Impact of CGIAR maize germplasm in Sub-Saharan Africa.

This study reports on the adoption and impacts of CGIAR-related maize varieties in 18 major maize-producing countries in sub-Saharan Africa (SSA) during 1995-2015. Of the 1345 maize varieties released during this timeframe, approximately 60% had a known CGIAR parentage. About 34% (9.5 million ha) of the total maize area in 2015 was cultivated with 'new' CGIAR-related maize varieties released between 1995 and 2015. In the same year, an additional 13% of the maize area was cultivated with 'old' CGIAR-related maize varieties released before 1995. The aggregate annual economic benefit of using new CGIAR-related maize germplasm for yield increase in SSA was estimated at US$1.1-1.6 billion in 2015, which we attributed equally to co-investments by CGIAR funders, public-sector national research and extension programs, and private sector partners. Given that the annual global investment in CGIAR maize breeding at its maximum was US$30 million, the benefit-cost ratios for the CGIAR investment and CGIAR-attributable portion of economic benefits varied from 12:1-17:1, under the assumption of a 5-year lag in the research investment to yield returns. The study also discusses the methodological challenges involved in large-scale impact assessments. Post-2015 CGIAR tropical maize breeding efforts have had a strong emphasis on stress tolerance.

Breeding crops for climate resilience.

In enhancing the resilience of our crops to the impacts of climate change, selection objectives need to address increased variability in the production environment. This encompasses the effects of more variable rainfall and temperatures than currently experienced, including extreme weather events, and changes in pest and pathogens distribution with the increased likelihood of major pest and disease outbreaks as well as occurrence of novel pathogens. Farmers manage the inevitable risks associated with cropping by planting varieties that deliver high yields and good quality under optimal conditions but minimise losses when the seasons are bad. Breeders and agronomists work to support farmers in specific target environments, but increased climate variability has meant that they need to broaden the adaptability of varieties grown and increase the yield stability to help minimise climate-induced risks and build resilience.

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

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

Genomic prediction in biparental tropical maize populations in water-stressed and well-watered environments using low-density and GBS SNPs.

One of the most important applications of genomic selection in maize breeding is to predict and identify the best untested lines from biparental populations, when the training and validation sets are derived from the same cross. Nineteen tropical maize biparental populations evaluated in multienvironment trials were used in this study to assess prediction accuracy of different quantitative traits using low-density (~200 markers) and genotyping-by-sequencing (GBS) single-nucleotide polymorphisms (SNPs), respectively. An extension of the Genomic Best Linear Unbiased Predictor that incorporates genotype × environment (GE) interaction was used to predict genotypic values; cross-validation methods were applied to quantify prediction accuracy. Our results showed that: (1) low-density SNPs (~200 markers) were largely sufficient to get good prediction in biparental maize populations for simple traits with moderate-to-high heritability, but GBS outperformed low-density SNPs for complex traits and simple traits evaluated under stress conditions with low-to-moderate heritability; (2) heritability and genetic architecture of target traits affected prediction performance, prediction accuracy of complex traits (grain yield) were consistently lower than those of simple traits (anthesis date and plant height) and prediction accuracy under stress conditions was consistently lower and more variable than under well-watered conditions for all the target traits because of their poor heritability under stress conditions; and (3) the prediction accuracy of GE models was found to be superior to that of non-GE models for complex traits and marginal for simple traits.

Out of America: tracing the genetic footprints of the global diffusion of maize.

Maize was first domesticated in a restricted valley in south-central Mexico. It was diffused throughout the Americas over thousands of years, and following the discovery of the New World by Columbus, was introduced into Europe. Trade and colonization introduced it further into all parts of the world to which it could adapt. Repeated introductions, local selection and adaptation, a highly diverse gene pool and outcrossing nature, and global trade in maize led to difficulty understanding exactly where the diversity of many of the local maize landraces originated. This is particularly true in Africa and Asia, where historical accounts are scarce or contradictory. Knowledge of post-domestication movements of maize around the world would assist in germplasm conservation and plant breeding efforts. To this end, we used SSR markers to genotype multiple individuals from hundreds of representative landraces from around the world. Applying a multidisciplinary approach combining genetic, linguistic, and historical data, we reconstructed possible patterns of maize diffusion throughout the world from American "contribution" centers, which we propose reflect the origins of maize worldwide. These results shed new light on introductions of maize into Africa and Asia. By providing a first globally comprehensive genetic characterization of landraces using markers appropriate to this evolutionary time frame, we explore the post-domestication evolutionary history of maize and highlight original diversity sources that may be tapped for plant improvement in different regions of the world.

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.

Quality control genotyping for assessment of genetic identity and purity in diverse tropical maize inbred lines.

Quality control (QC) genotyping is an important component in breeding, but to our knowledge there are not well established protocols for its implementation in practical breeding programs. The objectives of our study were to (a) ascertain genetic identity among 2-4 seed sources of the same inbred line, (b) evaluate the extent of genetic homogeneity within inbred lines, and (c) identify a subset of highly informative single-nucleotide polymorphism (SNP) markers for routine and low-cost QC genotyping and suggest guidelines for data interpretation. We used a total of 28 maize inbred lines to study genetic identity among different seed sources by genotyping them with 532 and 1,065 SNPs using the KASPar and GoldenGate platforms, respectively. An additional set of 544 inbred lines was used for studying genetic homogeneity. The proportion of alleles that differed between seed sources of the same inbred line varied from 0.1 to 42.3 %. Seed sources exhibiting high levels of genetic distance are mis-labeled, while those with lower levels of difference are contaminated or still segregating. Genetic homogeneity varied from 68.7 to 100 % with 71.3 % of the inbred lines considered to be homogenous. Based on the data sets obtained for a wide range of sample sizes and diverse genetic backgrounds, we recommended a subset of 50-100 SNPs for routine and low-cost QC genotyping, verified them in a different set of double haploid and inbred lines, and outlined a protocol that could be used to minimize errors in genetic analyses and breeding.

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.

Investigation of anticorrosive behaviour of novel tert-butyl 4-[(4-methyl phenyl) carbonyl] piperazine-1-carboxylate for carbon steel in 1M HCl.

The main focus of current research is on the synthesis and anticorrosive activity of novel heterocyclic compounds tert-butyl 4-[(4-methyl phenyl) carbonyl] piperazine-1-carboxylate [TBMPCPC]. Electrochemical, quantum chemical, and surface characterization studies at elevated temperatures (303-333 K) for carbon steel in 1M HCl solution studied this molecule's corrosion inhibition property. It is observed from the results of electrochemical studies that the TBMPCPC may be able to effectively protect the steel plate surface with an inhibition efficiency of 91.5 % at 25 ppm in corrosive media. The corrosion inhibition depends on concentration, as concentration also increases inhibition efficiency due to the strong and spontaneous adsorption on the metal's surface. The Tafel polarization measurements concluded that the inhibitor works as a mixed form to protect the carbon steel in the bulk solution from corrosion. The adsorption of the TBMPCPC onto the metal surface was in reliable with the isothermal model of the Langmuir adsorption. The scanning electron microscopy clearly showed that the inhibitor was substantially deposited on the metal surface, indicating substantial inhibition. The surface morphology of carbon steel in the absence and existence of an inhibitor in 1 M HCl is also studied using the Atomic Force Microscopic method.

Analysis of phenotypic and microsatellite-based diversity of maize landraces in India, especially from the north east Himalayan region.

The maize landraces in the North East Himalayan (NEH) region in India, especially in the Sikkim state, are morphologically highly diverse. The present study provides details of phenotypic and molecular characterization of a set of 48 selected maize landrace accessions, including the 'Sikkim Primitives' which have a unique habit of prolificacy (5-9 ears on a single stalk). Multi-location phenotypic evaluation of these 48 accessions revealed significant genetic variability for grain yield and its components, leading to identification of several promising accessions. Cluster analysis and PCA using nine morpho-agronomic characters clearly separated 'Sikkim Primitives' from the rest of the accessions. PCA revealed two principal components describing 90% of the total variation, with hundred kernel weight, ear length, ear diameter, number of kernels per ear and flowering behaviour forming the most discriminatory traits. The accessions were genotyped using 42 microsatellite or simple sequence repeat (SSR) markers using a 'population bulk DNA fingerprinting strategy', with allele resolution using an automated DNA Sequencer. The study revealed a high mean number of alleles per SSR locus (13.0) and high Polymorphism Information Content (PIC) value of 0.60. The analysis also led to identification of 163 private/unique alleles, differentiating 44 out of 48 accessions. Six highly frequent SSR alleles were detected at different loci (phi014, phi062, phi090, umc1266, umc1367 and umc2250) with individual frequencies >/=0.75. Some of these SSR loci were reported to tag specific genes/QTL for some important traits, indicating that chromosomal regions harboring these SSR alleles were not selectively neutral. Cluster analysis using Rogers' genetic distance also revealed distinct genetic identity of the 'Sikkim Primitives' from the rest of the accessions in India, including Sikkim. Mantel's test revealed significant and positive correlation between the phenotypic and molecular genetic dissimilarity matrices. The study was the first to portray the patterns of phenotypic and molecular diversity in the maize landraces from the NEH region in India.

Improving the Efficiency of Colchicine-Based Chromosomal Doubling of Maize Haploids.

Production and use of doubled haploids (DH) is becoming an essential part of maize breeding programs worldwide as DH lines offer several advantages in line development and evaluation. One of the critical steps in maize DH line production is doubling the chromosomes of in vivo-derived haploids so that naturally sterile haploids become reproductively fertile diploids (DH) to produce seed. This step of artificially doubling the chromosomes is labor-intensive and costly; hence, optimizing protocols to improve the doubling success is critical for achieving efficiencies in the DH production pipelines. Immersion of 3-4-day old germinating haploid seedlings in colchicine solution is commonly used for chromosome doubling in large-scale maize DH line production. This manuscript presents a new method of colchicine application to haploid seedlings that showed superior doubling rates compared to other methods like standard seedling immersion, seed immersion, root immersion, and direct application of colchicine solution to the seedlings at V2 stage in the greenhouse trays. The new method involves immersing the crown region of the haploid seedlings along with all the seedling roots at V2 stage in the colchicine solution. Further experiments to optimize this method indicated that increasing colchicine concentration had a very positive effect on overall success rate in chromosomal doubling, while not drastically affecting survival rate. The optimized method showed on average 5.6 times higher overall success rate (OSR) compared to the standard haploid seedling immersion method which was the second-best method in our experiments. This improved method of colchicine application saves resources by reducing the number of haploids to be generated and handled in a maize DH production pipeline.

Correction to: High-throughput method for ear phenotyping and kernel weight estimation in maize using ear digital imaging.

[This corrects the article DOI: 10.1186/s13007-018-0317-4.].

Identification of donors for low-nitrogen stress with maize lethal necrosis (MLN) tolerance for maize breeding in sub-Saharan Africa.

After drought, a major challenge to smallholder farmers in sub-Saharan Africa is low-fertility soils with poor nitrogen (N)-supplying capacity. Many challenges in this region need to be overcome to create a viable fertilizer market. An intermediate solution is the development of maize varieties with an enhanced ability to take up or utilize N in severely depleted soils, and to more efficiently use the small amounts of N that farmers can supply to their crops. Over 400 elite inbred lines from seven maize breeding programs were screened to identify new sources of tolerance to low-N stress and maize lethal necrosis (MLN) for introgression into Africa-adapted elite germplasm. Lines with high levels of tolerance to both stresses were identified. Lines previously considered to be tolerant to low-N stress ranked in the bottom 10% under low-N confirming the need to replace these lines with new donors identified in this study. The lines that performed best under low-N yielded about 0. 5 Mg ha-1 (20%) more in testcross combinations than some widely used commercial parent lines such as CML442 and CML395. This is the first large scale study to identify maize inbred lines with tolerance to low-N stress and MLN in eastern and southern Africa.

Genetic diversity among and within cultured cyanobionts of diverse species of Azolla.

The cyanobionts isolated from 10 Azolla accessions belonging to 6 species (Azolla mexicana, A. microphylla, A. rubra, A. caroliniana, A. filiculoides, A. pinnata) were cultured under laboratory conditions and analyzed on the basis of whole cell protein profiles and molecular marker dataset generated using repeat sequence primers (STRR(mod) and HipTG). The biochemical and molecular marker profiles of the cyanobionts were compared with those of the free-living cyanobacteria and symbiotic Nostoc strains from Anthoceros sp., Cycas sp. and Gunnera monoika. Cluster analysis revealed the genetic diversity among the selected strains, and identified 3 distinct clusters. Group 1 included cyanobionts from all the 10 accessions of Azolla, group 2 comprised all the symbiotic Nostoc strains, while group 3 included the free-living cyanobacteria belonging to the genera Nostoc and Anabaena. The interrelationships among the Azolla cyanobionts were further revealed by principal component analysis. Cyanobionts from A. caroliniana-A. microphylla grouped together while cyanobionts associated with A. mexicana-A. filiculoides along with A. pinnata formed another group. A. rubra cyanobionts had intermediate relationship with both the subgroups. This is the first study analyzing the diversity existing among the cultured cyanobionts of diverse Azolla species through the use of biochemical and molecular profiles and also the genetic distinctness of these free-living cyanobionts as compared to cyanobacterial strains of the genera Anabaena and Nostoc.

Developing and deploying climate-resilient maize varieties in the developing world.

In sub-Saharan Africa (SSA) and Asia maize yields remain variable due to climate shocks. Over the past decade extensive progress has been made on the development and delivery of climate-resilient maize. In 2016 over 70000 metric tonnes of drought-tolerant maize seed was commercialized in 13 countries in SSA, benefiting an estimated 53 million people. Significant progress is also being made with regard to the development and deployment of elite heat-tolerant maize varieties in South Asia. Increased genetic gain in grain yield under stress-prone environments, coupled with faster replacement of old/obsolete varieties, through intensive engagement with seed companies is essential to protect maize crops grown by smallholders from the changing climates in SSA and Asia.

High-throughput method for ear phenotyping and kernel weight estimation in maize using ear digital imaging.

BACKGROUND: Grain yield, ear and kernel attributes can assist to understand the performance of maize plant under different environmental conditions and can be used in the variety development process to address farmer's preferences. These parameters are however still laborious and expensive to measure. RESULTS: A low-cost ear digital imaging method was developed that provides estimates of ear and kernel attributes i.e., ear number and size, kernel number and size as well as kernel weight from photos of ears harvested from field trial plots. The image processing method uses a script that runs in a batch mode on ImageJ; an open source software. Kernel weight was estimated using the total kernel number derived from the number of kernels visible on the image and the average kernel size. Data showed a good agreement in terms of accuracy and precision between ground truth measurements and data generated through image processing. Broad-sense heritability of the estimated parameters was in the range or higher than that for measured grain weight. Limitation of the method for kernel weight estimation is discussed. CONCLUSION: The method developed in this work provides an opportunity to significantly reduce the cost of selection in the breeding process, especially for resource constrained crop improvement programs and can be used to learn more about the genetic bases of grain yield determinants.

Morphological, physiochemical and molecular characterization of Anabaena strains.

A set of 30 Anabaena strains, isolated from diverse geographical regions of India, were characterized using morphological and physiochemical attributes as well as molecular marker profiles. Significant differences were observed among the Anabaena strains with regard to the shape and size of trichomes and individual cells within a filament, besides qualitative and quantitative aspects of phycobiliprotein accumulation and activities of enzymes involved in nitrogen metabolism. Analyses of molecular polymorphisms in a selected set of 13 Anabaena strains, using primers based on repetitive sequences in the genome, led to unambiguous differentiation of the strains as well as understanding of their genetic relationships. Informative morphological, physio-chemical and molecular characters have been identified that could aid in differentiation and utilization of Anabaena strains as bioinoculants or as sources of pigments.

Unmanned aerial platform-based multi-spectral imaging for field phenotyping of maize.

BACKGROUND: Recent developments in unmanned aerial platforms (UAP) have provided research opportunities in assessing land allocation and crop physiological traits, including response to abiotic and biotic stresses. UAP-based remote sensing can be used to rapidly and cost-effectively phenotype large numbers of plots and field trials in a dynamic way using time series. This is anticipated to have tremendous implications for progress in crop genetic improvement. RESULTS: We present the use of a UAP equipped with sensors for multispectral imaging in spatial field variability assessment and phenotyping for low-nitrogen (low-N) stress tolerance in maize. Multispectral aerial images were used to (1) characterize experimental fields for spatial soil-nitrogen variability and (2) derive indices for crop performance under low-N stress. Overall, results showed that the aerial platform enables to effectively characterize spatial field variation and assess crop performance under low-N stress. The Normalized Difference Vegetation Index (NDVI) data derived from spectral imaging presented a strong correlation with ground-measured NDVI, crop senescence index and grain yield. CONCLUSION: This work suggests that the aerial sensing platform designed for phenotyping studies has the potential to effectively assist in crop genetic improvement against abiotic stresses like low-N provided that sensors have enough resolution for plot level data collection. Limitations and future potential uses are also discussed.

Chronic calcific pancreatitis of the tropics (CCPT): spectrum and correlates of exocrine and endocrine pancreatic dysfunction.

The exocrine and endocrine pathophysiology of chronic calcific pancreatitis of the tropics (CCPT) remains elusive. The objective of this study was to evaluate the spectrum and correlates of the exocrine and endocrine pancreatic dysfunction in CCPT. Thirty-seven consecutive patients with a clinico-radiological diagnosis of CCPT were stratified into three subgroups: CCPT-normal glucose tolerance (NGT), CCPT-abnormal glucose tolerance (IGT) and CCPT-diabetes mellitus (DM). Ten ketosis resistant young diabetic (KRDY) patients, 10 classical insulin dependent diabetes mellitus (IDDM) patients and 18 healthy matched controls were included for comparison. Fecal chymotrypsin (FCT) levels and blood C-peptide levels (basal and post i.v. glucagon stimulation) were estimated for assessing the exocrine and endocrine pancreatic functions, respectively. Sonography was performed to evaluate the pancreatic size and ductal diameter. Pancreatic exocrine-endocrine correlation was examined by studying the C-peptide/fecal chymotrypsin ratio (CP/FCT) (CP/FCT of normal controls = 1). Mean FCT levels in all 3 subgroups of CCPT (NGT: 3.4 micrograms/g; IGT: 0.82 microgram/g; DM: 2.4 micrograms/g) were very low (87-96% reduction in exocrine pancreatic dysfunction; mean FCT in healthy controls was 22.8 micrograms/g) (P < 0.0001). In contrast, KRDY and IDDM patients displayed 50-54% reduction in pancreatic acinar function (P < 0.001). Basal and stimulated C-peptide levels progressively fell in the 3 CCPT subsets (NGT: 0.23 and 0.46 > IGT: 0.14 and 0.29 > DM 0.10 and 0.14) (P < 0.01). CCPT patients exhibited pancreatic atrophy and ductal dilation (> 3 mm).(ABSTRACT TRUNCATED AT 250 WORDS)

Evaluation of Tolypothrix germplasm for phycobiliprotein content.

Twenty Tolypothrix strains, including 15 strains of T. tenuis, three strains of T. ceylonica and one strain each of T. nodosa and T. bouteillei, were evaluated for their phycobiliprotein content and composition. Significant differences among the Tolypothrix strains were found at both inter- and intra-specific levels in the production of phycobiliprotein constituents--phycocyanin (PC), allophycocyanin (APC) and phycoerythrin (PE). Four specific parameters, viz. PC or PE content, total phycobiliprotein and total protein content, and percentage of phycobiliproteins, in a mixture of total proteins were used to select four T. tenuis and one T. ceylonica strain as useful for phycobiliproteins production.