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

Abstract

Stalk lodging, breakage of the stalk at or below the ear, causes substantial yield losses in maize. The strength of the stalk rind, commonly measured as rind penetrometer resistance (RPR), is an important contributor to stalk lodging resistance. To enhance RPR genetic architecture, we conducted selection mapping on populations developed by 15 cycles of divergent selection for high (C15-H) and low (C15-L) RPR. We also performed time-course transcriptome and metabolic analyses on developing stalks of high (Hrpr1) and low (Lrpr1) RPR inbred lines derived from the C15-H and C15-L populations, respectively. Divergent selection significantly altered allele frequencies at 3,656 and 3,412 single nucleotide polymorphisms (SNP) in the C15-H and C15-L populations, respectively. While the majority of the SNPs under selection were unique, 110 SNPs were common in both populations indicating the fixation of alleles with alternative effects. Remarkably, preferential selection on the genomic regions associated with lignin and polysaccharide biosynthesis genes was observed in C15-H and C15-L populations, respectively. This observation was supported by higher lignification and lower extractability of cell wall-bound sugars in Hrpr1 compared to Lrpr1. Tricin, a monolignol important for incorporation of lignin in grass cell walls, emerged as a key determinant of the different cell wall properties of Hrpr1 and Lrpr1. Integration of selection mapping with transcriptomics and previous genetic studies on RPR identified 40 novel candidate genes including ZmMYB31, ZmNAC25, ZmMADS1, two PAL paralogues, two lichenases, ZmEXPA2, ZmIAA41, and Caleosin. Enhanced mechanistic and genetic understanding of RPR provides a foundation for improved stalk lodging resistance.

Integration of transcriptome and metabolome analyses reveals key lodging-resistance-related genes and metabolic pathways in maize

“…The content of lignin is associated with stem rigidity because lignin is only deposited in the secondary cell wall, which influences the structural integrity of the cell wall and stiffness of the stem ( Kumar et al, 2020 ). Our investigation of the lignin content of the three hybrid cultivars revealed that highly resistant JNK728 always accumulated greater amounts of lignin than the other two cultivars in response to stalk lodging ( Figure 1C ).…”

“…In addition to reducing yield, lodging can significantly diminish the quality and efficiencies of production and mechanical harvesting processes. More scuttling and climate change–driven extreme weather events such as heavy rainfalls and strong winds exacerbate stalk lodging associated crop yield losses ( Kumar et al, 2020 ) .…”