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A genome-wide association study reveals genes associated with fusarium ear rot resistance in a maize core diversity panel.

Zila CT, Samayoa LF, Santiago R, Butrón A, Holland JB - G3 (Bethesda) (2013)

Bottom Line: We performed association tests with 47,445 single-nucleotide polymorphisms (SNPs) while controlling for background genomic relationships with a mixed model and identified three marker loci significantly associated with disease resistance in at least one subset of environments.Each associated SNP locus had relatively small additive effects on disease resistance (±1.1% on a 0-100% scale), but nevertheless were associated with 3 to 12% of the genotypic variation within or across environment subsets.An analysis of associated allele frequencies within the major maize subpopulations revealed enrichment for resistance alleles in the tropical/subtropical and popcorn subpopulations compared with other temperate breeding pools.

View Article: PubMed Central - PubMed

Affiliation: Department of Crop Science, North Carolina State University, Raleigh, North Carolina 27695.

ABSTRACT
Fusarium ear rot is a common disease of maize that affects food and feed quality globally. Resistance to the disease is highly quantitative, and maize breeders have difficulty incorporating polygenic resistance alleles from unadapted donor sources into elite breeding populations without having a negative impact on agronomic performance. Identification of specific allele variants contributing to improved resistance may be useful to breeders by allowing selection of resistance alleles in coupling phase linkage with favorable agronomic characteristics. We report the results of a genome-wide association study to detect allele variants associated with increased resistance to Fusarium ear rot in a maize core diversity panel of 267 inbred lines evaluated in two sets of environments. We performed association tests with 47,445 single-nucleotide polymorphisms (SNPs) while controlling for background genomic relationships with a mixed model and identified three marker loci significantly associated with disease resistance in at least one subset of environments. Each associated SNP locus had relatively small additive effects on disease resistance (±1.1% on a 0-100% scale), but nevertheless were associated with 3 to 12% of the genotypic variation within or across environment subsets. Two of three identified SNPs colocalized with genes that have been implicated with programmed cell death. An analysis of associated allele frequencies within the major maize subpopulations revealed enrichment for resistance alleles in the tropical/subtropical and popcorn subpopulations compared with other temperate breeding pools.

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LD heatmaps showing LD measure (r2) calculated for each pairwise combination of SNPs in an approximately ±1 Mbp region surrounding each SNP significantly associated with ear rot resistance in the North Carolina analysis. (A) LD around chromosome 1 SNP. (B) LD around chromosome 5 SNP. (C) LD around chromosome 9 SNP. The significant SNP on each chromosome is highlighted by the perpendicular black lines within each heatmap. Colors indicate the magnitude of each pairwise r2 measure (r2 = 1 is red to r2 = 0 is white).
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fig2: LD heatmaps showing LD measure (r2) calculated for each pairwise combination of SNPs in an approximately ±1 Mbp region surrounding each SNP significantly associated with ear rot resistance in the North Carolina analysis. (A) LD around chromosome 1 SNP. (B) LD around chromosome 5 SNP. (C) LD around chromosome 9 SNP. The significant SNP on each chromosome is highlighted by the perpendicular black lines within each heatmap. Colors indicate the magnitude of each pairwise r2 measure (r2 = 1 is red to r2 = 0 is white).

Mentions: Genes containing or nearby SNPs significantly associated with ear rot resistance were characterized by the use of the filtered predicted gene set from the annotated B73 reference maize genome (Schnable et al. 2009). Two of the three genes identified in the North Carolina analysis have predicted functions that have been implicated in disease response pathways in other plant species (Tsunezuka et al. 2005; Hématy et al. 2009). The SNP at physical position 151,295,233 bp on chromosome 9, which was identified in both the North Carolina and combined analyses, is located in an intronic region of a cellulose synthase-like family A/mannan synthase gene (Table 3). Mean LD r2 between this SNP and other chromosome 9 SNPs dropped below 0.1 within approximately 100 kbp (Figure 2). The other two SNPs identified in the North Carolina analysis on chromosomes 1 and 5 were located inside of a gene of unknown function and nearby a heat-shock 60-kD protein (HSP60), respectively. Mean LD r2 between the chromosome 1 and chromosome 5 SNPs and other SNPs dropped below 0.1 within approximately 10 kbp and 100 kbp, respectively (Figure 2). Although the chromosome 1 and 9 SNPs were not significantly associated with ear rot resistance in Galicia, the allele effects at these loci were consistent between North Carolina and Galicia (Table 3). However, the allele effect at the chromosome 5 SNP locus showed a change in direction between North Carolina (+1.149%, Table 3) and Galicia (−0.017%).


A genome-wide association study reveals genes associated with fusarium ear rot resistance in a maize core diversity panel.

Zila CT, Samayoa LF, Santiago R, Butrón A, Holland JB - G3 (Bethesda) (2013)

LD heatmaps showing LD measure (r2) calculated for each pairwise combination of SNPs in an approximately ±1 Mbp region surrounding each SNP significantly associated with ear rot resistance in the North Carolina analysis. (A) LD around chromosome 1 SNP. (B) LD around chromosome 5 SNP. (C) LD around chromosome 9 SNP. The significant SNP on each chromosome is highlighted by the perpendicular black lines within each heatmap. Colors indicate the magnitude of each pairwise r2 measure (r2 = 1 is red to r2 = 0 is white).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3815068&req=5

fig2: LD heatmaps showing LD measure (r2) calculated for each pairwise combination of SNPs in an approximately ±1 Mbp region surrounding each SNP significantly associated with ear rot resistance in the North Carolina analysis. (A) LD around chromosome 1 SNP. (B) LD around chromosome 5 SNP. (C) LD around chromosome 9 SNP. The significant SNP on each chromosome is highlighted by the perpendicular black lines within each heatmap. Colors indicate the magnitude of each pairwise r2 measure (r2 = 1 is red to r2 = 0 is white).
Mentions: Genes containing or nearby SNPs significantly associated with ear rot resistance were characterized by the use of the filtered predicted gene set from the annotated B73 reference maize genome (Schnable et al. 2009). Two of the three genes identified in the North Carolina analysis have predicted functions that have been implicated in disease response pathways in other plant species (Tsunezuka et al. 2005; Hématy et al. 2009). The SNP at physical position 151,295,233 bp on chromosome 9, which was identified in both the North Carolina and combined analyses, is located in an intronic region of a cellulose synthase-like family A/mannan synthase gene (Table 3). Mean LD r2 between this SNP and other chromosome 9 SNPs dropped below 0.1 within approximately 100 kbp (Figure 2). The other two SNPs identified in the North Carolina analysis on chromosomes 1 and 5 were located inside of a gene of unknown function and nearby a heat-shock 60-kD protein (HSP60), respectively. Mean LD r2 between the chromosome 1 and chromosome 5 SNPs and other SNPs dropped below 0.1 within approximately 10 kbp and 100 kbp, respectively (Figure 2). Although the chromosome 1 and 9 SNPs were not significantly associated with ear rot resistance in Galicia, the allele effects at these loci were consistent between North Carolina and Galicia (Table 3). However, the allele effect at the chromosome 5 SNP locus showed a change in direction between North Carolina (+1.149%, Table 3) and Galicia (−0.017%).

Bottom Line: We performed association tests with 47,445 single-nucleotide polymorphisms (SNPs) while controlling for background genomic relationships with a mixed model and identified three marker loci significantly associated with disease resistance in at least one subset of environments.Each associated SNP locus had relatively small additive effects on disease resistance (±1.1% on a 0-100% scale), but nevertheless were associated with 3 to 12% of the genotypic variation within or across environment subsets.An analysis of associated allele frequencies within the major maize subpopulations revealed enrichment for resistance alleles in the tropical/subtropical and popcorn subpopulations compared with other temperate breeding pools.

View Article: PubMed Central - PubMed

Affiliation: Department of Crop Science, North Carolina State University, Raleigh, North Carolina 27695.

ABSTRACT
Fusarium ear rot is a common disease of maize that affects food and feed quality globally. Resistance to the disease is highly quantitative, and maize breeders have difficulty incorporating polygenic resistance alleles from unadapted donor sources into elite breeding populations without having a negative impact on agronomic performance. Identification of specific allele variants contributing to improved resistance may be useful to breeders by allowing selection of resistance alleles in coupling phase linkage with favorable agronomic characteristics. We report the results of a genome-wide association study to detect allele variants associated with increased resistance to Fusarium ear rot in a maize core diversity panel of 267 inbred lines evaluated in two sets of environments. We performed association tests with 47,445 single-nucleotide polymorphisms (SNPs) while controlling for background genomic relationships with a mixed model and identified three marker loci significantly associated with disease resistance in at least one subset of environments. Each associated SNP locus had relatively small additive effects on disease resistance (±1.1% on a 0-100% scale), but nevertheless were associated with 3 to 12% of the genotypic variation within or across environment subsets. Two of three identified SNPs colocalized with genes that have been implicated with programmed cell death. An analysis of associated allele frequencies within the major maize subpopulations revealed enrichment for resistance alleles in the tropical/subtropical and popcorn subpopulations compared with other temperate breeding pools.

Show MeSH
Related in: MedlinePlus