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WGS re-sequencing of 259 rice accessions

ABSTRACT: WGS re-sequencing of 259 rice accessions Raw sequence reads

PROVIDER: PRJNA597536 | ENA |

REPOSITORIES: ENA

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Project description:WGS resequencing for 259 rice accessions

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Expression data of 8 rice accessions under cold stress in seedling stage

Project description:Low temperature is one of the major abiotic stresses limiting rice growth and productivity, it is urgent to reveal the genetic and molecular mechanisms of plant responses to low temperature stress and to search for useful genetic resources for improving low-temperature tolerance. the 8 accessions from China Core Collection include 4 cold tolerance accessions, 3 sensitivity accessions and 1 intermediate type accession. We used microarrays to detail variation of the gene expression after cold treatment and screen more cold-response genes in rice.

2015-10-01 | GSE71680 | GEO

de novo re-construction of the core genome from ChIP-Seq for large-genome organisms

Project description:Genetic diversity in plants is remarkably high. Recent whole genome sequencing (WGS) of 67 rice accessions recovered 10,872 novel genes. Comparison of the genetic architecture among divergent populations or between crops and wild relatives is essential for obtaining functional components determining crucial traits. However, many major crops have gigabase-scale genomes, which are not well-suited to WGS. Existing cost-effective sequencing approaches including re-sequencing, exome-sequencing and restriction enzyme-based methods all have difficulty in obtaining long novel genomic sequences from highly divergent population with large genome size. The present study presented a reference-independent core genome targeted sequencing approach, CGT-seq, which employed epigenomic information from both active and repressive epigenetic marks to guide the assembly of the core genome mainly composed of promoter and intragenic regions. This method was relatively easily implemented, and displayed high accuracy, sensitivity and specificity for capturing the core genome of bread wheat. 95% intragenic and 89% promoter region from wheat were covered by CGT-seq read. We further demonstrated in rice that CGT-seq captured hundreds of novel genes and regulatory sequences from a previously unsequenced ecotype. Together, with specific enrichment and sequencing of regions within and nearby genes, CGT-seq is a time- and resource-effective approach to profiling functionally relevant regions in sequenced and non-sequenced populations with large genomes.

2018-05-27 | GSE107827 | GEO

WGS of rice accessions with contrast responses to salinity stress

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WGS of a serie of Arabidopsis thaliana tetrad's products to study the role of RECQ4A, RECQ4B, FIGL1 and FANCM genes in the rate, nature and distribution of meiotic recombination products (CO and NCO)

Project description:In this study, two accessions of Arabidopsis thaliana (Columbia and Landsberg erecta) were crossed and tetrads were obtained using thanks to the the quartet mutation, which keeps the 4 haploid pollen grains from a single meiosis attached together. By fertilising a plant (of ecotype Columbia) with a single tetrad, then selecting seeds from siliques containing exactly four seeds and finally sequencing the 4 developed plants, we can access the complete history of meiotic recombination events occurring in a single male meiosis. Comparison of the genomic sequences (WGS) of the 4 plants in a tetrad makes it possible to identify meiotic COs and NCOS events in each tetrad thanks to the numerous polymorphisms specific to each of the parental genomes. The analysis of the WGS tetrads data consists of genotyping a series of SNV markers (differentiating Columbia and Landsberg) positioned on the five chromosomes for the 4 (M1, M2, M3, M4) individuals of a tetrad, representing the 4 chromatids of each chromosomes. A total of 20 tetrads, the F1 and the two parental accessions Columbia and Landsberg erecta were sequenced.

2024-12-02 | E-MTAB-14435 | biostudies-arrayexpress

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