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. 2018 Jan 10;8(1):366.
doi: 10.1038/s41598-017-18690-3.

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

Zerka Rashid  1 , Pradeep Kumar Singh  1 , Hindu Vemuri  1 , Pervez Haider Zaidi  1 , Boddupalli Maruthi Prasanna  2 , Sudha Krishnan Nair  3
Affiliations

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

Zerka Rashid et al. Sci Rep. .

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.

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Conflict of interest statement

The authors declare that they have no competing interests.

Figures

Figure 1
Figure 1
Population structure based on the first three eigenvalues of principal component (PC) analysis of the CAAM panel using 63,546 SNPs. Clusters in dark blue represent moderate resistant (MR) lines, florescent green (CL02450) and black (CML474) dots represent tester lines of CIMMYT’s heterotic group A, red dots are moderately susceptible (MS) lines, pink are downy mildew resistant (DMR) lines, and clusters of florescent blue dots are susceptible lines (SUS), while yellow (CML451) and green (CML470) dots represent CIMMYT’s heterotic group B tester lines.
Figure 2
Figure 2
Linkage disequilibrium (LD) plot representing the average genome-wide LD decay of the CAAM panel using 37,043 genome-wide SNP markers. The values on the Y-axis represent the squared correlation coefficient r2 and the X-axis represents the genetic distance in kilobases (Kb).
Figure 3
Figure 3
(a) Inflation depicted by Q-Q plots of observed versus expected −log10 (P values) plots for SDM using the naïve association model (G-test), GLM (G + Q) and MLM (G + Q + K); G = genotype (fixed), Q = ten principal components (fixed), K = kinship matrix (random); (b) Highly significant SNPs identified from MLM model using Manhattan plot, plotted with the individual SNPs on the X-axis and −log10 P value of each SNP on the Y-axis. The blue vertical lines show the significant associations at previously reported QTLs.
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