Whole genome re-sequencing of allopolyploid cotton

Working group session: 
Breeding and Applied Genomics
Presentation type: 
oral
Authors: 
Page, Justin; Van Deynze, Allen; Stelly, David; Udall, Joshua
Presenter: 
Udall, Joshua
Correspondent: 
Udall, Joshua
Abstract: 
We re-sequenced the genomes of 13 G. hirsutum and 15 G. barbadense using Illumina PE 100bp reads. Reads from each accession were mapped to the D-genome reference and were categorized as belonging to either At- or Dt-genome. Based on the D-genome read alignments, we constructed a comprehensive map of SNPs (inter- and intra-specific), estimated relatedness of the sampled accessions, quantified regions of genomic conversion between the At- and Dt-genomes, identified coding sequence changes such as premature stop codons, estimated LD in both At- and Dt-genomes, identified of duplications and deletions between the two genomes, identified CNVs of genic and exonic regions that make up the core genome of polyploid cotton. Similar estimates were made based on alignments to the A-genome reference sequence. A summary of these population genomic results is presented.