The Identification of Two Head Smut Resistance-Related QTL in Maize by the Joint Approach of Linkage Mapping and Association Analysis.

Yong-Xiang Li,Chunhui Li,Yan-Chun Song,Xun Wu,Yu Li,Yun-Su Shi,Donghui Cui,Huaiyu Dong,Guanghui Hu,Jennifer Jaqueth,Bailin Li,Dengfeng Zhang,Tianyu Wang,Lewis Lukens

doi:10.1371/journal.pone.0145549

Abstract

Head smut, caused by the fungus Sphacelotheca reiliana (Kühn) Clint, is a devastating threat to maize production. In this study, QTL mapping of head smut resistance was performed using a recombinant inbred line (RIL) population from a cross between a resistant line “QI319” and a susceptible line “Huangzaosi” (HZS) with a genetic map constructed from genotyping-by-sequencing (GBS) data and composed of 1638 bin markers. Two head smut resistance QTL were identified, located on Chromosome 2 (q2.09HR) and Chromosome 5 (q5.03HR), q2.09HR is co-localized with a previously reported QTL for head smut resistance, and the effect of q5.03HR has been validated in backcross populations. It was also observed that pyramiding the resistant alleles of both QTL enhanced the level of resistance to head smut. A genome-wide association study (GWAS) using 277 diverse inbred lines was processed to validate the mapped QTL and to identify additional head smut resistance associations. A total of 58 associated SNPs were detected, which were distributed in 31 independent regions. SNPs with significant association to head smut resistance were detected within the q2.09HR and q5.03HR regions, confirming the linkage mapping results. It was also observed that both additive and epistastic effects determine the genetic architecture of head smut resistance in maize. As shown in this study, the combined strategy of linkage mapping and association analysis is a powerful approach in QTL dissection for disease resistance in maize.

Highlights

Among all stresses, maize diseases significantly threaten the achievement of high yield under the inevitable trend of monoculture
The objectives of this study are to: (1) identify quantitative trait loci (QTL) conferring head smut resistance using a recombinant inbred line (RIL) population derived from a resistant line “QI319” and a susceptible line “Huangzaosi” (HZS) with the genetic map constructed from genotyping-bysequencing (GBS) data; (2) validate the head smut resistance QTL in backcross populations; and (3) perform genome-wide association study (GWAS) to detect loci for head smut resistance and to provide evidence for the QTL identified by linkage mapping
Linkage disequilibrium (LD) within the QTL region was evaluated using the software of QTL mapping of head smut resistance with the genetic map constructed from GBS data Using the genetic map with 1638 bin markers, two head smut resistance-related QTL, located on Chromosome 2 and 5 and designated as q2.09HR and q5.03HR, were identified in a Qi319 x HZS RIL population

Summary

Introduction

Maize diseases significantly threaten the achievement of high yield under the inevitable trend of monoculture. Head smut, caused by the fungus Sphacelotheca reiliana (Kühn) Clint, constitutes a devastating threat to maize production, especially in regions with low temperatures or at high latitude [1,2]. In Northern China, head smut incidence varied from 7.0 to 35.0% and caused yield loss of up to 0.3 million tons annually [3, 4]. Several factors, including continuous cropping without rotation, planting of susceptible varieties, misuse of seed coating agents and increasing frequency of abnormal weather patterns, have intensified head smut occurrence since 2000. In 2002, the head smut infected area reached about one million hectares, accounting for 19.5% of the total planting area of the Northeast Spring Corn area of China [5]. Compared with traditional control strategies, such as chemical application and field management practices, the development of disease resistant varieties will be the most convenient, cost-effective and environmentally friendly approach

Objectives

Methods

Results

Conclusion