ABR-PG: Sequence Resources for Cotton, A Model System for Allopolyploid Crops.
About
This project focuses on resequencing 506 accessions of cotton, including a broad representation of the commercially important allopolyploid (AD-genome) species G. hirsutum and G. barbadense, and related wild species representing other allopolyploids and progenitor diploid (A, D) genomes. These DNA sequences will be analyzed to address fundamental biological questions of polyploidy genomes and the genetic diversity of cotton. Polyploidy is a prominent feature of plant genomes and is particularly prevalent in crop plants. Using allopolyploid cotton as a well-developed model, our research will address biological questions of broad relevance to polyploid plants, while at the same time revealing detailed information on genomic and phylogeographic patterns of diversity in cotton. The research will also advance our capacity to utilize an expanded gene pool for cotton improvement and in the process generate a Gossypium pan-genome. Fundamental questions for polyploid plant genomes will be addressed, including the distribution of genic and non-genic diversity among subgenomes, chromosomes, and homoeologs, the nature of linkage disequilibrium between co-resident genomes, the extent of homoeologous recombination and its intergenomic biases and effects on nucleotide and protein diversity, and the relative rates and distributions of copy number variations (deletions and duplications) among diploids and their descendant genomes in allopolyploids. In addition to addressing these broadly relevant questions, we will quantify patterns of genetic diversity in cotton. Specifically, we will determine the specific portion and proportion of wild genetic diversity that have been captured in modern breeding populations of G. hirsutum and G. barbadense, the degree to which historical interspecific introgression (G. hirsutum to G. barbadense and vice versa) has affected the distribution of intraspecific genetic variation, the responses of two different domesticated species to strong human directional selection under domestication and crop improvement, and the phylogenetic and genomic distribution of gene losses and gains during evolution of the cotton genus, subsequent to polyploid formation during evolutionary radiation of the allopolyploids, and subsequent to parallel domestication.
FUNDING AGENCY: NSF, PGRP (Plant Genome Resource Program)
ESTIMATED END DATE: March 31st, 2021
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