Genome-wide association study reveals novel QTLs and candidate genes for panicle number in rice

Frontiers in Genetics, Journal Year: 2024, Volume and Issue: 15

Published: Nov. 5, 2024

Introduction Panicle number (PN) is one of the three key yield components in rice, maintaining stable tiller and PN a crucial characteristic an ideal plant architecture. Understanding molecular mechanisms underlying essential for breeders aiming to improve rice yield. Methods To dissect genetic architecture panicle number, genome-wide association study (GWAS) was conducted 411 japonica varieties. GWAS analysis carried out with mixed linear model using 743,678 high-quality SNPs. Results Over two experimental years, we detected total seven quantitative trait loci (QTLs), located on chromosomes 1, 4, 6, 8, 11, 12; notably, qPN1.1 qPN8 were consistently both years. By combining haplotype expression analyses, OsCKX11 identified as candidate gene , while LOC_Os01g07870 LOC_Os01g07950 genes . Significant differences observed among haplotypes these genes. Additionally, qRT-PCR results showed that levels significantly lower accessions high numbers compared those low numbers. Discussion understand natural biological function genes, further research involving overexpression or silencing needed. Despite challenges, our will lay foundation development provide valuable resources developing high-panicle-number cultivars engineering breeding.

Language: Английский

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Comparative transcriptome profiling suggests the role of phytohormones in leaf stalk-stem angle in melon (Cucumis melo L.)

PeerJ, Journal Year: 2024, Volume and Issue: 12, P. e18467 - e18467

Published: Nov. 18, 2024

Leaf stalk-stem angle is an important agronomic trait influencing melon architecture, photosynthetic efficiency, and crop yield. However, the mechanisms governing leaf angle, particularly in melon, are not well understood. In this study, we explored comparative transcriptome expanded architecture line Y164 compact plant Z151 at 30 days after pollination. Phytohormones were measured stalk-angle site same time these two lines using liquid chromatography (LC) tandem mass spectrometry (MS) (LC-MS/MS). The phytohormones transcriptomes jointly analyzed. Differential hormone profiling revealed that levels of 1-aminocyclopropane-1-carboxylate (ACC) 12-oxophytodienoic acid (OPDA) large-angled significantly higher than those small-angled Z151. These differences quantified as 2.1- 2.8-fold increases, respectively. Conversely, content isopentenyl adenosine (IPA) was elevated Z151, with a 3.8-fold concentration relative to Y164. Transcriptome analysis identified total 1709 differently expressed genes (DEGs), predominant enrichment Kyoto Encyclopedia Genes Genomes (KEGG) pathways related photosynthesis signal transduction. Similarly, metabolic process predominantly enriched biological Gene Ontology (GO) terms. Further integration analyses substantiated close relationship between phytohormones, especially ACC, OPDA IPA. Selected DEGs from phytohormone transduction validated. Detailed highlighted potential role such GH3s ( LOC103490488 , LOC103490483 ), SUARs LOC107991561 LOC103497281 LOC103489067 ARFs LOC103503893 LOC103493078 ) five abscisic pathway. summary, our findings strongly suggest direct correlation angles melon.

Language: Английский

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Regulation of tillering and panicle branching in rice and wheat

Journal of genetics and genomics/Journal of Genetics and Genomics, Journal Year: 2024, Volume and Issue: unknown

Published: Dec. 1, 2024

Language: Английский

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Construction of a High-Density Paulownia Genetic Map and QTL Mapping of Important Phenotypic Traits Based on Genome Assembly and Whole-Genome Resequencing

International Journal of Molecular Sciences, Journal Year: 2023, Volume and Issue: 24(21), P. 15647 - 15647

Published: Oct. 27, 2023

Quantitative trait locus (QTL) mapping based on a genetic map is very effective method of marker-assisted selection in breeding, and whole-genome resequencing one the useful methods to obtain high-density maps. In this study, hybrid assembly Illumina, PacBio, chromatin interaction data was used construct high-quality chromosomal genome sequences Paulownia fortunei, with size 476.82 Mb, heterozygosity 0.52%, contig scaffold N50s 7.81 Mb 21.81 respectively. Twenty scaffolds total length 437.72 were assembled into 20 pseudochromosomes. Repeat 243.96 accounted for 51.16% entire genome. all, 26,903 protein-coding gene loci identified, 26,008 (96.67%) genes had conserved functional motifs. Further comparative genomics analysis preliminarily showed that split P. fortunei Tectona grandis likely occurred 38.8 (33.3-45.1) million years ago. Whole-genome merged linkage groups, 2993 bin markers (3,312,780 SNPs), 1675.14 cm, an average marker interval 0.56 cm. total, 73 QTLs important phenotypic traits identified (19 major variation explained ≥ 10%), including 10 diameter at breast height, 7 main trunk 56 branch-related traits. These results not only enrich genomic but also form solid foundation fine QTL key marker/gene mining Paulownia, which great significance directed improvement these species.

Language: Английский

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Waterlogging shifts ontogenic hormone dynamics in tomato leaves and petioles

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2022, Volume and Issue: unknown

Published: Dec. 3, 2022

Abstract Waterlogging leads to hypoxic conditions in the root zone that subsequently cause systemic adaptive responses shoot, including leaf epinasty. Waterlogging-induced epinasty tomato has long been ascribed coordinated action of ethylene and auxins. However, other hormonal signals have largely neglected, despite evidence their importance posture control. To adequately cover a large group growth regulators, we performed tissue-specific time-dependent hormonomics analysis. This analysis revealed multiple hormones are differentially affected throughout 48 h waterlogging treatment, and, more importantly, development defines framework which this control is regulated. In addition, could distinguish early might contribute fast towards oxygen deprivation from those potentially sustain response. For example, abscisic acid (ABA) levels peak petioles within first 12 while its metabolites only rise much later, suggesting ABA transport altered. At same time, cytokinins (CK) derivatives drastically decline during leaves all ages. drop CK possibly releases inhibition auxin mediated cell elongation establish epinastic bending. Auxins themselves substantially petiole mature leaves, but mostly after hypoxia. Based on our hormone profiling, propose act synergistically dynamically fine-tune balance IAA petiole, ultimately leading differential waterlogging.

Language: Английский

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