I am working with the aphid and nematode resistance genes in the soybean. I want to utilize the already generated SNP markers of the soybean genome in SoySNP50K iSelect BeadChip from soybean database. Can anyone provide the best tool and way for predicting the candidate genes?
I have been following this paper. I want to know how they did it?
http://journal.frontiersin.org/article/10.3389/fpls.2016.01214/full#B27
Hi,
you need to use the soybean population that has been genotyped (or you have to genotype this population yourself with the chip mentioned), the more the better >>100, e.g. RIL collection or different cultivars.
Then you perform your resistance assay in a quantitative manner, at least assigning numbers for disease symptoms. Then GWAS will correlate the two datasets and you may identify genomic regions which are associated with resistance/ susceptibility.
Good luck,
Tony Schaeffner
Munich, Germany
Hi. I totally agree with the steps to follow. To add something to the original question (Can anyone provide the best tool and way for predicting the candidate genes?), one of the simplest tool to perform GWAS is Tassel. Just load your genotyping and phenotyping data (in the required format), perform Union datasets and do GLM or MLM analysis. Regards.
- Badges
- Science topic
- Similar topics
- Biological Science
- Botany
- Plant Biology
- Plant Biotechnology