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Open AccessArticle

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

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Department of Agricultural Production, Makerere Univesity, P.O. Box 7062 Kampala, Uganda
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Cereals Program, National Crop Resource Research Institute, P.O. Box 7084 Kampala, Uganda
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Alliance Bioversity International-CIAT, P.O. Box 24384 Kampala, Uganda
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Laboratory of Applied Ecology, University of Abomey-Calavi, 01BP 526 Cotonou, Benin
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Department of Crop Science, University of Cape Coast, P.O. Box 5007 PMB Cape Coast, Ghana
*
Author to whom correspondence should be addressed.
Genes 2020, 11(6), 689; https://doi.org/10.3390/genes11060689
Received: 19 May 2020 / Revised: 30 May 2020 / Accepted: 1 June 2020 / Published: 24 June 2020
(This article belongs to the Special Issue Genetics and Physiology of Multiple-Stress Tolerance in Crops)
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. View Full-Text
Keywords: combined insect resistance; QTNs; functional prioritization; fall armyworm; maize weevil; stem borers combined insect resistance; QTNs; functional prioritization; fall armyworm; maize weevil; stem borers
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Badji, A.; Kwemoi, D.B.; Machida, L.; Okii, D.; Mwila, N.; Agbahoungba, S.; Kumi, F.; Ibanda, A.; Bararyenya, A.; Solemanegy, M.; Odong, T.; Wasswa, P.; Otim, M.; Asea, G.; Ochwo-Ssemakula, M.; Talwana, H.; Kyamanywa, S.; Rubaihayo, P. Genetic Basis of Maize Resistance to Multiple Insect Pests: Integrated Genome-Wide Comparative Mapping and Candidate Gene Prioritization. Genes 2020, 11, 689.

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