Mapping-by-Sequencing of Major Genes and QTLs in Allotetraploid Upland Cotton

The genomic reference sequences available to the cotton community have grown dramatically over the last few years, tracing an arc that many polyploid species can expect to follow.  Draft and reference quality genomes for related diploids were released, followed by draft tetraploid genomes.  At each step, we employed new strategies to identify candidate genes for the agronomic traits we study. The creation and sequencing of nearly isogenic lines and bulked segregant populations ensures that genetic diversity is largely limited to the regions under phenotypic selection.  However, the presence of similar homeologous sequences in polyploid genomes presents an analytic challenge, as does local rearrangements of chromosomes of the studied cultivars relative to the available reference sequences.  When suitable sub-genome read sorting and megabase-scale syntenous reference sequences are available for a genetic locus, simple binning of polymorphisms can identify a diverse region that is closely linked to the gene or QTL.  We have converted these polymorphisms to genetic markers that facilitated the fine mapping of genetic loci to the kilobase scale, revealing candidate genes.  I will discuss the genetic basis of end-use properties of non-woven fabrics including natural flame resistance.  I will present our progress on identification of major cotton fiber property genes and QTLs including short fiber mutants Li₁ and Li₂, the immature fiber mutant im, and fiber strength QTLs and look forward to the use of a MAGIC population for allele discovery.