iCottonQTL – An R/Shiny Web App for Streamlining Cotton Genetic Mapping

iCottonQTL, a newly publicly available R/Shiny App, was developed to streamline genetic mapping using community developed SNP arrays to assist in the analysis of multiple populations.  Preprocessing raw [CottonSNPchip] data from biparental populations into a format that is commonly used for linkage mapping, ie with the program JoinMap, for trait association is complicated and error-prone. The iCottonQTL app bundles numerous R functions into a visual interface that simplifies the process for various methods of filtering the raw data and providing multiple forms of output for downstream applications, including the input format for Joinmap.  The app seeks to make biparental analysis more accessible to researchers with less experience with bioinformatic methods.  Additionally, iCottonQTL provides a one click conversion of the data generated from the genotyping arrays to the format for uploading raw data to CottonGen and provides a built-in button for emailing the formatted data directly to CottonGen.  This was designed to provide an easier method for submitting genotyping data from raw chip data to CottonGen to assist with publication requirements.  Submission of this data is extremely useful for future chip development, supporting meta-analysis, and expanding the impact of your published results.

The App can be found here: https://gbru-ars.shinyapps.io/iCottonQTL/

1. Develop a publicly available R/Shiny App to streamline use of genotyping data obtained using SNP arrays.
2. Provide an easy method to convert and deposit genetic data into CottonGen.
3. Enable fast filtering and conversion of file formats to support genetic mapping.

PARTICIPANTS

Using iCottonQTL:

• IUPAC Converter Tab (CottonGen Upload Format) [view]:
• - To convert Illumina's exported format into the format required to submission to CottonGen 

1. Upload one Final Report from Illumina's Genome Studio exported following standard protocol listed at left panel of TAMU CottonSNP63K Array in .csv or .txt format 
2. Download the IUPAC formatted .csv. The user will need to open the file and input the species name for each sample under the 'species' column [view].
3. Please email the completed file to: jing.yu@wsu.edu The email button in the app opens Microsoft Outlook to a new email addresed to the CottonGen currator.

• JoinMap Convertor Tab (Generate Input File for JoinMap) [view]

1. Upload one or more Final Reports from Illumina's Genome Studio exported following standard protocol listed at TAMU CottonSNP63K Array in .csv or tab-delimited .txt format.  The Final Report should be in the same format as it was downloaded - the Shiny app expects the report to have the header. The app will double check that the file is in the appropriate format. If your file is not in the correct format, please refer back to GenomeStudio and export the Final Report as a tab-delimited .txt format according to the rules found from TAMU CottonSNP63K Array.
2. Optional: Upload a .txt list of the samples in the Final Report to subset the dataset if your project encompasses less samples than what is in the overall Final Report file.

• iCottonQTL - App for Streamlining Cotton Genetic Mapping
• This project developed a web app dedicated to the downstream analysis of genotyping data including selecting subsets of the Illumina's Genome Studio Final Reports generated from the CottonSNP63K array (Hulse-Kemp, et al., 2015), creating JoinMap .loc files from the filtered marker sets, and converting Final Reports into IUPAC format (as required to upload rawdata to CottonGen database).

• Schoonmaker, A.N.; Hulse-Kemp, A.M.; Youngblood, R.C.; Rahmat, Z.; Atif Iqbal, M.; Rahman, M.-u.; Kochan, K.J.; Scheffler, B.E.; Scheffler, J.A. Detecting Cotton Leaf Curl Virus Resistance Quantitative Trait Loci in Gossypium hirsutum and iCottonQTL a New R/Shiny App to Streamline Genetic Mapping. Plants 2023, 12, 1153. https://doi.org/10.3390/plants12051153

• Hulse-Kemp, A. M., Lemm, J., Plieske, J., Ashrafi, H., Buyyarapu, R., Fang, D. D.,  Stelly, D. M. (2015). Development of a 63K SNP Array for Cotton and High-Density Mapping of Intraspecific and Interspecific Populations of Gossypium spp. G3: Genes|Genomes|Genetics, 5(6), 1187–1209. https://doi.org/10.1534/g3.115.018416

App can be found here: https://gbru-ars.shinyapps.io/iCottonQTL/