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United States Department of Agriculture

Agricultural Research Service

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Research Project: Rosbreed: Enabling Marker-Assisted Breeding in Rosaceae

Location: National Clonal Germplasm Repository

2012 Annual Report

1a. Objectives (from AD-416):
Develop and apply marker assisted breeding in Rosaceae fruit crops more efficiently and rapidly.

1b. Approach (from AD-416):
We have organized a diverse team of researchers (genomicists, breeders, ag economists, and extension personnel)to: 1)increase the likelihood of new Rosaceae cultivar adoption, 2)integrate breeding and genomics resources by establishing a standardized statistical framework and breeding information management system, 3)establish sustainable infrastructure for an efficient Marker Assisted Breeding (MAB) pipeline in Rosaceae including crop-specific SNP genome scan platforms for breeding-relevant germplasm, 4)implement the MAB pipeline to demonstrate application of efficient MAB schemes in U.S. breeding programs, and 5)enhance sustainability of cultivar development by training of current and future Rosaceae plant breeders and active engagement of industry stakeholders and the allied research community.

3. Progress Report:
This project relates to objective 3b of the parent project. The purpose of this project was to develop markers for the genetically challenging octoploid strawberry. A pilot study demonstrated poor resolution of genotypes in the strawberry due to its higher ploidy (octoploid) and the need to improve software capabilities to accommodate polyploid plants. As a consequence we modified our marker detection criteria to prioritize selection of diploid-like loci. Also, in collaboration with a private company, the number of targeted markers to interrogate was increased by 15 fold and computer scripts that can generate better resolution of polyploid marker genotypes are being implemented. These approaches will enable by the end of the third year. The development of a genome scan for the first time in an octoploid crop. Genome scans using the high-throughput marker platforms were completed for 942 individuals representing important breeding parents and breeding populations for peach and cherry (sweet and tart) and 80% of the apple selections. The data from these marker platforms was quality checked to identify a robust set of informative genome wide markers for these three crop groups. These genomics resources will enable new marker-locus-trait association discovery and validation of associations in breeding germplasm for major Rosaceae crops.

4. Accomplishments

Last Modified: 10/16/2017
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