Breeding Investigations on Resistance to Fall Armyworm in Tropical Maize Germplasm

Abstract

Maize is the main staple food in Kenya and contributes significantly to the country’s food and nutrition security. However, significant economic yield losses attributed to fall armyworm (FAW) infestation have been reported in the country. Limited genetic studies have been conducted on FAW resistance in tropical maize. This study was carried out to i) determine the genetic diversity within tropical maize germplasm for resistance to FAW, ii) estimate gene action for fall armyworm resistance and agronomic traits in tropical maize inbred lines, and iii) identify genomic regions and candidate genes associated with resistance to FAW in tropical maize germplasm using genome-wide association studies (GWAS). In objective i), the genetic diversity and population structure of 140 tropical maize inbred lines for resistance to fall armyworm were determined using phenotypic traits and DArTseq-based single-nucleotide polymorphisms (SNP) markers. One hundred and forty maize inbred lines were evaluated for their agronomic traits and response to FAW under artificial infestation in a 14 x 10 alpha lattice design with two replications for two seasons at KALRO Kiboko station in Kenya. Highly significant differences (< 0.001) were observed among the genotypes for FAW leaf and cob damage scores, plant height, ear height, number of ears, ear aspect, and grain yield (t ha-1). Genotype and genotype by environment interaction (GEI) variances were highly significant for all traits. Significant negative correlation was observed between FAW damage parameters and grain yield/yield related parameters. The variation in performance of the genotypes signified that the tropical inbred lines were genetically diverse and may be used in maize breeding programs for crop improvement. The inbred lines were further genotyped using 24,741 SNP markers. The gene diversity (GD) recorded a mean of 0.35 with a range of between 0.1 and 0.5. The polymorphism information content (PIC) ranged from 0.10 to 0.38 with a mean of 0.28. Observed heterozygosity (Ho) ranged between 0.18 and 0.49, with a mean value of 0.25. Population pair wise fixation index ranged from 0.02 to 0.15. Genetic variation within the subpopulation (65%) was higher than among the subpopulation (35%). Population structure analysis based on cross-entropy criteria and neighbor joining hierarchical cluster analysis grouped the inbred lines into nine subpopulations (K=9) and 9 clusters, respectively. The wide genetic variability observed in this study indicated that the inbred lines were genetically diverse and may be important sources of beneficial genes for maize breeding programs. The second objective involved the estimation of gene action for FAW resistance and agronomic traits in tropical maize inbred lines. Combining ability analysis of 123 hybrids generated by North Carolina Design II (NCDII) mating design and 5 checks was performed in a 16 x 8 alpha lattice design with 2 replications, across 3 locations (Kiboko, Kirinyaga and Kakamega) for two seasons. Result showed that FAW leaf damage traits, cob damage and ear aspect were controlled by additive gene effects while plant height, ear height and ear rot were regulated by both additive and non-additive gene effects. Eleven lines in leaf damage score 1 (LD1), 9 in leaf damage score 2 (LD2), 6 in leaf damage score 3 (LD3) and 13 entries in cob damage exhibited significant negative general combining ability (GCA) male effects and 14 entries in LD1, 7 in LD2 and 13 in cob damage had significant negative female GCA effects for fall armyworm damage traits. Ten inbred lines recorded a significant negative GCA effect for ear rot. Lines with significant negative GCA effects for FAW and ear rot from the study can contribute favorable alleles for improvement of resistance to FAW and ear rot in maize, respectively. Twenty-three new superior hybrids with significant specific combining ability (SCA) effect in maize ear rot disease, 42 hybrids in plant height, 42 hybrids in ear height, and a single hybrid with significant SCA effect for grain yield were identified. The selected hybrids were recommended for further evaluation for improvement of their respective traits and preparation for release. In the third objective, 137 tropical maize inbred lines were evaluated for FAW leaf and cob damage, grain yield and ear rot infection. The lines were evaluated under artificial FAW infestation for two seasons and genotyped with the DArTseq platform. Genome-wide association study (GWAS) revealed that 8 SNPs were highly significantly associated with resistance to FAW damage traits, 10,950 candidate genes associated with FAW leaf damage, and 4,495 candidate genes associated with cob damage in maize. Thirty four pathways linked with FAW resistance and biological processes governed by 20 most significantly enriched genes associated with FAW damage were identified. The SNPs, candidate genes, pathways, and biological processes identified provided extensive genomic information that can be further investigated for FAW resistance in maize