Genome-wide association analysis reveals new insights into the genetic architecture of defensive, agro-morphological and quality-related traits in cassava

Ismail Yusuf Rabbi,Jean-Luc Jannink,Elizabeth Parkes,Peter Kulakow,Siraj Ismail Kayondo,Marnin Wolfe,Muyideen Yusuf,Ruth Uwugiaren,Cynthia Idhigu Aghogho,Prasad Peteti,Afolabi Agbona,Ezenwaka Lydia,Ikpan Andrew Smith,Chiedozie Egesi,Kayode Ogunpaimo,Guillaume Bauchet

doi:10.1007/s11103-020-01038-3

Abstract

Key messageMore than 40 QTLs associated with 14 stress-related, quality and agro-morphological traits were identified. A catalogue of favourable SNP markers for MAS and a list of candidate genes are provided.Cassava (Manihot esculenta) is one of the most important starchy root crops in the tropics due to its adaptation to marginal environments. Genetic progress in this clonally propagated crop can be accelerated through the discovery of markers and candidate genes that could be used in cassava breeding programs. We carried out a genome-wide association study (GWAS) using a panel of 5130 clones developed at the International Institute of Tropical Agriculture—Nigeria. The population was genotyped at more than 100,000 SNP markers via genotyping-by-sequencing (GBS). Genomic regions underlying genetic variation for 14 traits classified broadly into four categories: biotic stress (cassava mosaic disease and cassava green mite severity); quality (dry matter content and carotenoid content) and plant agronomy (harvest index and plant type) were investigated. We also included several agro-morphological traits related to leaves, stems and roots with high heritability. In total, 41 significant associations were uncovered. While some of the identified loci matched with those previously reported, we present additional association signals for the traits. We provide a catalogue of favourable alleles at the most significant SNP for each trait-locus combination and candidate genes occurring within the GWAS hits. These resources provide a foundation for the development of markers that could be used in cassava breeding programs and candidate genes for functional validation.

Highlights

Cassava (Manihot esculenta Crantz) is the most widely consumed starchy-root staple and an emerging multi-purpose and industrial crop in Africa, Asia, and Latin America (Parmar et al 2017)
The population composed of 5130 elite Institute of Tropical Agriculture (IITA) cassava breeding genotypes were phenotyped in a total of 53 field trials (Supplementary Table 1) for the 14 traits related to biotic stress; storage root quality; plant agronomy; and several agro-morphological traits related to leaves, stems and roots (Table 1)
We demonstrate that the use of a diverse association mapping panel consisting of landraces and improved cultivars from multiple breeding initiatives can identify single nucleotide polymorphism (SNP) variants associated with agronomically essential traits in cassava

Summary

Introduction

Cassava (Manihot esculenta Crantz) is the most widely consumed starchy-root staple and an emerging multi-purpose and industrial crop in Africa, Asia, and Latin America (Parmar et al 2017). While phenotype-based recurrent selection has made significant progress, the rate of genetic gain has been low due to several breeding complexities associated with the biology of the crop, including asynchronous flowering, low seed set per cross, a long cropping cycle of 12 to 24 months and low multiplication rate of planting materials (Ceballos et al 2012). These challenges hinder the breeding program’s abilities to rapidly respond to changing human needs under volatile climatic and environmental conditions

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