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ARS Home » Southeast Area » Stoneville, Mississippi » Genomics and Bioinformatics Research » Research » Research Project #443312

Research Project: Developing a Haplotype-assisted Breeding System for Upland Cotton - Stoneville

Location: Genomics and Bioinformatics Research

Project Number: 6066-21310-006-024-I
Project Type: Interagency Reimbursable Agreement

Start Date: Jun 1, 2022
End Date: May 31, 2025

To develop a genome-informed breeding system for upland cotton. The first objective will determine the haplotype structure across the entire genome of upland cotton. This information will be used to develop genomic prediction algorithms and test them in an upland cotton breeding program.

This project will leverage genetic data already being produced by USDA-ARS where about 170 G. hirsutum cotton accessions were selected to represent the trajectory of modern cotton breeding from the 1900s until now. These accessions have been deep sequenced by USDA-ARS and grown in the field for phenotype collection. The currently proposed project extends the initial aims of the work. Using young ovules already harvested from the field, we will characterize the variation in early cotton fiber morphology by microscopy. These data will be integrated with Advanced Fiber Information System (AFIS) data currently being collected, including calculation of mature fiber diameter, to look for a correlation between the ranges of early and mature diameter. This research will be broken into three specific aims as follows (1) Determine the correlations between early fiber diameter and mature fiber diameter, AFIS fineness, and genetic variation within a diverse group of U.S. G. hirsutum cotton accessions by measuring with high-throughput microscopy fiber tip sizes and using that phenotypic information to perform genome wide association analysis; (2) Reveal cell-type-specific transcriptomes for recently discovered narrow and wide fiber types in G. hirsutum by RNA-Seq transcriptome collection for the different types of G. hirsutum fibers using novel methods, with the aim of identifying key controlling genes, and (3) Begin to test the functionality of candidate genes for setting the diameter of Upland cotton fibers using virus induced gene silencing and in situ hybridization. These results can be compared with gene variants already called between the different accessions to implicate genes that will be tested for functional importance in the control of fiber diameter. ARS SY will be co-PI and primarily focus on co-advising researchers on the project under the direction of PI at North Carolina State University.