesting their potential roles influencing fruit size trichome formation. Intriguingly, our findings indicated high genetic divergence between two individual, tentatively named Actinidia × leiocacarpae, sect. Leiocacarpae. This likely hybrid heterozygous genome exhibited notable adaptations related resistance against bacterial canker, particularly through upregulation RPM1 gene, which contains specific SV, after infection by Pseudomonas syringae pv. actinidiae. In addition, also discussed interlineage hybridizations taxonomic treatments Actinidia. Overall, comprehensive here, along findings, lays foundation examining compositions markers, those SVs, facilitate breeding aimed at developing desired kiwifruits.

Language: Английский

Citations

0
Advances in basic biology of alfalfa (Medicago sativa L.): a comprehensive overview DOI Creative Commons
Yuanyuan Zhang, Lei Wang

Horticulture Research, Journal Year: 2025, Volume and Issue: 12(7)

Published: March 10, 2025

Abstract Alfalfa (Medicago sativa L.), a perennial legume forage, has been broadly cultivated owing to variety of favorable characteristics, including comprehensive ecological adaptability, superior nutritive value and palatability, nitrogen fixation capacity. The productivity traits alfalfa, specifically its biomass yield forage quality, are significantly influenced by series determinants, internal developmental factors external environmental cues. However, the regulatory mechanisms underlying fundamental biological problems alfalfa remain elusive. Here, we conducted review focusing on genomics advancements in gene-editing technologies, identification genes that control pivotal agronomic formation, nutritional flowering time, resistance various stresses. Moreover, molecular design roadmap for ‘ideal alfalfa’ proposed potential pangenomes, self-incompatibility mechanisms, de novo domestication, intelligent breeding strategies enhance alfalfa's yield, resilience were further discussed. This will provide information basic biology offer new insights cultivation ideal alfalfa.

Language: Английский

Citations

0
Pangenome charts the genomic path for wheat improvement DOI
Mahendar Thudi, Martin Mascher, Murukarthick Jayakodi

et al.

Trends in Plant Science, Journal Year: 2025, Volume and Issue: unknown

Published: March 1, 2025

Language: Английский

Citations

0
Evaluating Genome Assemblies for Optimized Completeness and Accuracy of Reference Gene Sequences in Wheat, Rye, and Triticale DOI Creative Commons
Mingke Yan, Guodong Yang, Dongming Yang

et al.

Plants, Journal Year: 2025, Volume and Issue: 14(7), P. 1140 - 1140

Published: April 6, 2025

Recent years have witnessed a surge in the publication of dozens genome assemblies for Triticeae crops, which significantly advanced gene-related research wheat, rye, and triticale. However, this progress has also introduced challenges selecting universally efficient applicable reference genomes genotypes with distant or ambiguous phylogenetic relationships. In study, we assessed completeness accuracy triticale using comparative benchmarking universal single-copy orthologue (BUSCO) analysis transcript mapping approaches. BUSCO revealed that proportion complete genes positively correlated RNA-seq read mappability, while frequency internal stop codons served as significant negative indicator assembly data mappability wheat. By integrated alignment rate, covered length, total depth from data, identified SY Mattis, Lo7, Mattis plus Lo7 most robust references studies triticale, respectively. Furthermore, recommend D sequence be incorporated bioinformatic analyses introgression, translocation, substitution into frequently occurs during breeding. The could help evaluating correctness published future, other findings are expected to support closely related species.

Language: Английский

Citations

0
Integrated review of Psathyrostachy huashanica: From phylogenetic research to wheat breeding application DOI
Yinghui Li,

Binwen Tan,

Jingyuan Yang

et al.

Molecular Breeding, Journal Year: 2025, Volume and Issue: 45(4)

Published: April 1, 2025

Language: Английский

Citations

0
Advancing wheat breeding using rye: a key contribution to wheat breeding history DOI Creative Commons

G C Han,

Hanwen Yan,

LI Li-hui

et al.

Trends in biotechnology, Journal Year: 2025, Volume and Issue: unknown

Published: April 1, 2025

Language: Английский

Citations

0