Genetic diversity and performance of maize varieties from Zimbabwe, Zambia and Malawi

Large scale and planned introduction of maize (Zea mays) in southern Africa was accomplished during the last 100 years. Since then, smallholder farmers and breeders have been selecting varieties best adapted to their specific growing conditions. Six studies were conducted to generate information on the current levels of genetic diversity and agronomic performance of both farmer-developed and commercially-bred maize varieties in Zimbabwe, Zambia and Malawi to help in the identification of sources of new alleles for improving yield, especially under the main abiotic stresses that prevail in the region. In the first study, 267 maize landraces were collected from smallholder farmers in different agro-ecological zones of the three countries for conservation and further studies. Passport data and information on why smallholder farmers continue to grow landraces despite the advent of modern varieties were also collected along with the landraces. The second study revealed considerable variation for phenological, morphological and agronomic characters, and inter-relationships among the landraces and their commercial counterparts. A core sample representing most of the diversity in the whole collection of landraces was selected for further detailed analyses. The third study revealed high levels of molecular diversity between landraces originating from different growing environments and between landraces and commercially-bred varieties. The Simple Sequence Repeat (SSR) data also showed that the genetic diversity introduced from the original gene pool from the USA about 100 years ago is still found in both the descendant landraces and commercially-bred varieties. The fourth study showed that in general, commercially-bred varieties outyielded landraces under both abiotic stress and nonstress conditions with some notable exceptions. Landraces were more stable across environments than improved varieties. The most promising landraces for pre-breeding and further investigation were also identified. The clustering patterns formed based on agronomic data were different from SSR markers, but in general the genotype groupings were consistent across the two methods of measuring diversity. In the fifth study, the more recently-bred maize varieties in Zimbabwe showed consistent improvement over older cultivars in grain yield. The apparent yearly rate of yield increase due to genetic improvement was positive under optimum growing conditions, low soil nitrogen levels and drought stress. The sixth study revealed that in general, genetic diversity in Zimbabwean maize has neither significantly decreased nor increased over time, and that the temporal changes observed in this study were more qualitative than quantitative. The results from the six studies confirm the origin of maize in southern Africa and reveals that considerable genetic variation exists in the region which could be used to broaden the sources of diversity for maize improvement under the current agro-ecological conditions in southern Africa

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

<p>Abstract</p> <p>Background</p> <p>Knowledge 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.</p> <p>Results</p> <p>Genetic 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.</p> <p>Conclusions</p> <p>There 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.</p

Genetic potential of tropically adapted exotic maize (Zea mays L.) heat-tolerant donor lines in sub-tropical breeding programs

Breeding for heat stress tolerance became a priority in sub-Saharan Africa (SSA), as projections are showing an increase in frequency, duration, and severity. In this study, 14 heat stress tolerant-donor lines (HSTDLs) sourced from CIMMYT-India (males) were crossed with 15 locally adapted elite lines (females) developed within the CIMMYT-Zimbabwe maize-breeding program using the North Carolina Design II mating scheme. The resultant 175 single crosses were evaluated alongside five commercial hybrids and adjacent to the trial of parental lines used in the crosses across two locations representing heat stress and optimal environments in Zimbabwe. The design II analysis showed significant (p < 0.01) general combining ability (GCA) effects for exotic heat donor lines and specific combining ability (SCA) effects on grain yield under heat stress, optimal conditions, and across locations; demonstrating additive and non-additive genetic inheritance of grain yield. High Baker’s ratios observed in this study indicate predominance of additive over non-additive gene effects. Three exotic HSTDLs, namely CAL14138, CAL152, and CAL1440, exhibited significant (p < 0.001) and positive GCA effects under heat stress conditions. The results imply that these exotic lines could serve as valuable genetic resources for introgression of heat tolerant alleles into local maize populations for accelerated yield genetic gains. Single crosses, DJ265-15 × VL1018816 and DJ267-9 × CAL1440, exhibited positive and significant (p < 0.01) and (p < 0.05) SCA effects for grain yield under heat stress conditions, respectively. These crosses can be used for further breeding and can contribute to grain yield performance under heat stress conditions. The exotic HSTDLs, CAL14138, CAL152, and VL109126 showed superior per se performance under heat, optimal conditions, and across environments. Overall data demonstrate the potential of exotic HSTDLs for improving the adaptation of maize to heat stress in sub-tropical breeding programs

Genome-Wide Association Mapping and Genomic Prediction Analyses Reveal the Genetic Architecture of Grain Yield and Flowering Time Under Drought and Heat Stress Conditions in Maize

Drought stress (DS) is a major constraint to maize yield production. Heat stress (HS) alone and in combination with DS are likely to become the increasing constraints. Association mapping and genomic prediction (GP) analyses were conducted in a collection of 300 tropical and subtropical maize inbred lines to reveal the genetic architecture of grain yield and flowering time under well-watered (WW), DS, HS, and combined DS and HS conditions. Out of the 381,165 genotyping-by-sequencing SNPs, 1549 SNPs were significantly associated with all the 12 trait-environment combinations, the average PVE (phenotypic variation explained) by these SNPs was 4.33%, and 541 of them had a PVE value greater than 5%. These significant associations were clustered into 446 genomic regions with a window size of 20 Mb per region, and 673 candidate genes containing the significantly associated SNPs were identified. In addition, 33 hotspots were identified for 12 trait-environment combinations and most were located on chromosomes 1 and 8. Compared with single SNP-based association mapping, the haplotype-based associated mapping detected fewer number of significant associations and candidate genes with higher PVE values. All the 688 candidate genes were enriched into 15 gene ontology terms, and 46 candidate genes showed significant differential expression under the WW and DS conditions. Association mapping results identified few overlapped significant markers and candidate genes for the same traits evaluated under different managements, indicating the genetic divergence between the individual stress tolerance and the combined drought and HS tolerance. The GP accuracies obtained from the marker-trait associated SNPs were relatively higher than those obtained from the genome-wide SNPs for most of the target traits. The genetic architecture information of the grain yield and flowering time revealed in this study, and the genomic regions identified for the different trait-environment combinations are useful in accelerating the efforts on rapid development of the stress-tolerant maize germplasm through marker-assisted selection and/or genomic selection

Genetic trends in the Zimbabwe’s national maize breeding program over two decades

Monitoring genetic gains within breeding programs is a critical component for continuous improvement. While several national breeding programs in Africa have assessed genetic gain using era studies, this study is the first to use two decades of historical data to estimate genetic trends within a national breeding program. The objective of this study was to assess genetic trends within the final two stages of Zimbabwe’s Department of Research &amp; Specialist Services maize breeding pipeline between 2002 and 2021. Data from 107 intermediate and 162 advanced variety trials, comprising of 716 and 398 entries, respectively, was analyzed. Trials were conducted under optimal, managed drought stress, low nitrogen stress, low pH, random stress, and disease pressure (maize streak virus (MSV), grey leaf spot (GLS), and turcicum leaf blight under artificial inoculation. There were positive and significant genetic gains for grain yield across management conditions (28–35 kg ha-1 yr-1), under high-yield potential environments (17–61 kg ha-1 yr-1), and under low-yield potential environments (0–16 kg ha-1 yr-1). No significant changes were observed in plant and ear height over the study period. Stalk and root lodging, as well as susceptibility to MSV and GLS, significantly decreased over the study period. New breeding technologies need to be incorporated into the program to further increase the rate of genetic gain in the maize breeding programs and to effectively meet future needs

Genetic trends in CIMMYT’s tropical maize breeding pipelines

Fostering a culture of continuous improvement through regular monitoring of genetic trends in breeding pipelines is essential to improve efficiency and increase accountability. This is the first global study to estimate genetic trends across the International Maize and Wheat Improvement Center (CIMMYT) tropical maize breeding pipelines in eastern and southern Africa (ESA), South Asia, and Latin America over the past decade. Data from a total of 4152 advanced breeding trials and 34,813 entries, conducted at 1331 locations in 28 countries globally, were used for this study. Genetic trends for grain yield reached up to 138 kg ha−1 yr−1 in ESA, 118 kg ha−1 yr−1 South Asia and 143 kg ha−1 yr−1 in Latin America. Genetic trend was, in part, related to the extent of deployment of new breeding tools in each pipeline, strength of an extensive phenotyping network, and funding stability. Over the past decade, CIMMYT’s breeding pipelines have significantly evolved, incorporating new tools/technologies to increase selection accuracy and intensity, while reducing cycle time. The first pipeline, Eastern Africa Product Profile 1a (EA-PP1a), to implement marker-assisted forward-breeding for resistance to key diseases, coupled with rapid-cycle genomic selection for drought, recorded a genetic trend of 2.46% per year highlighting the potential for deploying new tools/technologies to increase genetic gain

Potential of Temperate, Tropical, and Sub-Tropical Exotic Maize Germplasm for Increased Gains in Yield Performance in Sub-Tropical Breeding Programs

Exotic germplasm (i.e., germplasm beyond the breeder’s target area) has traditionally been used to broaden the genetic base of local (germplasm within the breeder’s target area) populations, but little has been done to assess gains that could be induced by this breeding practice in the sub-tropical regions of Africa. Here, eight maize (Zea mays L.) inbred lines developed from pedigree crosses of exotic and local (i.e., sub-tropically adapted lines; STALs) were inter-mated together with six elite STALs, in a partial diallel mating scheme, in order to depict yield gains that can be made when exotic genes are integrated within the sub-tropical maize germplasm pool. The crossing scheme yielded a total of 91 F1s which were evaluated together with nine commercial checks in multi-environmental trials (METs) at eight locations representing agro-ecologies in which maize is predominantly grown in Zimbabwe. Across site Analysis of Variance (ANOVA) showed differences in grain yield (GY) performance of the F1s. Significant genotype x environment effects was also detected for GY (i.e., GEI; p 1s of parents with a temperate background [i.e., P7 (S) x P2 (T)] showed the highest GY potential (e.g., G44; GY = 10.52 tha−1). Apart from showing high GY potential, G44 also demonstrated to be stable across diverse agro-ecologies and to mature earlier than the best commercial check hybrid. In conclusion, incorporation of exotic genes, especially those from temperate regions, may improve the yielding ability and stability and can introduce earliness in the maturity of maize populations in sub-tropical regions

Adaptability and Stability Analysis of Commercial Cultivars, Experimental Hybrids and Lines under Natural Fall Armyworm Infestation in Zimbabwe Using Different Stability Models

Fall armyworm (Spodoptera frugiperda (J.E. Smith); FAW)-resistant cultivars and breeding lines have been identified in sub-Saharan Africa. However, these genotypes have not been evaluated for their stability across environments with natural FAW infestation. The objectives of this study were to: (i) identify hybrids/open pollinated varieties combining high grain yield (GYD) and stability across environments with natural FAW infestation, (ii) select maize inbred lines with high GYD and stable FAW resistance, and (iii) identify the most discriminating environments for GYD performance and foliar FAW damage (FFAWD) under natural FAW infestation. The additive main effect and multiplicative interaction (AMMI) model was used to detect the presence of genotype-by-environment interaction (GEI) for GYD, and foliar and ear FAW damage. Seven stability analysis models were used to analyse adaptation and stability of genotypes across environments. The hybrids Mutsa-MN521 and CimExp55/CML334 were the best, combining adaptation and stability across FAW infested environments. Other acceptable hybrids were identified as 113WH330, Manjanja-MN421, CML338/CML334 and PAN53. The local inbred lines SV1P and CML491 combined adaptability and stable FAW resistance across environments. The best exotic donor lines exhibiting stable FAW resistance were CML67, CML346, CML121 and CML338. Harare and Gwebi were identified as the most discriminating sites for GYD performance, while Kadoma and Rattray-Arnold Research Stations were identified for FFAWD among inbred lines