African rice (Oryza glaberrima) genomic introgressions impacting upon panicle architecture in Asian rice (O. sativa) lead to the identification of key QTLs DOI Creative Commons
Hélène Adam, Andrés Gutiérrez‐Rodríguez, Marie Couderc

et al.

Research Square (Research Square), Journal Year: 2023, Volume and Issue: unknown

Published: May 11, 2023

Abstract Background: Developing high yielding varieties is a major challenge for breeders tackling the challenges of climate change in agriculture. The panicle (inflorescence) architecture rice one key components yield potential and displays inter- intra-specific variability. genus Oryza features two different crop species: Asian ( sativa L.) African O. glaberrima Steud). One main morphological differences between independently domesticated species structure (or complexity) panicle, with displaying highly branched which turn produces larger number grains than that . genetic interactions govern diversity complexity within are still poorly understood. Results: To identify factors linked to species, we used set 60 Chromosome Segment Substitution Lines (CSSLs) issued from third generation backcross (BC 3 DH) carrying genomic segments cv. MG12 background Tropical Japonica Caiapó. Phenotypic data were collected rachis primary branch length, primary, secondary tertiary spikelet number. A total 15 QTLs localized on chromosomes 1, 2, 3, 7, 11 12 associated enhanced numbers detected CSSLs. Furthermore, BC 4 F 3:5 lines combinations substituted produced decipher effects identified QTL regions variations architecture. detailed analysis phenotypes versus genotypes was carried out parental genomes these order understand how introgression events may lead alterations traits. Conclusion: Our led detection Caiapó traits specific These contain genes regulate development their interspecific explain phenotypic observed.

Language: Английский

Detecting novel plant pathogen threats to food system security by integrating the Plant Reactome and remote sensing DOI
Seth C. Murray, Aart Verhoef, Alper Adak

et al.

Current Opinion in Plant Biology, Journal Year: 2025, Volume and Issue: 83, P. 102684 - 102684

Published: Jan. 5, 2025

Language: Английский

Citations

1
Integrating GWAS and transcriptomics to identify candidate genes conferring heat tolerance in rice DOI Creative Commons
Pingping Li,

Jing Jiang,

Guogen Zhang

et al.

Frontiers in Plant Science, Journal Year: 2023, Volume and Issue: 13

Published: Jan. 9, 2023

Rice (Oryza sativa L.) production is being challenged by global warming. Identifying new loci and favorable alleles associated with heat tolerance crucial to developing rice heat-tolerant varieties.We evaluated the at seedling stage using 620 diverse accessions. A total of six were identified a genome-wide association study (GWAS) ~2.8 million single nucleotide polymorphisms (SNPs).Among detected loci, qHT7 harbored strongest signal most SNPs. By comparing transcriptomes two representative accessions contrasting tolerance, LOC_Os07g48710 (OsVQ30) was selected as promising candidate gene in due significant difference its expression level between Haplotype 4 (Hap4) determined haplotype for via gene-based analysis. The LOC_Os07g48710Hap4 highly enriched tropical Geng/Japonica accessions, frequency has decreased significantly during improvement process varieties.Based on GWAS transcriptomics integrated results, hypothetical model modulated response stress proposed. Our results provide valuable genes improving through molecular breeding.

Language: Английский

Citations

20
A barley pan-transcriptome reveals layers of genotype-dependent transcriptional complexity DOI Creative Commons
Robbie Waugh, Wenbin Guo, Miriam Schreiber

et al.

Research Square (Research Square), Journal Year: 2024, Volume and Issue: unknown

Published: Jan. 8, 2024

Abstract A pan-transcriptome describes the transcriptional and post-transcriptional consequences of genome diversity from multiple individuals within a species, revealing an assortment functions that drive biological outcomes. We developed barley using twenty inbred genotypes representing domesticated* by generating analysing extensive short- long-read RNA sequencing datasets tissues. To overcome single reference bias facilitate downstream analyses we constructed genotype-specific transcript (RTDs) integrated these into linear pan-genome framework to create pan-RTD. Categorising transcripts based upon presence or absence across defined them as core (expressed in all), shell (absent one more) cloud only one). Focusing on observed significant abundance variation among tissues between genotypes. show drivers this category include processing, gene copy number, large structural rearrangements degree conservation promotor motifs. reveal conserved patterns co-expression module-tissue correlations encompassing distinct functions, well frequent functional diversification. complement integrating diverse replicated public RNA-seq cultivar (cv.) Morex comprehensive gene-expression atlas

Language: Английский

Citations

4
Genome evolution and diversity of wild and cultivated rice species DOI Creative Commons
Weixiong Long, Qiang He,

Yitao Wang

et al.

Nature Communications, Journal Year: 2024, Volume and Issue: 15(1)

Published: Nov. 18, 2024

Wild species of crops serve as a valuable germplasm resource for breeding modern cultivars. Rice (Oryza sativa L.) is vital global staple food. However, research on genome evolution and diversity wild rice remains limited. Here, we present nearly complete genomes 13 representative species. By integrating with four previously published pangenome analysis, total 101,723 gene families are identified across the genus, including 9834 (9.67%) core families. Additionally, 63,881 absent in cultivated but discovered. Extensive structural rearrangements, sub-genomes exchanges, widespread allelic variations, regulatory sequence variations observed Interestingly, expanded less diverse disease resistance genes rice, likely due to loss some fixing amplification encoding specific diseases during domestication artificial selection. This study not only reveals natural gene-level studies selection also enhances our understanding domestication. The Oryza genus comprise two 20 extant Here authors assemble species, construct super by them reported reveal within genus.

Language: Английский

Citations

4
Interplay between quantitative trait loci for stem strength and agronomic traits in a wheat doubled-haploid population DOI Creative Commons
J. Allan Feurtado, Letitia Da Ros,

Shola Hassan Kareem

et al.

Field Crops Research, Journal Year: 2025, Volume and Issue: 327, P. 109892 - 109892

Published: April 8, 2025

Language: Английский

Citations

0
Developing Green Nutritious Super Rice for a healthy Anthropocene DOI
Qifa Zhang, Jauhar Ali, Howarth E. Bouis

et al.

Science Bulletin, Journal Year: 2025, Volume and Issue: unknown

Published: April 1, 2025

Language: Английский

Citations

0
Genome-wide association and epistasis studies reveal the genetic basis of saline-alkali tolerance at the germination stage in rice DOI Creative Commons

Guogen Zhang,

Zhiyuan Bi,

Jing Jiang

et al.

Frontiers in Plant Science, Journal Year: 2023, Volume and Issue: 14

Published: May 11, 2023

Introduction Saline-alkali stress is one of the main abiotic factors limiting rice production worldwide. With widespread use direct seeding technology, it has become increasingly important to improve saline-alkali tolerance at germination stage. Methods To understand genetic basis and facilitate breeding efforts for developing tolerant varieties, was dissected by phenotyping seven germination-related traits 736 diverse accessions under control conditions using genome-wide association epistasis analysis (GWAES). Results Totally, 165 main-effect quantitative trait nucleotides (QTNs) 124 additional epistatic QTNs were identified as significantly associated with tolerance, which explained a significant portion total phenotypic variation in accessions. Most these located genomic regions either harboring or known genes reported previously. Epistasis an validated best linear unbiased prediction inclusion both showed consistently better accuracy than alone. Candidate two pairs suggested based on combined evidence from high-resolution mapping plus their molecular functions. The first pair included glycosyltransferase gene LOC_Os02g51900 (UGT85E1) E3 ligase LOC_Os04g01490 (OsSIRP4) , while second comprised ethylene-responsive transcriptional factor, AP59 (LOC_Os02g43790) Bcl-2-associated athanogene gene, OsBAG1 (LOC_Os09g35630) salt tolerance. Detailed haplotype analyses promoter CDS candidate favorable combinations large effects can be used selective introgression. Discussion Our findings provided germplasm resources valuable information future functional

Language: Английский

Citations

8
Molecular analysis of broad-spectrum induced resistance in rice by the green leaf volatile Z-3-hexenyl acetate DOI
Willem Desmedt, Maarten Ameye, Osvaldo Filipe

et al.

Journal of Experimental Botany, Journal Year: 2023, Volume and Issue: 74(21), P. 6804 - 6819

Published: Aug. 25, 2023

Abstract Green leaf volatiles (GLVs), volatile organic compounds released by plants upon tissue damage, are key signaling molecules in plant immunity. The ability of exogenous GLV application to trigger an induced resistance (IR) phenotype against arthropod pests has been widely reported, but its effectiveness pathogens is less well understood. In this study, we combined mRNA sequencing-based transcriptomics and phytohormone measurements with multispectral imaging-based precision phenotyping gain insights into the molecular basis Z-3-hexenyl acetate-induced (Z-3-HAC-IR) rice. Furthermore, evaluated efficacy Z-3-HAC-IR a panel economically significant rice pathogens: Pyricularia oryzae, Rhizoctonia solani, Xanthomonas oryzae pv. Cochliobolus miyabeanus, Meloidogyne graminicola. Our data revealed rapid induction jasmonate metabolism systemic immune responses Z-3-HAC exposure, as transient allocation cost due accelerated chlorophyll degradation nutrient remobilization. proved effective all tested except for C. including (hemi)biotrophs M. graminicola, X. P. oryzae. was lost (JA)-deficient hebiba mutant, which confirms causal role JA Z-3-HAC-IR. Together, our results show that exposure induces broad-spectrum, JA-mediated disease limited costs, may thus be promising alternative crop protection approach.

Language: Английский

Citations

7
Functional differentiation and genetic diversity of rice cation exchanger (CAX) genes and their potential use in rice improvement DOI Creative Commons

Shangshu Lian,

Yanjun Chen,

Yanyan Zhou

et al.

Scientific Reports, Journal Year: 2024, Volume and Issue: 14(1)

Published: April 15, 2024

Abstract Cation exchanger (CAX) genes play an important role in plant growth/development and response to biotic abiotic stresses. Here, we tried obtain information on the functionalities phenotypic effects of CAX gene family by systematic analyses their expression patterns, genetic diversity (gene CDS haplotypes, structural variations, presence/absence variations) 3010 rice genomes nine parents 496 Huanghuazhan introgression lines, frequency shifts predominant gcHaps at these loci artificial selection during modern breeding, association with tolerances several Significant amounts variation also exist cis-regulatory elements (CREs) OsCAX promoters 50 high-quality genomes. The functional differentiation were reflected primarily tissue development specific patterns varied responses different treatments, unique sets CREs associations agronomic traits/abiotic stress tolerances. Our results indicated that OsCAX1a OsCAX2 as general signal transporters many processes diverse environments, but they might be less value improvement. OsCAX1b , OsCAX1c OsCAX3 OsCAX4 was expected potential improvement because traits, responsiveness stresses or phytohormones, relatively high gcHap CRE diversity. strategy demonstrated highly efficient genes/alleles can used systematically characterize other families.

Language: Английский

Citations

2
Genomic introgressions from African rice (Oryza glaberrima) in Asian rice (O. sativa) lead to the identification of key QTLs for panicle architecture DOI Creative Commons
Hélène Adam, Andrés Gutiérrez, Marie Couderc

et al.

BMC Genomics, Journal Year: 2023, Volume and Issue: 24(1)

Published: Oct. 4, 2023

Developing high yielding varieties is a major challenge for breeders tackling the challenges of climate change in agriculture. The panicle (inflorescence) architecture rice one key components yield potential and displays inter- intra-specific variability. genus Oryza features two different crop species: Asian (Oryza sativa L.) African (O. glaberrima Steud.). One main morphological differences between independently domesticated species structure (or complexity) panicle, with O. displaying highly branched which turn produces larger number grains than that glaberrima. gene regulatory network governs intra- interspecific diversity still under-studied.To identify genetic factors linked to species, we used set 60 Chromosome Segment Substitution Lines (CSSLs) issued from third generation backcross (BC3DH) carrying genomic segments cv. MG12 background Tropical Japonica Caiapó. Phenotypic data were collected rachis primary branch length, primary, secondary tertiary spikelet number. A total 15 QTLs localized on chromosomes 1, 2, 3, 7, 11 12, associated enhanced numbers detected CSSLs. Furthermore, BC4F3:5 lines combinations substituted produced decipher effects identified QTL regions variations architecture. detailed analysis phenotypes versus genotypes was carried out parental genomes within these order understand how introgression events may lead alterations traits.Our led detection Caiapó traits specific These contain genes regulate development their explain phenotypic observed.

Language: Английский

Citations

6