Whole-genome resequencing of F2 full hybrids populations from Arabidopsis (Col x Ler, wild type and recq4ab figl1 mutants)
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ABSTRACT: This experiment aims at analyzing crossover distribution in the Arabidopsis recq4ab figl1 compared to wild type. Hybrid lines were obtained through the crossing of Col plants bearing the recq4a, recq4b, and figl1 mutations and Ler plants bearing the recq4a and figl1 mutations. F1 plants either wild type or mutants were selected and F2 seeds were obtained by selfing. Leaf samples from the F2 plants were used for DNA purification and library preparation for Illumina sequencing (HiSeq 3000 2 × 150 bp), performed at the Max Planck-Genome-center (https://mpgc.mpipz.mpg.de/home/).
Project description:This experiment aims at analyzing crossover distribution in the Arabidopsis recq4ab figl1 compared to wild type. CSL_Chr4_C and CSL_Chr5_C populations were produced through successive crosses as: A first cross was done between recq4ab figl1+/- Col plants and parental homozygote CSLs with Chr4 and Chr5 pure Ler, respectively. The resulting plant was then backcrossed to the parental CSLs for Chr4 and Chr5. From the resultant BC1 plants, we selected the recq4ab figl1 +/- and we identified the lines with pure Ler Chr4 (or Chr5, respectively). The offspring from the selfing of the selected plant was crossed with Col recq4ab figl1 +/-. Among the resultant plants, we selected wild-type and recq4ab figl1 individuals as the parents of the populations used for recombination and QTL analyses. Leaf samples from the self-crossed population were used for DNA purification and library preparation for Illumina sequencing (HiSeq 3000 2 × 150 bp), performed at the Max Planck-Genome-center (https://mpgc.mpipz.mpg.de/home/).
Project description:This experiment aims at analyzing crossover distribution in the Arabidopsis recq4ab figl1 compared to wild type. CSL_Chr2_L and CSL_Chr5_L populations were produced through successive crosses as: A first cross was done between recq4ab figl1+/- Ler plants and parental homozygote CSLs with Chr2 and Chr5 pure Col, respectively. The resulting plant was then backcrossed to the parental CSLs for Chr2 and Chr5. From the resultant BC1 plants, we selected the recq4ab figl1 +/- and we identified the lines with pure Col Chr4 (or Chr5, respectively). The offspring from the selfing of the selected plant was crossed with Ler recq4ab figl1 +/-. Among the resultant plants, we selected wild-type and recq4ab figl1 individuals as the parents of the populations used for recombination and QTL analyses. Leaf samples from the self-crossed population were used for DNA purification and library preparation for Illumina sequencing (HiSeq 3000 2 × 150 bp), performed at the Max Planck-Genome-center (https://mpgc.mpipz.mpg.de/home/).
Project description:This experiment aims at analyzing genotype profiles of wild-type and apomictic BRS CIRAD-302 rice. Leaf samples from plants of the parental, F1, F2, T0, T1, and T2 were used for DNA purification and library preparation for Illumina sequencing (2x150 bp), performed by the Max Planck-Genome-centre Cologne, Germany (https://mpgc.mpipz.mpg.de/home/).
Project description:Genomic DNA from 96 recq4ab Col x recq4a Ler F2 individuals was extracted using CTAB and used to generate sequencing libraries as described (Rowan et al; Yelina et al), with the following modifications. DNA was extracted from 3 rosette leaves of 5 week old plants and 150 ng of DNA used as input for each library. DNA shearing was carried out for 20 minutes at 37°C with 0.4U of DNA Shearase (Zymo research). The barcoded adapters used for library construction are listed in Rowan et al. Each set of 96 libraries was sequenced on one lane of an Illumina NextSeq500 instrument (300-cycle Mid Output run). Sequencing data was analysed to identify crossovers as previously reported, using the TIGER pipeline. These data can be compared to a set of wild type control libraries available at E-MTAB-10168.
Project description:Genomic DNA from 96 pJ3-J3(G155R) recq4ab Col x recq4a Ler F2 individuals was extracted using CTAB and used to generate sequencing libraries as described (Rowan et al; Yelina et al), with the following modifications. DNA was extracted from 3 rosette leaves of 5 week old plants and 150 ng of DNA used as input for each library. DNA shearing was carried out for 20 minutes at 37°C with 0.4U of DNA Shearase (Zymo research). The barcoded adapters used for library construction are listed in Rowan et al. Each set of 96 libraries was sequenced on one lane of an Illumina NextSeq500 instrument (300-cycle Mid Output run). Sequencing data was analysed to identify crossovers as previously reported, using the TIGER pipeline. These data can be compared to a set of wild type control libraries available at E-MTAB-10168.
Project description:This experiment aims at analyzing crossover distribution in female and male meiosis, in the Arabidopsis scep1 compared to wild type. The heterozygous scep1-1+/- plants were crossed with heterozygous scep1-7+/- plants to produce scep1-1/scep1-7 heteroallelic homozygous mutant. These plants were backcrossed as male or female with wild-type Col to generate the sequencing populations. Leaf samples from the back-crossed population were used for DNA purification and library preparation for Illumina sequencing (HiSeq 3000 2 × 150 base pairs [bp]), performed at the Max Planck-Genome-center (https://mpgc.mpipz.mpg.de/home/).
Project description:This experiment aims at analyzing crossover distribution in female and male meiosis, in the Arabidopsis mlh1 compared to wild type. Plants heterozygous for the mlh1-2 mutation (Col-0) were crossed as females with plants heterozygous for the mlh1-3 mutation (Ler). Wild-type and mlh1-2/mlh1-3 plants were selected among the F1s and crossed as female or as male with wild-type Col-0. Leaf samples from the four back-crossed populations were used for DNA purification and library preparation for Illumina sequencing (NextSeq 2000 2×150 base pairs [bp]), performed at the Max Planck-Genome-center (https://mpgc.mpipz.mpg.de/home/).
Project description:This experiment aims at analyzing crossover distribution in male and female meiosis, in the Arabidopsis heip1 compared to wild type. Plants heterozygous for the heip1-4 mutation (Col.0) were crossed as females with plants heterozygous for the heip1-5 mutation (Ler). Wild-type and heip1-4/heip1-5 plants were selected among the F1s and crossed as male or as female with wild-type Col.0. Leaf samples from the four back-crossed populations were used for DNA purification and library preparation for Illumina sequencing (HiSeq 3000 2 × 150 base pairs [bp]), performed at the Max Planck-Genome-center (https://mpgc.mpipz.mpg.de/home/).
Project description:This experiment aims at analyzing crossover distribution in male and female meiosis, in the Arabidopsis hei10+/- compared to wild type. Plants heterozygous for the hei10-2 mutation (Col-0) were crossed as females with Ler as males. Wild-type and hei10+/- plants were selected among the F1s and crossed as female or as male with wild-type Col-0. Leaf samples from the four back-crossed populations were used for DNA purification and library preparation for Illumina sequencing (NextSeq 2000 2×150 base pairs [bp]), performed at the Max Planck-Genome-center (https://mpgc.mpipz.mpg.de/home/).
Project description:This experiment aims at analyzing crossover distribution in male and female meiosis, in the Arabidopsis zyp1 mutant compared to wild type. Plants heterozygous for the zyp1-1 mutation (Col) were crossed as female with plants heterozygous for the zyp1-6 mutation (Ler). Wild type and zyp1-1/zyp-6 plants were selected among the F1s, and crossed as male or as female with wild-type Col. Leaf samples from plants from the four obtained BC1 populations were used for DNA purification and library preparation for Illumina sequencing (HiSeq 3000 2x150 bp), performed by the Max Planck-Genome-centre Cologne, Germany (https://mpgc.mpipz.mpg.de/home/).