Mapping and molecular marker development for the BnaSBT gene controlling inflorescence and plant architectures in B. napus
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1247395 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR32999859_1.fastq.gz | Fastqsanger.gz | |||
| SRR32999859_2.fastq.gz | Fastqsanger.gz | |||
| SRR32999860_1.fastq.gz | Fastqsanger.gz | |||
| SRR32999860_2.fastq.gz | Fastqsanger.gz | |||
| SRR32999861_1.fastq.gz | Fastqsanger.gz |
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Project description:Exploring the molecular mechanism underlying plant architecture and breeding new varieties suitable for mechanized harvesting are primary objectives for rapeseed breeders in China. However, few genes controlling plant architecture have been cloned in Brassica napus. In this study, SX3, a scattered-bud B. napus line with a dwarf and compact plant architecture, was characterized. To identify the genes underlying bud arrangement, plant height and branch angle, segregating populations were constructed by crossing SX3 with two clustered-bud lines with a tall and loose plant architecture. Genetic analysis revealed that the scattered-bud trait (SBT) was controlled by a single dominant gene, BnaSBT. BnaSBT is likely a pleiotropic gene that simultaneously controls plant height and branch angle. Using BSA-seq analysis, BnaSBT was mapped to a 4.15 Mb region on ChrA10. Owing to the lack of recombinants within this region, it was infeasible to finely map BnaSBT. RNA-seq analysis of BC2 plants with contrasting inflorescence and plant architectures revealed that the upregulation of genes involved in amino acid and lipid metabolism and genes encoding MADS-box transcription factors is related to the the phenotype of SX3. These findings together with comparative sequencing indicated that BnaA10.SEP1, BnaA10.AGL15, BnaA10.GLN1-4 and BnaA10.AGP15 are candidate genes for BnaSBT. Markers closely linked to the scattered-bud trait were developed for selecting dwarf and compact plants. These findings provide molecular markers and germplasms for breeding new varieties with ideal plant types and lay a theoretical foundation for cloning key genes and elucidating the genetic basis of inflorescence and plant architectures in B. napus.
2025-04-23 | GSE293898 | GEO
Project description:The effect of the number of pods on the main inflorescence (NPMIs) on seed yield in Brassica napus plants grown at high density is a topic of great economic and scientific interest. We sought to identify patterns of gene expression that are associated with inflorescence and PMI differentiation and development in Brassica napus.
2014-12-31 | GSE57886 | GEO
Project description:In this study we used the maize (Zea mays) inflorescence to investigate gene networks that modulate determinacy, specifically the decision to allow branch growth. We characterized developmental transitions by associating spatiotemporal expression profiles with morphological changes resulting from genetic perturbations that disrupt steps in a pathway controlling branching. These are the RNA-seq datasets used in this study.
2013-11-27 | GSE51047 | GEO
Project description:In this study we used the maize (Zea mays) inflorescence to investigate gene networks that modulate determinacy, specifically the decision to allow branch growth. We characterized developmental transitions by associating spatiotemporal expression profiles with morphological changes resulting from genetic perturbations that disrupt steps in a pathway controlling branching. These are the RNA-seq datasets used in this study. We profiled changes in gene expression during normal maize ear and tassel development and in developing maize ear primordia upon genetic perturbation of the RAMOSA branching pathway. For the wild-type ear and tassel developmental series, greenhouse-grown B73 inbred plants were used. 10mm ears were collected and sectioned as follows from tip to base along the developmental gradient: tip 1mm sampled (tip; Inflorescence Meristem/Spikelet Pair Meristem), next 1mm discarded, next 1mm sampled (mid; Spikelet Meristem), next 2mm discarded, next 2 mm sampled (base; Floral Meristem), and immediately frozen in liquid nitrogen. Sections from ~30 sampled ears were pooled for each of 2 biological replicates to represent tip, mid, and base stages. Tassels were hand-dissected, measured, separated by stage: 1-2mm (stg1), 3-4mm (stg2), and 5-7mm (stg3), and immediately frozen in liquid N. For each stage, ~20-30 tassels were pooled for each of 2 biological replicates. For ramosa mutant series, segregating families (1:1) of ra1-R, ra2-R, and ra3-fea1 mutant alleles, all introgressed at least 6 times into the B73 inbred background, were grown at CSHL Uplands Farm. Field-grown plants were genotyped and collected 6-7 weeks after germination (V7-V8 stage). First and second ear primordia were immediately hand-dissected, measured, and frozen in liquid nitrogen. For ra1, ra2 and ra3 mutants and wild-type controls, ears were pooled into two size classes: 1) 1mm class included a range of 0.7-1.5mm sized ears and nine ears were pooled for each of 2 biological replicates; 2) 2mm class included a range of 1.8-2.5mm sized ears and six ears were pooled for each of three biological replicates. Wild-type samples were proportional mixtures of heterozygote siblings segregating in ra1, ra2, and ra3 populations. Variability factors (e.g. ear size within class, ear rank on the plant, and time of collection) were distributed evenly across pooled samples.
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2012-07-04 | E-MTAB-4309 | biostudies-arrayexpress
Project description:Rapeseed (Brassica napus L.) is a globally significant oil-producing crop, and its structural variations (SVs) are fundamental to the enhancement and domestication of important agronomic traits. However, the effects of SVs on agronomic traits in allotetraploid rapeseed are still largely unexplored. Here, we conducted a whole-genome identification of SVs based on 300 re-sequenced rapeseed accessions and found 42,384 high-quality SVs consisted of 34,442 deletions, 6,653 insertions, 828 duplications and 461 inversions. Onset of inflorescence formation and subsequent flower opening at the proper time is crucial for successful propagation. To uncover significant SVs associated with inflorescence development, we performed genome-wide association study based on SVs (SV-GWAS) and identified seven significant SVs. Through analysis of each SV and referencing previous studies, we explored the SV in the second intron of LEAFY on Chromosome C3 (BnaC3.LFY), which is one of homologs of Arabidopsis floral identification gene LFY (AtLFY). BnaC3.LFY Hap1 is significantly related to early inflorescence development due to increased gene expression of BnaC3.LFY. By the CRISPR/Cas9 application in the wild-type spring accession Westar, multiple deletions in intron 2 region of BnaC3.LFY were received and the phenotype of delayed flowering opening was observed. Additionally, we discovered the conserved function of the second intron in Arabidopsis. This study demonstrates the whole-genome layout of SVs in Brassica napus genomes and highlights the conserved role of the second intron of BnaC3.LFY in influencing the timing of inflorescence formation and flower opening, with significant agronomic implications.
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Project description:Rapeseed (Brassica napus L.) is a globally significant oil-producing crop, and its structural variations (SVs) are fundamental to the enhancement and domestication of important agronomic traits. However, the effects of SVs on agronomic traits in allotetraploid rapeseed are still largely unexplored. Here, we conducted a whole-genome identification of SVs based on 300 re-sequenced rapeseed accessions and found 42,384 high-quality SVs consisted of 34,442 deletions, 6,653 insertions, 828 duplications and 461 inversions. Onset of inflorescence formation and subsequent flower opening at the proper time is crucial for successful propagation. To uncover significant SVs associated with inflorescence development, we performed genome-wide association study based on SVs (SV-GWAS) and identified seven significant SVs. Through analysis of each SV and referencing previous studies, we explored the SV in the second intron of LEAFY on Chromosome C3 (BnaC3.LFY), which is one of homologs of Arabidopsis floral identification gene LFY (AtLFY). BnaC3.LFY Hap1 is significantly related to early inflorescence development due to increased gene expression of BnaC3.LFY. By the CRISPR/Cas9 application in the wild-type spring accession Westar, multiple deletions in intron 2 region of BnaC3.LFY were received and the phenotype of delayed flowering opening was observed. Additionally, we discovered the conserved function of the second intron in Arabidopsis. This study demonstrates the whole-genome layout of SVs in Brassica napus genomes and highlights the conserved role of the second intron of BnaC3.LFY in influencing the timing of inflorescence formation and flower opening, with significant agronomic implications.
2025-06-25 | GSE285927 | GEO
Project description:Rapeseed (Brassica napus L.) is a globally significant oil-producing crop, and its structural variations (SVs) are fundamental to the enhancement and domestication of important agronomic traits. However, the effects of SVs on agronomic traits in allotetraploid rapeseed are still largely unexplored. Here, we conducted a whole-genome identification of SVs based on 300 re-sequenced rapeseed accessions and found 42,384 high-quality SVs consisted of 34,442 deletions, 6,653 insertions, 828 duplications and 461 inversions. Onset of inflorescence formation and subsequent flower opening at the proper time is crucial for successful propagation. To uncover significant SVs associated with inflorescence development, we performed genome-wide association study based on SVs (SV-GWAS) and identified seven significant SVs. Through analysis of each SV and referencing previous studies, we explored the SV in the second intron of LEAFY on Chromosome C3 (BnaC3.LFY), which is one of homologs of Arabidopsis floral identification gene LFY (AtLFY). BnaC3.LFY Hap1 is significantly related to early inflorescence development due to increased gene expression of BnaC3.LFY. By the CRISPR/Cas9 application in the wild-type spring accession Westar, multiple deletions in intron 2 region of BnaC3.LFY were received and the phenotype of delayed flowering opening was observed. Additionally, we discovered the conserved function of the second intron in Arabidopsis. This study demonstrates the whole-genome layout of SVs in Brassica napus genomes and highlights the conserved role of the second intron of BnaC3.LFY in influencing the timing of inflorescence formation and flower opening, with significant agronomic implications.
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Project description:Microarray expression analysis of the main inflorescence in B. napus
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Project description:As a desirable agricultural trait, multi-inflorescence (MI) fulfills the requirement of mechanized harvesting and yield increase in rapeseed (Brassica napus L.). However, the genetic mechanism underlying the multi-inflorescence trait remain poorly understood. We previously identified a difference of one pair of dominant genes between the two mapping parental materials. In this study, phenotype and expression analysis indicated that the imbalance of the CLAVATA (CLV)-WUSCHEL (WUS) feedback loop may contribute to the abnormal development of the shoot apical meristem (SAM). BnaMI was fine-mapped to a 55 kb genomic region combining with genotype and phenotype of 5768 BCF1 individuals using a traditional mapping approach. Through comparative and expression analyses, combined with the annotation in Arabidopsis, five genes in this interval were identified as candidate genes. The present findings may provide assistance in functional analysis of the mechanism associated with multi-inflorescence and yield increase in rapeseed.
| S-EPMC9266383 | biostudies-literature