Global Vitamin Enhancement of Maize Grain: Wonderful Opportunities for Genomic Selection

Advances in understanding the genetic basis of variation for levels of total carotenoids and provitamin A carotenoids in maize grain have been made recently. Provitamin A carotenoids are converted to retinol or Vitamin A in the human body. Global Vitamin A deficiencies are widespread. Vitamin A deficiency can result in night blindness and increased susceptibility to infections and can eventually result in death. It is estimated that 250,000 to 500,000 children become blind every year as a result of vitamin A deficiency, and that half of these die within one year of losing their eyesight (www.who.int/nutrition/topics/vad/en/). Fortunately the genes that control levels of provitamin A in maize grain have been discovered. Maize is a major food staple in Sub-Saharan Africa where vitamin deficiencies are prevalent. Initial selection of favorable forms of two carotenoid biosynthetic genes have dramatically increased provitamin A concentrations in experimental hybrids grown in Zambia. However, there are needs for a major widespread selection initiative and program to convert most all of the maize throughout Sub-Saharan Africa to high provitamin A concentrations. Developments in genomic prediction and selection based on DNA sequence variation are emerging and could greatly help this goal. Artificial Intelligence may be very useful in designing very efficient selection programs. More and more DNA sequence data will become available as technology advances. The entire genome of maize plants in breeding programs will be routinely DNA sequenced. However, the rate of increase of DNA sequence data is already making it challenging for humans to effectively handle and use all this information. How AI may help a global breeding effort for more nutritious maize grain effort will be discussed, including efforts to increase other vitamins, such as Vitamin E. Some consideration will be given to possible negative consequences of AI driven selection programs to enhance vitamin concentrations in maize grain throughout the developing and developed world

Genome-Wide Association Study and Pathway-Level Analysis of Kernel Color in Maize.

Rapid development and adoption of biofortified, provitamin A-dense orange maize (Zea mays L.) varieties could be facilitated by a greater understanding of the natural variation underlying kernel color, including as it relates to carotenoid biosynthesis and retention in maize grain. Greater abundance of carotenoids in maize kernels is generally accompanied by deeper orange color, useful for distinguishing provitamin A-dense varieties to consumers. While kernel color can be scored and selected with high-throughput, low-cost phenotypic methods within breeding selection programs, it remains to be well established as to what would be the logical genetic loci to target for selection for kernel color. We conducted a genome-wide association study of maize kernel color, as determined by colorimetry, in 1,651 yellow and orange inbreds from the Ames maize inbred panel. Associations were found with y1, encoding the first committed step in carotenoid biosynthesis, and with dxs2, which encodes the enzyme responsible for the first committed step in the biosynthesis of the isoprenoid precursors of carotenoids. These genes logically could contribute to overall carotenoid abundance and thus kernel color. The lcyE and zep1 genes, which can affect carotenoid composition, were also found to be associated with colorimeter values. A pathway-level analysis, focused on genes with a priori evidence of involvement in carotenoid biosynthesis and retention, revealed associations for dxs3 and dmes1, involved in isoprenoid biosynthesis; ps1 and vp5, within the core carotenoid pathway; and vp14, involved in cleavage of carotenoids. Collectively, these identified genes appear relevant to the accumulation of kernel color

A foundation for provitamin A biofortification of maize: genome-wide association and genomic prediction models of carotenoid levels.

Efforts are underway for development of crops with improved levels of provitamin A carotenoids to help combat dietary vitamin A deficiency. As a global staple crop with considerable variation in kernel carotenoid composition, maize (Zea mays L.) could have a widespread impact. We performed a genome-wide association study (GWAS) of quantified seed carotenoids across a panel of maize inbreds ranging from light yellow to dark orange in grain color to identify some of the key genes controlling maize grain carotenoid composition. Significant associations at the genome-wide level were detected within the coding regions of zep1 and lut1, carotenoid biosynthetic genes not previously shown to impact grain carotenoid composition in association studies, as well as within previously associated lcyE and crtRB1 genes. We leveraged existing biochemical and genomic information to identify 58 a priori candidate genes relevant to the biosynthesis and retention of carotenoids in maize to test in a pathway-level analysis. This revealed dxs2 and lut5, genes not previously associated with kernel carotenoids. In genomic prediction models, use of markers that targeted a small set of quantitative trait loci associated with carotenoid levels in prior linkage studies were as effective as genome-wide markers for predicting carotenoid traits. Based on GWAS, pathway-level analysis, and genomic prediction studies, we outline a flexible strategy involving use of a small number of genes that can be selected for rapid conversion of elite white grain germplasm, with minimal amounts of carotenoids, to orange grain versions containing high levels of provitamin A

Food biofortification : reaping the benefits of science to overcome hidden hunger

Biofortification is a process of increasing the density of minerals and vitamins in a food crop through conventional plant breeding, genetic engineering, or agronomic practices (primarily use of fertilizers and foliar sprays). Biofortified staple food crops, when substituted consistently for non-biofortified staple food crops, can generate measurable improvements in human nutrition and health. This monograph describes the progress made in developing, testing, and disseminating biofortified staple food crops, primarily through the use of conventional plant breeding, summarizing the activities of two consortiums of inter-disciplinary collaborating institutions led the HarvestPlus program and the International Potato Center (CIP). We focus on laying out the evidence base proving the effectiveness and impact to date of biofortified crops. Results of a large number of nutritional bioavailability and efficacy trials are summarized (Chapter 2), crop development techniques and activities are presented and variety releases documented for a dozen staple food crops in low and middle income countries (LMICs) in Africa, Asia, and Latin America (Chapter 3), and strategies for promoting the uptake of specific biofortified crops are discussed, concurrent with policy advocacy to encourage key institutions to mainstream the promotion, and use of biofortified crops in their core activities (Chapters 4 and 5). Statistics will be presented on numbers of farm households adopting biofortified crops (Chapters 3 and 4), now available to farmers in 40 low and middle income countries (LMICs). Each section will outline the way forward on additional future activities required to enhance the development and impact the biofortification through conventional plant breeding. No biofortified staple food crop developed through transgenic techniques has been fully de-regulated for release to farmers in LMICs. Yet transgenic techniques hold the potential for a several-fold increase in the impact/benefits of biofortified crops. This potential is described in Chapter 6 which discusses developmental research already completed, including achieving higher densities of single nutrients than is possible with conventional breeding, combining multiple nutrient traits in single events, slowing down/reducing the level of degradation of vitamins after harvesting, and combining superior agronomic traits with nutrient traits in single events. A final chapter summarizes and discusses key questions and issues that will influence the ultimate mainstreaming of biofortified crops in food systems in LMICs and will allow maximization of the benefits of biofortification

Rare genetic variation at Zea mays crtRB1 increases β-carotene in maize grain

Breeding to increase β-carotene levels in cereal grains, termed provitamin A biofortification, is an economical approach to address dietary vitamin A deficiency in the developing world. Experimental evidence from association and linkage populations in maize (Zea maysL.) demonstrate that the gene encoding β-carotene hydroxylase 1 (crtRB1) underlies a principal quantitative trait locus associated with β-carotene concentration and conversion in maize kernels. crtRB1 alleles associated with reduced transcript expression correlate with higher β-carotene concentrations. Genetic variation at crtRB1 also affects hydroxylation efficiency among encoded allozymes, as observed by resultant carotenoid profiles in recombinant expression assays. The most favorable crtRB1 alleles, rare in frequency and unique to temperate germplasm, are being introgressed via inexpensive PCR marker-assisted selection into tropical maize germplasm adapted to developing countries, where it is most needed for human health

The effect of artificial selection on phenotypic plasticity in maize

Remarkable productivity has been achieved in crop species through artificial selection and adaptation to modern agronomic practices. Whether intensive selection has changed the ability of improved cultivars to maintain high productivity across variable environments is unknown. Understanding the genetic control of phenotypic plasticity and genotype by environment (G × E) interaction will enhance crop performance predictions across diverse environments. Here we use data generated from the Genomes to Fields (G2F) Maize G × E project to assess the effect of selection on G × E variation and characterize polymorphisms associated with plasticity. Genomic regions putatively selected during modern temperate maize breeding explain less variability for yield G × E than unselected regions, indicating that improvement by breeding may have reduced G × E of modern temperate cultivars. Trends in genomic position of variants associated with stability reveal fewer genic associations and enrichment of variants 0–5000 base pairs upstream of genes, hypothetically due to control of plasticity by short-range regulatory elements

Maize Genomes to Fields: 2014 and 2015 field season genotype, phenotype, environment, and inbred ear image datasets

Objectives: Crop improvement relies on analysis of phenotypic, genotypic, and environmental data. Given large, well-integrated, multi-year datasets, diverse queries can be made: Which lines perform best in hot, dry environments? Which alleles of specific genes are required for optimal performance in each environment? Such datasets also can be leveraged to predict cultivar performance, even in uncharacterized environments. The maize Genomes to Fields (G2F) Initiative is a multi-institutional organization of scientists working to generate and analyze such datasets from existing, publicly available inbred lines and hybrids. G2F’s genotype by environment project has released 2014 and 2015 datasets to the public, with 2016 and 2017 collected and soon to be made available. Data description: Datasets include DNA sequences; traditional phenotype descriptions, as well as detailed ear, cob, and kernel phenotypes quantified by image analysis; weather station measurements; and soil characterizations by site. Data are released as comma separated value spreadsheets accompanied by extensive README text descriptions. For genotypic and phenotypic data, both raw data and a version with outliers removed are reported. For weather data, two versions are reported: a full dataset calibrated against nearby National Weather Service sites and a second calibrated set with outliers and apparent artifacts removed

Distinct Genetic Architectures for Male and Female Inflorescence Traits of Maize

We compared the genetic architecture of thirteen maize morphological traits in a large population of recombinant inbred lines. Four traits from the male inflorescence (tassel) and three traits from the female inflorescence (ear) were measured and studied using linkage and genome-wide association analyses and compared to three flowering and three leaf traits previously studied in the same population. Inflorescence loci have larger effects than flowering and leaf loci, and ear effects are larger than tassel effects. Ear trait models also have lower predictive ability than tassel, flowering, or leaf trait models. Pleiotropic loci were identified that control elongation of ear and tassel, consistent with their common developmental origin. For these pleiotropic loci, the ear effects are larger than tassel effects even though the same causal polymorphisms are likely involved. This implies that the observed differences in genetic architecture are not due to distinct features of the underlying polymorphisms. Our results support the hypothesis that genetic architecture is a function of trait stability over evolutionary time, since the traits that changed most during the relatively recent domestication of maize have the largest effects

Plant Breeding Basics

Non-PRIFPRI2; CRP4; HarvestPlusHarvestPlus; A4NHCGIAR Research Program on Agriculture for Nutrition and Health (A4NH