Computational protocol: Identification of major QTLs underlying tomato spotted wilt virus resistance in peanut cultivar Florida-EPTM ‘113’

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Protocol publication

[…] Two parental lines (Florida-EPTM ‘113’ and Georgia Valencia) plus 10 F6 lines samples were selected for GBS. Among the 10 F6 lines, five lines consistently showed disease resistance for 3 years and the other five lines showed susceptibility. The 12 DNA samples with high quality and a concentration higher than 50 ng/ul were delivered to Cornell University, Institute of biotechnology (Genomic Diversity Facility) for 96-plex GBS library preparation (in combination with other 83 samples unrelated with this experiment) and sequencing with Illumina HiSeq 2000 platform following the optimized protocol []. The restriction enzyme, ApeKI was used for reduced representation library preparation.The Tassel-GBS pipeline was utilized for SNP calling []. Trimmed and cleaned sequence tags were aligned to peanut A and B genomes respectively [] using Bowtie2 []. The minor allele frequency (MAF) cutoff was set at 0.01. Raw SNPs were called and the resulting HapMap.hmp.txt files were input into TASSEL software [] for further filtering. SNPs with more than 25 % missing data were removed. The remaining SNPs were applied for single marker analysis first. Then association mapping analysis was conducted. The general linear model (GLM) was performed and a Manhattan plot was generated by Tassel v5.0 after inputting phenotyping data of 12 samples [, ]. […]

Pipeline specifications

Software tools TASSEL-GBS, Bowtie2, TASSEL
Application GBS analysis
Organisms