Linkage mapping and genomic prediction of grain quality traits in tropical maize (Zea mays L.).

The suboptimal productivity of maize systems in sub-Saharan Africa (SSA) is a pressing issue, with far-reaching implications for food security, nutrition, and livelihood sustainability within the affected smallholder farming communities. Dissecting the genetic basis of grain protein, starch and oil content can increase our understanding of the governing genetic systems, improve the efficacy of future breeding schemes and optimize the end-use quality of tropical maize. Here, four bi-parental maize populations were evaluated in field trials in Kenya and genotyped with mid-density single nucleotide polymorphism (SNP) markers. Genotypic (G), environmental (E) and G×E variations were found to be significant for all grain quality traits. Broad sense heritabilities exhibited substantial variation (0.18-0.68). Linkage mapping identified multiple quantitative trait loci (QTLs) for the studied grain quality traits: 13, 7, 33, 8 and 2 QTLs for oil content, protein content, starch content, grain texture and kernel weight, respectively. The co-localization of QTLs identified in our research suggests the presence of shared genetic factors or pleiotropic effects, implying that specific genomic regions influence the expression of multiple grain quality traits simultaneously. Genomic prediction accuracies were moderate to high for the studied traits. Our findings highlight the polygenic nature of grain quality traits and demonstrate the potential of genomic selection to enhance genetic gains in maize breeding. Furthermore, the identified genomic regions and single nucleotide polymorphism markers can serve as the groundwork for investigating candidate genes that regulate grain quality traits in tropical maize. This, in turn, can facilitate the implementation of marker-assisted selection (MAS) in breeding programs focused on improving grain nutrient levels.

Genetic trends for yield and key agronomic traits in pre-commercial and commercial maize varieties between 2008 and 2020 in Uganda.

Estimating genetic gains is vital to optimize breeding programs for increased efficiency. Genetic gains should translate into productivity gains if returns to investments in breeding and impact are to be realized. The objective of this study was to estimate genetic gain for grain yield and key agronomic traits in pre-commercial and commercial maize varieties from public and private breeding programs tested in (i) national performance trials (NPT), (ii) era trial and, (iii) compare the trends with the national average. The study used (i) historical NPT data on 419 improved maize varieties evaluated in 23 trials at 6-8 locations each between 2008 and 2020, and (ii) data from an era trial of 54 maize hybrids released between 1999 and 2020. The NPT data was first analyzed using a mixed model and resulting estimate for each entry was regressed onto its first year of testing. Analysis was done over all entries, only entries from National Agricultural Research Organization (NARO), International Maize and Wheat Improvement Center (CIMMYT), or private seed companies. Estimated genetic gain was 2.25% or 81 kg ha-1 year-1 from the NPT analysis. A comparison of genetic trends by source indicated that CIMMYT entries had a gain of 1.98% year-1 or 106 kg ha-1 year-1. In contrast, NARO and private sector maize entries recorded genetic gains of 1.30% year-1 (59 kg ha-1 year-1) and 1.71% year-1 (79 kg ha-1 year-1), respectively. Varieties from NARO and private sector showed comparable mean yields of 4.56 t ha-1 and 4.62 t ha-1, respectively, while hybrids from CIMMYT had a mean of 5.37 t ha-1. Era analysis indicated significant genetic gain of 1.69% year-1 or 55 kg ha-1 year-1, while a significant national productivity gain of 1.48% year-1 (37 kg ha-1 year-1) was obtained. The study, thus, demonstrated the importance of public-private partnerships in development and delivery of new genetics to farmers in Uganda.

Genetic analyses of tropical maize lines under artificial infestation of fall armyworm and foliar diseases under optimum conditions.

Development and deployment of high-yielding maize varieties with native resistance to Fall armyworm (FAW), turcicum leaf blight (TLB), and gray leaf spot (GLS) infestation is critical for addressing the food insecurity in sub-Saharan Africa. The objectives of this study were to determine the inheritance of resistance for FAW, identity hybrids which in addition to FAW resistance, also show resistance to TLB and GLS, and investigate the usefulness of models based on general combining ability (GCA) and SNP markers in predicting the performance of new untested hybrids. Half-diallel mating scheme was used to generate 105 F1 hybrids from 15 parents and another 55 F1 hybrids from 11 parents. These were evaluated in two experiments, each with commercial checks in multiple locations under FAW artificial infestation and optimum management in Kenya. Under artificial FAW infestation, significant mean squares among hybrids and hybrids x environment were observed for most traits in both experiments, including at least one of the three assessments carried out for foliar damage caused by FAW. Interaction of GCA x environment and specific combining ability (SCA) x environment interactions were significant for all traits under FAW infestation and optimal conditions. Moderate to high heritability estimates were observed for GY under both management conditions. Correlation between GY and two of the three scorings (one and three weeks after infestation) for foliar damage caused by FAW were negative (-0.27 and -0.38) and significant. Positive and significant correlation (0.84) was observed between FAW-inflicted ear damage and the percentage of rotten ears. We identified many superior-performing hybrids compared to the best commercial checks for both GY and FAW resistance associated traits. Inbred lines CML312, CML567, CML488, DTPYC9-F46-1-2-1-2, CKDHL164288, CKDHL166062, and CLRCY039 had significant and positive GCA for GY (positive) and FAW resistance-associated traits (negative). CML567 was a parent in four of the top ten hybrids under optimum and FAW conditions. Both additive and non-additive gene action were important in the inheritance of FAW resistance. Both GCA and marker-based models showed high correlation with field performance, but marker-based models exhibited considerably higher correlation. The best performing hybrids identified in this study could be used as potential single cross testers in the development of three-way FAW resistance hybrids. Overall, our results provide insights that help breeders to design effective breeding strategies to develop FAW resistant hybrids that are high yielding under FAW and optimum conditions.

Low-Density Reference Fingerprinting SNP Dataset of CIMMYT Maize Lines for Quality Control and Genetic Diversity Analyses.

CIMMYT maize lines (CMLs), which represent the tropical maize germplasm, are freely available worldwide. All currently released 615 CMLs and fourteen temperate maize inbred lines were genotyped with 180 kompetitive allele-specific PCR single nucleotide polymorphisms to develop a reference fingerprinting SNP dataset that can be used to perform quality control (QC) and genetic diversity analyses. The QC analysis identified 25 CMLs with purity, identity, or mislabeling issues. Further field observation, purification, and re-genotyping of these CMLs are required. The reference fingerprinting SNP dataset was developed for all of the currently released CMLs with 152 high-quality SNPs. The results of principal component analysis and average genetic distances between subgroups showed a clear genetic divergence between temperate and tropical maize, whereas the three tropical subgroups partially overlapped with one another. More than 99% of the pairs of CMLs had genetic distances greater than 0.30, showing their high genetic diversity, and most CMLs are distantly related. The heterotic patterns, estimated with the molecular markers, are consistent with those estimated using pedigree information in two major maize breeding programs at CIMMYT. These research findings are helpful for ensuring the regeneration and distribution of the true CMLs, via QC analysis, and for facilitating the effective utilization of the CMLs, globally.

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.

Host plant resistance for fall armyworm management in maize: relevance, status and prospects in Africa and Asia.

KEY MESSAGE: Sustainable control of fall armyworm (FAW) requires implementation of effective integrated pest management (IPM) strategies, with host plant resistance as a key component. Significant opportunities exist for developing and deploying elite maize cultivars with native genetic resistance and/or transgenic resistance for FAW control in both Africa and Asia. The fall armyworm [Spodoptera frugiperda (J.E. Smith); FAW] has emerged as a serious pest since 2016 in Africa, and since 2018 in Asia, affecting the food security and livelihoods of millions of smallholder farmers, especially those growing maize. Sustainable control of FAW requires implementation of integrated pest management strategies, in which host plant resistance is one of the key components. Significant strides have been made in breeding elite maize lines and hybrids with native genetic resistance to FAW in Africa, based on the strong foundation of insect-resistant tropical germplasm developed at the International Maize and Wheat Improvement Center, Mexico. These efforts are further intensified to develop and deploy elite maize cultivars with native FAW tolerance/resistance and farmer-preferred traits suitable for diverse agro-ecologies in Africa and Asia. Independently, genetically modified Bt maize with resistance to FAW is already commercialized in South Africa, and in a few countries in Asia (Philippines and Vietnam), while efforts are being made to commercialize Bt maize events in additional countries in both Africa and Asia. In countries where Bt maize is commercialized, it is important to implement a robust insect resistance management strategy. Combinations of native genetic resistance and Bt maize also need to be explored as a path to more effective and sustainable host plant resistance options. We also highlight the critical gaps and priorities for host plant resistance research and development in maize, particularly in the context of sustainable FAW management in Africa and Asia.

Genomic Analysis of Resistance to Fall Armyworm (Spodoptera frugiperda) in CIMMYT Maize Lines.

The recent invasion, rapid spread, and widescale destruction of the maize crop by the fall armyworm (FAW; Spodoptera frugiperda (J.E. Smith)) is likely to worsen the food insecurity situation in Africa. In the present study, a set of 424 maize lines were screened for their responses to FAW under artificial infestation to dissect the genetic basis of resistance. All lines were evaluated for two seasons under screen houses and genotyped with the DArTseq platform. Foliar damage was rated on a scale of 1 (highly resistant) to 9 (highly susceptible) and scored at 7, 14, and 21 days after artificial infestation. Analyses of variance revealed significant genotypic and genotype by environment interaction variances for all traits. Heritability estimates for leaf damage scores were moderately high and ranged from 0.38 to 0.58. Grain yield was negatively correlated with a high magnitude to foliar damage scores, ear rot, and ear damage traits. The genome-wide association study (GWAS) revealed 56 significant marker-trait associations and the predicted functions of the putative candidate genes varied from a defense response to several genes of unknown function. Overall, the study revealed that native genetic resistance to FAW is quantitative in nature and is controlled by many loci with minor effects.

Reproductive potential of fall armyworm Spodoptera frugiperda (J.E. Smith) and effects of feeding on diverse maize genotypes under artificial infestation.

Fall armyworm (FAW) Spodoptera frugiperda (J.E. Smith) has become a major threat to maize production in Africa. In this study, six maize genotypes were assessed for their resistance to FAW under artificial infestation in both laboratory and net house conditions. These included two FAW-tolerant hybrids (CKHFAW180294 and CKH191221), two commercial hybrids (WE2115 and CKH10717), and two open-pollinated varieties (ZM523 and KDV4). Larval development time and reproductive potential were assessed on maize leaves in the laboratory and a life table for FAW was constructed. The maize genotypes were also artificially infested with three FAW neonates at two phenological stages (V5 and V7) and reproductive stage (R1) in the net house. Leaf and ear damage scores were recorded on a scale of 1-9. Larval development time varied significantly between maize genotypes with the highest on CKH191221 (16.4 days) and the lowest on KDV4 (13.7 days). The intrinsic rate of natural increase for life tables varied from 0.24 on CKH191221 to 0.41 on KDV4. Mean generation time of FAW ranged from 17.6 to 22.8 days on KDV4 and CKH191221, respectively. Foliar damage was the lowest on CKH191221, and the highest on KDV4 at V7 infestation stage in week 1. CKH191221 had the lowest ear damage score, whereas ZM523 had the highest scores at V5 infestation stage. The highest and lowest yield reductions were observed on ZM523 (64%) at V7 infestation stage and CKHFAW180294 (6%) at R1 infestation stage, respectively. The results indicated the potential for developing tropical mid-altitude maize germplasm with native genetic resistance to FAW.

Beat the stress: breeding for climate resilience in maize for the tropical rainfed environments.

KEY MESSAGE: Intensive public sector breeding efforts and public-private partnerships have led to the increase in genetic gains, and deployment of elite climate-resilient maize cultivars for the stress-prone environments in the tropics. Maize (Zea mays L.) plays a critical role in ensuring food and nutritional security, and livelihoods of millions of resource-constrained smallholders. However, maize yields in the tropical rainfed environments are now increasingly vulnerable to various climate-induced stresses, especially drought, heat, waterlogging, salinity, cold, diseases, and insect pests, which often come in combinations to severely impact maize crops. The International Maize and Wheat Improvement Center (CIMMYT), in partnership with several public and private sector institutions, has been intensively engaged over the last four decades in breeding elite tropical maize germplasm with tolerance to key abiotic and biotic stresses, using an extensive managed stress screening network and on-farm testing system. This has led to the successful development and deployment of an array of elite stress-tolerant maize cultivars across sub-Saharan Africa, Asia, and Latin America. Further increasing genetic gains in the tropical maize breeding programs demands judicious integration of doubled haploidy, high-throughput and precise phenotyping, genomics-assisted breeding, breeding data management, and more effective decision support tools. Multi-institutional efforts, especially public-private alliances, are key to ensure that the improved maize varieties effectively reach the climate-vulnerable farming communities in the tropics, including accelerated replacement of old/obsolete varieties.

Evaluation of early-generation tropical maize testcrosses for grain-yield potential and weevil (Sitophilus zeamais Motschulsky) resistance.

Smallholder maize farmers in Africa experience pre- and post-harvest production stresses either individually or in combination at different stages of the crop cycle. The maize weevil is among the major post-harvest storage pests. A strategy to address this problem is to develop and promote high yielding maize germplasm with resistance to multiple stresses. A study was conducted to: 1) assess yield and agronomic performance of testcross hybrids developed from early generation lines; and 2) assess the response of the testcross hybrids to infestation with Sitophilus zeamais. Fifty-eight drought-tolerant testcross hybrids were evaluated for agronomic performance and weevil resistance at four environments in Uganda in 2016. Hybrid G39 (L2/T2) had the best grain yield performance; it significantly out-performed the best check by 11.4% in all environments. Hybrid grain from field trials was subjected to Sitophilus zeamais infestation in a choice and no choice test under laboratory conditions. Hybrids G56 (L49/T2) and G58 (L51/T2) had the least weevil damage and were rated as resistant to Sitophilus zeamais. The numbers of damaged kernels, number of exit holes and ear aspect were positively correlated with the grain weight loss. The results suggest possibilities for simultaneous selection for high grain yield and storage insect pest resistance among drought-tolerant genotypes. Use of high-yielding and resistant maize hybrids to storage insect pest should be promoted for increased maize production and managing post-harvest losses due to the maize weevil in smallholder farming communities in Africa.

Genetic dissection of Striga hermonthica (Del.) Benth. resistance via genome-wide association and genomic prediction in tropical maize germplasm.

KEY MESSAGE: Genome-wide association revealed that resistance to Striga hermonthica is influenced by multiple genomic regions with moderate effects. It is possible to increase genetic gains from selection for Striga resistance using genomic prediction. Striga hermonthica (Del.) Benth., commonly known as the purple witchweed or giant witchweed, is a serious problem for maize-dependent smallholder farmers in sub-Saharan Africa. Breeding for Striga resistance in maize is complicated due to limited genetic variation, complexity of resistance and challenges with phenotyping. This study was conducted to (i) evaluate a set of diverse tropical maize lines for their responses to Striga under artificial infestation in three environments in Kenya; (ii) detect quantitative trait loci associated with Striga resistance through genome-wide association study (GWAS); and (iii) evaluate the effectiveness of genomic prediction (GP) of Striga-related traits. An association mapping panel of 380 inbred lines was evaluated in three environments under artificial Striga infestation in replicated trials and genotyped with 278,810 single-nucleotide polymorphism (SNP) markers. Genotypic and genotype x environment variations were significant for measured traits associated with Striga resistance. Heritability estimates were moderate (0.42) to high (0.92) for measured traits. GWAS revealed 57 SNPs significantly associated with Striga resistance indicator traits and grain yield (GY) under artificial Striga infestation with low to moderate effect. A set of 32 candidate genes physically near the significant SNPs with roles in plant defense against biotic stresses were identified. GP with different cross-validations revealed that prediction of performance of lines in new environments is better than prediction of performance of new lines for all traits. Predictions across environments revealed high accuracy for all the traits, while inclusion of GWAS-detected SNPs led to slight increase in the accuracy. The item-based collaborative filtering approach that incorporates related traits evaluated in different environments to predict GY and Striga-related traits outperformed GP for Striga resistance indicator traits. The results demonstrated the polygenic nature of resistance to S. hermonthica, and that implementation of GP in Striga resistance breeding could potentially aid in increasing genetic gain for this important trait.

The impact of adopting stress-tolerant maize on maize yield, maize income, and food security in Tanzania.

Productivity growth emanating from scientific advances offered by biotechnology and other plant breeding initiatives offers great promise for meeting the growing food demand worldwide. This justifies investments in agricultural research and development that have led to the development of stress-tolerant maize varieties (STMVs) in Africa. While most literature has documented the average impacts of STMVs on productivity, this paper is premised on the fact that benefits from technology adoption are not the same across household. The paper addresses this information gap by examining potential heterogeneity in yield, income, and food security benefits from of adopting STMVs using a sample of 720 maize-producing households from Tanzania. The dose-response continuous treatment effect method supported by an endogenous switching probit model was used to estimate the heterogenous impact of STMV adoption on the three outcomes of interest. Results show that, overall, the adoption of stress-tolerant maize varieties increased maize grain yield by about 1 ton/ha, maize income by about $62/ha. The adoption of STMVs also reduced the propensity to report mild, moderate, and severe food insecurity by 34%, 17%, and 6%, respectively. There are substantial idiosyncratic variations in the productivity, income, and food security effects depending on the scale of adoption, with a higher impact at lower dose levels of adoption. The heterogenous and pro-poor nature of STMV adoption is also revealed through nonparametric results showing higher productivity benefits among households that are less endowed with wealth and knowledge. These findings underscore the need for further scaling of stress-tolerant maize varieties for greater impact on the livelihoods of poor small-scale farmers in Tanzania.

Genetic Dissection of Resistance to Gray Leaf Spot by Combining Genome-Wide Association, Linkage Mapping, and Genomic Prediction in Tropical Maize Germplasm.

Gray leaf spot (GLS) is one of the major maize foliar diseases in sub-Saharan Africa. Resistance to GLS is controlled by multiple genes with additive effect and is influenced by both genotype and environment. The objectives of the study were to dissect the genetic architecture of GLS resistance through linkage mapping and genome-wide association study (GWAS) and assessing the potential of genomic prediction (GP). We used both biparental populations and an association mapping panel of 410 diverse tropical/subtropical inbred lines that were genotyped using genotype by sequencing. Phenotypic evaluation in two to four environments revealed significant genotypic variation and moderate to high heritability estimates ranging from 0.43 to 0.69. GLS was negatively and significantly correlated with grain yield, anthesis date, and plant height. Linkage mapping in five populations revealed 22 quantitative trait loci (QTLs) for GLS resistance. A QTL on chromosome 7 (qGLS7-105) is a major-effect QTL that explained 28.2% of phenotypic variance. Together, all the detected QTLs explained 10.50, 49.70, 23.67, 18.05, and 28.71% of phenotypic variance in doubled haploid (DH) populations 1, 2, 3, and F3 populations 4 and 5, respectively. Joint linkage association mapping across three DH populations detected 14 QTLs that individually explained 0.10-15.7% of phenotypic variance. GWAS revealed 10 significantly (p < 9.5 × 10-6) associated SNPs distributed on chromosomes 1, 2, 6, 7, and 8, which individually explained 6-8% of phenotypic variance. A set of nine candidate genes co-located or in physical proximity to the significant SNPs with roles in plant defense against pathogens were identified. GP revealed low to moderate prediction correlations of 0.39, 0.37, 0.56, 0.30, 0.29, and 0.38 for within IMAS association panel, DH pop1, DH pop2, DH pop3, F3 pop4, and F3 po5, respectively, and accuracy was increased substantially to 0.84 for prediction across three DH populations. When the diversity panel was used as training set to predict the accuracy of GLS resistance in biparental population, there was 20-50% reduction compared to prediction within populations. Overall, the study revealed that resistance to GLS is quantitative in nature and is controlled by many loci with a few major and many minor effects. The SNPs/QTLs identified by GWAS and linkage mapping can be potential targets in improving GLS resistance in breeding programs, while GP further consolidates the development of high GLS-resistant lines by incorporating most of the major- and minor-effect genes.

Combination of Linkage Mapping, GWAS, and GP to Dissect the Genetic Basis of Common Rust Resistance in Tropical Maize Germplasm.

Common rust (CR) caused by Puccina sorghi is one of the destructive fungal foliar diseases of maize and has been reported to cause moderate to high yield losses. Providing CR resistant germplasm has the potential to increase yields. To dissect the genetic architecture of CR resistance in maize, association mapping, in conjunction with linkage mapping, joint linkage association mapping (JLAM), and genomic prediction (GP) was conducted on an association-mapping panel and five F3 biparental populations using genotyping-by-sequencing (GBS) single-nucleotide polymorphisms (SNPs). Analysis of variance for the biparental populations and the association panel showed significant genotypic and genotype x environment (GXE) interaction variances except for GXE of Pop4. Heritability (h2) estimates were moderate with 0.37-0.45 for the individual F3 populations, 0.45 across five populations and 0.65 for the association panel. Genome-wide association study (GWAS) analyses revealed 14 significant marker-trait associations which individually explained 6-10% of the total phenotypic variances. Individual population-based linkage analysis revealed 26 QTLs associated with CR resistance and together explained 14-40% of the total phenotypic variances. Linkage mapping revealed seven QTLs in pop1, nine QTL in pop2, four QTL in pop3, five QTL in pop4, and one QTL in pop5, distributed on all chromosomes except chromosome 10. JLAM for the 921 F3 families from five populations detected 18 QTLs distributed in all chromosomes except on chromosome 8. These QTLs individually explained 0.3 to 3.1% and together explained 45% of the total phenotypic variance. Among the 18 QTL detected through JLAM, six QTLs, qCR1-78, qCR1-227, qCR3-172, qCR3-186, qCR4-171, and qCR7-137 were also detected in linkage mapping. GP within population revealed low to moderate correlations with a range from 0.19 to 0.51. Prediction correlation was high with r = 0.78 for combined analysis of the five F3 populations. Prediction of biparental populations by using association panel as training set reveals positive correlations ranging from 0.05 to 0.22, which encourages to develop an independent but related population as a training set which can be used to predict diverse but related populations. The findings of this study provide valuable information on understanding the genetic basis of CR resistance and the obtained information can be used for developing functional molecular markers for marker-assisted selection and for implementing GP to improve CR resistance in tropical maize.

Hybrid Breeding for MLN Resistance: Heterosis, Combining Ability, and Hybrid Prediction.

Prior knowledge on heterosis and quantitative genetic parameters on maize lethal necrosis (MLN) can help the breeders to develop numerous resistant or tolerant hybrids with optimum resources. Our objectives were to (1) estimate the quantitative genetic parameters for MLN disease severity, (2) investigate the efficiency of the prediction of hybrid performance based on parental per se and general combining ability (GCA) effects, and (3) examine the potential of hybrid prediction for MLN resistance or tolerance based on markers. Fifty elite maize inbred lines were selected based on their response to MLN under artificial inoculation. Crosses were made in a half diallel mating design to produce 307 F1 hybrids. All hybrids were evaluated in MLN quarantine facility in Naivasha, Kenya for two seasons under artificial inoculation. All 50 inbreds were genotyped with genotyping-by-sequencing (GBS) SNPs. The phenotypic variation was significant for all traits and the heritability was moderate to high. We observed that hybrids were superior to the mean performance of the parents for disease severity (-14.57%) and area under disease progress curve (AUDPC) (14.9%). Correlations were significant and moderate between line per se and GCA; and mean of parental value with hybrid performance for both disease severity and AUDPC value. Very low and negative correlation was observed between parental lines marker based genetic distance and heterosis. Nevertheless, the correlation of GCA effects was very high with hybrid performance which can suggests as a good predictor of MLN resistance. Genomic prediction of hybrid performance for MLN is high for both traits. We therefore conclude that there is potential for prediction of hybrid performance for MLN. Overall, the estimated quantitative genetic parameters suggest that through targeted approach, it is possible to develop outstanding lines and hybrids for MLN resistance.

Performance of elite maize genotypes under selected sustainable intensification options in Kenya.

Combining different cropping and tillage systems with different genotypes across several cropping seasons can reveal opportunities for sustainable intensification (SI). The objective of this study was to assess the performance of six maize genotypes under intercropping with conservation tillage (no-till) - two promising options for SI. The experiment was carried out over three years (or six cropping seasons) at Kiboko Research Station, Kenya with sole cropping and mouldboard ploughing as baseline production systems. Results showed that maize genotypes and cropping systems had a significant effect on yield, but the effect of tillage was not significant. Moreover, there was no significant interactive effects of the tested factors on maize yield. The maize genotype CKH10085 had the highest yield of 7.7 t ha-1 under sole cropping yet it also recorded the largest yield penalty due to intercropping of 1.1 t ha-1. On the other hand, genotype CKH10717 maintained the same average yield of 7.1 t ha-1 in both conventional and conservation tillage systems. The commercial genotype genotype CKH10080 and CKH08051 were more stable than the other experimental genotypes under the variable growing and management conditions. These two genotypes are of intermediate maturity and drought tolerance, two critical attributes to improved maize production. Intercropping reduced maize yields due to increased competition, for example the overall yield of sole cropping was 7.1 t ha-1 compared with 6.4 t ha-1 under intercropping; representing an overall yield penalty of 0.7 t ha-1. The differences in performance of maize genotypes revealed opportunities to deploy genotypes to reduce risk or maximize yield, depending on the biophysical circumstances and the production objective of the farmer.

Maize lethal necrosis (MLN): Efforts toward containing the spread and impact of a devastating transboundary disease in sub-Saharan Africa.

Maize lethal necrosis (MLN), a complex viral disease, emerged as a serious threat to maize production and the livelihoods of smallholders in eastern Africa since 2011, primarily due to the introduction of maize chlorotic mottle virus (MCMV). The International Maize and Wheat Improvement Center (CIMMYT), in close partnership with national and international partners, implemented a multi-disciplinary and multi-institutional strategy to curb the spread of MLN in sub-Saharan Africa, and mitigate the impact of the disease. The strategy revolved around a) intensive germplasm screening and fast-tracked development and deployment of MLN-tolerant/resistant maize hybrids in Africa-adapted genetic backgrounds; b) optimizing the diagnostic protocols for MLN-causing viruses, especially MCMV, and capacity building of relevant public and private sector institutions on MLN diagnostics and management; c) MLN monitoring and surveillance across sub-Saharan Africa in collaboration with national plant protection organizations (NPPOs); d) partnership with the private seed sector for production and exchange of MLN pathogen-free commercial maize seed; and e) awareness creation among relevant stakeholders about MLN management, including engagement with policy makers. The review concludes by highlighting the need to keep continuous vigil against MLN-causing viruses, and preventing any further spread of the disease to the major maize-growing countries that have not yet reported MLN in sub-Saharan Africa.

On-farm performance and farmers' participatory assessment of new stress-tolerant maize hybrids in Eastern Africa.

The development and deployment of high-yielding stress tolerant maize hybrids are important components of the efforts to increase maize productivity in eastern Africa. This study was conducted to: i) evaluate selected, stress-tolerant maize hybrids under farmers' conditions; ii) identify farmers' selection criteria in selecting maize hybrids; and iii) have farmers evaluate the new varieties according to those criteria. Two sets of trials, one with 12 early-to-intermediate maturing and the other with 13 intermediate-to-late maturing hybrids, improved for tolerance to multiple stresses common in farmers' fields in eastern Africa (drought, northern corn leaf blight, gray leaf spot, common rust, maize streak virus), were evaluated on-farm under smallholder farmers' conditions in a total of 42 and 40 environments (site-year-management combinations), respectively, across Kenya, Uganda, Tanzania and Rwanda in 2016 and 2017. Farmer-participatory variety evaluation was conducted at 27 sites in Kenya and Rwanda, with a total of 2025 participating farmers. Differential performance of the hybrids was observed under low-yielding (<3 t ha-1) and high-yielding (>3 t ha-1) environments. The new stress-tolerant maize hybrids had a much better grain-yield performance than the best commercial checks under smallholder farmer growing environments but had a comparable grain-yield performance under optimal conditions. These hybrids also showed better grain-yield stability across the testing environments, providing an evidence for the success of the maize-breeding approach. In addition, the new stress- tolerant varieties outperformed the internal genetic checks, indicating genetic gain under farmers' conditions. Farmers gave high importance to grain yield in both farmer-stated preferences (through scores) and farmer-revealed preferences of criteria (revealed by regressing the overall scores on the scores for the individual criteria). The top-yielding hybrids in both maturity groups also received the farmers' highest overall scores. Farmers ranked yield, early maturity, cob size and number of cobs as the most important traits for variety preference. The criteria for the different hybrids did not differ between men and women farmers. Farmers gave priority to many different traits in addition to grain yield, but this may not be applicable across all maize-growing regions. Farmer-stated importance of the different criteria, however, were quite different from farmer- revealed importance. Further, there were significant differences between men and women in the revealed-importance of the criteria. We conclude that incorporating farmers' selection criteria in the stage-gate advancement process of new hybrids by the breeders is useful under the changing maize-growing environments in sub-Saharan Africa, and recommended to increase the turnover of new maize hybrids.

Identification and diversity of tropical maize inbred lines with resistance to common rust (Puccinia sorghi Schwein).

Common rust (CR) caused by Puccinia sorghi Schwein is one of the major foliar diseases of maize (Zea mays L.) in Eastern and Southern Africa. This study was conducted to (i) evaluate the response of elite tropical adapted maize inbred lines to Puccinia sorghi and identify resistant lines (ii) examine associations between CR disease parameters and agronomic traits, and (iii) assess the genetic diversity of the inbred lines. Fifty inbred lines were evaluated in field trials for three seasons (2017-2019) in Uganda under artificial inoculation. Disease severity was rated on a 1-9 scale at 21 (Rust 1), 28 (Rust 2), and 35 (Rust 3) days after inoculation. Area under disease progress curve (AUDPC) was calculated. The genetic diversity of the lines was assessed using 44,975 single nucleotide polymorphism markers. Combined ANOVA across seasons showed significant (P < .001) line mean squares for the three rust scores and AUDPC. Heritability was high for Rust 2 (0.90), Rust 3 (0.83), and AUDPC (0.93). Of the 50 lines, 12 were highly resistant to CR. Inbred lines CKL1522, CKL05010, and CKL05017 had significantly lower Rust 3 scores and AUDPC compared to the resistant check CML444 and are potential donors of CR resistance alleles. The genetic correlations between CR disease resistance parameters were positive and strong. A neighbor-joining (NJ) tree and STRUCTURE suggested the presence of three major groups among the lines, with lines highly resistant to CR spread across the three groups. The genetic diversity among the highly resistant lines can be exploited by recycling genetically distant lines to develop new multiple disease resistant inbred lines for hybrid development and deployment.

Genome-Wide Analyses and Prediction of Resistance to MLN in Large Tropical Maize Germplasm.

Maize lethal necrosis (MLN), caused by co-infection of maize chlorotic mottle virus and sugarcane mosaic virus, can lead up to 100% yield loss. Identification and validation of genomic regions can facilitate marker assisted breeding for resistance to MLN. Our objectives were to identify marker-trait associations using genome wide association study and assess the potential of genomic prediction for MLN resistance in a large panel of diverse maize lines. A set of 1400 diverse maize tropical inbred lines were evaluated for their response to MLN under artificial inoculation by measuring disease severity or incidence and area under disease progress curve (AUDPC). All lines were genotyped with genotyping by sequencing (GBS) SNPs. The phenotypic variation was significant for all traits and the heritability estimates were moderate to high. GWAS revealed 32 significantly associated SNPs for MLN resistance (at p < 1.0 × 10-6). For disease severity, these significantly associated SNPs individually explained 3-5% of the total phenotypic variance, whereas for AUDPC they explained 3-12% of the total proportion of phenotypic variance. Most of significant SNPs were consistent with the previous studies and assists to validate and fine map the big quantitative trait locus (QTL) regions into few markers' specific regions. A set of putative candidate genes associated with the significant markers were identified and their functions revealed to be directly or indirectly involved in plant defense responses. Genomic prediction revealed reasonable prediction accuracies. The prediction accuracies significantly increased with increasing marker densities and training population size. These results support that MLN is a complex trait controlled by few major and many minor effect genes.