Project description:For developing the more SNPs and new high-density genetic linkage map of tea plant, two parents and their 326 progenies and 147 registered tea cultivars was sequencing by newly developed Affymetrix Axiom genotyping technology
Project description:The F1 population of Phalaenopsis Intermedia, which established from the cross between P. equestris and P. aphrodite was applied to build a high-density genetic map based on SSRs and SNPs from GBS methodology, with the digestion of by Hinp1 I and Hae III. In addition, another GBS was performed with enzymes ApeK I and Hae II to increase the SNP number for the GWAS analysis. We identified 10 SNPs highly associated with floral aesthetic trait, and among them, 4 were associated with flower color related. Genes with function related to anthocyanin biosynthesis were identified as the candidate genes. In addition, the flowering time-related gene SOC1 may contribute to flower color regulation in our discovery.
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:High density linkage map of eggplant
