Ontology highlight
ABSTRACT:
PROVIDER: PRJNA839214 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:<p>Pigmented rice (<em>Oryza sativa L.</em>) is a rich source of nutrients, but pigmented lines typically have long life cycles and limited productivity. Here we generated genome assemblies of 5 pigmented rice varieties and evaluated the genetic variation among 51 pigmented rice varieties by resequencing an additional 46 varieties. Phylogenetic analyses divided the pigmented varieties into four varietal groups: Geng-japonica, Xian-indica, circum-Aus and circum-Basmati. Metabolomics and ionomics profiling revealed that black rice varieties are rich in aromatic secondary metabolites. We established a regeneration and transformation system and used CRISPR-Cas9 to knock out three flowering time repressors (Hd2, Hd4 and Hd5) in the black Indonesian rice Cempo Ireng, resulting in an early maturing variety with shorter stature. Our study thus provides a multi-omics resource for understanding and improving Asian pigmented rice.</p>
2023-03-27 | MTBLS3320 | MetaboLights
Project description:Intercropping is a sustainable agricultural practice widely used around the world for enhancing resource use efficiency. However, short crops often grow in shade condition underneath the canopy of tall crops. Soybean is one of the most important oil crops and usually is planted in intercropping patterns. However, little is known about the acclimation responses of soybean leaves to shade in intercropping condition at the transcriptome level.
2013-07-11 | E-MTAB-4279 | biostudies-arrayexpress
Project description:MicroRNAs (miRNAs) are a class of endogenous small non-coding RNAs (19–24 nt) that regulates de gene expression, mainly through mRNA targets cleavage and translation inhibition. In plants, miRNAs have been shown to play pivotal roles in a wide variety of metabolic and biological processes like plant growth, development, and response to biotic and abiotic stress. Soybean is one of the most important crops worldwide, due to the production of oil and its high protein content. The reproductive phase is considered the most important for the yield of soybean, which is mainly intended to produce the grains. The identification of miRNAs is not yet saturated in soybeans, and there are no studies linking them to the different floral organs. In this study, three different soybean floral whorls were used in the construction of sRNA libraries. The sequencing of petal, carpel and stamen libraries by the Solexa platform generated a total of 10,165,661 sequences. Subsequently analyses detected 200 miRNAs sequences, from those 41 were novel miRNAs never detected before, 80 were conserved soybean miRNAs, 31 were new antisense conserved soybean miRNAs and 46 soybean miRNAs isoforms. We also found a new miRNA conserved in other plant species, and finally one miRNA-sibling of a soybean conserved miRNA. Conserved and novel miRNAs were evaluated by RT-qPCR. We observed a differential expression across the three whorls for six miRNAs analyzed. A computational prediction of targets for miRNAs analyzed by RT-qPCR was performed. Many of the predicted targets have described functions related to the reproductive process in plants. In summary, the increased accumulation of specific and novel miRNAs in different whorls indicates that miRNAs are an important part of the regulatory network in soybean flower.
2018-05-25 | GSE69572 | GEO
Project description:Soybean is a self-pollinating crop species that has relatively low nucleotide polymorphism rates compared to other crop plant species. Despite the appearance of a low intervarietal nucleotide polymorphism rate, a wide range of heritable phenotypic variation exists. There is even evidence for heritable phenotypic variation among individuals within some varieties. ‘Williams 82,’ the soybean variety used to produce the reference genome sequence, was derived from backcrossing a phytophthora root rot resistance locus from the donor parent ‘Kingwa’ into the recurrent parent ‘Williams.’ To explore the genetic basis of intravarietal variation, we investigated the nucleotide, structural and gene content variation of different Williams 82 individuals. Williams 82 individuals exhibited variation in the number and size of introgressed Kingwa loci. In these regions of genomic heterogeneity, the reference Williams 82 genome sequence consists of a mosaic of Williams and Kingwa haplotypes. Genomic structural variation between Williams and Kingwa was maintained between the Williams 82 individuals within the regions of heterogeneity. Additionally, the regions of heterogeneity exhibited gene content differences between Williams 82 individuals. Collectively, these findings show that genetic heterogeneity in Williams 82 primarily originated from the differential segregation of polymorphic chromosomal regions following the backcross and single-seed descent generations of the breeding process. We conclude that soybean haplotypes can possess a high rate of structural and gene content variation, and the impact of intravarietal genetic heterogeneity may be much greater than previously assumed. This detailed characterization will be useful for interpreting soybean genomic data sets and highlights important considerations for research communities that are utilizing or working towards developing a reference genome sequence. Soybean variety Williams 82 (Wm82) was derived from a Williams x Kingwa BC6F3 population. CGH was performed to detect regions of Kingwa genomic introgression in Wm82; Williams was hybridized as a common reference against Kingwa and four different Wm82 individuals. Two different Wm82 individuals (SGC and ISU) were also hybridized with one another. The soybean tiling array consists of 700k probes, spaced at approximately 1.1 kb intervals.
2010-12-14 | E-GEOD-25294 | biostudies-arrayexpress
Project description:Soybean aphids are phloem-feeding pests that can cause significant yield losses in soybean plants. Soybean aphids thrive on susceptible soybean lines but not on resistant lines. We used microarrays to characterize the soybean plant's transcriptional defense against aphids in two related cultivars, a susceptible line and a resistant line with the Rag1 aphid-resistance gene. We measured trancript levels in leaves after one and seven days of aphid infestation. This was a full-factorial experiment with three factors: soybean variety (susceptible SD01-76R,resistant LD05-16060), aphid treatment (control, aphids), and infestation duration (1 day, 7 days). There were three replicates per treatment, for a total of 24 samples. The experiment was carried out in a growth chamber. At the V3 growth stage, thirty aphids were added to the third trifoliate leaves of the aphid-treated plants. Each plant had a net to prevent aphid movement among different plants. The aphids were removed prior to sampling.
2012-01-31 | E-GEOD-35427 | biostudies-arrayexpress