High-resolution linkage map and chromosome-scale genome assembly for cassava (Manihot esculenta Crantz) from 10 populations

Abstract

Cassava (Manihot esculenta Crantz) is a major staple crop in Africa, Asia, and South America,
\nand its starchy roots provide nourishment for 800 million people worldwide. Although native to South
\nAmerica, cassava was brought to Africa 400–500 years ago and is now widely cultivated across sub-Saharan
\nAfrica, but it is subject to biotic and abiotic stresses. To assist in the rapid identification of markers for
\npathogen resistance and crop traits, and to accelerate breeding programs, we generated a framework map
\nfor M. esculenta Crantz from reduced representation sequencing [genotyping-by-sequencing (GBS)]. The
\ncomposite 2412-cM map integrates 10 biparental maps (comprising 3480 meioses) and organizes 22,403
\ngenetic markers on 18 chromosomes, in agreement with the observed karyotype. We used the map to
\nanchor 71.9% of the draft genome assembly and 90.7% of the predicted protein-coding genes. The
\nchromosome-anchored genome sequence will be useful for breeding improvement by assisting in the rapid
\nidentification of markers linked to important traits, and in providing a framework for genomic selectionenhanced
\nbreeding of this important crop.