Association analysis for resistance to Striga hermonthica in diverse tropical maize inbred lines

Abstract

Striga hermonthica is a widespread, destructive parasitic plant that causes substantial yield loss to maize productivity in sub-Saharan Africa. Under severe Striga infestation, yield losses can range from 60 to 100% resulting in abandonment of farmers’ lands. Diverse methods have been proposed for Striga management; however, host plant resistance is considered the most effective and affordable to small-scale famers. Thus, conducting a genome-wide association study to identify quantitative trait nucleotides controlling S. hermonthica resistance and mining of relevant candidate genes will expedite the improvement of Striga resistance breeding through marker-assisted breeding. For this study, 150 diverse maize inbred lines were evaluated under Striga infested and non-infested conditions for two years and genotyped using the genotyping-by-sequencing platform. Heritability estimates of Striga damage ratings, emerged Striga plants and grain yield, hereafter referred to as Striga resistance-related traits, were high under Striga infested condition. The mixed linear model (MLM) identified thirty SNPs associated with the three Striga resistance-related traits based on the multi-locus approaches (mrMLM, FASTmrMLM, FASTmrEMMA and pLARmEB). These SNPs explained up to 14% of the total phenotypic variation. Under non-infested condition, four SNPs were associated with grain yield, and these SNPs explained up to 17% of the total phenotypic variation. Gene annotation of significant SNPs identified candidate genes (Leucine-rich repeats, putative disease resistance protein and VQ proteins) with functions related to plant growth, development, and defense mechanisms. The marker-effect prediction was able to identify alleles responsible for predicting high yield and low Striga damage rating in the breeding panel. This study provides valuable insight for marker validation and deployment for Striga resistance breeding in maize.

Mapping quantitative trait loci and predicting candidate genes for Striga resistance in maize using resistance donor line derived from Zea diploperennis

“…Some of the QTLs identified in this study have been reported in previous studies. For example, QTLs qSD 2.3 and qSD 5 detected for Striga damage, qSC 2.1 and qSC 2.2 for Striga emergence counts in this study have been previously reported by Stanley et al (2021) . The authors identified significant SNP markers S5_70442824 and S2_188120710 to be associated with Striga damage ratings as well as S2_135038935 and S2_208978140 associated with number of emerged Striga plants in a genome-wide association study to detect SNP markers linked with Striga resistance traits in late maturing maize germplasm.…”

“…Several well-studied plant transcription factor families, including ethylene response factor (ERF), basic-domain leucine-zipper protein (bZIP), MYB, WRKY, NAC, and members of the basic helix-loop-helix (bHLH) transcription factors associated with defense responses in plants were identified in our study to be associated with Striga resistance adaptive traits. Stanley et al (2021) identified the bHLH transcription factors, putative leucine-rich repeat protein and bZIP transcription factors in a GWAS to identify Striga resistance linked markers using the IITA intermediate and late maturing maize inbred lines under artificial Striga infestation. Similarly; Gowda et al (2021) found the bHLH transcription factors to be associated with Striga resistance traits in maize.…”

“…QTLs/markers have been identified for Striga resistance traits by maize breeders at the IITA and the International Maize and Wheat Improvement Centre (CIMMYT). However, most of the QTLs/markers have minor effects, though linked to genes associated with plant defense mechanisms under Striga infestation ( Badu-Apraku et al, 2020a ; Adewale et al, 2020 ; Badu-Apraku et al, 2020b ; Gowda et al, 2021 ; Stanley et al, 2021 ). There is, therefore, the need to identify more Striga resistance QTLs particularly using germplasm extracted from wild maize sources ( Zea diploperennis ) to ensure successful resistance breeding through gene pyramiding.…”

Association mapping for broomrape resistance in sunflower

“…in maize and sorghum, most association mapping studies were based on population sizes not very far from our population size, e.g. n=132 ( Adewale et al., 2020 ), n=150 ( Stanley et al., 2021 ), n=169 ( Okunola et al., 2022 ), or n=173 (Kavuloko et al., 2021), in most cases using a single Striga population. Other studies used larger population sizes, e.g.…”

Elucidating the patterns of pleiotropy and its biological relevance in maize

“…A highly pleiotropic locus in GAP mass features included empty pericarp2 (Zm00001d005675), which is involved in embryo morphogenesis, shoot development, and the negative regulation of the heat shock response [49][50][51]. GAP expression data showed ZIMtranscription factor 8 (zim8, Zm00001d004277), a candidate gene for Striga damage [52], and kernel composition and popping expansion [53].…”