Genome-wide association study in Asia-adapted tropical maize reveals novel and explored genomic regions for sorghum downy mildew resistance

Zerka Rashid,Boddupalli Maruthi Prasanna,Pervez Haider Zaidi,Hindu Vemuri,Pradeep Kumar Singh,Sudha Krishnan Nair

doi:10.1038/s41598-017-18690-3

Abstract

Globally, downy mildews are among the important foliar diseases of maize that cause significant yield losses. We conducted a genome-wide association study for sorghum downy mildew (SDM; Peronosclerospora sorghi) resistance in a panel of 368 inbred lines adapted to the Asian tropics. High density SNPs from Genotyping-by-sequencing were used in GWAS after controlling for population structure and kinship in the panel using a single locus mixed model. The study identified a set of 26 SNPs that were significantly associated with SDM resistance, with Bonferroni corrected P values ≤ 0.05. Among all the identified SNPs, the minor alleles were found to be favorable to SDM resistance in the mapping panel. Trend regression analysis with 16 independent genetic variants including 12 SNPs and four haplotype blocks identified SNP S2_6154311 on chromosome 2 with P value 2.61E-24 and contributing 26.7% of the phenotypic variation. Six of the SNPs/haplotypes were within the same chromosomal bins as the QTLs for SDM resistance mapped in previous studies. Apart from this, eight novel genomic regions for SDM resistance were identified in this study; they need further validation before being applied in the breeding pipeline. Ten SNPs identified in this study were co-located in reported mildew resistance genes.

Highlights

Maize is the world’s leading cereal in terms of production, with 1,016 million metric tons (MMT) produced on 184 million hectares (M ha) globally[1]
Four genetically broad-based populations were developed for downy mildew resistance (DMR) by the CIMMYT Asian Regional Maize Program (ARMP) and two sets of CIMMYT maize lines (CMLs) resistant to downy mildews (DMs) were released for use in DM resistance breeding in Asia
DM resistant inbred lines developed in Thailand and Philippines as well as lines developed from DM resistant maize populations, such as early white DMR (EW-DMR), early yellow DMR (EY-DMR), late white DMR (LW-DMR) and late yellow DMR (LY-DMR) are included in the CIMMYT Asia Association Mapping (CAAM) panel

Summary

Introduction

Maize is the world’s leading cereal in terms of production, with 1,016 million metric tons (MMT) produced on 184 million hectares (M ha) globally[1]. Maize grown in the Asian tropics, especially during the monsoon season, is constrained an array of diseases, including downy mildews, leaf blights, rusts, stalk rots and ear rots. Six genomic regions on chromosomes 1, 2, 6, 7 and 10 were identified for downy mildew resistance, including a major QTL on chromosome 6 that influenced resistance to five different DMs in the Asian region. A genome-wide association study (GWAS) is a powerful tool that identifies specific allele variants that confer improved resistance to various diseases in maize. CIMMYT developed a panel of elite Asia-adapted tropical and subtropical maize inbred lines, called CIMMYT Asia Association Mapping (CAAM) panel This panel enables association mapping studies for an array of major agronomic, biotic and abiotic stress tolerance traits in the region. The main objective of the present study was to identify genomic regions associated with SDM resistance and to validate previously reported QTL responsible for DM resistance in maize

Objectives

Methods

Results

Discussion

Conclusion