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

<div><p>Head smut, caused by the fungus <i>Sphacelotheca reiliana</i> (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 (<i>q2</i>.<i>09HR)</i> and Chromosome 5 (<i>q5</i>.<i>03HR</i>), <i>q2</i>.<i>09HR</i> is co-localized with a previously reported QTL for head smut resistance, and the effect of <i>q5</i>.<i>03HR</i> 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 <i>q2</i>.<i>09HR</i> and <i>q5</i>.<i>03HR</i> 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.</p></div

Genetic effects of head smut resistant QTL <i>q2</i>.<i>09HR</i> and <i>q5</i>.<i>03HR</i> in BC₄F₁ population.

<p>HZS stands for the allele contributed by susceptible parent HZS, QI319 stands for the allele contributed by the resistant parent QI319, the lighter gray part in the pie stands for the percentage of resistant plants within each group with the same genotype, the bracketed numbers stands for the total plants of each group. The probabilities of Analysis of Variance (ANOVA) among different allele combinations are noted in the brackets of pie right.</p

Distributions of head smut resistance QTL on chromosome 2 and 5 for the RIL population of QI319×HZS.

<p>Distributions of head smut resistance QTL on chromosome 2 and 5 for the RIL population of QI319×HZS.</p

Single marker-trait testing for both the BC₅F₂ families and plants.

<p>The x-axes represents the genetic position of tested SNPs within the <i>q5</i>.<i>03HR</i> region, and the y-axes represents the negative log P value of t-test.</p

Validation of head smut resistance QTL <i>q5</i>.<i>03HR</i> with a BC₄F₁ population.

<p>Validation of head smut resistance QTL <i>q5</i>.<i>03HR</i> with a BC₄F₁ population.</p

Detection of marker-resistance associations within the regions of <i>q2</i>.<i>09HR</i> (a) and <i>q5</i>.<i>03H</i> (b).

<p>The horizontal dashed line shows the significance with stringent threshold of–log₁₀ (0.00001).</p

LD heat-map for the region around the most significant SNP PZE-105072717 in <i>q5</i>.<i>03HR</i>.

<p>Numbers for each entry are the linkage disequilibrium (LD) level evaluated with D’. Colors varied from white to deep red mean that the LD level in pair-SNPs is increasing from 0% to 100%. The markers within triangle cycles are tightly linked together (with D’ more than 90%).</p