Multi-environment mixed QTL model
A total of 18 QTL were identified for panicle morphology traits with the multi-environment mixed model analyses (Figure 4, Table 4). Seven QTL were identified for PL, distributed across seven different chromosomes. Among these, five QTL (2K@77.89, 4K@26.26, 5K@76.02, 5N@36.27 and 9N@38.02) had consistent effects across field sites (Figure 5a). In contrast, two QTL (3N@62.06 and 6N@54.19) show interaction with the environment (QTL x E). The additive effects for QTL 3N@62.06 changed in magnitude across geographic regions. Further, QTL 6N@54.19 had the largest effects at the most northern and southern site and smaller effect at mid-latitude sites. QTL 6N@54.19 (A x B cross) also had a trade-off pattern, with the allelic effects changing sign from southern to northern sites.
Seven QTL were identified for PBN that are also distributed on 7 chromosomes. Four QTL (2K@74.02, 2N@66.12, 5N@84.04 and 9N@26.03) had consistent effects across locations, while three QTL (3K@38, 5K@14.06, and 7N@54.06) had QTL x E interactions, including both changes of magnitude (3K@38 and 7N@54.06) and direction (5K@14.06) from the allelic effect across geographic regions (Figure 5b). Four QTL were identified for SBN. Three QTL (2N@72.03, 5K@95.5 and 9N@36.02) had consistent effects across locations, while there was a magnitude changing interactions for QTL 9K@51.96 (Figure 5c). We also observed that two QTL for PBN (2K@74.02 and 9N@26.03) co-localized with PL QTL on chromosome 2K and 9N, based on overlapping confidence intervals (Figure 4). QTL 9N@38.02 for SBN co-localized with the QTL of PL and PBN on chromosome 9N (Figure 4).