Improving root characterisation for genomic prediction in cassava

Bilan Omar Yonis,Marnin Wolfe,Jean-Luc Jannink,Peter Kulakow,Dunia Pino Del Carpio,Ismail Rabbi

doi:10.1038/s41598-020-64963-9

Abstract

Cassava is cultivated due to its drought tolerance and high carbohydrate-containing storage roots. The lack of uniformity and irregular shape of storage roots poses constraints on harvesting and post-harvest processing. Here, we phenotyped the Genetic gain and offspring (C1) populations from the International Institute of Tropical Agriculture (IITA) breeding program using image analysis of storage root photographs taken in the field. In the genome-wide association analysis (GWAS), we detected for most shape and size-related traits, QTL on chromosomes 1 and 12. In a previous study, we found the QTL on chromosome 12 to be associated with cassava mosaic disease (CMD) resistance. Because the root uniformity is important for breeding, we calculated the standard deviation (SD) of individual root measurements per clone. With SD measurements we identified new significant QTL for Perimeter, Feret and Aspect Ratio on chromosomes 6, 9 and 16. Predictive accuracies of root size and shape image-extracted traits were mostly higher than yield trait prediction accuracies. This study aimed to evaluate the feasibility of the image phenotyping protocol and assess GWAS and genomic prediction for size and shape image-extracted traits. The methodology described and the results are promising and open up the opportunity to apply high-throughput methods in cassava.

Highlights

Cassava is cultivated due to its drought tolerance and high carbohydrate-containing storage roots
The frequency distribution of the mean value per plot of the Genetic Gain (GG) and C1 populations is presented in Supplementary Fig. 2 and the mean values per trait within a population are presented in Supplementary Table 1
Cassava root characterisation has been the subject of several studies[31,32,33], the genetic architecture underlying cassava root shape remains unexplored

Summary

Introduction

Cassava is cultivated due to its drought tolerance and high carbohydrate-containing storage roots. The lack of uniformity and irregular shape of storage roots poses constraints on harvesting and postharvest processing. In the genome-wide association analysis (GWAS), we detected for most shape and size-related traits, QTL on chromosomes 1 and 12. Cassava storage roots are morphologically diverse, the lack of uniformity and irregular shape between and within genotypes poses significant constraints on harvesting and post-harvest processing. Several studies have attempted to characterize cassava root shape to support the development of peeling mechanization[6,7]. Routine assessment of storage root size and shape in breeding plots relies on visual scores (www.cassavabase.org/search/traits). The shape scoring is based on the most common observation in a plot.

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Conclusion