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Genome-wide association study (GWAS) for root traits as an a

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Diego Ortiz

on 20 November 2013

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Transcript of Genome-wide association study (GWAS) for root traits as an a

Materials and Methods

Root traits in maize DH lines
(Volume, length, Surface Area, Dry weight)
Summary and conclusion

GWAS was performed for root length, root surface area, root dry weight, and root volume on 317 maize accessions and 37,861 SNP markers using TASSEL software.
Genome-wide association study (GWAS) for root traits as an avenue to increase nitrogen use efficiency in maize (
Zea mays

317 maize doubled haploid lines (crosses between exotic landraces and 2 maize inbred lines (PHB47 and PHZ51)
GEM Project
Genome Wide Association Studies (GWAS)
Used to find genetic factors that contribute for an observable trait


Discover SNP markers responsible for root dry weight, total root length, root surface area, and root volume in maize.

Darlene Sanchez
Diego Ortiz

Uses Single Nucleotide Polymorphism (SNP) markers, which are abundant and can be found across the genome
Recent tool in plant and animal breeding programs for predicting an important trait in the offspring more accurately
important role in water and nutrient acquisition

They were evaluated for root traits and genotyped using more than 600,000 SNPs
(after filtering = 37831 SNPs)
Association Analysis (GLM and
Genomic Selection (Ridge Regression)
Linkage Disequilibrium Analysis
Missing Data Imputation (genotype and phenotype)
SNP Extraction, filtering, numericalization, formatting
(Hapmap, Plink, Flapjack, BLOB and Phylip)
Diversity Analysis
Kinship and Principal Component Analysis
TASSEL : Tools for Genetic Research
Association of SNP markers and root traits in 317 maize accessions
Quantile-quantile plots for root traits in 317 maize accessions
SNP markers associated with root traits in 317 maize accessions
Gene harboring the SNP marker S7_165574687 (from MaizeGDB)

Bradbury, P. J., Zhang, Z., Kroon, D. E., Casstevens, T. M., Ramdoss, Y., & Buckler, E. S. (2007). TASSEL: software for association mapping of complex traits in diverse samples. Bioinformatics, 23(19), 2633-2635.

Lawrence, C. J., Dong, Q., Polacco, M. L., Seigfried, T. E., & Brendel, V. (2004). MaizeGDB, the community database for maize genetics and genomics.Nucleic acids research, 32(suppl 1), D393-D397.


The association between the SNP marker S7_165574687 and root surface area was significant with a
–log10p = 5.19 .
The strongest associated SNPs for the traits studied are all found in Chromosome 7.
Thomas Lübberstedt

Jen (Jieyun Hu)
Full transcript