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United States Department of Agriculture

Agricultural Research Service

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Research Project: SNP DISCOVERY IN SUGARCANE USING BSA-SEQ

Location: Sugarcane Production Research

2011 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 the in house objective 3: Identify alleles or genes that can be used in molecular marker-assisted selection to complement the conventional approach of sugarcane cultivar development.

Hybrid sugarcane clones showing resistance or susceptibility to brown rust of sugarcane caused by the pathogen Puccinia melanocephala were identified from a wide cross mapping population that is maintained in replicated plots at Canal Point. Brown rust susceptibility data was examined from multiple years of experiments. Leaf tissue from resistant and susceptible clones and the two respective parents were sampled according to protocols supplied and mailed to Syngenta.

Progress was monitored via site visits, emails and phone calls.


Last Modified: 4/23/2014
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