Location: Crop Germplasm Research
Project Number: 3091-21000-038-01-N
Project Type: Nonfunded Cooperative Agreement
Start Date: Oct 1, 2013
End Date: Sep 30, 2018
Jointly develop, analyze, and utilize the genome sequence resources for the Upland cotton (Gossypium hirsutum) genetic standard, TM-1, to advance cotton genomics that contributes to an increased understanding and improvement of the cotton plant.
Through cooperative and coordinated research, genomic DNA libraries of a highly homozygous inbred genetic standard, TM-1, will be prepared and sequenced using the high-throughput next-generation Illumina HiSeq 2000 platform. The whole genome shotgun TM-1 sequence reads will be assembled into scaffolds with assistance of sequenced bacterial artificial chromosome (BAC) clones and genetically mapped single nucleotide polymorphism (SNP) markers on each of the 26 tetraploid cotton chromosomes. In addition to deep sequencing of TM-1, restriction-site associated DNA (RAD) sequencing of 3-79, the genetic standard of Sea Island cotton, G. barbadense, and recombinant inbred line (RIL) progeny of the TM-1 X 3-79 population will be conducted to assist in scaffolding genome assemblies through linkage mapping. Two diploid cotton progenitors, A and D genomes, and an integrated tetraploid cotton map, AD genome, will be used to assist in the TM-1 genome assembly. The assembled sequence will be annotated for functional genes and other genetic elements to provide the reference genome sequence with the gene content and distribution in Upland cotton. Genetic applications of the TM-1 genome sequence will be conducted in cotton breeding populations to improve the traits of interest.