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

и другие.

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2023, Номер unknown

Опубликована: Апрель 28, 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.

Язык: Английский

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

Jing Jiang,

Guogen Zhang

и другие.

Frontiers in Plant Science, Год журнала: 2023, Номер 13

Опубликована: Янв. 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.

Язык: Английский

Процитировано

20
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

и другие.

Current Opinion in Plant Biology, Год журнала: 2025, Номер 83, С. 102684 - 102684

Опубликована: Янв. 5, 2025

Язык: Английский

Процитировано

1
Genome evolution and diversity of wild and cultivated rice species DOI Creative Commons
Weixiong Long, Qiang He,

Yitao Wang

и другие.

Nature Communications, Год журнала: 2024, Номер 15(1)

Опубликована: Ноя. 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.

Язык: Английский

Процитировано

6
A barley pan-transcriptome reveals layers of genotype-dependent transcriptional complexity DOI Creative Commons
Robbie Waugh, Wenbin Guo, Miriam Schreiber

и другие.

Research Square (Research Square), Год журнала: 2024, Номер unknown

Опубликована: Янв. 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

Язык: Английский

Процитировано

4
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

и другие.

Scientific Reports, Год журнала: 2024, Номер 14(1)

Опубликована: Апрель 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.

Язык: Английский

Процитировано

3
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

и другие.

Field Crops Research, Год журнала: 2025, Номер 327, С. 109892 - 109892

Опубликована: Апрель 8, 2025

Язык: Английский

Процитировано

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

и другие.

Science Bulletin, Год журнала: 2025, Номер unknown

Опубликована: Апрель 1, 2025

Язык: Английский

Процитировано

0
Genome-wide association mapping for salinity recovery of rice seedlings grown in hydroponic and field conditions DOI
M. A. Siddique, Marjorie De Ocampo,

Efren Bagunu

и другие.

Philosophical Transactions of the Royal Society B Biological Sciences, Год журнала: 2025, Номер 380(1927)

Опубликована: Май 29, 2025

Salinity stress significantly impacts global food production by hindering crop growth and reducing cultivable land. Efforts to develop salinity-tolerant rice varieties have faced challenges due the complexity of salinity tolerance traits a lack suitable genetic donors. One is that fluctuating degrees severity often occur over growing season, which may require plants recover quickly as levels temporarily decrease. This study evaluated recovery in 256 diverse accessions, including 230 from 3K Rice Genomes Project. Key physiological were measured, indicating accessions outperformed variety FL478, three common both field hydroponics: BRRI dhan 47, Kalar Kar WAS 170-B-B-1-1. Genome-wide association mapping identified significant single nucleotide polymorphisms linked recovery-related traits, with four genes ( LOC_Os01g71350 , LOC_Os02g56510 LOC_Os03g53150 LOC_Os04g40410 ) consistently greenhouse. Based on colocating loci, favourable haplotype for was chr 3. The good genes/loci here will provide useful information future studies genetics breeding salt tolerant/resilient rice. article part theme issue ‘Crops under stress: can we mitigate climate change agriculture launch ‘Resilience Revolution’?’.

Язык: Английский

Процитировано

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

и другие.

Frontiers in Plant Science, Год журнала: 2023, Номер 14

Опубликована: Май 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

Язык: Английский

Процитировано

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

и другие.

Journal of Experimental Botany, Год журнала: 2023, Номер 74(21), С. 6804 - 6819

Опубликована: Авг. 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.

Язык: Английский

Процитировано

7