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PROVIDER: PRJNA1190497 | ENA |
REPOSITORIES: ENA
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Project description:Purpose: The goal of this study is to construct an interspecific genetic linkage map using SNP markers generated using a genotyping by sequencing transcript approach. Methods: mRNA profiles of 14-day-old parents and 140 recombinant inbred lines were generated by high-throughput sequencing using Illumina HiSeq 3000 system. The sequence reads that passed filtering were mapped to lentil cultivar Cassab reference transcriptome using Burrows Wheeler Aligner and the SNPs generated were then clustered to linkage groups (LG) to construct a high-density linkage map using the ‘mstmap’ function from within the ASMap R package (v1.0-4) (Taylor and Butler, 2017). Results: A total of 694,694,624 paired end reads (150-bp) were generated by sequencing multiplexed cDNA libraries on the Illumina HiSeq 3000 platform with an average of 4,997,803 reads per RIL progeny. Variant calling and sequential filtering led to identification of 2,363 SNP markers which were used to construct a genetic linkage map spanning 545.5 cM with 8 linkage groups. Conclusions: The study has utilized a novel interspecific-derived RIL population to add an array of SNPs to the existing marker data for lentil, which will be of use in future genetic and genomic analyses.
2021-06-09 | GSE176412 | GEO
Project description:Guizotia abyssinica cultivar:noug Genome sequencing and assembly
| PRJNA1193105 | ENA
Project description:Bone marrow macrophages were cultured from 16 week old apoE-deficient F2 mice from an AKRxDBA/2 intercross; Gene expression profiling was performed using Affy 430v2 arrays, and 1967 informative SNP markers were genotyped for each mouse; Supplementary file of SNP data attached below from ParAllele 5K mouse linkage panel Experiment Overall Design: Expression QTLs and sex effects on gene expression and eQTLs were determined
2008-06-16 | E-GEOD-8512 | biostudies-arrayexpress
Project description:To accelerate genetic studies in sugarcane, an Axiom Sugarcane100K single nucleotide polymorphism (SNP) array was designed and customized in this study. Target enrichment sequencing 300 sugarcane accessions selected from the world collection of sugarcane and related grass species yielded more than four million SNPs, from which a total of 31,449 single dose (SD) SNPs and 68,648 low dosage (33,277 SD and 35,371 double dose) SNPs from two datasets respectively were selected and tiled on Affymetrix Axiom SNP array. Most of selected SNPs (91.77%) were located within genic regions (12,935 genes), with an average of 7.1 SNPs/gene according to sorghum gene models. This newly developed array was used to genotype 469 sugarcane clones, including one F1 population derived from cross between Green German and IND81-146, one selfing population derived from CP80-1827, and 11 diverse sugarcane accessions as controls. Results of genotyping revealed a high polymorphic SNP rate (77.04%) among the 469 samples. Three linkage maps were constructed by using SD SNP markers, including a genetic map for Green German with 3,482 SD SNP markers spanning 3,336 cM, a map for IND81-146 with 1,513 SD SNP markers spanning 2,615 cM, and a map for CP80-1827 with 536 SD SNP markers spanning 3,651 cM. Quantitative trait loci (QTL) analysis identified a total of 18 QTLs controlling Sugarcane yellow leaf virus resistance segregating in the two mapping populations, harboring 27 disease resistant genes. This study demonstrated the successful development and utilization of a SNP array as an efficient genetic tool for high throughput genotyping in highly polyploid sugarcane.
2019-12-17 | GSE128450 | GEO
Project description:Guizotia abyssinica cultivar:RCR-18 variety Raw sequence reads
| PRJNA430159 | ENA