A SNP-Based High-Density Genetic Map Reveals Reproducible QTLs for Tassel-Related Traits in Maize (Zea mays L.)

The tassel architecture of maize (Zea mays L.), which plays an important role in F1 hybrid seed production and yield performance, is genetically controlled by quantitative trait loci (QTLs). Here, we constructed a high-density SNP-based genetic map using an F2 population containing 148 individuals. This genetic map included 7613 SNPs whose average genetic distance was 0.19 cM. On account of the F2 population, we detected 14 QTLs responsible for tassel branch number (TBN), tassel weight (TW), central spike length (CSL), and meristem length (ML); eight of these QTLs demonstrated a relatively high level of phenotypic variation explanation (PVE) (PVE ≥ 10%), at a high level of significance. qTW-2 was a major QTL (LOD = 10.11 and PVE = 28.82%), and this QTL and qTBN-2 shared the same region, indicating a possible pleiotropic effect. An F2:3 population was developed to further verify QTLs in the F2 population. Finally, qTBN-5, qTW-2 and qCSL_N-10 were detected reproducibly. To help screen potential candidate genes, we chose 12 genes within the regions of qTBN-5, qML-6, qCSL_N-7 and qTW-2 and that were possibly involved in tassel morphogenesis according to Gene Ontology (GO) annotation analysis and performed quantitative real-time polymerase chain reaction (qRT-PCR). The expression of eight of the 12 genes was significantly (P < 0.05) or extremely significantly different (P < 0.01) between parents of the F2 population during the young tassel development stage, suggesting that those eight were possible candidate genes. These results provide insights into the genetic mechanisms controlling tassel architecture and will benefit both tassel-related QTL fine mapping and causal gene cloning in maize.