scholarly journals Optimizing Genomic-Enabled Prediction in Small-Scale Maize Hybrid Breeding Programs: A Roadmap Review

2021 ◽  
Vol 12 ◽  
Author(s):  
Roberto Fritsche-Neto ◽  
Giovanni Galli ◽  
Karina Lima Reis Borges ◽  
Germano Costa-Neto ◽  
Filipe Couto Alves ◽  
...  
Keyword(s):  
Molecular Markers ◽  
Hybrid Breeding ◽  
Small Scale ◽  
Environment Interaction ◽  
Large Set ◽  
Tropical Maize ◽  
Breeding Programs ◽  
Maize Hybrid ◽  
Maize Hybrids ◽  
Tropical Conditions

The usefulness of genomic prediction (GP) for many animal and plant breeding programs has been highlighted for many studies in the last 20 years. In maize breeding programs, mostly dedicated to delivering more highly adapted and productive hybrids, this approach has been proved successful for both large- and small-scale breeding programs worldwide. Here, we present some of the strategies developed to improve the accuracy of GP in tropical maize, focusing on its use under low budget and small-scale conditions achieved for most of the hybrid breeding programs in developing countries. We highlight the most important outcomes obtained by the University of São Paulo (USP, Brazil) and how they can improve the accuracy of prediction in tropical maize hybrids. Our roadmap starts with the efforts for germplasm characterization, moving on to the practices for mating design, and the selection of the genotypes that are used to compose the training population in field phenotyping trials. Factors including population structure and the importance of non-additive effects (dominance and epistasis) controlling the desired trait are also outlined. Finally, we explain how the source of the molecular markers, environmental, and the modeling of genotype–environment interaction can affect the accuracy of GP. Results of 7 years of research in a public maize hybrid breeding program under tropical conditions are discussed, and with the great advances that have been made, we find that what is yet to come is exciting. The use of open-source software for the quality control of molecular markers, implementing GP, and envirotyping pipelines may reduce costs in an efficient computational manner. We conclude that exploring new models/tools using high-throughput phenotyping data along with large-scale envirotyping may bring more resolution and realism when predicting genotype performances. Despite the initial costs, mostly for genotyping, the GP platforms in combination with these other data sources can be a cost-effective approach for predicting the performance of maize hybrids for a large set of growing conditions.

Boosting predictive ability of tropical maize hybrids via genotype‐by‐environment interaction under multivariate GBLUP models

Crop Science ◽  
2020 ◽  
Vol 60 (6) ◽  
pp. 3049-3065
Author(s):  
Matheus Dalsente Krause ◽  
Kaio Olímpio das Graças Dias ◽  
Jhonathan Pedroso Rigal dos Santos ◽  
Amanda Avelar Oliveira ◽  
Lauro José Moreira Guimarães ◽  
...  
Keyword(s):  
Predictive Ability ◽  
Genotype By Environment Interaction ◽  
Environment Interaction ◽  
Tropical Maize ◽  
Maize Hybrids ◽  
Genotype By Environment

scholarly journals Interpreting genotype × environment interaction in tropical maize using linked molecular markers and environmental covariables

1999 ◽  
Vol 99 (3-4) ◽  
pp. 611-625 ◽  
Author(s):  
J. Crossa ◽  
M. Vargas ◽  
F. A. van Eeuwijk ◽  
C. Jiang ◽  
G. O. Edmeades ◽  
...  
Keyword(s):  
Molecular Markers ◽  
Environment Interaction ◽  
Tropical Maize ◽  
Genotype Environment Interaction

scholarly journals Unravelling the Effect of Provitamin A Enrichment on Agronomic Performance of Tropical Maize Hybrids

Plants ◽  
2021 ◽  
Vol 10 (8) ◽  
pp. 1580
Author(s):  
Abebe Menkir ◽  
Ibnou Dieng ◽  
Wende Mengesha ◽  
Silvestro Meseka ◽  
Bussie Maziya-Dixon ◽  
...  
Keyword(s):  
Provitamin A ◽  
Agronomic Performance ◽  
Tropical Maize ◽  
Maize Hybrid ◽  
Maize Hybrids ◽  
Diverse Field ◽  
The Difference ◽  
Growing Conditions ◽  
Β Carotene ◽  
Traditional Diets

Maize is consumed in different traditional diets as a source of macro- and micro-nutrients across Africa. Significant investment has thus been made to develop maize with high provitamin A content to complement other interventions for alleviating vitamin A deficiencies. The current breeding focus on increasing β-carotene levels to develop biofortified maize may affect the synthesis of other beneficial carotenoids. The changes in carotenoid profiles, which are commonly affected by environmental factors, may also lead to a trade-off with agronomic performance. The present study was therefore conducted to evaluate provitamin A biofortified maize hybrids across diverse field environments. The results showed that the difference in accumulating provitamin A and other beneficial carotenoids across variable growing environments was mainly regulated by the genetic backgrounds of the hybrids. Many hybrids, accumulating more than 10 µg/g of provitamin A, produced higher grain yields (>3600 kg/ha) than the orange commercial maize hybrid (3051 kg/ha). These hybrids were also competitive, compared to the orange commercial maize hybrid, in accumulating lutein and zeaxanthins. Our study showed that breeding for enhanced provitamin A content had no adverse effect on grain yield in the biofortified hybrids evaluated in the regional trials. Furthermore, the results highlighted the possibility of developing broadly adapted hybrids containing high levels of beneficial carotenoids for commercialization in areas with variable maize growing conditions in Africa.

Morphological and molecular markers based screening of maize hybrids against northern corn leaf blight

2020 ◽  
Vol 53 (1) ◽  
Author(s):  
Sadaf Naeem ◽  
Muhammad Tahir ◽  
Kiramat Khan ◽  
Amjad Hasan ◽  
Rafiq Ahmad
Keyword(s):  
Molecular Markers ◽  
Leaf Blight ◽  
Maize Hybrids ◽  
Northern Corn Leaf Blight ◽  
Corn Leaf Blight

scholarly journals Disclosing the Nutritional Quality Diversity of Portuguese Common Beans—The Missing Link for Their Effective Use in Protein Quality Breeding Programs

Agronomy ◽  
2021 ◽  
Vol 11 (2) ◽  
pp. 221
Author(s):  
Elsa Mecha ◽  
Sofia Natalello ◽  
Bruna Carbas ◽  
Andreia Bento da Silva ◽  
Susana T. Leitão ◽  
...  
Keyword(s):  
Heat Stress ◽  
Amino Acid ◽  
Nutritional Quality ◽  
Dietary Habits ◽  
Protein Quality ◽  
Trypsin Inhibitor Activity ◽  
Environment Interaction ◽  
Individual Amino Acid ◽  
Common Beans ◽  
Breeding Programs

The common bean (Phaseolus vulgaris L.) represents a sustainable and affordable source of protein, namely, to populations with vegetarian dietary habits. Despite the national germplasm genetic diversity, little is known about the Portuguese accessions’ nutritional and protein quality, leading to their underuse in breeding programs. To fill this gap, a representative collection (106 accessions) was cropped under two contrasting environments (traditional versus heat stress) and evaluated in terms of nutritional quality by near-infrared spectroscopy. Protein quality was assessed, under the stressful environment, considering the individual amino acid contents and the activity of trypsin inhibitors through mass spectrometry (LC-MS/MS) and spectrophotometry, respectively. On top of strong genotypic control, the nutritional composition (protein, fat, fiber, moisture and ash) was also highly influenced by the environment and by genotype × environment interaction, with a clear nutritional quality ranking change for the accessions in heat stress conditions. Classified into three clusters, the accessions from the cluster with the highest individual amino acid and protein contents also showed higher trypsin inhibitor activity (TIA). Since different levels of TIA had no translation into contrasting protein digestibility, breeders focusing on common beans’ protein quality improvement, especially under challenging warming climate conditions, may take advantage of this group of accessions.

scholarly journals Evaluating Genotype × Environment Interactions of Yield Traits and Adaptability in Rice Cultivars Grown under Temperate, Subtropical and Tropical Environments

Agriculture ◽  
2021 ◽  
Vol 11 (6) ◽  
pp. 558
Author(s):  
Xing Huang ◽  
Su Jang ◽  
Backki Kim ◽  
Zhongze Piao ◽  
Edilberto Redona ◽  
...  
Keyword(s):  
Yield Component ◽  
Yield Potential ◽  
High Yield ◽  
Environment Interaction ◽  
Accurate Identification ◽  
Rice Varieties ◽  
Panicle Number ◽  
Tropical Conditions ◽  
Component Traits ◽  
Yield Component Traits

Rice yield is a complex trait that is strongly affected by environment and genotype × environment interaction (GEI) effects. Consideration of GEI in diverse environments facilitates the accurate identification of optimal genotypes with high yield performance, which are adaptable to specific or diverse environments. In this study, multiple environment trials were conducted to evaluate grain yield (GY) and four yield-component traits: panicle length, panicle number, spikelet number per panicle, and thousand-grain weight. Eighty-nine rice varieties were cultivated in temperate, subtropical, and tropical regions for two years. The effects of both GEI (12.4–19.6%) and environment (23.6–69.6%) significantly contributed to the variation of all yield-component traits. In addition, 37.1% of GY variation was explained by GEI, indicating that GY performance was strongly affected by the different environmental conditions. GY performance and genotype stability were evaluated using simultaneous selection indexing, and 19 desirable genotypes were identified with high productivity and broad adaptability across temperate, subtropical, and tropical conditions. These optimal genotypes could be recommended for cultivation and as elite parents for rice breeding programs to improve yield potential and general adaptability to climates.

scholarly journals A Rapid Pipeline for Pollen- and Anther-Specific Gene Discovery Based on Transcriptome Profiling Analysis of Maize Tissues

2021 ◽  
Vol 22 (13) ◽  
pp. 6877
Author(s):  
Yannan Shi ◽  
Yao Li ◽  
Yongchao Guo ◽  
Eli James Borrego ◽  
Zhengyi Wei ◽  
...  
Keyword(s):  
Seed Production ◽  
Late Stage ◽  
Mature Pollen ◽  
Hybrid Breeding ◽  
Large Set ◽  
Male Sterile ◽  
Reproductive Process ◽  
Maize Pollen ◽  
Cis Element ◽  
Mature Anther

Recently, crop breeders have widely adopted a new biotechnology-based process, termed Seed Production Technology (SPT), to produce hybrid varieties. The SPT does not produce nuclear male-sterile lines, and instead utilizes transgenic SPT maintainer lines to pollinate male-sterile plants for propagation of nuclear-recessive male-sterile lines. A late-stage pollen-specific promoter is an essential component of the pollen-inactivating cassette used by the SPT maintainers. While a number of plant pollen-specific promoters have been reported so far, their usefulness in SPT has remained limited. To increase the repertoire of pollen-specific promoters for the maize community, we conducted a comprehensive comparative analysis of transcriptome profiles of mature pollen and mature anthers against other tissue types. We found that maize pollen has much less expressed genes (>1 FPKM) than other tissue types, but the pollen grain has a large set of distinct genes, called pollen-specific genes, which are exclusively or much higher (100 folds) expressed in pollen than other tissue types. Utilizing transcript abundance and correlation coefficient analysis, 1215 mature pollen-specific (MPS) genes and 1009 mature anther-specific (MAS) genes were identified in B73 transcriptome. These two gene sets had similar GO term and KEGG pathway enrichment patterns, indicating that their members share similar functions in the maize reproductive process. Of the genes, 623 were shared between the two sets, called mature anther- and pollen-specific (MAPS) genes, which represent the late-stage pollen-specific genes of the maize genome. Functional annotation analysis of MAPS showed that 447 MAPS genes (71.7% of MAPS) belonged to genes encoding pollen allergen protein. Their 2-kb promoters were analyzed for cis-element enrichment and six well-known pollen-specific cis-elements (AGAAA, TCCACCA, TGTGGTT, [TA]AAAG, AAATGA, and TTTCT) were found highly enriched in the promoters of MAPS. Interestingly, JA-responsive cis-element GCC box (GCCGCC) and ABA-responsive cis-element-coupling element1 (ABRE-CE1, CCACC) were also found enriched in the MAPS promoters, indicating that JA and ABA signaling likely regulate pollen-specific MAPS expression. This study describes a robust and straightforward pipeline to discover pollen-specific promotes from publicly available data while providing maize breeders and the maize industry a number of late-stage (mature) pollen-specific promoters for use in SPT for hybrid breeding and seed production.

Stability Analysis of Agronomic Traits for Maize (Zea Mays L.) Genotypes Based on Ammi Model

2021 ◽  
Vol 50 (2) ◽  
pp. 343-350
Author(s):  
Meijin Ye ◽  
Zhaoyang Chen ◽  
Bingbing Liu ◽  
Haiwang Yue
Keyword(s):  
Grain Yield ◽  
Agronomic Traits ◽  
Interaction Model ◽  
Genotype By Environment Interaction ◽  
Kernel Weight ◽  
Environment Interaction ◽  
Maize Hybrids ◽  
Genotype By Environment ◽  
Ammi Model ◽  
The Ideal

Stability and adaptability of promising maize hybrids in terms of three agronomic traits (grain yield, ear weight and 100-kernel weight) in multi-environments trials were evaluated. The analysis of AMMI model indicated that the all three agronomic traits showed highly significant differences (p < 0.01) on genotype, environment and genotype by environment interaction. Results showed that genotypes Hengyu321 (G9), Yufeng303 (G10) and Huanong138 (G3) were of higher stability on grain yield, ear weight and 100-kernel weight, respectively. Genotypes Hengyu1587 (G8) and Hengyu321 (G9) showed good performance in terms of grain yield, whereas Longping208 (G2) and Weike966 (G12) showed broad adaptability for ear weight. It was also found that the genotypes with better adaptability in terms of 100-kernel weight were Zhengdan958 (G5) and Weike966 (G12). The genotype and environment interaction model based on AMMI analysis indicated that Hengyu1587 and Hengyu321 were the ideal genotypes, due to extensive adaptability and high grain yield under both testing sites. Bangladesh J. Bot. 50(2): 343-350, 2021 (June)

Kalmag: a high spatio temporal model of the Geomagnetic field

2021 ◽  
Author(s):  
Julien Baerenzung ◽  
Matthias Holschneider
Keyword(s):  
Geomagnetic Field ◽  
Learning Algorithm ◽  
Dynamical Evolution ◽  
Small Scale ◽  
Large Set ◽  
The Core ◽  
Resolution Model ◽  
Auto Regressive ◽  
Spatio Temporal ◽  
Marine Vessels

&lt;p&gt;We present a new high resolution model of the Geomagnetic field spanning the last 121 years. The model derives from a large set of data taken by low orbiting satellites, ground based observatories, marine vessels, airplane and during land surveys. It is obtained by combining a Kalman filter to a smoothing algorithm. Seven different magnetic sources are taken into account. Three of them are of internal origin. These are the core, the lithospheric &amp;#160;and the induced / residual ionospheric fields. The other four sources are of external origin. They are composed by a close, a remote and a fluctuating magnetospheric fields as well as a source associated with field aligned currents. The dynamical evolution of each source is prescribed by an auto regressive process of either first or second order, except for the lithospheric field which is assumed to be static. The parameters of the processes were estimated through a machine learning algorithm with a sample of data taken by the low orbiting satellites of the CHAMP and Swarm missions. In this presentation we will mostly focus on the rapid variations of the core field, and the small scale lithospheric field.&amp;#160; We will also discuss the nature of model uncertainties and the limitiations they imply.&lt;/p&gt;

scholarly journals Nickel Toxicity Induced Changes in Nutrient Dynamics and Antioxidant Profiling in Two Maize (Zea mays L.) Hybrids

Plants ◽  
2019 ◽  
Vol 9 (1) ◽  
pp. 5 ◽  
Author(s):  
Muhammad Amjad ◽  
Hasan Raza ◽  
Behzad Murtaza ◽  
Ghulam Abbas ◽  
Muhammad Imran ◽  
...  
Keyword(s):  
Nutrient Solution ◽  
Elevated Level ◽  
Nutrient Dynamics ◽  
Zea Mays L ◽  
Nutrient Concentrations ◽  
Nickel Toxicity ◽  
Maize Hybrid ◽  
Maize Hybrids ◽  
Growth Physiology ◽  
Induced Changes

Nickel (Ni) is among the essential micronutrient heavy metals utilized by plants. However, an elevated level of Ni causes serious concerns for plants’ physiology and their survival. This study evaluated the mechanisms influencing the growth, physiology, and nutrient dynamics in two commercial maize hybrids (Syngenta and Pioneer) exposed to Ni treatments in hydroponics nutrient solution (NS). Seedlings were raised in plastic trays with quartz sand, and subsequently transferred to Hoagland’s NS at the two leaves stage. After three days of transplantation, Ni levels of 0, 20, and 40 mg L−1 were maintained in the nutrient solution. After 30 days of Ni treatments, seedlings were harvested and different growth, physiological, and nutrient concentrations were determined. The results showed that with increasing Ni concentration, the growth of maize hybrids was significantly reduced, and the maize hybrid, Pioneer, showed significantly higher growth than that of Syngenta at all levels of Ni. Higher growth in Pioneer is ascribed to elevated levels of antioxidant enzymes (SOD, CAT, GR, APX, and POX), lower damage to cellular membranes (i.e., higher MSI and lower MDA), and higher tissue nutrient concentrations (N, P, K, Ca, Mg, Fe, Mn, Zn, and Cu). Furthermore, the maize hybrids showed a difference in nutrient translocation from root to shoot which could be one of the factors responsible for differential response of these hybrids against Ni treatments.

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