Linkage and genome-wide association mapping using next-generation genotyping-by-sequencing in clonally propagated cassava

Abstract

Until recently, cassava (Manihot esculenta L.) has been considered an orphan crop characterized by an understudied genome and a limited number of genetic markers. However, the rapid advances in next-generation sequencing technologies opens up unprecedented opportunities for genetic improvement of this crop that is important to food security of millions of households in the tropics. To capitalize on these advances, we used Genotyping-by-Sequencing (GBS) to discover and genotype thousands of SNPs in a F1 mapping population and a collection of improved varieties of cassava held by the International Institute of Tropical Agriculture (IITA). The generated GBS markers were used to carry out high-resolution interval mapping and genome-wide association study in the F1 and the breeding populations, respectively. Quantitative trait loci (QTLs) underlying several traits including resistance to the devastating cassava mosaic disease, increased provitamin-A content, dry-matter content, and several morphological traits were identified. Markers with strongest signals in the QTL analyses were found close to either known candidate genes or previously published QTLs for several target traits. Moreover, we have developed a dense linkage map with 2360 SNPs located in more than 900 unique scaffolds, thereby contributing towards anchoring of the cassava genome sequence that is currently made up of nearly 13000 scaffolds. The successful implementation of next-generation sequencing-based genotyping in cassava shows that this approach is perfectly suited to studying the genetic architecture of key agronomic traits in this highly heterozygous and clonally propagated species and will lead to more efficient breeding using genomic-assisted selection strategy.

Citation

Rabbi, I.; Gedil, M.; Kulakow, P.; Ly, D.; Hamblin, M.; Jannink, J.L. Linkage and genome-wide association mapping using next-generation genotyping-by-sequencing in clonally propagated cassava. Presented at XXI Plant and Animal Genome Conference, San Diego, USA, 12-16 January 2013. (2013)

Linkage and genome-wide association mapping using next-generation genotyping-by-sequencing in clonally propagated cassava

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