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The strength of the stalk rind, measured as rind penetrometer resistance (RPR), is an important contributor to stalk lodging resistance. To enhance the genetic architecture of RPR, we combined selection mapping on populations developed by 15 cycles of divergent selection for high and low RPR with time-course transcriptomic and metabolic analyses of the stalks. Divergent selection significantly altered allele frequencies of 3,656 and 3,412 single- nucleotide polymorphisms (SNPs) in the high and low RPR populations, respectively. Surprisingly, only 110 (1.56%) SNPs under selection were common in both populations, while the majority (98.4%) were unique to each population. This result indicated that high and low RPR phenotypes are produced by biologically distinct mechanisms. Remarkably, regions harboring lignin and polysaccharide genes were preferentially selected in high and low RPR populations, respectively. The preferential selection was manifested as higher lignification and increased saccharification of the high and low RPR stalks, respectively. The evolution of distinct gene classes according to the direction of selection was unexpected in the context of parallel evolution and demonstrated that selection for a trait, albeit in different directions, does not necessarily act on the same genes. Tricin, a grass-specific monolignol that initiates the incorporation of lignin in the cell walls, emerged as a key determinant of RPR. Integration of selection mapping and transcriptomic analyses with published genetic studies of RPR identified several candidate genes including ZmMYB31, ZmNAC25, ZmMADS1, ZmEXPA2, ZmIAA41 and hk5. These findings provide a foundation for an enhanced understanding of RPR and the improvement of stalk lodging resistance.

Genetic Architecture of Maize Rind Strength Revealed by the Analysis of Divergently Selected Populations