Cassava SNPY-Array a Power Tool to Evaluate Diversity, Variety Identification, Redundancy and Population Structure

The study of genomic variation is an essential part to understand the crop’s species diversity, conservation and breeding. DNA polymorphisms can be used directly to indicate relationships between individuals within populations and between populations, providing a pivotal information for the crop’s genetic resources management and crop breeding strategies. Next generation sequencing among Latin American cassava landraces unraveled more than 12000 SNPs with different levels of genetic information. Of these SNPs a core set of 180 SNPs were selected and converted in a nanofluidic array (SNPY-array) for regular use in genotype characterization.

Here, we reported the results of four study cases where the SNPY–array was used for accurate identification of 5,740 cassava accession collected in Latin America from the Cauca region going through the Amazon communities of Colombia across the lowland forest of Peru and in Vietnam. The data obtained helped to understand the cassava variety composition of traditionally conserved landraces both in Cauca and the Amazon and assist the Peruvian and Vietnamese agricultural national program in the germplasm management and conservation decisions processes. These data also allowed us to understand the patterns of traditional versus improved varieties dissemination and adoption, as well as inferring their population genetics relationships at local and continental level. The SNPY-Array proved to be an effective tool to accurately identify thousands of informative genetic variations quickly and cost effectively in cassava.

Keyword:RAD-Sequencing, Gene banks, Variety identification

 

 

Title: Cassava SNPY-Array a power tool to evaluate diversity, variety identification, redundancy and population structure

Submitter's E-mail Address:t.m.ovalle@cgiar.org

Session Selection:Marker Systems Diversity: SNP

Authors:

Tatiana Ovalle ¹, Claudia Perea², Ana Maria Leiva¹, Janneth Gutierrez¹, Adriana Alzate¹, Augusto Becerra López-Lavalle¹.

¹ Cassava Genetics Program, (CIAT), AA 6713 Cali - Colombia

²Leuven University, Belgium

First author

Presenting Author

Tatiana Ovalle
CIAT
Email: t.m.ovalle@cgiar.org