Dan Makumbi

Prediction of genetic values of quantitative traits in plant breeding using pedigree and molecular markers

The availability of dense molecular markers has made possible the use of genomic selection (GS) for plant breeding. However, the evaluation of models for GS in real plant populations is very limited. This article evaluates the performance of parametric and semiparametric models for GS using wheat (Triticum aestivum L.) and maize (Zea mays) data in which different traits were measured in several environmental conditions. The findings, based on extensive cross-validations, indicate that models including marker information had higher predictive ability than pedigree-based models. In the wheat data set, and relative to a pedigree model, gains in predictive ability due to inclusion of markers ranged from 7.7 to 35.7%. Correlation between observed and predictive values in the maize data set achieved values up to 0.79. Estimates of marker effects were different across environmental conditions, indicating that genotype × environment interaction is an important component of genetic variability. These results indicate that GS in plant breeding can be an effective strategy for selecting among lines whose phenotypes have yet to be observed.

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.

Maize systems under climate change in sub-Saharan Africa

Purpose – The purpose of this study is to examine the biophysical and socioeconomic impacts of climate change on maize production and food security in sub-Saharan Africa (SSA) using adapted improved maize varieties and well-calibrated and validated bioeconomic models. Design/methodology/approach – Using the past climate (1950-2000) as a baseline, the study estimated the biophysical impacts of climate change in 2050 (2040-2069) and 2080 (2070-2099) under the A1B emission scenario and three nitrogen levels, and the socioeconomic impacts in 2050. Findings – Climate change will affect maize yields across SSA in 2050 and 2080, and the extent of the impact at a given period will vary considerably between input levels, regions and maize mega environments (MMEs). Greater relative yield reductions may occur under medium and high-input intensification than under low intensification, in Western and Southern Africa than in Eastern and Central Africa and in lowland and dry mid-altitude than in highland and wet mid-alt...

Genome-wide association mapping reveals novel sources of resistance to northern corn leaf blight in maize

BackgroundNorthern corn leaf blight (NCLB) caused by Exserohilum turcicum is a destructive disease in maize. Using host resistance to minimize the detrimental effects of NCLB on maize productivity is the most cost-effective and appealing disease management strategy. However, this requires the identification and use of stable resistance genes that are effective across different environments.ResultsWe evaluated a diverse maize population comprised of 999 inbred lines across different environments for resistance to NCLB. To identify genomic regions associated with NCLB resistance in maize, a genome-wide association analysis was conducted using 56,110 single-nucleotide polymorphism markers. Single-marker and haplotype-based associations, as well as Anderson-Darling tests, identified alleles significantly associated with NCLB resistance. The single-marker and haplotype-based association mappings identified twelve and ten loci (genes), respectively, that were significantly associated with resistance to NCLB. Additionally, by dividing the population into three subgroups and performing Anderson-Darling tests, eighty one genes were detected, and twelve of them were related to plant defense. Identical defense genes were identified using the three analyses.ConclusionAn association panel including 999 diverse lines was evaluated for resistance to NCLB in multiple environments, and a large number of resistant lines were identified and can be used as reliable resistance resource in maize breeding program. Genome-wide association study reveals that NCLB resistance is a complex trait which is under the control of many minor genes with relatively low effects. Pyramiding these genes in the same background is likely to result in stable resistance to NCLB.

Genetic relationships and structure among open-pollinated maize varieties adapted to eastern and southern Africa using microsatellite markers

Abstract Molecular characterization of open-pollinated maize varieties (OPVs) is fundamentally important in maize germplasm improvement. We investigated the extent of genetic differences, patterns of relationships, and population structure among 218 diverse OPVs widely used in southern and eastern Africa using the model-based population structure, analysis of molecular variance, cluster analysis, principal component analysis, and discriminant analysis. The OPVs were genotyped with 51 microsatellite markers and the fluorescent detection system of the Applied Biosystems 3730 Capillary Sequencer. The number of alleles detected in each OPV varied from 72 to 155, with an overall mean of 127.6. Genetic distance among the OPVs varied from 0.051 to 0.434, with a mean of 0.227. The different multivariate methods suggest the presence of 2–4 possible groups, primarily by maturity groups but also with overlapping variation between breeding programs, mega-environments, and specific agronomic traits. Nearly all OPVs in group 1 and group 2 belong to the intermediate-late and early maturity groups, respectively. Group 3 consisted of mainly intermediate maturing OPVs, while group 4 contained OPVs of different maturity groups. The OPVs widely used in eastern Africa either originated from the southern African maize breeding programs, or the majority of inbred lines used as parents by the two breeding programs in developing the OPVs might be genetically related. Some of the OPVs are much older than others, but they still did not show a clear pattern of genetic differentiation as compared with the recently developed ones, which is most likely due to recycling of the best parental lines in forming new OPVs.

Field evaluation of resistance to aflatoxin accumulation in maize inbred lines in Kenya and South Africa

ABSTRACT Aflatoxin, a carcinogenic toxin, is produced mainly by Aspergillus flavus and Aspergillus parasiticus. Contamination of maize (Zea mays L.) grain by these fungi occurs before harvest, and the easiest strategy to prevent this is to develop/use maize varieties resistant to Aspergillus spp. and aflatoxin accumulation. The objective of this investigation was to identify potential sources of resistance among 23 maize inbred lines (13 obtained from the MAIZE Competitive Grants Initiative, International Maize and Wheat Improvement Centre and 10 from Agricultural Research Council, South Africa). The inbred lines were planted in a randomized complete-block design at two locations each in Kenya and South Africa. Maize ears were inoculated at silking with three toxigenic strains of A. flavus. The inoculated ears in each plot were harvested at 12–18% moisture, dried, and visually assessed for Aspergillus ear rot (AER). Aflatoxin concentration in the kernels was determined using liquid chromatography–tandem mass spectrometry. Significant variation for both AER and aflatoxin concentration existed among the inbred lines at both locations in Kenya and one location in South Africa. Combined analysis revealed a significant (p < 0.001) lines × locations interaction for both AER and aflatoxin concentration. Higher incidences of AER (0–86.0%) and aflatoxin concentration (0.21–6.51 µg/kg) were recorded at Kiboko in Kenya than at the other three locations. A stronger genetic correlation (rG = 0.936, p < 0.0001) between the AER and aflatoxin concentration was recorded in Potchefstroom than at the other three locations. Repeatability of aflatoxin concentration was high at Kiboko (0.87) and Potchefstroom in South Africa (0.74). Three inbred lines, CML247, CML444, and CML495, emerged as potentially useful sources of resistance to AER and aflatoxin accumulation as they showed low levels of aflatoxin contamination in both localities in Kenya and in South Africa.

Genetic analysis of early-maturing maize (Zea Mays L.) inbred lines under stress and nonstress conditions

ABSTRACT Early-maturing maize (Zea Mays L.) germplasm developed from diverse sources has the potential for use in developing maize hybrids suitable for increasing maize production in the dry ecologies of eastern Africa. A diallel study was conducted to estimate general combining ability (GCA) of 12 early-maturing maize inbred lines, identify potential single-cross hybrids for use as parents, assess genetic diversity among the inbred lines, and relate genetic distance to specific combining ability (SCA) and hybrid performance. Sixty-six F1 diallel hybrids were evaluated under optimal and drought stress conditions at four locations in Kenya and Uganda. The parental inbred lines were genotyped using 94 single nucleotide polymorphism (SNP) markers. Additive gene action was more important than nonadditive gene action for inheritance of grain yield (GY) under optimal conditions. However, nonadditive gene effects were more important in the inheritance of GY under drought and across all environments. Inbred lines CKL0722, VL058014, and CZL0724 were among the best with positive GCA effects for GY across both optimal and drought stress conditions. The correlation between SCA and both genetic distance and F1 GY was significant under both drought stress and across all environments. Inbred lines with desirable GCA effects for GY and other agronomic traits and hybrids with good performance under both optimal and drought stress conditions are potential parents for development of various types of high-yielding, stress-tolerant, and early-maturing hybrids.

Genetic analysis of tropical quality protein maize (Zea mays L.) germplasm

Maize (Zea mays L.) is an important source of carbohydrates and protein in the diet in sub-Saharan Africa. The objectives of this study were to (i) estimate general (GCA) and specific combining abilities (SCA) of 13 new quality protein maize (QPM) lines in a diallel under stress and non-stress conditions, (ii) compare observed and predicted performance of QPM hybrids, (iii) characterize genetic diversity among the 13 QPM lines using single nucleotide polymorphism (SNP) markers and assess the relationship between genetic distance and hybrid performance, and (iv) assess diversity and population structure in 116 new QPM inbred lines as compared to eight older tropical QPM lines and 15 non-QPM lines. The GCA and SCA effects were significant for most traits under optimal conditions, indicating that both additive and non-additive genetic effects were important for inheritance of the traits. Additive genetic effects appeared to govern inheritance of most traits under optimal conditions and across environments. Non-additive genetic effects were more important for inheritance of grain yield but additive effects controlled most agronomic traits under drought stress conditions. Inbred lines CKL08056, CKL07292, and CKL07001 had desirable GCA effects for grain yield across drought stress and non-stress conditions. Prediction efficiency for grain yield was highest under optimal conditions. The classification of 139 inbred lines with 95 SNPs generated six clusters, four of which contained 10 or fewer lines, and 16 lines of mixed co-ancestry. There was good agreement between Neighbor Joining dendrogram and Structure classification. The QPM lines used in the diallel were nearly uniformly spread throughout the dendrogram. There was no relationship between genetic distance and grain yield in either the optimal or stressed environments in this study. The genetic diversity in mid-altitude maize germplasm is ample, and the addition of the QPM germplasm did not increase it measurably.

Pre-harvest management is a critical practice for minimizing aflatoxin contamination of maize

Maize, the main dietary staple in Kenya, is one of the crops most susceptible to contamination by aflatoxin. To understand sources of aflatoxin contamination for home grown maize, we collected 789 maize samples from smallholder farmers’ fields in Eastern and South Western, two regions in Kenya representing high and low aflatoxin risk areas, respectively, and determined aflatoxin B1 (AFB1) using ELISA with specific polyclonal antibodies. AFB1 was detected in 274 of the 416 samples from Eastern Kenya at levels between 0.01 and 9091.8 μg kg−1 (mean 67.8 μg kg−1). In South Western, AFB1 was detected in 233 of the 373 samples at levels between 0.98 and 722.2 μg kg−1 (mean 22.3 μg kg−1). Of the samples containing AFB1, 153 (55.8%) from Eastern and 102 (43.8%) from South Western exceeded the maximum allowable limit of AFB1 (5 μg kg−1) in maize for human consumption in Kenya. The probable daily intake (PDI) of AFB1 in Eastern Kenya ranged from 0.07 to 60612 ng kg−1 bw day−1 (mean 451.8 ng kg−1 bw day−1), while for South Western, PDI ranged from 6.53 to 4814.7 ng kg−1 bw day−1 (mean 148.4 ng kg−1 bw day−1). The average PDI for both regions exceeded the estimated provisional maximum tolerable daily intake of AFB1, which is a health concern for the population in these regions. These results revealed significant levels of preharvest aflatoxin contamination of maize in both regions. Prevention of preharvest infection of maize by toxigenic A. flavus strains should be a critical focal point to prevent aflatoxin contamination and exposure.

Assessment of management options on striga infestation and maize grain yield in Kenya

Abstract The parasitic purple witchweed [Striga hermonthica (Del.) Benth.] is a serious constraint to maize production in sub-Saharan Africa, especially in poor soils. Various Striga spp. control measures have been developed, but these have not been assessed in an integrated system. This study was conducted to evaluate a set of promising technologies for S. hermonthica management in western Kenya. We evaluated three maize genotypes either intercropped with peanut (Arachis hypogaea L.), soybean [Glycine max (L.) Merr.], or silverleaf desmodium [Desmodium uncinatum (Jacq.) DC] or as a sole crop at two locations under artificial S. hermonthica infestation and at three locations under natural S. hermonthica infestation between 2011 and 2013. Combined ANOVA showed significant (P<0.05) cropping system and cropping system by environment interactions for most traits measured. Grain yield was highest for maize grown in soybean rotation (3,672 kg ha-1) under artificial infestation and in D. uncinatum and peanut cropping systems (3,203 kg ha-1 and 3,193 kg ha-1) under natural infestation. Grain yield was highest for the Striga spp.-resistant hybrid under both methods of infestation. A lower number of emerged S. hermonthica plants per square meter were recorded at 10 and 12 wk after planting on maize grown under D. uncinatum in the artificial S. hermonthica infestation. A combination of herbicide-resistant maize varieties intercropped with legumes was a more effective method for S. hermonthica control than individualcomponent technologies. Herbicide-resistant and Striga spp.-resistant maize integrated with legumes would help reduce the Striga spp. seedbank in the soil. Farmers should be encouraged to adopt an integrated approach to control Striga spp. for better maize yields.