Stephen Mugo

Molecular characterization of diverse CIMMYT maize inbred lines from eastern and southern Africa using single nucleotide polymorphic markers

BackgroundKnowledge of germplasm diversity and relationships among elite breeding materials is fundamentally important in crop improvement. We genotyped 450 maize inbred lines developed and/or widely used by CIMMYT breeding programs in both Kenya and Zimbabwe using 1065 SNP markers to (i) investigate population structure and patterns of relationship of the germplasm for better exploitation in breeding programs; (ii) assess the usefulness of SNPs for identifying heterotic groups commonly used by CIMMYT breeding programs; and (iii) identify a subset of highly informative SNP markers for routine and low cost genotyping of CIMMYT germplasm in the region using uniplex assays.ResultsGenetic distance for about 94% of the pairs of lines fell between 0.300 and 0.400. Eighty four percent of the pairs of lines also showed relative kinship values ≤ 0.500. Model-based population structure analysis, principal component analysis, neighbor-joining cluster analysis and discriminant analysis revealed the presence of 3 major groups and generally agree with pedigree information. The SNP markers did not show clear separation of heterotic groups A and B that were established based on combining ability tests through diallel and line x tester analyses. Our results demonstrated large differences among the SNP markers in terms of reproducibility, ease of scoring, polymorphism, minor allele frequency and polymorphic information content. About 40% of the SNPs in the multiplexed chip-based GoldenGate assays were found to be uninformative in this study and we recommend 644 of the 1065 for low to medium density genotyping in tropical maize germplasm using uniplex assays.ConclusionsThere were high genetic distance and low kinship coefficients among most pairs of lines, clearly indicating the uniqueness of the majority of the inbred lines in these maize breeding programs. The results from this study will be useful to breeders in selecting best parental combinations for new breeding crosses, mapping population development and marker assisted breeding.

Meta-analyses of QTL for grain yield and anthesis silking interval in 18 maize populations evaluated under water-stressed and well-watered environments

BackgroundIdentification of QTL with large phenotypic effects conserved across genetic backgrounds and environments is one of the prerequisites for crop improvement using marker assisted selection (MAS). The objectives of this study were to identify meta-QTL (mQTL) for grain yield (GY) and anthesis silking interval (ASI) across 18 bi-parental maize populations evaluated in the same conditions across 2-4 managed water stressed and 3-4 well watered environments.ResultsThe meta-analyses identified 68 mQTL (9 QTL specific to ASI, 15 specific to GY, and 44 for both GY and ASI). Mean phenotypic variance explained by each mQTL varied from 1.2 to 13.1% and the overall average was 6.5%. Few QTL were detected under both environmental treatments and/or multiple (>4 populations) genetic backgrounds. The number and 95% genetic and physical confidence intervals of the mQTL were highly reduced compared to the QTL identified in the original studies. Each physical interval of the mQTL consisted of 5 to 926 candidate genes.ConclusionsMeta-analyses reduced the number of QTL by 68% and narrowed the confidence intervals up to 12-fold. At least the 4 mQTL (mQTL2.2, mQTL6.1, mQTL7.5 and mQTL9.2) associated with GY under both water-stressed and well-watered environments and detected up to 6 populations may be considered for fine mapping and validation to confirm effects in different genetic backgrounds and pyramid them into new drought resistant breeding lines. This is the first extensive report on meta-analysis of data from over 3100 individuals genotyped using the same SNP platform and evaluated in the same conditions across a wide range of managed water-stressed and well-watered environments.

Resistance of maize varieties to the maize weevil Sitophilus zeamais (Motsch.) (Coleoptera: Curculionidae)

of susceptibility was used to group the varieties. The variety, ‘BHQP-542’, had the least index of susceptibility and was regarded as resistant. The varieties, ‘Katumani’, ‘Melkasa-I’, ‘Melkasa-II’, ‘Melkasa-III’, ‘Coree’, ‘BH-541’, ‘BH-660’, ‘BH-540’, ‘Rare-I’, ‘Awasa-511’, ‘ACV3’ and ‘ACV6’, were moderately resistant. Weevils fed with the resistant variety produced low numbers of F1 progeny, had a high median developmental time and a low percentage of seed damage and seed weight loss. Maize varieties with a high F1 progeny tended to have a short median developmental time. An increasing number of F1 progeny resulted in an increasing seed damage and seed weight loss. We found an inverse relationship between the susceptibility index and percent mortality and median developmental time; however, the numbers of F1 progeny, percent seed damage and seed weight loss were positively related with the susceptibility index. The use of resistant varieties should be promoted in managing S. zeamais in stored maize under subsistence farming conditions in Africa.

Resistance of three-way cross experimental maize hybrids to post-harvest insect pests, the larger grain borer (Prostephanus truncatus) and maize weevil (Sitophilus zeamais)

The larger grain borer Prostephanus truncatus Horn and the maize weevil Sitophilus zeamais Motschulsky are important pests of stored maize in the tropics, particularly where maize is stored on-farm with little control of moisture content and without use of pesticides. This study was undertaken to determine level of resistance among new experimental maize hybrids against P. truncatus and S. zeamais. Out of the 54 experimental hybrids tested, eight hybrids were resistant, six were susceptible and the remaining 40 hybrids were moderately resistant. Five hybrids showed considerable reduction in losses for both P. truncatus and S. zeamais (CKPH08013, CKPH08021, CKPH08003, CKPH08004 and CKPH08009), suggesting that they contained genes that confer resistance to the two pests. Low grain weight loss, powder production and low insect multiplication on resistant grains reduce the negative impact of the two beetle pests. Therefore, host plant resistance can be used as a vital component of an integrated pest management strategy against P. truncatus and S. zeamais.

Yield stability of stem borer resistant maize hybrids evaluated in regional trials in East Africa

Twenty-seven stem borer-resistant maize hybrids and three checks were evaluated in 14 locations in Kenya and Ethiopia to study the genotype x environment interaction (GEI) and yield stability. An analysis of variance was conducted for grain yield, number of days to silking, plant height, ear height and grain moisture content, and reaction to turcicum leaf blight, gray leaf spot, maize streak virus diseases and common rust. The yield stability and adaptation pattern of genotypes were examined with genotype plus genotype x environment (GGE) interaction biplot. Variations due to location, genotype and GEI effects were highly significant for all traits. Location variance among the hybrids was the most important source of variation for all traits, accounting for 58 to 90% of the total variance. The genotypic variance was higher than the GEI variance for turcicum leaf blight, plant height and silking date. The GEI variance was higher than the genotypic variance for grain yield, ear height, gray leaf spot, common rust and grain moisture content. The GGE biplot showed that 50% of the entries had positive PC1 scores suggesting above average performance, and 50% of them had negative PC1 scores indicating below average performance. Based on the mean grain yield and stability parameters, hybrid CKIR07003 (5.5 t/ha), CKIR07004 (5.5 t/ha) and CKIR07005 (5.6 t /ha) were identified as high-yielding and stable genotypes, and could be nominated for national performance trials for commercial release in various countries.

The Water Efficient Maize for Africa Project as an Example of a Public–Private Partnership

The Water Efficient Maize for Africa (WEMA) project was started in 2008 with the main objective of developing drought tolerant white hybrid maize for smallholder farmers of sub-Saharan Africa (SSA) that yields at least 20 % more under drought conditions compared to commercial check hybrids. To achieve this, a combination of breeding and biotech approaches are followed to introduce drought tolerance in African maize varieties. To protect the yield benefit, the insect protection trait (Bt) was added in the year 2011. This work is conducted through a public–private partnership led by the African Agricultural Technology Foundation based in Kenya with collaborating partners that include the International Maize and Wheat Improvement Center, Monsanto Company, and five National Agricultural Research Systems for Tanzania, Kenya, Mozambique, Uganda, and the Republic of South Africa. Among the key achievements for the first 5 years of the project (Phase 1) include the successful running of confined field trials for transgenic maize varieties in Kenya, Uganda, and South Africa and the submission of conventional drought tolerant maize hybrids into the national performance trials in Kenya. The next Phase 2 of the program (2013–2017) involves the deployment of the WEMA products. The first WEMA conventional drought tolerant maize hybrids are scheduled to be released to farmers in the year 2013. These are WEMA hybrids that outperformed some of the best local check hybrids on the market. Next for release in 2016/2017, subject to receiving appropriate regulatory approvals, will be the transgenic products of WEMA which will carry two biotech traits, Bt insect protection trait and the drought tolerance trait from the cold shock protein B (cspB). The overall impact of WEMA project will be the availability of both transgenic and non-transgenic drought tolerant maize hybrids for use by smallholder farmers in SSA.

Options in developing stemborer-resistant maize: CIMMYT's approaches and experiences

Various insect pests, of which stemborers are the most widely distributed and damaging, affect about 30 out of the 35 million hectares planted with maize in developing countries. Chemical control, biological control, cultural methods and host plant resistance constitute the four general approaches to stemborer control. The use of stemborer-resistant maize increases farming efficiency by both reducing yield losses from stemborer damage and reducing or eliminating the cost of insecticides and other inputs. In the past, CIMMYT followed conventional breeding methods to develop germplasm resistant to stemborers and molecular technology, quantitative trait loci (QTL) in marker-assisted selection (MAS) to select for improved stemborer resistance in elite lines. More recently, CIMMYT has developed the capacity to produce transgenic maize with resistance factor(s) derived from genes that encode delta-endotoxins derived from the soil bacterium Bacillus thuringiensis (Bt). A sub-tropical source population with multiple borer resistance (MBR population) was developed by recombination and recurrent selection under infestation with four stemborer species. Marker-assisted selection is being used in two African countries to promote the transfer of resistance into elite and adapted germplasm. The Insect Resistant Maize for Africa (IRMA) project is pursuing the transfer of Bt-based resistance to adapted maize germplasm, initially in Kenya, but later to other interested African countries. CIMMYT’s varietal release strategy is to pyramid Bt genes into maize populations with existing multigenic pest resistance, in order to enhance both the levels and durability of plant resistance to maize pests. This paper discusses the various approaches used at CIMMYT to develop stemborer-resistant maize germplasm.RésuméPlusieurs espèces d’insectes infestent environ 30 sur 35 million d’hectares plantés de maïs dans les pays en voie de développement. Parmi ceux-ci, les foreurs sont les plus destructifs et les plus largement repartis. La lutte chimique, biologique, les méthodes culturales et l’utilisation des plantes résistantes forment les quatres approches courantes de lutte contre les foreurs. L’utilisation du maïs résistant aux foreurs augmentent l’efficacité culturale en réduisant les pertes en récoltes dues aux foreurs grâce à la réduction ou l’élimination des dépenses en insecticides ou autres entrants agricoles. Dans le passé CIMMYT a suivi la méthode conventionnelle des multiplications pour développer du matériel génétique résistant aux foreurs, la technologie moleculaire, l’aspect quantitatif du loci (QTL) des marqueurs assistés (MAS) aide à selectionner dans les lignes elites une meilleure resistance aux foreurs. Plus recemment, le CIMMYT a dévéloppé la capacité de produire un maïs transgénique avec des facteurs de résistance dérivés des gènes qui codent pour une delta-endotoxin dérivée des bactéries du sol Bacillus thuringiensis (Bt). Une souche sous tropicale avec une résistance multiple aux foreurs a été dévéloppée par recombinaison et selection recurrente sous une infestation de quatres espèces de foreurs. La sélection par marqueur assisté est actuellement utilisée dans 2 pays africains pour promouvoir le transfert de la résistance dans le matériel génétique élite adapté. Le projet sur la résistance du maïs aux insects (IRMA) suit le transfert de la résistance basée sur Bt au matériel génétique de maïs adapté, initiallement au Kenya, et après aux autres pays africains qui s’y intéresseraient. La stratégie de propogation des variétés de CIMMYT est d’insérer le gène de Bt dans les populations de maïs ayant des gènes multiples de résistances aux ravageurs dans l’optique d’améliorer les niveaux et la durée de la résistances des plantes aux ravageurs du maïs. Cet article discute des différentes approches utilisées par CIMMYT pour dévélopper un materiel génétiquement résistant aux foreurs de tiges de maïs.

Responses of tropical maize landraces to damage by Chilo partellus stem borer

The potential to manage insect pests using host-plant resistance exists, but has not been exploited adequately. The objective of this study was to determine the resistance of 75 tropical maize landraces through artificial infestation with Chilo partellus Swinhoe. The trial was laid in alpha-lattice design and each seedling was infested with five neonates three weeks after planting, over two seasons in 2009 and 2010. The number of exit holes, tunnel length, ear diameter, ear length, plant height, stem diameter, stem lodging and grain yield were measured and a selection index computed. GUAT 1050 was the most resistant with an index of 0.56, while BRAZ 2179 was the most susceptible with an index of 1.66. Ear characteristics were negatively correlated with damage parameters. The principal component biplot suggested that exit holes, cumulative tunnel length, leaf damage, cob diameter, stem lodging, selection index, ear and plant height contributed 71.2% of the variation in resistance. The mean number of exit holes and tunnel length for resistant landraces and resistant hybrid checks were similar; at 5.5 and 2.48 cm, respectively. The identified resistant landraces (GUAT 1050, GUAT 280, GUAT 1093, GUAT 1082, GUAT 1014, CHIS 114, and GUAN 34) could be used to develop C. partellus stem borer-resistant maize genotypes. Key words: Chilo partellus , ear length, exit holes, stem borer resistance, tunnel length.

Resistance of Bt-maize (MON810) against the stem borers Busseola fusca (Fuller) and Chilo partellus (Swinhoe) and its yield performance in Kenya

A study was conducted to assess the performance of maize hybrids with Bt event MON810 (Bt-hybrids) against the maize stem borer Busseola fusca (Fuller) in a biosafety greenhouse (BGH) and against the spotted stem borer Chilo partellus (Swinhoe) under confined field trials (CFT) in Kenya for three seasons during 2013–2014. The study comprised 14 non-commercialized hybrids (seven pairs of near-isogenic Bt and non-Bt hybrids) and four non-Bt commercial hybrids. Each plant was artificially infested twice with 10 first instar larvae. In CFT, plants were infested with C. partellus 14 and 24 days after planting; in BGH, plants were infested with B. fusca 21 and 31 days after planting. In CFT, the seven Bt hybrids significantly differed from their non-Bt counterparts for leaf damage, number of exit holes, percent tunnel length, and grain yield. When averaged over three seasons, Bt-hybrids gave the highest grain yield (9.7 t ha−1), followed by non-Bt hybrids (6.9 t ha−1) and commercial checks (6 t ha−1). Bt-hybrids had the least number of exit holes and percent tunnel length in all the seasons as compared to the non-Bt hybrids and commercial checks. In BGH trials, Bt-hybrids consistently suffered less leaf damage than their non-Bt near isolines. The study demonstrated that MON810 was effective in controlling B. fusca and C. partellus. Bt-maize, therefore, has great potential to reduce the risk of maize grain losses in Africa due to stem borers, and will enable the smallholder farmers to produce high-quality grain with increased yield, reduced insecticide inputs, and improved food security.

Combining ability and testcross performance of drought-tolerant maize inbred lines under stress and non-stress environments in Kenya

Abstract Drought and poor soil fertility are among the major abiotic stresses affecting maize productivity in sub‐Saharan Africa. Maize breeding efforts at the International Maize and Wheat Improvement Center (CIMMYT) have focused on incorporating drought stress tolerance and nitrogen‐use efficiency (NUE) into tropical maize germplasm. The objectives of this study were to estimate the general combining ability (GCA) and specific combining ability (SCA) of selected maize inbred lines under drought stress (DS), low‐nitrogen (LN) and optimum moisture and nitrogen (optimum) conditions, and to assess the yield potential and stability of experimental hybrids under these management conditions. Forty‐nine experimental three‐way cross hybrids, generated from a 7 × 7 line by tester crosses, and six commercial checks were evaluated across 11 optimum, DS and LN sites in Kenya in 2014 using an alpha lattice design with two replicates per entry at each site. DS reduced both grain yield (GY) and plant height (PH), while anthesis–silking interval (ASI) increased under both DS and LN. Hybrids ‘L4/T2’ and ‘L4/T1’ were found to be superior and stable, while inbreds ‘L4’ and ‘L6’ were good combiners for GY and other secondary traits across sites. Additive variance played a greater role for most traits under the three management conditions, suggesting that further progress in the improvement of these traits should be possible. GY under optimum conditions was positively correlated with GY under both DS and LN conditions, but GY under DS and LN was not correlated. Our results suggest the feasibility for simultaneous improvement in grain yield performance of genotypes under optimum, DS and LN conditions.