Person: Semagn, K.
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Semagn
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K.
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Semagn, K.
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0000-0001-6486-5685 3 results
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- Discovery and validation of genomic regions associated with resistance to maize lethal necrosis in four biparental populations(Springer Verlag, 2018) Gowda, M.; Beyene, Y.; Makumbi, D.; Semagn, K.; Olsen, M.; Jumbo, M.B; Das, B.; Mugo, S.N.; Suresh, L.M.; Prasanna, B.M.In sub-Saharan Africa, maize is the key determinant of food security for smallholder farmers. The sudden outbreak of maize lethal necrosis (MLN) disease is seriously threatening the maize production in the region. Understanding the genetic basis of MLN resistance is crucial. In this study, we used four biparental populations applied linkage mapping and joint linkage mapping approaches to identify and validate the MLN resistance-associated genomic regions. All populations were genotyped with low to high density markers and phenotyped in multiple environments against MLN under artificial inoculation. Phenotypic variation for MLN resistance was significant and heritability was moderate to high in all four populations for both early and late stages of disease infection. Linkage mapping revealed three major quantitative trait loci (QTL) on chromosomes 3, 6, and 9 that were consistently detected in at least two of the four populations. Phenotypic variance explained by a single QTL in each population ranged from 3.9% in population 1 to 43.8% in population 2. Joint linkage association mapping across three populations with three biometric models together revealed 16 and 10 main effect QTL for MLN-early and MLN-late, respectively. The QTL identified on chromosomes 3, 5, 6, and 9 were consistent with the QTL identified by linkage mapping. Ridge regression best linear unbiased prediction with five-fold cross-validation revealed high accuracy for prediction across populations for both MLN-early and MLN-late. Overall, the study discovered and validated the presence of major effect QTL on chromosomes 3, 6, and 9 which can be potential candidates for marker-assisted breeding to improve the MLN resistance.
Publication - Genome‑wide association and genomic prediction of resistance to maize lethal necrosis disease in tropical maize germplasm(Springer, 2015) Gowda, M.; Das, B.; Makumbi, D.; Babu, R.; Semagn, K.; Mahuku, G.; Olsen, M.; Jumbo, M.B; Beyene, Y.; Prasanna, B.M.The maize lethal necrosis disease (MLND) caused by synergistic interaction of Maize chlorotic mottle virus and Sugarcane mosaic virus, and has emerged as a serious threat to maize production in eastern Africa since 2011. Our objective was to gain insights into the genetic architecture underlying the resistance to MLND by genome-wide association study (GWAS) and genomic selection. We used two association mapping (AM) panels comprising a total of 615 diverse tropical/subtropical maize inbred lines. All the lines were evaluated against MLND under artificial inoculation. Both the panels were genotyped using genotyping-by-sequencing. Phenotypic variation for MLND resistance was significant and heritability was moderately high in both the panels. Few promising lines with high resistance to MLND were identified to be used as potential donors. GWAS revealed 24 SNPs that were significantly associated (P < 3 × 10−5) with MLND resistance. These SNPs are located within or adjacent to 20 putative candidate genes that are associated with plant disease resistance. Ridge regression best linear unbiased prediction with five-fold cross-validation revealed higher prediction accuracy for IMAS-AM panel (0.56) over DTMA-AM (0.36) panel. The prediction accuracy for both within and across panels is promising; inclusion of MLND resistance associated SNPs into the prediction model further improved the accuracy. Overall, the study revealed that resistance to MLND is controlled by multiple loci with small to medium effects and the SNPs identified by GWAS can be used as potential candidates in MLND resistance breeding program.
Publication - Improving maize grain yield under drought stress and non-stress environments in Sub-Saharan Africa using marker-assisted recurrent selection(Crop Science Society of America (CSSA), 2016) Beyene, Y.; Semagn, K.; Crossa, J.; Mugo, S.N.; Atlin, G.; Tarekegne, A.T.; Meisel, B.; Sehabiague, P.; Vivek, B.; Oikeh, S.O.; Alvarado Beltrán, G.; Machida, L.; Olsen, M.; Prasanna, B.M.; Banziger, M.In marker-assisted recurrent selection (MARS), a subset of molecular markers significantly associated with target traits of interest are used to predict the breeding value of individual plants, followed by rapid recombination and selfing. This study estimated genetic gains in grain yield (GY) using MARS in 10 biparental tropical maize (Zea may L.) populations. In each population, 148 to 184 F2:3 (defined as C0) progenies were derived, crossed with a single-cross tester, and evaluated under water-stressed (WS) and well-watered (WW) environments in sub- Saharan Africa (SSA). The C0 populations were genotyped with 190 to 225 single-nucleotide polymorphism (SNP) markers. A selection index based on marker data and phenotypic data was used for selecting the best C0 families for recombination. Individual plants from selected families were genotyped using 55 to 87 SNPs tagging specific quantitative trait loci (QTL), and the best individuals from each cycle were either intercrossed (to form C1) or selfed (to form C1S1 and C1S2). A genetic gain study was conducted using test crosses of lines from the different cycles F1 and founder parents. Test crosses, along with five commercial hybrid checks were evaluated under four WS and four WW environments. The overall gain for GY using MARS across the 10 populations was 105 kg ha−1 yr−1 under WW and 51 kg ha−1 yr−1 under WS. Across WW environments, GY of C1S2–derived hybrids were 8.7, 5.9, and 16.2% significantly greater than those of C0, founder parents, and commercial checks, respectively. Results demonstrate the potential of MARS for increasing genetic gain under both drought and optimum environments in SSA.
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