The quantitative trait locus stiff2 controls stalk bending strength and root architecture in maize

Stalk lodging is a major threat to global maize production, which causes great annual yield losses. Stalk bending strength (SBS) is highly associated with resistance to stalk lodging in maize. However, the genetic basis of SBS remains largely unknown. In this study, we identify a quantitative trait locus (QTL), stiff2, corresponding to a known flowering-time gene ZmCCT, by integrating QTL mapping and association mapping. A 5-kilobase (kb) transposable element inserted in the promoter region of ZmCCT significantly reduces SBS, while upregulated expression of ZmCCT through transformation significantly enhances SBS. Gene regulatory network analysis reveals that ZmCCT may indirectly regulate a set of downstream genes, which contain nrt5 for nitrogen transport, Tu1, d8, and d9 for stalk elongation, ub2, ub3, and ch1 for stalk thickening, and myb69 and bm4 for lignin biosynthesis. These genes collectively increase stalk strength and improve lodging resistance aboveground. Additionally, stiff2 regulates not only aboveground resistance to stalk bending and breakage but also influences root system architecture, which enhances resistance to root lodging belowground. The identification of stiff2 and its downstream targets provides critical insights into the genetic control of maize lodging and offers powerful tools for breeding lodging-resistant cultivars.