Genetic Basis of Maize Resistance to Multiple Insect Pests: Integrated Genome-Wide Comparative Mapping and Candidate Gene Prioritization

Abstract

Several species of herbivores feed on maize in field and storage setups, making the development of multiple insect resistance a critical breeding target. In this study, an association mapping panel of 341 tropical maize lines was evaluated in three field environments for resistance to fall armyworm (FAW), whilst bulked grains were subjected to a maize weevil (MW) bioassay and genotyped with Diversity Array Technology’s single nucleotide polymorphisms (SNPs) markers. A multi-locus genome-wide association study (GWAS) revealed 62 quantitative trait nucleotides (QTNs) associated with FAW and MW resistance traits on all 10 maize chromosomes, of which, 47 and 31 were discovered at stringent Bonferroni genome-wide significance levels of 0.05 and 0.01, respectively, and located within or close to multiple insect resistance genomic regions (MIRGRs) concerning FAW, SB, and MW. Sixteen QTNs influenced multiple traits, of which, six were associated with resistance to both FAW and MW, suggesting a pleiotropic genetic control. Functional prioritization of candidate genes (CGs) located within 10–30 kb of the QTNs revealed 64 putative GWAS-based CGs (GbCGs) showing evidence of involvement in plant defense mechanisms. Only one GbCG was associated with each of the five of the six combined resistance QTNs, thus reinforcing the pleiotropy hypothesis. In addition, through in silico co-functional network inferences, an additional 107 network-based CGs (NbCGs), biologically connected to the 64 GbCGs, and differentially expressed under biotic or abiotic stress, were revealed within MIRGRs. The provided multiple insect resistance physical map should contribute to the development of combined insect resistance in maize.

Global warming and increasing maize cultivation demand comprehensive efforts in disease and insect resistance breeding in north‐western Europe

“…Postharvest insect pest resistance is especially important in coun- Schön et al (1993), Bohn et al (2000), and Badji et al (2020and Badji et al ( , 2021, thus restricting gain from selection.…”

“…The detected QTLs displayed large confidence intervals and their effects were usually not consistent across maize populations, thus the stability of the resistance is lacking. Nevertheless, presumably in the future, GS will provide more success in increasing insect resistance in plants including maize (Badji et al, 2020(Badji et al, , 2021, suggesting that entomologists and breeders should not be discouraged by less promising results at this early stage of research.…”

Factors Influencing Genomic Prediction Accuracies of Tropical Maize Resistance to Fall Armyworm and Weevils

“…In addition, genetic linkage and genome-wide association mapping studies have seldom been explored in African germplasm [ 8 , 24 ], which further impedes the application of MAS in the development of insect resistance maize germplasm in Africa. In a previous study, we discovered several quantitative trait nucleotides and genes that are putatively associated with FAW and MW resistance, confirming the quantitative nature of these traits, hence the difficulty in improving these traits through MAS [ 25 ]. An alternative to both PS and MAS is genomic selection (GS), which uses whole-genome markers to perform genomic prediction (GP) of breeding values of unphenotyped genotypes, from which one can select superior candidate genotypes for crossing to produce hybrids or to advance to the next generation [ 26 ].…”

“…The differential performances of the different GP algorithms on the insect resistance traits evaluated in this study could be due to differences in the genetic structures (extent of additive vs. non-additive gene action) of the respective traits [ 23 , 38 , 47 , 49 ]. Maize resistance to FAW, which was moderately heritable across environments [ 25 ], would be expected to be controlled by both additive and non-additive genetic factors, including epistasis [ 102 , 103 , 104 ], whereas, MW-resistance traits such as GWL, AP, and AK with heritability values above 90% [ 25 ] were most likely characterized by a prevalence of additive gene action [ 105 , 106 ] in the current panel.…”

“…Genotyping of the panel and SNP quality were described in our previous study [ 25 ]. In brief, maize leaves at the sixth-leaf stage of development were harvested from 341 of the 358 lines of the panel (5–10 plants per line) in 2017B and 2018A (for lines not captured in 2017B).…”