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United States Department of Agriculture

Agricultural Research Service

Research Project: SNP DISCOVERY IN SUGARCANE USING BSA-SEQ
2012 Annual Report


1a.Objectives (from AD-416):
Develop and test technology and methodology towards genomic based Single Nucleotide Polymorphism (SNP) marker discovery and trait association in sugar cane.


1b.Approach (from AD-416):
The parties will test whether a sequence based bulk segregant analysis (seqBSA) pooling strategies, methods, and analytical algorithms developed and validated in other crops can be applied to sugar cane for both marker discovery and trait association using the Solexa GA2 technology platform.

Solexa sequence data will be generated by the cooperator from DNA/RNA bulked from genotypes selected by ARS and segregating for resistance to brown and orange rust of sugarcane as well as their respective parents.

Criteria used by ARS to select the populations will be as follows: High quality and accurate and Replicated spatially and/or over time.

The Cooperator will evaluate Solexa sequencing for marker discovery, mapping and marker trait association using sugar cane material and phenotypic data.


3.Progress Report:

This research relates to inhouse objective 2: Develop better agronomic practices for the Florida sugarcane industry.

Brown rust reactions were determined in a population resulting from the cross, Green German X Ind 81-146. Parental clones and bulks were analyzed and sequenced to develop potential molecular markers (non-Bru1) for brown rust resistant genes. Potential markers are being evaluated.


Last Modified: 11/26/2014
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