Genetic Control and Phenotypic Characterization of Panicle Architecture and Grain Yield Related Traits in Foxtail Millet (Setaria Italica)

Panicle architecture and grain weight, both of which are influenced by genetic and environmental factors, have significant effects on grain yield potential. Here, we used a recombinant inbred line population (RIL) of 333 lines, which were grown in 13 trials with varying environmental conditions, to identify quantitative trait loci (QTL) that control differences in 9 agronomic traits related to panicle architecture and grain yield. We find that panicle weight, grain weight per panicle, panicle length, panicle diameter, and panicle exsertion length varied across different geographical locations. QTL mapping revealed 159 QTL for nine traits, of these, 34 QTL were identified in 2 to 12 environments, suggesting that the genetic control of panicle architecture in foxtail millet is sensitive to photoperiod or other environmental factors. 88 QTL controlling different traits formed 34 co-located QTL clusters, including the triple QTL cluster qPD9.2/qPL9.5/qPEL9.3, the genomic region of which was detected by 23 times in 13 environments. Several candidate genes were identified in the genomic intervals of multi-environmental QTL or co-located QTL clusters, including Seita.2G388700, Seita.3G136000, Seita.4G185300, Seita.5G241500, Seita.5G243100, Seita.9G281300, and Seita.9G342700. Among these, Seita.9G342700 was the candidate gene of qPD9.2/qPL9.5/qPEL9.3 QTL cluster, it is homologous to rice OsMADS56, which encodes a putative MADS-box transcription factor that determines inflorescence architecture in rice. These results not only provided a basis for further fine mapping, functional studies and marker-assisted selection of panicle architecture related traits in foxtail millet, but also benefited comparative genomics of cereal crops.