However, the molecular genetic basis of maize stalk strength remains unclear, and improvement methods remain inefficient. Here, we combined map-based cloning and association mapping and identified the gene stiff1 underlying a major quantitative trait locus for stalk strength in maize. A 27.2-kb transposable element insertion was present in the promoter of the stiff1 gene, which encodes an F-box domain protein. This transposable element insertion repressed the transcription of stiff1, leading to the increased cellulose and lignin contents in the cell wall and consequently greater stalk strength. Furthermore, a precisely edited allele of stiff1 generated through the CRISPR/Cas9 system resulted in plants with a stronger stalk than the unedited control. Nucleotide diversity analysis revealed that the promoter of stiff1 was under strong selection in the maize stiff-stalk group. Our cloning of stiff1 reveals a case in which a transposable element played an important role in maize improvement. The identification of stiff1 and our edited stiff1 allele pave the way for efficient improvement of maize stalk strength.
(A) QTL mapping identified a major QTL for stalk strength on chromosome 6, accounting for 23.8 and 15.6% of the total phenotypic variation in stalk BS and RPR, respectively. The blue and green lines represent the BS and RPR traits, respectively. The red dashed line represents the significant logarithm of the odds (LOD) threshold (3.2).
(B) High-resolution mapping of stiff1. Only 4 of 14 markers for fine-mapping (Supplemental Figure 5) are presented. The comparison of BS between two NILs (St72-56-1 and St72-56-2) originated from a recombination event narrowed down stiff1 to a 58-kb fragment between two markers: P7 and P10 (P = 1.0 × 10−10). Orange arrows represent molecular markers for fine-mapping, and the positions of these markers are presented below these orange arrows. Blue and green bars indicate the chromosomal fragments of the parental lines B73 and Ki11. The red flag indicates the target region of stiff1.
(C) Sequence analysis of the 58-kb fragment between two parent lines, B73 and Ki11. Two insertions of 27.2 kb and 578 bp were present in B73 at positions −1094 and −392 in the promoter of the target gene Zm00001d036653 using the Ki11 sequence as a reference. The start codon was regarded as position 0. The two insertions are highlighted in red and purple. Blue and dark bars represent stiff1 gene exons and introns, respectively. Bar = 1 kb.
(D) Association mapping with a mixed linear model revealed that the large insertion/deletion at position −1094 in the stiff1 promoter was strongly correlated with stalk BS. The red dashed line is the 1% significance threshold after Bonferroni correction for 58 tests. The stiff1 gene structure is presented on the x axis.
(E) stiff1 protein sequence alignment between B73 and Ki11. The F-box domain is highlighted with the red dashed line.