Computational protocol: Unraveling the Complex Trait of Harvest Index with Association Mapping in Rice (Oryza sativa L.)

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Protocol publication

[…] Genetic distance was calculated from the 155 molecular markers using Nei distance . Phylogenetic reconstruction was based on the UPGMA method implemented in PowerMarker version 3.25 . PowerMarker was also used to calculate the average number of alleles, gene diversity, and polymorphism information content (PIC) values. The tree to visualize the phylogenetic distribution of accessions and ancestry groups was constructed using MEGA version 4 .Each of the 14 phenotypic traits was modeled independently with the MIXED procedure in SASv.9.2, where genotype, location and interaction of location with genotype were defined as fixed effects while replication within a location (block effect) was a random effect. Broad-sense heritability was calculated using formula H2 = σg2/(σg2+σe2/n), where σg2 as the genotypic variance, σe2 as the environmental variance and n as the number of replications . Spearman rank correlation coefficients between each pair of the 14 traits were calculated using the mean of 9 plants, 3 in each of three replications for an accession, using the CORR procedure in SASv.9.2. Correlation coefficients for the traits that significantly correlated with harvest index were displayed graphically using principal components analysis (PCA) performed with NTSYSpc software version 2.11 . [...] Following the procedures previously recommended , for various mixed models, we tested a subpopulation membership percentage (Q), PCA as fixed covariates and kinship (K) as a random effect. The kinship was calculated using SPAGeDi . Phenotypic data were also incorporated into the process to determine the final number of dimensions for PCA based on Bayesian information criterion (BIC) . The best fit model for each trait was determined based on the BIC among six models, naive, Kinship, PCA, PCA+Kinship, Q and Q+Kinship , . The selected model was then used to map the SSR markers significantly associated with harvest index's traits. The association analysis was conducted using the MIXED procedure in SASv.9.2. For multiple testing, P values were compared to the Bonferroni threshold (1/155 = 6.45×10−3) to identify statistically significant loci. Allelic effects at marker loci were compared using the LSMEANS and pdiff option in the MIXED procedure, using Saxton's PDMIX800 SAS macro . […]

Pipeline specifications

Software tools PowerMarker, MEGA, NTSYSpc, SPAGeDi
Applications Phylogenetics, Population genetic analysis
Organisms Oryza sativa