Additional file 1 of Multi-locus genome-wide association mapping for spike-related traits in bread wheat (Triticum aestivum L.)
Creators: name: Malik, Parveen
name: Kumar, Jitendra
name: Sharma, Shiveta
name: Sharma, Rajiv
name: Sharma, Shailendra
Publisher: name: figshare
Year: 2021
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 1: Table S1: List of 225 spring wheat reference set genotypes. Table S2: Comparative analysis of environmental factors in two different environments/years using t-test. Fig. S1. The biological meaning of spike layer uniformity (the consistency of the spike distribution in the vertical space) related traits (SLURTs) shown with wheat plants having similar tillers height (a) and different tiller height (b). In (a) only one spike layer can be seen from the vertical perspective (SLN = 1) as spikes per plant have consistent vertical distribution (SLU = 1) and the SLT was identical to one spike length (SL) whereas in (b) two spike layer can be seen from the vertical perspective (SLN = 2) as spikes per plant have inconsistent vertical distribution (SLU = 0.5) and the SLT was identical to two spike length. A detailed description of SLURTs is provided in Table 1. Note: In the figure, immature wheat plants are shown just to illustrate the biological meaning of SLURTs. However, data for SLURTs were recorded on mature plants. In the figure scaling is approximate. The figure is based on the publication by Zhao et al. [12]. Fig. S2. Pairwise Pearson correlation among the eight SLURTs in E1 and grain yield (GYPP). A single asterisk (*) represents 0.05 level of significance. A double asterisk (**) represents 0.01 level of significance and a triple asterisk (***) represents 0.001 level of significance. Fig. S3. Pairwise Pearson correlation among the eight SLURTs in E2 and grain yield (GYPP). A single asterisk (*) represents 0.05 level of significance. A double asterisk (**) represents 0.01 level of significance and a triple asterisk (***) represents 0.001 level of significance. Fig. S4. Pairwise Pearson correlation among the eight SLURTs and grain yield (GYPP) for the combined E1 and E2 environments. A single asterisk (*) represents 0.05 level of significance. A double asterisk (**) represents 0.01 level of significance and a triple asterisk (***) represents 0.001 level of significance. Fig. S5. Manhattan plots obtained after using FarmCPU for eight SLURTs (a) GWPS (b) LTH (c) NSPP (d) NSPS (e) SL (f) SLN (g) SLT (h) SLU under E1 (above numbers) and E2 (below numbers) conditions. Numbers correspond to wheat chromosome. Fig. S6. QQ-plots to visualize the deviation of observed p values from expected p values (based on null hypothesis) for eight SLURTs (a) GWPS (b) LTH (c) NSPP (d) NSPS (e) SL (f) SLN (g) SLT (h) SLU under E1 and E2 conditions. Fig. S7 (i-v). Comparison of MTAs or MTA groups, detected in the present study, with historical QTLs/MTAs in different chromosomes; MTAs detected in known flanking regions or locations of QTLs/MTAs for same traits or grain yield are depicted in green color and MTAs found near to flanking regions or locations (less than 50 Mb) of QTLs/MTAs depicted in red colour. Flanking markers are shown with the same colour and with the reference details of the previous study. Novel MTAs detected in the present study are presented without any colour. The corresponding physical distances (Mb) of the QTL/MTA regions on each chromosome were obtained by blasting the flanking sequences of markers, depicted on the right side of each figure, to the Chinese Spring RefSeq v1.0. GY; grain yield, TN; tiller number.