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.

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.

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.

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.

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.

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.

Genetic architecture of maize chlorotic mottle virus and maize lethal necrosis through GWAS, linkage analysis and genomic prediction in tropical maize germplasm.

KEY MESSAGE: Analysis of the genetic architecture of MCMV and MLN resistance in maize doubled-haploid populations revealed QTLs with major effects on chromosomes 3 and 6 that were consistent across genetic backgrounds and environments. Two major-effect QTLs, qMCMV3-108/qMLN3-108 and qMCMV6-17/qMLN6-17, were identified as conferring resistance to both MCMV and MLN. Maize lethal necrosis (MLN) is a serious threat to the food security of maize-growing smallholders in sub-Saharan Africa. The ability of the maize chlorotic mottle virus (MCMV) to interact with other members of the Potyviridae causes severe yield losses in the form of MLN. The objective of the present study was to gain insights and validate the genetic architecture of resistance to MCMV and MLN in maize. We applied linkage mapping to three doubled-haploid populations and a genome-wide association study (GWAS) on 380 diverse maize lines. For all the populations, phenotypic variation for MCMV and MLN was significant, and heritability was moderate to high. Linkage mapping revealed 13 quantitative trait loci (QTLs) for MCMV resistance and 12 QTLs conferring MLN resistance. One major-effect QTL, qMCMV3-108/qMLN3-108, was consistent across populations for both MCMV and MLN resistance. Joint linkage association mapping (JLAM) revealed 18 and 21 main-effect QTLs for MCMV and MLN resistance, respectively. Another major-effect QTL, qMCMV6-17/qMLN6-17, was detected for both MCMV and MLN resistance. The GWAS revealed a total of 54 SNPs (MCMV-13 and MLN-41) significantly associated (P ≤ 5.60 × 10-05) with MCMV and MLN resistance. Most of the GWAS-identified SNPs were within or adjacent to the QTLs detected through linkage mapping. The prediction accuracy for within populations as well as the combined populations is promising; however, the accuracy was low across populations. Overall, MCMV resistance is controlled by a few major and many minor-effect loci and seems more complex than the genetic architecture for MLN resistance.

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.

Combined linkage and association mapping reveal QTL for host plant resistance to common rust (Puccinia sorghi) in tropical maize.

BACKGROUND: Common rust, caused by Puccinia sorghi, is an important foliar disease of maize that has been associated with up to 50% grain yield loss. Development of resistant maize germplasm is the ideal strategy to combat P. sorghi. RESULTS: Association mapping performed using a mixed linear model (MLM), integrating population structure and family relatedness identified 25 QTL (P < 3.12 × 10- 5) that were associated with resistance to common rust and distributed on chromosomes 1, 3, 5, 6, 8, and 10. We identified three QTLs associated with all three disease parameters (final disease rating, mean disease rating, and area under disease progress curve) located on chromosomes 1, 3, and 8. A total of 5 QTLs for resistance to common rust were identified in the RIL population. Nine candidate genes located on chromosomes 1, 5, 6, 8, and 10 for resistance to common rust associated loci were identified through detailed annotation. CONCLUSIONS: Using a diverse set of inbred lines genotyped with high density markers and evaluated for common rust resistance in multiple environments, it was possible to identify QTL significantly associated with resistance to common rust and several candidate genes. The results point to the need for fine mapping common rust resistance by targeting regions identified in common between this study and others using diverse germplasm.

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

BACKGROUND: Northern 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. RESULTS: We 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. CONCLUSION: An 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.

Genome-wide association and genomic prediction of resistance to maize lethal necrosis disease in tropical maize germplasm.

KEY MESSAGE: Genome-wide association analysis in tropical and subtropical maize germplasm revealed that MLND resistance is influenced by multiple genomic regions with small to medium effects. The maize lethal necrosis disease (MLND) caused by synergistic interaction of Maize chlorotic mottle virus and Sugarcane mosaic virus, and has emerged as a serious threat to maize production in eastern Africa since 2011. Our objective was to gain insights into the genetic architecture underlying the resistance to MLND by genome-wide association study (GWAS) and genomic selection. We used two association mapping (AM) panels comprising a total of 615 diverse tropical/subtropical maize inbred lines. All the lines were evaluated against MLND under artificial inoculation. Both the panels were genotyped using genotyping-by-sequencing. Phenotypic variation for MLND resistance was significant and heritability was moderately high in both the panels. Few promising lines with high resistance to MLND were identified to be used as potential donors. GWAS revealed 24 SNPs that were significantly associated (P < 3 × 10(-5)) with MLND resistance. These SNPs are located within or adjacent to 20 putative candidate genes that are associated with plant disease resistance. Ridge regression best linear unbiased prediction with five-fold cross-validation revealed higher prediction accuracy for IMAS-AM panel (0.56) over DTMA-AM (0.36) panel. The prediction accuracy for both within and across panels is promising; inclusion of MLND resistance associated SNPs into the prediction model further improved the accuracy. Overall, the study revealed that resistance to MLND is controlled by multiple loci with small to medium effects and the SNPs identified by GWAS can be used as potential candidates in MLND resistance breeding program.

Fine mapping of Msv1, a major QTL for resistance to Maize Streak Virus leads to development of production markers for breeding pipelines.

Msv1 , the major QTL for MSV resistance was delimited to an interval of 0.87 cM on chromosome 1 at 87 Mb and production markers with high prediction accuracy were developed. Maize streak virus (MSV) disease is a devastating disease in the Sub-Saharan Africa (SSA), which causes significant yield loss in maize. Resistance to MSV has previously been mapped to a major QTL (Msv1) on chromosome 1 that is germplasm and environment independent and to several minor loci elsewhere in the genome. In this study, Msv1 was fine-mapped through QTL isogenic recombinant strategy using a large F 2 population of CML206 × CML312 to an interval of 0.87 cM on chromosome 1. Genome-wide association study was conducted in the DTMA (Drought Tolerant Maize for Africa)-Association mapping panel with 278 tropical/sub-tropical breeding lines from CIMMYT using the high-density genotyping-by-sequencing (GBS) markers. This study identified 19 SNPs in the region between 82 and 93 Mb on chromosome 1(B73 RefGen_V2) at a P < 1.00E-04, which coincided with the fine-mapped region of Msv1. Haplotype trend regression identified a haplotype block significantly associated with response to MSV. Three SNPs in this haplotype block at 87 Mb on chromosome 1 had an accuracy of 0.94 in predicting the disease reaction in a collection of breeding lines with known responses to MSV infection. In two biparental populations, selection for resistant Msv1 haplotype demonstrated a reduction of 1.03-1.39 units on a rating scale of 1-5, compared to the susceptible haplotype. High-throughput KASP assays have been developed for these three SNPs to enable routine marker screening in the breeding pipeline for MSV resistance.

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 in the Kenya Highland Maize Breeding Program between 1999 and 2020.

Optimization of a breeding program requires assessing and quantifying empirical genetic trends made through past efforts relative to the current breeding strategies, germplasm, technologies, and policy. To establish the genetic trends in the Kenyan Highland Maize Breeding Program (KHMP), a two-decade (1999-2020) historical dataset from the Preliminary Variety Trials (PVT) and Advanced Variety Trials (AVT) was analyzed. A mixed model analysis was used to compute the genetic gains for traits based on the best linear unbiased estimates in the PVT and AVT evaluation stages. A positive significant genetic gain estimate for grain yield of 88 kg ha-1 year-1 (1.94% year-1) and 26 kg ha-1 year-1 (0.42% year-1) was recorded for PVT and AVT, respectively. Root lodging, an important agronomic trait in the Kenya highlands, had a desired genetic gain of -2.65% year-1 for AVT. Results showed improvement in resistance to Turcicum Leaf Blight (TLB) with -1.19% and -0.27% year-1 for the PVT and AVT, respectively. Similarly, a significant genetic trend of -0.81% was noted for resistance to Gray Leaf Spot (GLS) in AVT. These findings highlight the good progress made by KHMP in developing adapted maize hybrids for Kenya's highland agroecology. Nevertheless, the study identified significant opportunities for the KHMP to make even greater genetic gains for key traits with introgression of favorable alleles for various traits, implementing a continuous improvement plan including marker-assisted forward breeding, sparse testing, and genomic selection, and doubled haploid technology for line development.

Genomic prediction of the performance of tropical doubled haploid maize lines under artificial Striga hermonthica (Del.) Benth. infestation.

Striga hermonthica (Del.) Benth., a parasitic weed, causes substantial yield losses in maize production in sub-Saharan Africa. Breeding for Striga resistance in maize is constrained by limited genetic diversity for Striga resistance within the elite germplasm and phenotyping capacity under artificial Striga infestation. Genomics-enabled approaches have the potential to accelerate identification of Striga resistant lines for hybrid development. The objectives of this study were to evaluate the accuracy of genomic selection for traits associated with Striga resistance and grain yield (GY) and to predict genetic values of tested and untested doubled haploid maize lines. We genotyped 606 doubled haploid lines with 8,439 rAmpSeq markers. A training set of 116 doubled haploid lines crossed to 2 testers was phenotyped under artificial Striga infestation at 3 locations in Kenya. Heritability for Striga resistance parameters ranged from 0.38-0.65 while that for GY was 0.54. The prediction accuracies for Striga resistance-associated traits across locations, as determined by cross-validation (CV) were 0.24-0.53 for CV0 and from 0.20 to 0.37 for CV2. For GY, the prediction accuracies were 0.59 and 0.56 for CV0 and CV2, respectively. The results revealed 300 doubled haploid lines with desirable genomic estimated breeding values for reduced number of emerged Striga plants (STR) at 8, 10, and 12 weeks after planting. The genomic estimated breeding values of doubled haploid lines for Striga resistance-associated traits in the training and testing sets were similar in magnitude. These results highlight the potential application of genomic selection in breeding for Striga resistance in maize. The integration of genomic-assisted strategies and doubled haploid technology for line development coupled with forward breeding for major adaptive traits will enhance genetic gains in breeding for Striga resistance in maize.

QTL mapping in three tropical maize populations reveals a set of constitutive and adaptive genomic regions for drought tolerance.

Despite numerous published reports of quantitative trait loci (QTL) for drought-related traits, practical applications of such QTL in maize improvement are scarce. Identifying QTL of sizeable effects that express more or less uniformly in diverse genetic backgrounds across contrasting water regimes could significantly complement conventional breeding efforts to improve drought tolerance. We evaluated three tropical bi-parental populations under water-stress (WS) and well-watered (WW) regimes in Mexico, Kenya and Zimbabwe to identify genomic regions responsible for grain yield (GY) and anthesis-silking interval (ASI) across multiple environments and diverse genetic backgrounds. Across the three populations, on average, drought stress reduced GY by more than 50 % and increased ASI by 3.2 days. We identified a total of 83 and 62 QTL through individual environment analyses for GY and ASI, respectively. In each population, most QTL consistently showed up in each water regime. Across the three populations, the phenotypic variance explained by various individual QTL ranged from 2.6 to 17.8 % for GY and 1.7 to 17.8 % for ASI under WS environments and from 5 to 19.5 % for GY under WW environments. Meta-QTL (mQTL) analysis across the three populations and multiple environments identified seven genomic regions for GY and one for ASI, of which six mQTL on chr.1, 4, 5 and 10 for GY were constitutively expressed across WS and WW environments. One mQTL on chr.7 for GY and one on chr.3 for ASI were found to be 'adaptive' to WS conditions. High throughput assays were developed for SNPs that delimit the physical intervals of these mQTL. At most of the QTL, almost equal number of favorable alleles was donated by either of the parents within each cross, thereby demonstrating the potential of drought tolerant × drought tolerant crosses to identify QTL under contrasting water regimes.

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.

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.

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

BACKGROUND: 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. RESULTS: 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. CONCLUSIONS: 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.