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Successes and insights of an industry biotech program to enhance maize agronomic traits.
Simmons, CR, Lafitte, HR, Reimann, KS, Brugière, N, Roesler, K, Albertsen, MC, Greene, TW, Habben, JE
Plant science : an international journal of experimental plant biology. 2021;:110899
Abstract
Corteva Agriscience™ ran a discovery research program to identify biotech leads for improving maize Agronomic Traits such as yield, drought tolerance, and nitrogen use efficiency. Arising from many discovery sources involving thousands of genes, this program generated over 3331 DNA cassette constructs involving a diverse set of circa 1671 genes, whose transformed maize events were field tested from 2000 to 2018 under managed environments designed to evaluate their potential for commercialization. We demonstrate that a subgroup of these transgenic events improved yield in field-grown elite maize breeding germplasm. A set of at least 22 validated gene leads are identified and described which represent diverse molecular and physiological functions. These leads illuminate sectors of biology that could guide crop improvement in maize and perhaps other crops. In this review and interpretation, we share some of our approaches and results, and key lessons learned in discovering and developing these maize Agronomic Traits leads.
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Cold Atmospheric Pressure Plasma Treatment of Maize Grains-Induction of Growth, Enzyme Activities and Heat Shock Proteins.
Holubová, Ľ, Švubová, R, Slováková, Ľ, Bokor, B, Chobotová Kročková, V, Renčko, J, Uhrin, F, Medvecká, V, Zahoranová, A, Gálová, E
International journal of molecular sciences. 2021;(16)
Abstract
Zea mays L. is one of the most produced crops, and there are still parts of the world where maize is the basic staple food. To improve agriculture, mankind always looks for new, better methods of growing crops, especially in the current changing climatic conditions. Cold atmospheric pressure plasma (CAPP) has already showed its potential to enhance the culturing of crops, but it still needs more research for safe implementation into agriculture. In this work, it was shown that short CAPP treatment of maize grains had a positive effect on the vitality of grains and young seedlings, which may be connected to stimulation of antioxidant and lytic enzyme activities by short CAPP treatment. However, the prolonged treatment had a negative impact on the germination, growth, and production indexes. CAPP treatment caused the increased expression of genes for heat shock proteins HSP101 and HSP70 in the first two days after sowing. Using comet assay it was observed that shorter treatment times (30-120 s) did not cause DNA damage. Surface diagnostics of plasma-treated grains showed that plasma increases the hydrophilicity of the surface but does not damage the chemical bonds on the surface.
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Beat the stress: breeding for climate resilience in maize for the tropical rainfed environments.
Prasanna, BM, Cairns, JE, Zaidi, PH, Beyene, Y, Makumbi, D, Gowda, M, Magorokosho, C, Zaman-Allah, M, Olsen, M, Das, A, et al
TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik. 2021;(6):1729-1752
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Abstract
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.
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Genetic basis of maize kernel oil-related traits revealed by high-density SNP markers in a recombinant inbred line population.
Fang, H, Fu, X, Ge, H, Zhang, A, Shan, T, Wang, Y, Li, P, Wang, B
BMC plant biology. 2021;(1):344
Abstract
BACKGROUND Maize (Zea mays ssp. mays) is the most abundantly cultivated and highly valued food commodity in the world. Oil from maize kernels is highly nutritious and important for the diet and health of humans, and it can be used as a source of bioenergy. A better understanding of genetic basis for maize kernel oil can help improve the oil content and quality when applied in breeding. RESULTS In this study, a KUI3/SC55 recombinant inbred line (RIL) population, consisting of 180 individuals was constructed from a cross between inbred lines KUI3 and SC55. We phenotyped 19 oil-related traits and subsequently dissected the genetic architecture of oil-related traits in maize kernels based on a high-density genetic map. In total, 62 quantitative trait loci (QTLs), with 2 to 5 QTLs per trait, were detected in the KUI3/SC55 RIL population. Each QTL accounted for 6.7% (qSTOL1) to 31.02% (qBELI6) of phenotypic variation and the total phenotypic variation explained (PVE) of all detected QTLs for each trait ranged from 12.5% (OIL) to 52.5% (C16:0/C16:1). Of all these identified QTLs, only 5 were major QTLs located in three genomic regions on chromosome 6 and 9. In addition, two pairs of epistatic QTLs with additive effects were detected and they explained 3.3 and 2.4% of the phenotypic variation, respectively. Colocalization with a previous GWAS on oil-related traits, identified 19 genes. Of these genes, two important candidate genes, GRMZM2G101515 and GRMZM2G022558, were further verified to be associated with C20:0/C22:0 and C18:0/C20:0, respectively, according to a gene-based association analysis. The first gene encodes a kinase-related protein with unknown function, while the second gene encodes fatty acid elongase 2 (fae2) and directly participates in the biosynthesis of very long chain fatty acids in Arabidopsis. CONCLUSIONS Our results provide insights on the genetic basis of oil-related traits and a theoretical basis for improving maize quality by marker-assisted selection.
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Hyperspectral reflectance-based phenotyping for quantitative genetics in crops: Progress and challenges.
Grzybowski, M, Wijewardane, NK, Atefi, A, Ge, Y, Schnable, JC
Plant communications. 2021;(4):100209
Abstract
Many biochemical and physiological properties of plants that are of interest to breeders and geneticists have extremely low throughput and/or can only be measured destructively. This has limited the use of information on natural variation in nutrient and metabolite abundance, as well as photosynthetic capacity in quantitative genetic contexts where it is necessary to collect data from hundreds or thousands of plants. A number of recent studies have demonstrated the potential to estimate many of these traits from hyperspectral reflectance data, primarily in ecophysiological contexts. Here, we summarize recent advances in the use of hyperspectral reflectance data for plant phenotyping, and discuss both the potential benefits and remaining challenges to its application in plant genetics contexts. The performances of previously published models in estimating six traits from hyperspectral reflectance data in maize were evaluated on new sample datasets, and the resulting predicted trait values shown to be heritable (e.g., explained by genetic factors) were estimated. The adoption of hyperspectral reflectance-based phenotyping beyond its current uses may accelerate the study of genes controlling natural variation in biochemical and physiological traits.
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Nitrogen fixation in maize: breeding opportunities.
Sheoran, S, Kumar, S, Kumar, P, Meena, RS, Rakshit, S
TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik. 2021;(5):1263-1280
Abstract
Maize (Zea mays L.) is a highly versatile crop with huge demand of nitrogen (N) for its growth and development. N is the most essential macronutrient for crop production. Despite being the highest abundant element in the atmosphere (~ 78%), it is scarcely available for plant growth. To fulfil the N demand, commercial agriculture is largely dependent on synthetic fertilizers. Excessive dependence on inorganic fertilizers has created extensive ecological as well as economic problems worldwide. Hence, for a sustainable solution to nitrogenous fertilizer use, development of biological nitrogen fixation (BNF) in cereals will be the best alternative. BNF is a well-known mechanism in legumes where diazotrophs convert atmospheric nitrogen (N≡N) to plant-available form, ammonium (NH4+). From many decades, researchers have dreamt to develop a similar symbiotic partnership as in legumes to the cereal crops. A large number of endophytic diazotrophs have been found associated with maize. Elucidation of the genetic and molecular aspects of their interaction will open up new avenues to introgress BNF in maize breeding. With the advanced understanding of N-fixation process, researchers are at a juncture of breeding and engineering this symbiotic relationships in cereals. Different breeding, genetic engineering, omics, gene editing, and synthetic biology approaches will be discussed in this review to make BNF a reality in cereals. It will help to provide a road map to develop/improve the BNF in maize to an advance step for the sustainable production system to achieve the food and nutritional security.
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Biofortified and fortified maize consumption reduces prevalence of low milk retinol, but does not increase vitamin A stores of breastfeeding Zambian infants with adequate reserves: a randomized controlled trial.
Palmer, AC, Jobarteh, ML, Chipili, M, Greene, MD, Oxley, A, Lietz, G, Mwanza, R, Haskell, MJ
The American journal of clinical nutrition. 2021;(5):1209-1220
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Abstract
BACKGROUND Replacement of conventional staples with biofortified or industrially fortified staples in household diets may increase maternal breast milk retinol content and vitamin A intakes from complementary foods, improving infant total body stores (TBS) of vitamin A. OBJECTIVES To determine whether biofortified or industrially fortified maize consumption by Zambian women and their breastfeeding infants could improve milk retinol concentration and infant TBS. METHODS We randomly assigned 255 lactating women and their 9-mo-old infants to a 90-d intervention providing 0 µg retinol equivalents (RE)/d as conventional maize or ∼315 µg RE/d to mothers and ∼55 µg RE/d to infants as provitamin A carotenoid-biofortified maize or retinyl palmitate-fortified maize. Outcomes were TBS, measured by retinol isotope dilution in infants (primary), and breast milk retinol, measured by HPLC in women (secondary). RESULTS The intervention groups were comparable at baseline. Loss to follow-up was 10% (n = 230 mother-infant pairs). Women consumed 92% of the intended 287 g/d and infants consumed 82% of the intended 50 g/d maize. The baseline geometric mean (GM) milk retinol concentration was 1.57 μmol/L (95% CI: 1.45, 1.69 μmol/L), and 24% of women had milk retinol <1.05 μmol/L. While mean milk retinol did not change in the biofortified arm (β: 0.11; 95% CI: -0.02, 0.24), the intervention reduced low milk retinol (RR: 0.42; 95% CI: 0.21, 0.85). Fortified maize increased mean milk retinol (β: 0.17; 95% CI: 0.04, 0.30) and reduced the prevalence of low milk retinol (RR: 0.46; 95% CI: 0.25, 0.82). The baseline GM TBS was 178 μmol (95% CI: 166, 191 μmol). This increased by 24 µmol (± 136) over the 90-d intervention period, irrespective of treatment group. CONCLUSIONS Both biofortified and fortified maize consumption improved milk retinol concentration. This did not translate into greater infant TBS, most likely due to adequate TBS at baseline. This trial was registered at clinicaltrials.gov as NCT02804490.
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Maize endosperm development.
Dai, D, Ma, Z, Song, R
Journal of integrative plant biology. 2021;(4):613-627
Abstract
Recent breakthroughs in transcriptome analysis and gene characterization have provided valuable resources and information about the maize endosperm developmental program. The high temporal-resolution transcriptome analysis has yielded unprecedented access to information about the genetic control of seed development. Detailed spatial transcriptome analysis using laser-capture microdissection has revealed the expression patterns of specific populations of genes in the four major endosperm compartments: the basal endosperm transfer layer (BETL), aleurone layer (AL), starchy endosperm (SE), and embryo-surrounding region (ESR). Although the overall picture of the transcriptional regulatory network of endosperm development remains fragmentary, there have been some exciting advances, such as the identification of OPAQUE11 (O11) as a central hub of the maize endosperm regulatory network connecting endosperm development, nutrient metabolism, and stress responses, and the discovery that the endosperm adjacent to scutellum (EAS) serves as a dynamic interface for endosperm-embryo crosstalk. In addition, several genes that function in BETL development, AL differentiation, and the endosperm cell cycle have been identified, such as ZmSWEET4c, Thk1, and Dek15, respectively. Here, we focus on current advances in understanding the molecular factors involved in BETL, AL, SE, ESR, and EAS development, including the specific transcriptional regulatory networks that function in each compartment during endosperm development.
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ConnecTF: A platform to integrate transcription factor-gene interactions and validate regulatory networks.
Brooks, MD, Juang, CL, Katari, MS, Alvarez, JM, Pasquino, A, Shih, HJ, Huang, J, Shanks, C, Cirrone, J, Coruzzi, GM
Plant physiology. 2021;(1):49-66
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Abstract
Deciphering gene regulatory networks (GRNs) is both a promise and challenge of systems biology. The promise lies in identifying key transcription factors (TFs) that enable an organism to react to changes in its environment. The challenge lies in validating GRNs that involve hundreds of TFs with hundreds of thousands of interactions with their genome-wide targets experimentally determined by high-throughput sequencing. To address this challenge, we developed ConnecTF, a species-independent, web-based platform that integrates genome-wide studies of TF-target binding, TF-target regulation, and other TF-centric omic datasets and uses these to build and refine validated or inferred GRNs. We demonstrate the functionality of ConnecTF by showing how integration within and across TF-target datasets uncovers biological insights. Case study 1 uses integration of TF-target gene regulation and binding datasets to uncover TF mode-of-action and identify potential TF partners for 14 TFs in abscisic acid signaling. Case study 2 demonstrates how genome-wide TF-target data and automated functions in ConnecTF are used in precision/recall analysis and pruning of an inferred GRN for nitrogen signaling. Case study 3 uses ConnecTF to chart a network path from NLP7, a master TF in nitrogen signaling, to direct secondary TF2s and to its indirect targets in a Network Walking approach. The public version of ConnecTF (https://ConnecTF.org) contains 3,738,278 TF-target interactions for 423 TFs in Arabidopsis, 839,210 TF-target interactions for 139 TFs in maize (Zea mays), and 293,094 TF-target interactions for 26 TFs in rice (Oryza sativa). The database and tools in ConnecTF will advance the exploration of GRNs in plant systems biology applications for model and crop species.
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A local-ingredients-based supplement is an alternative to corn-soy blends plus for treating moderate acute malnutrition among children aged 6 to 59 months: A randomized controlled non-inferiority trial in Wolaita, Southern Ethiopia.
Nane, D, Hatløy, A, Lindtjørn, B
PloS one. 2021;(10):e0258715
Abstract
BACKGROUND Globally, moderate acute malnutrition (MAM) affects approximately 5% of children below five years of age. MAM is a persistent public health problem in Ethiopia. The current approach in Ethiopia for managing MAM is a supplementary feeding program; however, this is only provided to chronically food-insecure areas. The objective of the study was to compare a local-ingredients-based supplement (LIBS) with the standard corn-soy blend plus (CSB+) in treating MAM among children aged 6 to 59 months to test the hypothesis that the recovery rate achieved with LIBS will not be more than 7% worse than that achieved with CSB+. METHODS AND FINDINGS We used an individual randomized controlled non-inferiority trial design with two arms, involving 324 children with MAM aged 6 to 59 months in Wolaita, Southern Ethiopia. One hundred and sixty-two children were randomly assigned to each of the two arms. In the first arm, 125.2 g of LIBS with 8 ml of refined deodorized and cholesterol-free sunflower oil/day was provided. In the second arm, 150 g of CSB+ with 16 ml of refined deodorized and cholesterol-free sunflower oil/day was provided. Each child was provided with a daily ration of either LIBS or CSB+ for 12 weeks. Both intention-to-treat (ITT) and per-protocol (PP) analyses were done. ITT and PP analyses showed non-inferiority of LIBS compared with CSB+ for recovery rate [ITT risk difference = 4.9% (95% CI: -4.70, 14.50); PP risk difference = 3.7% (95% CI: -5.91, 13.31)]; average weight gain [ITT risk difference = 0.10 g (95% CI: -0.33 g, 0.53 g); PP risk difference = 0.04 g (95% CI: -0.38 g, 0.47 g)]; and recovery time [ITT risk difference = -2.64 days (95% CI: -8.40 days, 3.13 days); PP difference -2.17 days (95% CI: -7.97 days, 3.64 days]. Non-inferiority in MUAC gain and length/height gain was also observed in the LIBS group compared with the CSB+ group. CONCLUSIONS LIBS can be used as an alternative to the standard CSB+ for the treatment of MAM. Thus, the potential of scaling up the use of LIBS should be promoted. TRIAL REGISTRATION Pan-African Clinical Trial Registration number: PACTR201809662822990.