Semester of Graduation
First Major Professor
Master of Science (MS)
Peanut is an essential food supply plant that is an allotetroploid, which means its genome contains four copies of each chromosome from two distinct ancestral diploid species. Genotyping is the process of detecting the alleles present at the variable sites in a genome, and phasing is the process of linking the alleles into haplotypes, four haplotypes in an allotetraploid individual. When jointly genotyping and phasing allotetraploid individuals from noisy short read data, the four copies of each chromosome means the number of possible haplotypes quickly expands and overwhelms computational resources. Here, we introduce a novel, efficient strategy to genotype and phase allotetroploid individuals by prescreening the data to detect the truly variable sites. We then derive, implement, and apply an EM algorithm to estimate the haplotypes only at the loci with evidence of variation.
Embargo Period (admin only)
Wang, Hongxu, "Approximated EM algorithm for Genotyping of Allotetraploid" (2021). Creative Components. 822.
Available for download on Saturday, May 07, 2022