Boddupalli M. Prasanna

Maize HapMap2 identifies extant variation from a genome in flux

Whereas breeders have exploited diversity in maize for yield improvements, there has been limited progress in using beneficial alleles in undomesticated varieties. Characterizing standing variation in this complex genome has been challenging, with only a small fraction of it described to date. Using a population genetics scoring model, we identified 55 million SNPs in 103 lines across pre-domestication and domesticated Zea mays varieties, including a representative from the sister genus Tripsacum. We find that structural variations are pervasive in the Z. mays genome and are enriched at loci associated with important traits. By investigating the drivers of genome size variation, we find that the larger Tripsacum genome can be explained by transposable element abundance rather than an allopolyploid origin. In contrast, intraspecies genome size variation seems to be controlled by chromosomal knob content. There is tremendous overlap in key gene content in maize and Tripsacum, suggesting that adaptations from Tripsacum (for example, perennialism and frost and drought tolerance) can likely be integrated into maize.

Crops that feed the world 6. Past successes and future challenges to the role played by maize in global food security

Maize is one of the most important food crops in the world and, together with rice and wheat, provides at least 30% of the food calories to more than 4.5 billion people in 94 developing countries. In parts of Africa and Mesoamerica, maize alone contributes over 20% of food calories. Maize is also a key ingredient in animal feed and is used extensively in industrial products, including the production of biofuels. Increasing demand and production shortfalls in global maize supplies have worsened market volatility and contributed to surging global maize prices. Climatic variability and change, and the consequent rise in abiotic and biotic stresses, further confound the problem. Unless concerted and vigorous measures are taken to address these challenges and accelerate yield growth, the outcome will be hunger and food insecurity for millions of poor consumers. We review the research challenges of ensuring global food security in maize, particularly in the context of climate change. The paper summarizes the importance of maize for food, nutrition and livelihood security and details the historical productivity of maize, consumption patterns and future trends. We show how crop breeding to overcome biotic and abiotic stresses will play a key role in meeting future maize demand. Attention needs to be directed at the generation of high yielding, stress-tolerant and widely-adapted maize varieties through judicious combination of conventional and molecular breeding approaches. The use of improved germplasm per se will not, however, be enough to raise yields and enhance adaptation to climate change, and will need to be complemented by improved crop and agronomic practices. Faced with emasculated state extension provision and imperfect markets, new extension approaches and institutional innovations are required that enhance farmers’ access to information, seeds, other inputs, finance and output markets. Over the long-term, large public and private sector investment and sustained political commitment and policy support for technology generation and delivery are needed to overcome hunger, raise the incomes of smallholder farmers and meet the challenges of growing demand for maize at the global level.

Adapting maize production to climate change in sub-Saharan Africa

Given the accumulating evidence of climate change in sub-Saharan Africa, there is an urgent need to develop more climate resilient maize systems. Adaptation strategies to climate change in maize systems in sub-Saharan Africa are likely to include improved germplasm with tolerance to drought and heat stress and improved management practices. Adapting maize systems to future climates requires the ability to accurately predict future climate scenarios in order to determine agricultural responses to climate change and set priorities for adaptation strategies. Here we review the projected climate change scenarios for Africa’s maize growing regions using the outputs of 19 global climate models. By 2050, air temperatures are expected to increase throughout maize mega- environments within sub-Saharan Africa by an average of 2.1°C. Rainfall changes during the maize growing season varied with location. Given the time lag between the development of improved cultivars until the seed is in the hands of farmers and adoption of new management practices, there is an urgent need to prioritise research strategies on climate change resilient germplasm development to offset the predicted yield declines.

Maize Production in a Changing Climate: Impacts, Adaptation, and Mitigation Strategies

Abstract Plant breeding and improved management options have made remarkable progress in increasing crop yields during the past century. However, climate change projections suggest that large yield losses will be occurring in many regions, particularly within sub-Saharan Africa. The development of climate-ready germplasm to offset these losses is of the upmost importance. Given the time lag between the development of improved germplasm and adoption in farmers’ fields, the development of improved breeding pipelines needs to be a high priority. Recent advances in molecular breeding provide powerful tools to accelerate breeding gains and dissect stress adaptation. This review focuses on achievements in stress tolerance breeding and physiology and presents future tools for quick and efficient germplasm development. Sustainable agronomic and resource management practices can effectively contribute to climate change mitigation. Management options to increase maize system resilience to climate-related stresses and mitigate the effects of future climate change are also discussed.

Whole-genome strategies for marker-assisted plant breeding

Molecular breeding for complex traits in crop plants requires understanding and manipulation of many factors influencing plant growth, development and responses to an array of biotic and abiotic stresses. Molecular marker-assisted breeding procedures can be facilitated and revolutionized through whole-genome strategies, which utilize full genome sequencing and genome-wide molecular markers to effectively address various genomic and environmental factors through a representative or complete set of genetic resources and breeding materials. These strategies are now increasingly based on understanding of specific genomic regions, genes/alleles, haplotypes, linkage disequilibrium (LD) block(s), gene networks and their contribution to specific phenotypes. Large-scale and high-density genotyping and genome-wide selection are two important components of these strategies. As components of whole-genome strategies, molecular breeding platforms and methodologies should be backed up by high throughput and precision phenotyping and e-typing (environmental assay) with strong support systems such as breeding informatics and decision support tools. Some basic strategies are discussed in this article, including (1) seed DNA-based genotyping for simplifying marker-assisted selection (MAS), reducing breeding cost and increasing scale and efficiency, (2) selective genotyping and phenotyping, combined with pooled DNA analysis, for capturing the most important contributing factors, (3) flexible genotyping systems, such as genotyping by sequencing and arraying, refined for different selection methods including MAS, marker-assisted recurrent selection and genomic selection (GS), (4) marker-trait association analysis using joint linkage and LD mapping, and (5) sequence-based strategies for marker development, allele mining, gene discovery and molecular breeding.

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.

Maize Production in a Changing Climate

Abstract Plant breeding and improved management options have made remarkable progress in increasing crop yields during the past century. However, climate change projections suggest that large yield losses will be occurring in many regions, particularly within sub-Saharan Africa. The development of climate-ready germplasm to offset these losses is of the upmost importance. Given the time lag between the development of improved germplasm and adoption in farmers’ fields, the development of improved breeding pipelines needs to be a high priority. Recent advances in molecular breeding provide powerful tools to accelerate breeding gains and dissect stress adaptation. This review focuses on achievements in stress tolerance breeding and physiology and presents future tools for quick and efficient germplasm development. Sustainable agronomic and resource management practices can effectively contribute to climate change mitigation. Management options to increase maize system resilience to climate-related stresses and mitigate the effects of future climate change are also discussed.

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

BackgroundKnowledge of germplasm diversity and relationships among elite breeding materials is fundamentally important in crop improvement. We genotyped 450 maize inbred lines developed and/or widely used by CIMMYT breeding programs in both Kenya and Zimbabwe using 1065 SNP markers to (i) investigate population structure and patterns of relationship of the germplasm for better exploitation in breeding programs; (ii) assess the usefulness of SNPs for identifying heterotic groups commonly used by CIMMYT breeding programs; and (iii) identify a subset of highly informative SNP markers for routine and low cost genotyping of CIMMYT germplasm in the region using uniplex assays.ResultsGenetic distance for about 94% of the pairs of lines fell between 0.300 and 0.400. Eighty four percent of the pairs of lines also showed relative kinship values ≤ 0.500. Model-based population structure analysis, principal component analysis, neighbor-joining cluster analysis and discriminant analysis revealed the presence of 3 major groups and generally agree with pedigree information. The SNP markers did not show clear separation of heterotic groups A and B that were established based on combining ability tests through diallel and line x tester analyses. Our results demonstrated large differences among the SNP markers in terms of reproducibility, ease of scoring, polymorphism, minor allele frequency and polymorphic information content. About 40% of the SNPs in the multiplexed chip-based GoldenGate assays were found to be uninformative in this study and we recommend 644 of the 1065 for low to medium density genotyping in tropical maize germplasm using uniplex assays.ConclusionsThere were high genetic distance and low kinship coefficients among most pairs of lines, clearly indicating the uniqueness of the majority of the inbred lines in these maize breeding programs. The results from this study will be useful to breeders in selecting best parental combinations for new breeding crosses, mapping population development and marker assisted breeding.

Meta-analyses of QTL for grain yield and anthesis silking interval in 18 maize populations evaluated under water-stressed and well-watered environments

BackgroundIdentification of QTL with large phenotypic effects conserved across genetic backgrounds and environments is one of the prerequisites for crop improvement using marker assisted selection (MAS). The objectives of this study were to identify meta-QTL (mQTL) for grain yield (GY) and anthesis silking interval (ASI) across 18 bi-parental maize populations evaluated in the same conditions across 2-4 managed water stressed and 3-4 well watered environments.ResultsThe meta-analyses identified 68 mQTL (9 QTL specific to ASI, 15 specific to GY, and 44 for both GY and ASI). Mean phenotypic variance explained by each mQTL varied from 1.2 to 13.1% and the overall average was 6.5%. Few QTL were detected under both environmental treatments and/or multiple (>4 populations) genetic backgrounds. The number and 95% genetic and physical confidence intervals of the mQTL were highly reduced compared to the QTL identified in the original studies. Each physical interval of the mQTL consisted of 5 to 926 candidate genes.ConclusionsMeta-analyses reduced the number of QTL by 68% and narrowed the confidence intervals up to 12-fold. At least the 4 mQTL (mQTL2.2, mQTL6.1, mQTL7.5 and mQTL9.2) associated with GY under both water-stressed and well-watered environments and detected up to 6 populations may be considered for fine mapping and validation to confirm effects in different genetic backgrounds and pyramid them into new drought resistant breeding lines. This is the first extensive report on meta-analysis of data from over 3100 individuals genotyped using the same SNP platform and evaluated in the same conditions across a wide range of managed water-stressed and well-watered environments.

Maize Lethal Necrosis (MLN), an Emerging Threat to Maize-Based Food Security in Sub-Saharan Africa

In sub-Saharan Africa, maize is a staple food and key determinant of food security for smallholder farming communities. Pest and disease outbreaks are key constraints to maize productivity. In September 2011, a serious disease outbreak, later diagnosed as maize lethal necrosis (MLN), was reported on maize in Kenya. The disease has since been confirmed in Rwanda and the Democratic Republic of Congo, and similar symptoms have been reported in Tanzania, Uganda, South Sudan, and Ethiopia. In 2012, yield losses of up to 90% resulted in an estimated grain loss of 126,000 metric tons valued at