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

Abstract

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 enhanced understanding of RPR and the improvement of stalk lodging resistance.

Genetic basis of maize stalk strength decoded via linkage and association mapping

“…These findings suggest that Zm00001d052294 and Zm00001d037041 probably play a role in influencing stalk strength or lodging in maize. In addition, we found that the expression patterns of Zm0000 1d046455 and Zm00001d036051 were altered in the internodes of high-RPR lines at most developmental stages relative to low-RPR lines (Kumar et al, 2021), providing additional evidence to support their association with RPR. Beyond, we also identified two transcription factors with multiple cross-validations, Zm00001d013258 and Zm0000 1d036711, whose expression levels were not significantly different between high-and low-RPR lines.…”

Characterization and Fine Mapping of qRPR1-3 and qRPR3-1, Two Major QTLs for Rind Penetrometer Resistance in Maize

“…In the maize breeding, stalk strength plays an important role in maintaining grain yield. In many maize synthetic populations, stalk strength has been successfully enhanced based on phenotypic selection for RPR (Masole, 1993 ; Zhang et al, 2020 ; Kumar et al, 2021 ). Marker-assisted selection (MAS) as an alternative way could improve the target agronomic traits in maize varieties, making breeding more efficient and rapid (Zhao et al, 2012 ; Liu et al, 2015 ; Kage et al, 2016 ).…”

The Crop Clamp – A non-destructive electromechanical pinch test to evaluate stalk lodging resistance

“…This creates instability in the global maize supply and results in substantial economic losses for farmers [2] . It is therefore desirable to breed for maize varieties that are more resistant to stalk lodging [3] , [4] , [5] . It has been well established that stalk lodging in maize is related to stalk structural features [2] , [3] , [6] , [7] , [8] , [9] , [10] , [11] , [12] , [13] , [14] .…”

“…It is therefore desirable to breed for maize varieties that are more resistant to stalk lodging [3][4][5]. It has been well established that stalk lodging in maize is related to stalk structural features [2,3,[6][7][8][9][10][11][12][13][14].…”