The publically available genotype data were downloaded from
the Gramene Web site (http://www.gramene.org/) on March 10,
2013. During downloading, we removed the reference genome
data firstly, and we then filtered sites with the following parameters:
minimum count was 16 out of 20 sequences, and minimum
frequency was set at 0.25. Finally, a total of 32 655 SNPs distributed
in 12 chromosomes were downloaded (Xu et al., 2014).
Association mapping was performed with GAPIT (Lipka et al.,
2012). Comparison of models and selection of the best model
was referred to Xu et al. (2014). The results with the best model
were presented at the significance level of P < 0.005.