Genome-Wide Analyses and Prediction of Resistance to MLN in Large Tropical Maize Germplasm.

Manje Gowda,Jumbo M Bright,Yoseph Beyene,L M Suresh,Biswanath Das,Christine Nyaga,Dan Makumbi,Michael S Olsen,Wilson T Muriithi,Boddupalli M Prasanna

doi:10.3390/genes11010016

Abstract

Maize lethal necrosis (MLN), caused by co-infection of maize chlorotic mottle virus and sugarcane mosaic virus, can lead up to 100% yield loss. Identification and validation of genomic regions can facilitate marker assisted breeding for resistance to MLN. Our objectives were to identify marker-trait associations using genome wide association study and assess the potential of genomic prediction for MLN resistance in a large panel of diverse maize lines. A set of 1400 diverse maize tropical inbred lines were evaluated for their response to MLN under artificial inoculation by measuring disease severity or incidence and area under disease progress curve (AUDPC). All lines were genotyped with genotyping by sequencing (GBS) SNPs. The phenotypic variation was significant for all traits and the heritability estimates were moderate to high. GWAS revealed 32 significantly associated SNPs for MLN resistance (at p < 1.0 × 10−6). For disease severity, these significantly associated SNPs individually explained 3–5% of the total phenotypic variance, whereas for AUDPC they explained 3–12% of the total proportion of phenotypic variance. Most of significant SNPs were consistent with the previous studies and assists to validate and fine map the big quantitative trait locus (QTL) regions into few markers’ specific regions. A set of putative candidate genes associated with the significant markers were identified and their functions revealed to be directly or indirectly involved in plant defense responses. Genomic prediction revealed reasonable prediction accuracies. The prediction accuracies significantly increased with increasing marker densities and training population size. These results support that MLN is a complex trait controlled by few major and many minor effect genes.

Highlights

Maize (Zea mays L.) is an important cereal crop and a major determinant of food security inSub-Saharan Africa (SSA) [1]
ANOVA across environments revealed significant genotypic variance for both maize lethal necrosis (MLN)-disease severity (DS) and MLN-area under disease progress curve (AUDPC) (Table 1). For both MLN-DS and AUDPC values, GxE interaction variances were significant at p < 0.05
Heritability was moderate for MLN-DS with 0.42 and high for AUDPC with 0.86

Summary

Introduction

Maize (Zea mays L.) is an important cereal crop and a major determinant of food security inSub-Saharan Africa (SSA) [1]. Maize is grown around 25 million hectares in SSA translating to 38 million metric tons of grain yield. Maize lethal necrosis (MLN) has led to complete yield losses and affected food security negatively [3]. In 2011, MLN was first reported in Bomet District in Kenya with 30–100% yield losses and in 2012 similar symptoms. Genes 2020, 11, 16 were observed in Chepalungu, Narok, and Naivasha districts in Kenya [4]. It was later confirmed in several countries such as Rwanda [5], Ethiopia [1], DRC [6], and Uganda [4]

Objectives

Methods

Results