Genome-wide association mapping and genomic prediction for CBSD resistance in Manihot esculenta

Siraj Ismail Kayondo,Marnin Wolfe,Morag Ferguson,Yona Baguma,Vernon Gracen,Roberto Lozano,Robert Kawuki,Samuel Offei,Dunia Pino Del Carpio,Jean-Luc Jannink,Alfred Ozimati

doi:10.1038/s41598-018-19696-1

Abstract

Cassava (Manihot esculenta Crantz) is an important security crop that faces severe yield loses due to cassava brown streak disease (CBSD). Motivated by the slow progress of conventional breeding, genetic improvement of cassava is undergoing rapid change due to the implementation of quantitative trait loci mapping, Genome-wide association mapping (GWAS), and genomic selection (GS). In this study, two breeding panels were genotyped for SNP markers using genotyping by sequencing and phenotyped for foliar and CBSD root symptoms at five locations in Uganda. Our GWAS study found two regions associated to CBSD, one on chromosome 4 which co-localizes with a Manihot glaziovii introgression segment and one on chromosome 11, which contains a cluster of nucleotide-binding site-leucine-rich repeat (NBS-LRR) genes. We evaluated the potential of GS to improve CBSD resistance by assessing the accuracy of seven prediction models. Predictive accuracy values varied between CBSD foliar severity traits at 3 months after planting (MAP) (0.27–0.32), 6 MAP (0.40–0.42) and root severity (0.31–0.42). For all traits, Random Forest and reproducing kernel Hilbert spaces regression showed the highest predictive accuracies. Our results provide an insight into the genetics of CBSD resistance to guide CBSD marker-assisted breeding and highlight the potential of GS to improve cassava breeding.

Highlights

Cassava (Manihot esculenta Crantz) is a primary source of income and dietary calories for millions of people, and the high starch content of its storage roots is exploited in industry[1]
The characterization of QTL regions associated with cassava brown streak disease (CBSD) resistance in the Tanzanian local cultivar Namikonga and the Tanzanian landrace Kiroba, suggest that some of those regions were introgressed from Manihot glaziovii[19,20]
Efforts to understand CBSD resistance have focused on population development and QTL mapping, viral strain characterization, development of transgenic lines and evaluation of local and elite cassava genotypes to identify possible sources of resistance[10,19,20,39,40]

Summary

Introduction

Cassava (Manihot esculenta Crantz) is a primary source of income and dietary calories for millions of people, and the high starch content of its storage roots is exploited in industry[1]. Cassava is a resilient crop, its production in East Africa is often constrained by viral diseases including cassava brown streak virus disease (CBSD) which causes significant yield loses[2,3,4]. This disease is caused by two virus species of the genus Ipomovirus, family Potyviridae: cassava brown streak virus (CBSV) and Ugandan cassava brown streak virus (UCBSV)[5,6,7]. The characterization of QTL regions associated with CBSD resistance in the Tanzanian local cultivar Namikonga and the Tanzanian landrace Kiroba, suggest that some of those regions were introgressed from Manihot glaziovii[19,20]

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Conclusion