Genome-Wide Association Mapping and Genomic Prediction Analyses Reveal the Genetic Architecture of Grain Yield and Flowering Time Under Drought and Heat Stress Conditions in Maize.

Yibing Yuan,Cosmos Magorokosho,Raman Babu,Zhuanfang Hao,Yanli Lu,Jill E Cairns,Nan Wang,Xuecai Zhang,Dan Makumbi,Ao Zhang,Felix San Vicente,Manje Gowda,Michael S Olsen,Yubo Liu,Boddupalli M Prasanna

doi:10.3389/fpls.2018.01919

Abstract

Drought stress (DS) is a major constraint to maize yield production. Heat stress (HS) alone and in combination with DS are likely to become the increasing constraints. Association mapping and genomic prediction (GP) analyses were conducted in a collection of 300 tropical and subtropical maize inbred lines to reveal the genetic architecture of grain yield and flowering time under well-watered (WW), DS, HS, and combined DS and HS conditions. Out of the 381,165 genotyping-by-sequencing SNPs, 1549 SNPs were significantly associated with all the 12 trait-environment combinations, the average PVE (phenotypic variation explained) by these SNPs was 4.33%, and 541 of them had a PVE value greater than 5%. These significant associations were clustered into 446 genomic regions with a window size of 20 Mb per region, and 673 candidate genes containing the significantly associated SNPs were identified. In addition, 33 hotspots were identified for 12 trait-environment combinations and most were located on chromosomes 1 and 8. Compared with single SNP-based association mapping, the haplotype-based associated mapping detected fewer number of significant associations and candidate genes with higher PVE values. All the 688 candidate genes were enriched into 15 gene ontology terms, and 46 candidate genes showed significant differential expression under the WW and DS conditions. Association mapping results identified few overlapped significant markers and candidate genes for the same traits evaluated under different managements, indicating the genetic divergence between the individual stress tolerance and the combined drought and HS tolerance. The GP accuracies obtained from the marker-trait associated SNPs were relatively higher than those obtained from the genome-wide SNPs for most of the target traits. The genetic architecture information of the grain yield and flowering time revealed in this study, and the genomic regions identified for the different trait-environment combinations are useful in accelerating the efforts on rapid development of the stress-tolerant maize germplasm through marker-assisted selection and/or genomic selection.

Highlights

Maize is the major source of food security and economic development in the major developing countries in sub-Saharan Africa, Latin America and Asia (Cairns and Prasanna, 2018)
Drought stress (DS), Heat stress (HS), and drought and heat stress (DHS) have been recognized as the major abiotic constraints to maize yields in the main production regions
Previous studies indicated that maize is highly susceptible to abiotic stresses during flowering time, secondary traits including AD and ASI, with strong genetic correlation with GY, are potential to be included in the breeding program to facilitate the effective selection on GY (Bennetzen and Hake, 2008; Lu et al, 2010)

Summary

Introduction

Maize is the major source of food security and economic development in the major developing countries in sub-Saharan Africa, Latin America and Asia (Cairns and Prasanna, 2018). Heat stress (HS) alone and in combination with DS are likely to become the increasing constraints to maize production in the region of maize-dependent countries (Cairns et al, 2013a). This highlight the need to develop and deploy climate-resilient maize varieties in the tropical world. Breeding for HS in maize in sub-Saharan Africa was only initiated in 2011 and, to date, genetic gain in grain yield has not been quantified under HS. Understanding the genetic architecture of DS or HS tolerance alone or in a combination, by identifying and validating genomic regions conferring tolerance to stresses and developing production molecular markers can significantly accelerate the development of stress-resilient maize varieties through markerassisted selection or genomic selection (GS)

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