Limits...
Genome-Wide Association Implicates Candidate Genes Conferring Resistance to Maize Rough Dwarf Disease in Maize.

Chen G, Wang X, Hao J, Yan J, Ding J - PLoS ONE (2015)

Bottom Line: Fifteen candidate genes associated with MRDD resistance were identified, including ten genes with annotated protein encoding functions.The homologous of nine candidate genes were predicted to relate to plant defense in different species based on published results.The results in present study also imply the candidate genes in defense pathway play an important role in resistance to MRDD in maize.

View Article: PubMed Central - PubMed

Affiliation: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China.

ABSTRACT
Maize rough dwarf disease (MRDD) is a destructive viral disease in China, which results in 20-30% of the maize yield losses in affected areas and even as high as 100% in severely infected fields. Understanding the genetic basis of resistance will provide important insights for maize breeding program. In this study, a diverse maize population comprising of 527 inbred lines was evaluated in four environments and a genome-wide association study (GWAS) was undertaken with over 556000 SNP markers. Fifteen candidate genes associated with MRDD resistance were identified, including ten genes with annotated protein encoding functions. The homologous of nine candidate genes were predicted to relate to plant defense in different species based on published results. Significant correlation (R2 = 0.79) between the MRDD severity and the number of resistance alleles was observed. Consequently, we have broadened the resistant germplasm to MRDD and identified a number of resistance alleles by GWAS. The results in present study also imply the candidate genes in defense pathway play an important role in resistance to MRDD in maize.

No MeSH data available.


Related in: MedlinePlus

Quantile-quantile plot resulting from the GWAS results for disease severity index of MRDD.
© Copyright Policy
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4631334&req=5

pone.0142001.g002: Quantile-quantile plot resulting from the GWAS results for disease severity index of MRDD.

Mentions: To minimize the effect of environmental variation, phenotypic BLUPs across environments (i.e., the phenotypic data from 2012 and 2013 together with the extremely resistant lines in 2011) were used for association studies. To detect the genotypic variation underlying the resistance to MRDD, the significance of association between DSI and the genome-wide 556809 SNPs with MAF≥0.05 was evaluated by MLM analysis using kinship relationship (K matrix) and population structure (Q matrix) as covariate. The manhattan plot indicated that a total of 17 loci reached the genome-wide significance threshold of P≤1.79×10−6 (Table 2 and Fig 1). The quantile-quantile (QQ) plots were generated to detect inflation of statistics due to population stratification (Fig 2). The numbers of significant loci varied from chromosome to chromosome, and the maximum number of significant loci was observed on chromosomes 1 and 6, on which five each significant loci were detected, followed by three on chromosome 5, two on chromosome 8 and one each on chromosomes 2 and 7. For all the 17 loci significantly associated with MRDD DSI, five resistance alleles had relatively low frequences than their counterparts, and phenotypic effect explained by each allele varied from 5.4% to 7.8% in the association panel.


Genome-Wide Association Implicates Candidate Genes Conferring Resistance to Maize Rough Dwarf Disease in Maize.

Chen G, Wang X, Hao J, Yan J, Ding J - PLoS ONE (2015)

Quantile-quantile plot resulting from the GWAS results for disease severity index of MRDD.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4631334&req=5

pone.0142001.g002: Quantile-quantile plot resulting from the GWAS results for disease severity index of MRDD.
Mentions: To minimize the effect of environmental variation, phenotypic BLUPs across environments (i.e., the phenotypic data from 2012 and 2013 together with the extremely resistant lines in 2011) were used for association studies. To detect the genotypic variation underlying the resistance to MRDD, the significance of association between DSI and the genome-wide 556809 SNPs with MAF≥0.05 was evaluated by MLM analysis using kinship relationship (K matrix) and population structure (Q matrix) as covariate. The manhattan plot indicated that a total of 17 loci reached the genome-wide significance threshold of P≤1.79×10−6 (Table 2 and Fig 1). The quantile-quantile (QQ) plots were generated to detect inflation of statistics due to population stratification (Fig 2). The numbers of significant loci varied from chromosome to chromosome, and the maximum number of significant loci was observed on chromosomes 1 and 6, on which five each significant loci were detected, followed by three on chromosome 5, two on chromosome 8 and one each on chromosomes 2 and 7. For all the 17 loci significantly associated with MRDD DSI, five resistance alleles had relatively low frequences than their counterparts, and phenotypic effect explained by each allele varied from 5.4% to 7.8% in the association panel.

Bottom Line: Fifteen candidate genes associated with MRDD resistance were identified, including ten genes with annotated protein encoding functions.The homologous of nine candidate genes were predicted to relate to plant defense in different species based on published results.The results in present study also imply the candidate genes in defense pathway play an important role in resistance to MRDD in maize.

View Article: PubMed Central - PubMed

Affiliation: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China.

ABSTRACT
Maize rough dwarf disease (MRDD) is a destructive viral disease in China, which results in 20-30% of the maize yield losses in affected areas and even as high as 100% in severely infected fields. Understanding the genetic basis of resistance will provide important insights for maize breeding program. In this study, a diverse maize population comprising of 527 inbred lines was evaluated in four environments and a genome-wide association study (GWAS) was undertaken with over 556000 SNP markers. Fifteen candidate genes associated with MRDD resistance were identified, including ten genes with annotated protein encoding functions. The homologous of nine candidate genes were predicted to relate to plant defense in different species based on published results. Significant correlation (R2 = 0.79) between the MRDD severity and the number of resistance alleles was observed. Consequently, we have broadened the resistant germplasm to MRDD and identified a number of resistance alleles by GWAS. The results in present study also imply the candidate genes in defense pathway play an important role in resistance to MRDD in maize.

No MeSH data available.


Related in: MedlinePlus