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ARS Home » Southeast Area » Stoneville, Mississippi » Crop Genetics Research » Research » Research Project #431667

Research Project: Molecular Approaches to Identify Genes Associated with Reniform Nematode Resistance in Cotton

Location: Crop Genetics Research

Project Number: 6066-22000-075-04-S
Project Type: Non-Assistance Cooperative Agreement

Start Date: Sep 26, 2016
End Date: Dec 31, 2019

The objectives of this research are to (1) complete the genome sequencing effort for the diploid cotton species Gossypium herbaceum utilizing enhanced sequencing on high throughput Illumina platform to achieve greater than 99% sequence coverage and (2) develop DNA markers associated with reniform nematode resistance gene(s) identified in Gossypium herbaceum germplasm accessions using DNA sequencing data.

This research will be accomplished by sharing existing sequence data between Alabama A&M University (AAMU) and USDA ARS Crop Genetics Research Unit (ARS) scientists to complete the genome sequence of Gossypium herbaceum. De Novo sequencing will be undertaken by AAMU to improve coverage of the G. herbaceum genome in collaboration with ARS scientists. Seeds of the G. herbaceum accessions PI630014 (A1-141) will be provided by ARS scientists for DNA isolation to complete the genome sequencing. The sequence data will be mapped to the 13 chromosomes of the D5 reference genome with high quality contigs assembled, screened for contamination, annotated, analyzed, and evaluated for repeat content. BLAST searches of the sequence data will be conducted and results analyzed for gene ontology (GO) distributions. Top hits and species distribution of genomic data will also be performed. High throughput genotype by sequencing (GBS) data and corresponding reniform nematode resistance data for a set of approximately 85 G. herbaceum accessions will be provided by ARS scientists. Utilizing the G. herbaceum genome sequence data and GBS data, QTL analysis will be conducted to identify SNPs associated with resistance to reniform nematode. These markers will be tested in populations developed by ARS scientists from crosses between reniform nematode resistant and susceptible G. herbaceum accessions to identify markers useful for marker-assisted breeding.