Additional file 1 of Genome-wide association studies revealed complex genetic architecture and breeding perspective of maize ear traits
Creators: name: Khatun, Mita
name: Monir, Md Mamun
name: Lou, Xiangyang
name: Zhu, Jun
name: Xu, Haiming
Publisher: name: figshare
Year: 2022
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 1: Text S1. Details about the statistical models used for analyses. Table S1. Highly significant SNPs identified by using the base model with no G × E effects for four maize ear traits Effect: a = additive effect, d = dominance effect,. aa = additive × additive interaction effect, dd = dominance × dominance interaction effect. SE: standard error of estimated effect/predicted effect. –Log10P: minus log10 (P-value), h2: estimated heritability. Bold underlined SNPs are strongly associated with family structure and were not identified in the principal component adjusted model. SNPs written in regular word were detected in both base and principal component adjusted model. Table S2. Highly significant SNPs identified by using the base model with G × E effects for four maize ear traits. Effect: a = additive effect, d = dominance effect, ae1 = additive by environment 1 (Urbana) specific effect, ae2 = additive by environment 2 (Aurora) specific effect, ae3 = additive by environment 3 (Clayton) specific effect, ae4 = additive by environment 4 (Homestead) specific effect. SE: standard error of predicted effect. –Log10P: minus log10 (experiment-wise P-value), h2: estimated heritability. Bold underlined SNPs are strongly associated with family structure and were not identified in the principal component adjusted model. SNPs written in regular word were detected in both base and principal component adjusted model. Table S3. Highly significant SNPs identified by using the PC adjusted model for four maize ear traits. Effect: a = additive effect, d = dominance effect, ae1 = additive by environment 1 (Urbana) specific effect, ae2 = additive by environment 2 (Aurora) specific effect, ae3 = additive by environment 3 (Clayton) specific effect, ae4 = additive by environment 4 (Homestead) specific effect. SE: standard error of predicted effect. –Log10P: minus log10 (experiment-wise P-value), h2: estimated heritability. Bold underlined SNPs were newly identified in the principal component adjusted models, which were not identified in the base model. SNPs written in regular word were detected in both base and principal component adjusted model. Table S4. Superior lines and hybrids predicted by using full genetic model for four ear traits of maize. GSL = general superior line for four locations, SL (+)1 = superior line for Urbana, SL (+)2 = superior line for Aurora, SL (+)3 = superior line for Clayton, SL (+)4 = superior line for Homestead; GSH = general superior hybrid line for four locations, SH (+)1 = superior hybrid for Urbana, SH (+)2 = superior hybrid for Aurora, SH (+)3 = superior hybrid for Clayton, SH (+)4 = superior hybrid four Homestead; (+) = positive genotypic value. Fig. S1. Tree map of gene ontology terms of the identified genes. Tree map was plotted using the generated R-script from Revigo. Different child terms were clustered into several parents’ gene ontology terms. Fig. S2. Expression data of the identified genes in Ear and Tassel retrieved from Maize inflorescence database. Tip of the ear (ear_tip), middle of the ear (ear_mid), base of the ear (ear_base), tassel at stage 1 (tassel_stg1), tassel at stage 2 (tassel_stg2), and tassel at stage 3 (tassel_stg3) from experiments in ear and tassel development series; wild type ear at 2 mm (wt_2mm_ear) from experiments in fascinated ear (fea4); and wild type ear 2–5 mm from experiments in knotted1. (A) Expression of a set of identified genes in Ear. We plotted heat map based on expression values of the genes with continuous color scale, where white color represents low expression, yellow represent mid-level expression and red color represents high expression And (B) Expression of a set of identified genes in Tassel. Here different color had same meaning as Fig. A.