Project Number: 3096-21000-022-02-N
Project Type: Non-Funded Cooperative Agreement
Start Date: Sep 20, 2016
End Date: Sep 19, 2019
1. Continue with development of robust high-density linkage maps of sequence-based cotton genome markers. 2. Use linkage maps to marker-trait associations, marker-assisted selection (MAS), genome selection, gene discovery and/or cotton genome assembly. 3. Identify chromosome segments or linkage blocks associated with creating barriers for genetic recombination and gene introgression. 4. Validate and/or develop new SNP marker-sets associated with plant stress tolerance and disease resistance for assisting breeding through the use of diverse technologies.
A high-density genetic linkage map with robust spaced-sequence molecular markers provides an excellent framework for discovering loci and/or genes responsible for traits of interest; can help correct placement of scaffolds and gene sequences during genome assembly; and can eventually lead to genetic improvement especially in organisms with complex genomes such as the modern cottons, Upland and Pima [Gossypium hirsutum L., 2n=52, 2(AD)1 and G. barbadense L. 2n=52, 2(AD)2]. Several recombined inbred lines (RILs) mapping populations will be genotyped using the CottonSNP63K Illumina Infinium array, previously developed by Cooperator, and genotype by sequencing approach will be performed on selected RILs to generate the linkage genetic framework-map. To assess the genetic response to drought or disease resistance of these populations, field experiments will typically use a randomized complete block or incomplete block design with three or four replication. When seed availability is a limiting factor, experiments use two replications or use an augmented design. Plant stress such as drought tolerance and disease resistance evaluations have been performed by USDA/ARS on some of the mapping populations and will be performed on additional selected populations. In-house ongoing research and previous published results from both parties in breeding of diploid and polyploid crops, germplasm introgression, genetic analysis, marker development (SSRs, SNPs), marker assisted selection, and genomics will allow us to further address the barriers for genetic recombination and gene introgression and to validate and develop SNP marker-sets associated with plant stress tolerance and disease resistance. Genotyping will be based on proven technologies and well-developed expertise for KASP simplex and/or low-plex genotyping (e.g., 48 or 96-) and/or high-plex CottonSNP63K Infinium II array (63,000-plex). Simplex genotyping by KASP is especially applicable to single-seed and/or seedling MAS using inexpensively prepared DNA; other methods are complementary. Other genotyping methods may supplant or supplement existing methods, if they offer significantly superior returns per investment for specific applications. This project will support the recently published G. hirsutum L. acc. TM-1 genome references and ancestor diploids G. raimondii and G. arboreum reference genomes, to further fine tune the genome assembly of cotton, and provide the foundation for fine mapping and genetic dissection of candidate genes and quantitative trait loci (QTL) for important traits such as yield, fiber quality traits, plant stress tolerance, and pest/disease resistance. This research effort will overall provide to the cotton community a platform for integrated trait genetic analysis and genomics.