Introgressed Manihot glaziovii Alleles in Modern Cassava Germplasm Benefit Important Traits and Are Under Balancing Selection

Abstract

1.Introgression of alleles from wild relatives has often been adaptive, usually for disease resistance, in plant breeding. However, the significance of historical hybridization events in modern breeding is often not clear. Cassava (Manihot esculenta) is among the most important staple foods in the world, sustaining hundreds of millions of people in the tropics, especially in sub-Saharan Africa. Widespread genotyping makes cassava a model for clonally-propagated root and tuber crops in the developing world and provides an opportunity to study the modern benefits and consequences of historical introgression. We detected large introgressed M. glaziovii genome-segments in a collection of 2742 modern cassava landraces and elite germplasm, the legacy of 1930s era breeding to combat epidemics disease. African landraces and improved varieties were on average 3.8% (max 13.6%) introgressed. Introgressions accounted for significant (mean 20%, max 56%) portion of the heritability of tested traits M. glaziovii alleles on the distal 10Mb of chr. 1 increased dry matter and root number. On chr. 4, introgressed alleles in a 20Mb region improved harvest index and brown streak disease tolerance. Three cycles of selection initially doubled the introgression frequency on chr. 1. Later stage variety trials selectively excluded homozygotes which indicates a heterozygous advantage. We show that maintaining large recombination-suppressed introgressions in the heterozygous state allows the accumulation of deleterious mutations. We conclude that targeted recombination of introgression segments would therefore increase the efficiency of cassava breeding by allowing simultaneous fixation of beneficial alleles and purging of genetic load.\n\nSignificance StatementCrosses to wild relatives have often been adaptive for crop breeding, but their modern importance is usually poorly understood. Cassava (Manihot esculenta) is an important staple crop, feeding hundreds of millions in the developing world, and is a model for vegetatively-propagated non-inbred crops. In the 1930s, crossing to M. glaziovii averted mosaic disease epidemic in Africa. We reveal that large genome segments, the legacy of those crosses, benefit a number of traits including yield in modern cassava and are consistently favored during selection. Elite cultivars are almost exclusively heterozygous for wild alleles; homozygotes are rejected during early stage trials, suggesting inbreeding depression. More recombination around beneficial wild alleles will allow purging of genetic load and increase genetic gain in cassava.