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United States Department of Agriculture

Agricultural Research Service

Research Project: Enhancing Breeding of Small Grains through Improved Bioinformatics

Location: Plant, Soil and Nutrition Research

Title: Genetic mapping using genotyping-by-sequencing in the clonally-propagated cassava

Authors
item Rabbi, Ismail -
item Hamblin, Martha -
item Gedil, Melaku -
item Kulakow, Peter -
item Ferguson, Morag -
item Ikpan, Andrew -
item Ly, Delphine -
item Jannink, Jean-Luc

Submitted to: Crop Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: January 14, 2014
Publication Date: January 24, 2014
Citation: Rabbi, I., Hamblin, M., Gedil, M., Kulakow, P., Ferguson, M., Ikpan, A.S., Ly, D., Jannink, J. 2014. Genetic mapping using genotyping-by-sequencing in the clonally-propagated cassava. Crop Science. DOI: 10.2135/cropsci2013.07.0482.

Interpretive Summary: Cassava (Manihot esculenta L.) is one of the most important food crops in the tropics, but yields are far below their potential. The gene-pool of cassava contains natural genetic diversity relevant to many important breeding goals, but breeding progress has been slow, partly due to insufficient genomic resources. Genotyping by sequencing (GBS) is a method to assess differences in genes between individuals using high-throughput sequencing. As a first step toward implementing genome-wide genetic studies that will facilitate rapid genetic gain through breeding, we genotyped-by-sequencing a family of 182 full-sibs progeny from a cross between parents that differed for several traits: resistance to the cassava mosaic disease (CMD) and yield under CMD pressure; carotenoid content in storage roots; color of stem exterior and anthocyanin pigmentation in the petioles, inner root skin and apical leaves. Using an established GBS protocol, we obtained 2478 variable DNA markers of which 1257 passed standard filtering for missing genotypes and deviation from expected genotypic frequencies. We mapped 772 markers. Most of the studied morphological traits as well as resistance to CMD and root carotenoid content showed qualitative inheritance. As expected, analysis for these traits revealed single loci surrounded by small confidence intervals. Yield under CMD was associated with the CMD resistance locus. We show that GBS is a powerful genotyping tool that provides a sufficient number of markers for unraveling the genetic architecture of Mendelian traits in cassava families. The genetic map we developed was also useful in improving the existence reference sequence of cassava.

Technical Abstract: Cassava (Manihot esculenta L.) is one of the most important food crops in the tropics, but yields are far below their potential. The gene-pool of cassava contains natural genetic diversity relevant to many important breeding goals, but breeding progress has been slow, partly due to insufficient genomic resources. As a first step toward implementing genome-wide genetic studies that will facilitate rapid genetic gain through breeding, we genotyped-by-sequencing a set of 182 full-sibs population of cassava that segregated in several traits: resistance to the cassava mosaic disease (CMD) and yield under CMD pressure; increased carotenoid content in storage roots; color of stem exterior and anthocyanin pigmentation in the petioles, inner root skin and apical leaves. Employing a rare-cutting restriction enzyme, PstI in GBS library preparation, we obtained 2478 segregating SNPs of which 1257 passed standard filtering for missing genotypes and deviation from expected genotypic frequencies. We mapped 772 SNPs across 19 linkage groups and anchored 313 unique scaffolds from the version 4.1 of the cassava genome assembly. Most of the studied morphological traits as well as resistance to CMD and root carotenoid content showed qualitative inheritance. As expected, QTL analysis for these traits revealed single loci surrounded by small confidence intervals. Yield under CMD was associated with the CMD resistance locus. We show that GBS is a powerful genotyping tool that provides sufficient number of markers for unraveling the genetic architecture of Mendelian traits in cassava in addition to the development of robust genetic map that can help anchor unassembled genomic scaffolds.

Last Modified: 11/21/2014
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