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1.
Integrating genomic-enabled prediction and high-throughput phenotyping in breeding for climate-resilient bread wheat.
Juliana, P, Montesinos-López, OA, Crossa, J, Mondal, S, González Pérez, L, Poland, J, Huerta-Espino, J, Crespo-Herrera, L, Govindan, V, Dreisigacker, S, et al
TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik. 2019;(1):177-194
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Abstract
Genomic selection and high-throughput phenotyping (HTP) are promising tools to accelerate breeding gains for high-yielding and climate-resilient wheat varieties. Hence, our objective was to evaluate them for predicting grain yield (GY) in drought-stressed (DS) and late-sown heat-stressed (HS) environments of the International maize and wheat improvement center's elite yield trial nurseries. We observed that the average genomic prediction accuracies using fivefold cross-validations were 0.50 and 0.51 in the DS and HS environments, respectively. However, when a different nursery/year was used to predict another nursery/year, the average genomic prediction accuracies in the DS and HS environments decreased to 0.18 and 0.23, respectively. While genomic predictions clearly outperformed pedigree-based predictions across nurseries, they were similar to pedigree-based predictions within nurseries due to small family sizes. In populations with some full-sibs in the training population, the genomic and pedigree-based prediction accuracies were on average 0.27 and 0.35 higher than the accuracies in populations with only one progeny per cross, indicating the importance of genetic relatedness between the training and validation populations for good predictions. We also evaluated the item-based collaborative filtering approach for multivariate prediction of GY using the green normalized difference vegetation index from HTP. This approach proved to be the best strategy for across-nursery predictions, with average accuracies of 0.56 and 0.62 in the DS and HS environments, respectively. We conclude that GY is a challenging trait for across-year predictions, but GS and HTP can be integrated in increasing the size of populations screened and evaluating unphenotyped large nurseries for stress-resilience within years.
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Genebank genomics bridges the gap between the conservation of crop diversity and plant breeding.
Mascher, M, Schreiber, M, Scholz, U, Graner, A, Reif, JC, Stein, N
Nature genetics. 2019;(7):1076-1081
Abstract
Genebanks have the long-term mission of preserving plant genetic resources as an agricultural legacy for future crop improvement. Operating procedures for seed storage and plant propagation have been in place for decades, but there is a lack of effective means for the discovery and transfer of beneficial alleles from landraces and wild relatives into modern varieties. Here, we review the prospects of using molecular passport data derived from genomic sequence information as a universal monitoring tool at the single-plant level within and between genebanks. Together with recent advances in breeding methodologies, the transformation of genebanks into bio-digital resource centers will facilitate the selection of useful genetic variation and its use in breeding programs, thus providing easy access to past crop diversity. We propose linking catalogs of natural genetic variation and enquiries into biological mechanisms of plant performance as a long-term joint research goal of genebanks, plant geneticists and breeders.
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3.
Accelerating Climate Resilient Plant Breeding by Applying Next-Generation Artificial Intelligence.
Harfouche, AL, Jacobson, DA, Kainer, D, Romero, JC, Harfouche, AH, Scarascia Mugnozza, G, Moshelion, M, Tuskan, GA, Keurentjes, JJB, Altman, A
Trends in biotechnology. 2019;(11):1217-1235
Abstract
Breeding crops for high yield and superior adaptability to new and variable climates is imperative to ensure continued food security, biomass production, and ecosystem services. Advances in genomics and phenomics are delivering insights into the complex biological mechanisms that underlie plant functions in response to environmental perturbations. However, linking genotype to phenotype remains a huge challenge and is hampering the optimal application of high-throughput genomics and phenomics to advanced breeding. Critical to success is the need to assimilate large amounts of data into biologically meaningful interpretations. Here, we present the current state of genomics and field phenomics, explore emerging approaches and challenges for multiomics big data integration by means of next-generation (Next-Gen) artificial intelligence (AI), and propose a workable path to improvement.
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State-of-the-art and novel developments of in vivo haploid technologies.
Kalinowska, K, Chamas, S, Unkel, K, Demidov, D, Lermontova, I, Dresselhaus, T, Kumlehn, J, Dunemann, F, Houben, A
TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik. 2019;(3):593-605
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Abstract
The ability to generate (doubled) haploid plants significantly accelerates the crop breeding process. Haploids have been induced mainly through the generation of plants from cultivated gametophic (haploid) cells and tissues, i.e., in vitro haploid technologies, or through the selective loss of a parental chromosome set upon inter- or intraspecific hybridization. Here, we focus our review on the mechanisms responsible for the in vivo formation of haploids in the context of inter- and intraspecific hybridization. The application of a modified CENH3 for uniparental genome elimination, the IG1 system used for paternal as well as the BBM-like and the patatin-like phospholipase essential for maternal haploidy induction are discussed in detail.
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Stay-Green Trait: A Prospective Approach for Yield Potential, and Drought and Heat Stress Adaptation in Globally Important Cereals.
Kamal, NM, Alnor Gorafi, YS, Abdelrahman, M, Abdellatef, E, Tsujimoto, H
International journal of molecular sciences. 2019;(23)
Abstract
The yield losses in cereal crops because of abiotic stress and the expected huge losses from climate change indicate our urgent need for useful traits to achieve food security. The stay-green (SG) is a secondary trait that enables crop plants to maintain their green leaves and photosynthesis capacity for a longer time after anthesis, especially under drought and heat stress conditions. Thus, SG plants have longer grain-filling period and subsequently higher yield than non-SG. SG trait was recognized as a superior characteristic for commercially bred cereal selection to overcome the current yield stagnation in alliance with yield adaptability and stability. Breeding for functional SG has contributed in improving crop yields, particularly when it is combined with other useful traits. Thus, elucidating the molecular and physiological mechanisms associated with SG trait is maybe the key to defeating the stagnation in productivity associated with adaptation to environmental stress. This review discusses the recent advances in SG as a crucial trait for genetic improvement of the five major cereal crops, sorghum, wheat, rice, maize, and barley with particular emphasis on the physiological consequences of SG trait. Finally, we provided perspectives on future directions for SG research that addresses present and future global challenges.
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Doubled haploid technology for line development in maize: technical advances and prospects.
Chaikam, V, Molenaar, W, Melchinger, AE, Boddupalli, PM
TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik. 2019;(12):3227-3243
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Abstract
Increased efficiencies achieved in different steps of DH line production offer greater benefits to maize breeding programs. Doubled haploid (DH) technology has become an integral part of many commercial maize breeding programs as DH lines offer several economic, logistic and genetic benefits over conventional inbred lines. Further, new advances in DH technology continue to improve the efficiency of DH line development and fuel its increased adoption in breeding programs worldwide. The established method for maize DH production covered in this review involves in vivo induction of maternal haploids by a male haploid inducer genotype, identification of haploids from diploids at the seed or seedling stage, chromosome doubling of haploid (D0) seedlings and finally, selfing of fertile D0 plants. Development of haploid inducers with high haploid induction rates and adaptation to different target environments have facilitated increased adoption of DH technology in the tropics. New marker systems for haploid identification, such as the red root marker and high oil marker, are being increasingly integrated into new haploid inducers and have the potential to make DH technology accessible in germplasm such as some Flint, landrace, or tropical material, where the standard R1-nj marker is inhibited. Automation holds great promise to further reduce the cost and time in haploid identification. Increasing success rates in chromosome doubling protocols and/or reducing environmental and human toxicity of chromosome doubling protocols, including research on genetic improvement in spontaneous chromosome doubling, have the potential to greatly reduce the production costs per DH line.
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Speed breeding orphan crops.
Chiurugwi, T, Kemp, S, Powell, W, Hickey, LT
TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik. 2019;(3):607-616
Abstract
This review explores how speed breeding protocols that hasten plant growth and development could be applied to shorten breeding cycles and accelerate research activities in orphan crops. There is a growing need for the agri-food sector to sustainably produce larger quantities of higher-quality food, feed and fuel using fewer resources, within the context of changing agroclimatic conditions. Meeting this challenge will require the accelerated development and dissemination of improved plant varieties and substantial improvement of agricultural practices. Speed breeding protocols that shorten plant generation times can hasten breeding and research to help fulfil the ever-increasing demands. Global agri-food systems rely on a relatively small number of plant species; however, there are calls to widen the scope of globally important crops to include orphan crops, which are currently grown and used by the world's poorest people or marketed as niche products for affluent consumers. Orphan crops can supply global diets with key nutrients, support economic development in the world's poorest regions, and bolster the resilience of the global agri-food sector to biotic and abiotic stresses. Little research effort has been invested in orphan crops, with farmers growing landraces that are sourced and traded through poorly structured market systems. Efforts are underway to develop breeding resources and techniques to improve orphan crops. Here, we highlight the current efforts and opportunities to speed breed orphan crops and discuss alternative approaches to deploy speed breeding in the less-resourced regions of the world. Speed breeding is a tool that, when used together with other multidisciplinary R&D approaches, can contribute to the rapid creation of new crop varieties, agricultural practices and products, supporting the production and utilisation of orphan crops at a commercial scale.
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QTLian breeding for climate resilience in cereals: progress and prospects.
Choudhary, M, Wani, SH, Kumar, P, Bagaria, PK, Rakshit, S, Roorkiwal, M, Varshney, RK
Functional & integrative genomics. 2019;(5):685-701
Abstract
The ever-rising population of the twenty-first century together with the prevailing challenges, such as deteriorating quality of arable land and water, has placed a big challenge for plant breeders to satisfy human needs for food under erratic weather patterns. Rice, wheat, and maize are the major staple crops consumed globally. Drought, waterlogging, heat, salinity, and mineral toxicity are the key abiotic stresses drastically affecting crop yield. Conventional plant breeding approaches towards abiotic stress tolerance have gained success to limited extent, due to the complex (multigenic) nature of these stresses. Progress in breeding climate-resilient crop plants has gained momentum in the last decade, due to improved understanding of the physiochemical and molecular basis of various stresses. A good number of genes have been characterized for adaptation to various stresses. In the era of novel molecular markers, mapping of QTLs has emerged as viable solution for breeding crops tolerant to abiotic stresses. Therefore, molecular breeding-based development and deployment of high-yielding climate-resilient crop cultivars together with climate-smart agricultural practices can pave the path to enhanced crop yields for smallholder farmers in areas vulnerable to the climate change. Advances in fine mapping and expression studies integrated with cheaper prices offer new avenues for the plant breeders engaged in climate-resilient plant breeding, and thereby, hope persists to ensure food security in the era of climate change.
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Manipulation of oxalate metabolism in plants for improving food quality and productivity.
Kumar, V, Irfan, M, Datta, A
Phytochemistry. 2019;:103-109
Abstract
Oxalic acid is a naturally occurring metabolite in plants and a common constituent of all plant-derived human diets. Oxalic acid has diverse unrelated roles in plant metabolism, including pH regulation in association with nitrogen metabolism, metal ion homeostasis and calcium storage. In plants, oxalic acid is also a pathogenesis factor and is secreted by various fungi during host infection. Unlike those of plants, fungi and bacteria, the human genome does not contain any oxalate-degrading genes, and therefore, the consumption of large amounts of plant-derived oxalate is considered detrimental to human health. In this review, we discuss recent biotechnological approaches that have been used to reduce the oxalate content of plant tissues.
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Phyto-miRNA: A molecule with beneficial abilities for plant biotechnology.
Sabzehzari, M, Naghavi, MR
Gene. 2019;:28-34
Abstract
The discovery of the phenomenon of gene silencing in 1990s opened new doors to biotechnology and plant breeding in order to supply food security. Food Security, as defined by FAO, it exists when all people, at all times, have economic access to safe, sufficient and nutritious food to meet their dietary needs and food preferences for a healthy and active life. Due to the need to ensure food security and also gene silencing potentials, research in this field began with astonishing speed and even it still continues. In this field, miRNA-associated gene silencing especially attracted the attention of scientists in order to decrypt the genes involved in process such as plant growth and development, metabolism, signal transduction, response against environmental stresses, nodule development in legumes and inducement male sterility. In addition, miRNA found a lot of applications in plant biotechnology like miRNA-based molecular markers and miRNA-based molecular breeding for plants improvement. Given to the growing importance of plant miRNAs (Phyto-miRNAs) in biotechnology and expansion of their applications in molecular breeding, it is necessary to review miRNA in an up-to-date schema. In this study, it was presented both the necessary foundations of miRNAs and their important uses in plant sciences, such as molecular markers and metabolic engineering. As a result, we hope to expand the use of artificial miRNAs in plants engineering.