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ARS Home Southeast Area New Orleans, Louisiana Southern Regional Research Center Cotton Fiber Bioscience and Utilization Research Research





- Fang, David
- Naoumkina, Marina
- Thyssen, Gregory
- Kim, Hee-Jin
- 2023
- Publications
- Plant Genetic Resources, Genomics and Genetic Improvement (301)

Research Project: **Location:
                            Cotton Fiber Bioscience and Utilization Research** Project Number: 6054-21000-019-000-D
                        
                        Project Type: In-House Appropriated Start Date: Apr 6, 2023
                        
                        End Date: Apr 5, 2028 **Objective:**
                        
                        1. Conduct research to identify genes and/or loci with large effects on fiber and yield traits, develop associated DNA markers to select cotton plants with enhanced fiber quality and yield under various environmental conditions, and work with breeders for introgression of superior alleles to develop new cotton varieties. 
1.A. Use genome-wide association study to identify genetic variants that are associated with cotton fiber maturity and yield trait QTLs.
1.B. Assess the stability and transferability of fiber QTLs in diverse genetic backgrounds and work with breeders to evaluate their effectiveness for simultaneous improvement of fiber quality and yield.

2. Conduct research to integrate transcriptome-wide association (TWAS) with genome-wide association (GWAS) to identify expression QTL and candidate genes controlling fiber quality traits, and determine how expression of these alleles with small effects are linked to produce superior cotton fiber phenotypes.
2.A. Integrate TWAS with GWAS to identify expression QTL and candidate genes controlling fiber quality traits, and determine how expression of these alleles with small effects are linked to produce superior cotton fiber phenotypes.
2.B. Investigate the effect of cotton leafroll dwarf virus infection on fiber quality and expression of fiber genes.

3. Conduct research to functionally characterize candidate fiber genes and develop methods to facilitate allele mining for breeding and gene editing applications in cotton. **Approach:**
                        
                        1. Analyzing and dissecting the genomes of a recombinant inbred population that segregates in fiber quality and yield will identify genetic loci or genomic regions controlling these traits.

2. Selection of DNA markers physically adjacent to the superior alleles of the fiber genes (or genetic loci) will enable breeders to more efficiently and effectively breed a cotton genotype with improved fiber quality.

3. By correlating DNA genotype and gene expression to phenotypic traits we will be able to identify fiber genes and their epistatic interactions.

4. CLRDV infection may result in changes in fiber gene expressions, and subsequently affects fiber quality.

5. Allelic differences in the fiber gene sequence might affect the protein structure and therefore can alter fiber properties.


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