Improving grain yield, stress resilience and quality of bread wheat using large-scale genomics

Nature Genetics, Journal Year: 2019, Volume and Issue: 51(10), P. 1530 - 1539

Published: Sept. 23, 2019

Language: Английский

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Reap the crop wild relatives for breeding future crops

Trends in biotechnology, Journal Year: 2021, Volume and Issue: 40(4), P. 412 - 431

Published: Oct. 9, 2021

Crop wild relatives (CWRs) have provided breeders with several 'game-changing' traits or genes that boosted crop resilience and global agricultural production. Advances in breeding genomics accelerated the identification of valuable CWRs for use improvement. The enhanced genetic diversity pools carrying optimum combinations favorable alleles targeted crop-growing regions is crucial to sustain gain. In parallel, growing sequence information on genomes combination precise gene-editing tools provide a fast-track route transform into ideal future crops. Data-informed germplasm collection management strategies together adequate policy support will be equally important improve access their sustainable meet food nutrition security targets.

Language: Английский

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Enhancing Genetic Gain through Genomic Selection: From Livestock to Plants

Plant Communications, Journal Year: 2019, Volume and Issue: 1(1), P. 100005 - 100005

Published: Oct. 17, 2019

Although long-term genetic gain has been achieved through increasing use of modern breeding methods and technologies, the rate needs to be accelerated meet humanity's demand for agricultural products. In this regard, genomic selection (GS) considered most promising improvement complex traits controlled by many genes each with minor effects. Livestock scientists pioneered GS application largely due livestock's significantly higher individual values greater reduction in generation interval that can GS. Large-scale plants refining field management improve heritability estimation prediction accuracy developing optimum models consideration genotype-by-environment interaction non-additive effects, along significant cost reduction. Moreover, it would more effective integrate other tools platforms accelerating process thereby further enhancing gain. addition, establishing an open-source network transdisciplinary approaches essential efficiency small- medium-sized enterprises research systems countries. New strategies centered on need developed.

Language: Английский

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Accelerating Climate Resilient Plant Breeding by Applying Next-Generation Artificial Intelligence

Trends in biotechnology, Journal Year: 2019, Volume and Issue: 37(11), P. 1217 - 1235

Published: June 21, 2019

Language: Английский

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Developing Climate-Resilient Chickpea Involving Physiological and Molecular Approaches With a Focus on Temperature and Drought Stresses

Frontiers in Plant Science, Journal Year: 2020, Volume and Issue: 10

Published: Feb. 25, 2020

Chickpea is one of the most economically important food legumes, and a significant source proteins. It cultivated in more than 50 countries across Asia, Africa, Europe, Australia, North America, South America. production limited by various abiotic stresses (cold, heat, drought, salt, etc.). Being winter-season crop northern south Asia some parts chickpea faces low-temperature stress (0–15οC) during reproductive stage that causes substantial loss flowers, thus pods, to inhibit its yield potential 30–40%. The winter-sown Mediterranean, however, cold at vegetative stage. In late-sown environments, high-temperature pod filling stages, causing considerable losses. Both low high temperatures reduce pollen viability, germination on stigma, tube growth resulting poor set. also experiences drought stages; terminal along with heat flowering seed can yields 40–45%. southern Australia regions lack chilling tolerance cultivars delays set, usually exposed drought. incidences temperature extremes (cold heat) as well inconsistent rain fall patterns are expected increase near future owing climate change thereby necessitating development stress-tolerant climate-resilient having region specific traits, which perform under and/or stress. Different approaches, such genetic variability, genomic selection, molecular markers involving QTLs, whole genome sequencing transcriptomics analysis have been exploited improve extreme environments. Biotechnological tools broadened our understanding basis plants' responses chickpea, opened opportunities develop tolerant chickpea.

Language: Английский

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Heterosis and Hybrid Crop Breeding: A Multidisciplinary Review

Frontiers in Genetics, Journal Year: 2021, Volume and Issue: 12

Published: Feb. 24, 2021

Although hybrid crop varieties are among the most popular agricultural innovations, rationale for breeding is sometimes misunderstood. Hybrid slower and more resource-intensive than inbred breeding, but it allows systematic improvement of a population by recurrent selection exploitation heterosis simultaneously. Inbred parental lines can identically reproduce both themselves their F

Language: Английский

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Smart breeding driven by big data, artificial intelligence, and integrated genomic-enviromic prediction

Molecular Plant, Journal Year: 2022, Volume and Issue: 15(11), P. 1664 - 1695

Published: Sept. 7, 2022

The first paradigm of plant breeding involves direct selection-based phenotypic observation, followed by predictive using statistical models for quantitative traits constructed based on genetic experimental design and, more recently, incorporation molecular marker genotypes. However, performance or phenotype (P) is determined the combined effects genotype (G), envirotype (E), and environment interaction (GEI). Phenotypes can be predicted precisely training a model data collected from multiple sources, including spatiotemporal omics (genomics, phenomics, enviromics across time space). Integration 3D information profiles (G-P-E), each with multidimensionality, provides both tremendous opportunities great challenges. Here, we review innovative technologies breeding. We then evaluate multidimensional that integrated strategy, particularly envirotypic data, which have largely been neglected in collection are nearly untouched construction. propose smart scheme, genomic-enviromic prediction (iGEP), as an extension genomic prediction, multiomics information, big technology, artificial intelligence (mainly focused machine deep learning). discuss how to implement iGEP, models, environmental indices, factorial structure cross-species prediction. A strategy proposed prediction-based crop redesign at macro (individual, population, species) micro (gene, metabolism, network) scales. Finally, provide perspectives translating into gain through integrative platforms open-source initiatives. call coordinated efforts institutional partnerships, technological support.

Language: Английский

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Complex plant responses to drought and heat stress under climate change

The Plant Journal, Journal Year: 2024, Volume and Issue: 117(6), P. 1873 - 1892

Published: Jan. 3, 2024

SUMMARY Global climate change is predicted to result in increased yield losses of agricultural crops caused by environmental conditions. In particular, heat and drought stress are major factors that negatively affect plant development reproduction, previous studies have revealed how these stresses induce responses at physiological molecular levels. Here, we provide a comprehensive overview current knowledge concerning drought, heat, combinations conditions the status plants, including crops, affecting such as stomatal conductance, photosynthetic activity, cellular oxidative conditions, metabolomic profiles, signaling mechanisms. We further discuss stress‐responsive regulatory transcription factors, which play critical roles adaptation both potentially function ‘hubs’ and/or responses. Additionally, present recent findings based on forward genetic approaches reveal natural variations traits under Finally, an application decades study results actual fields strategy increase tolerance. This review summarizes our understanding

Language: Английский

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Addressing Research Bottlenecks to Crop Productivity

Trends in Plant Science, Journal Year: 2021, Volume and Issue: 26(6), P. 607 - 630

Published: April 21, 2021

More symmetrical investment in crop research will create opportunities to improve models, combine new alleles through prebreeding, and suggest novel management practices.Consensus among public private sectors is that more needed understanding of hormone crosstalk, recombination rate, maintenance respiration, root structure function, source–sink balance.Greater these areas expected benefit a wide range crops across most environments.New phenomics, genomics, bioinformatics make it feasible explore the vast untapped collections genetic resources trait combinations.Filling knowledge gaps enable much integrated yield adaptation, improving breeding models. Asymmetry leads lost accelerate gain identifying sources combinations traits alleles. On basis consultation with scientists from major seed companies, we identified several three common features: (i) relatively underrepresented literature; (ii) high probability boosting productivity environments; (iii) could be researched 'precompetitive' space, leveraging previous knowledge, thereby models guide decisions. Areas included into hormones, recombination, roots, source–sink, which, along bioinformatics, strategies. Research growth adaptation under diverse cultivation scenarios has underpinned global food security, especially since Green Revolution, during which time population than doubled. During same time, area cultivated cereals, account for 70% total calories consumed by humans, barely changed while yields have tripled.i These two statistics alone clearly support impact on agronomy as well effective policy decisions agility farmers adopt technologies [1.Stewart B.A. Lal R. Increasing world average cereal crops: it's all about water.in: Sparks D.L. Advances Agronomy. Vol. 151. Elsevier, 2018: 1-44Google Scholar,2.Fischer T. et al.Crop Yields Global Food Security: Will Yield Increase Continue Feed World?. Australian Centre International Agricultural Research, 2014Google Scholar]. Nonetheless, challenges agriculture now faces are not just feed 10+ billion people within generation, but do so harsher less predictable climate, many cases water declining soil quality Clearly, research, breeding, must even effective. Crop integrates crossing strategies combined efficient selection progeny [3.Van Ginkel M. Ortiz Cross best best, select best: HELP selfing crops.Crop Sci. 2018; 58: 17-30Crossref Scopus (11) Google To date, impactful objectives been maintain resistance ever-evolving spectrum pests diseases (e.g., [4.Singh R.P. al.Emergence spread races wheat stem rust fungus: continued threat security prospects control.Phytopathology. 2015; 105: 872-884Crossref PubMed (173) Scholar,5.Donatelli al.Modelling impacts agricultural systems.Agric. Syst. 2017; 155: 213-224Crossref (91) Scholar]), an array consumer-driven characteristics, such storability, baking quality, forth [6.Guzmán C. al.Genetic improvement grain CIMMYT semi-dwarf spring bread varieties developed 1965–2015: 50 years breeding.Field Crops Res. 210: 192-196Crossref (24) Scholar]). However, or environments require specific filled context. The technology exists apply allelic phenotype genotype at scale. Due large numbers involved screening (from thousands single cross millions double haploids), evaluation represent target (TPE) (see Glossary) expedient, genomic [7.Juliana P. al.Integrating genomic-enabled prediction high-throughput phenotyping climate-resilient wheat.Theor. Appl. Genet. 2019; 132: 177-194Crossref (23) Scholar], phenomic [8.Araus J.L. al.Translating gain.Trends Plant 23: 451-466Abstract Full Text PDF (170) modeling tools [9.Cooper al.Predicting future plant breeding: complementing empirical prediction.Crop Pasture 2014; 65: 311-336Crossref (148) advanced stage commercial In short, practical discipline focused products. upstream tends favor cutting-edge challenges, some methodological nature. focusing near- medium-term gains typically strategic enough warrant funding, too risk funds allocated breeding. As result, translation pure science [10.Reynolds al.Translational climate resilient, higher yielding Breed. Genom. 1e190016Google Some notable exceptions include photosynthesis [11.Long S.P. al.Meeting demand engineering potential.Cell. 161: 56-66Abstract (381) application tomography capture roots images [12.Morris E.C. al.Shaping 3D system architecture.Curr. Biol. 27: PR919-R930Abstract (54) gene editing [13.Gao H. al.Superior field performance waxy corn engineered using CRISPR-Cas9.Nat. Biotechnol. 2020; 38: 579-581Crossref (0) novelty significant driving force academia, including technologies. does grow symmetrically, creating instead islands necessarily connected [14.Borrell A. Reynolds Integrating greater synergy efficiency research.Food Energy Secur. 6: 26-32Crossref (3) While this approach works pushing back frontiers requires systematic achieve harvestable products seeds, fruits, tubers). For example, order crop's photosynthetic potential boost yield, extra photo-assimilates also distributed way optimizes development edible organs. case cereals other crops, expressed harvest index (HI). expression HI in, modern cultivars, approximately 0.4 0.55, attendant negative correlation between biomass [15.Aisawi K.A.B. al.The physiological progress cultivars 1966 2009.Crop 55: 1749-1764Crossref (86) attest apparent underutilization current capacity. partitioning reproductive match if value effectively translate security. There conundrums point asymmetrical knowledge. definition considers only above-ground biomass. This quite arbitrary, there being no scientific reason exclude below-ground one, analysis can easily performed structures compared those soil. Since important improvement, source error trivial. study wheat, differed 7% 20%, depending genotype, when considering versus biomass, [16.Reynolds M.P. al.Drought-adaptive derived wild relatives landraces.J. Exp. Bot. 2007; 177-186Crossref Another example asymmetry crop-focused academic emphasis over despite variation respiration associated [17.Wilson D. Response dark rate mature leaves Lolium perenne its effects young plants simulated swards.Ann. 1982; 49: 303-312Crossref (66) Furthermore, number studies show express significantly stronger relationship night temperature day [18.Lobell D.B. Ortiz-Monasterio J.I. Impacts temperatures yields: comparison CERES model predictions locations.Agron. J. 99: 469-477Crossref (123) Scholar,19.Shi W. al.High day- night-time affect dynamics contrasting rice genotypes.J. 68: 5233-5245Crossref (38) Because affects processes, flowering response, response key gap. needs renewed focus how manipulation photorespiration influence yields, degree effort great respiration. Indeed, recent work highlighted transgenic use alternative photorespiratory pathways exhibit improvements net CO2 uptake, accumulation, [20.South P.F. al.Synthetic glycolate metabolism stimulate field.Science. 636eaat9077Crossref (165) Scholar,21.Shen B.-R. al.Engineering chloroplastic bypass increase rice.Mol. Plant. 12: 199-214Abstract (40) importance environment influencing arising modifications addressed [22.Hammer G.L. al.Biological reality parsimony – why need both improvement! silico.Plants. 1diz010Google Asymmetrical crop-related additional conundrums. A literature search keywords 'photosynthesis' 'drought' identifies studies. deficit certainly inhibits gas exchange severe stress damage machinery, primary determinants access [23.White J.W. Castillo J.A. Relative effect shoot genotypes bean drought stress.Crop 1989; 29: 360-362Crossref (50) Scholar] budgeting [24.Messina C.D. al.Limited-transpiration may maize tolerance US Corn Belt.Agronomy. 107: 1978-1986Crossref (79) Subtle cultivar-level differences sensitivity apparatus marginal best; mundane analogy would tuning carburetor motor overcome block fuel line. exist, objective review illustrate crop-oriented better leveraged filling gaps. exist varying degrees, our premise addressing species environments. Therefore, processes they improved tandem. factor influences agenda difficulty working realistic environments, partially controlled. Lack control hampers rigorous production scenarios, where fields growing seasons ever completely same. Galileo's guideline 'measure what measurable, measurable so' applied advances remote sensing geographical information services. addition, generation molecular permit real-time estimates DNA metabolic monitored tissue taken directly experiments. (CGMs) provide mathematical framework integrate conduct quantitative evaluations TPE Scholar,24.Messina Scholar,25.Messina science: foundation advancing predictive agriculture.Crop 60: 544-546Crossref (6) providing dynamic help researching basic biology. unprecedented fill join investments. No matter component problem, whether cropping whole, broad maximize impact. An illuminating was showing zinc deficiency exacerbates due essential role detoxifying reactive oxygen species, leading foliar applications Zn 4 million ha Turkey [26.Bagci S.A. al.Effects field-grown Central Anatolia.J. Agron. 193: 198-206Crossref Before breakthrough, per se seriously confounded achieved (Figure 1) [27.Cakmak I. al.Zinc critical problem Anatolia.Plant Soil. 1996; 180: 165-172Crossref Perhaps overcoming bottleneck opens up possibilities introduction semidwarf genes cereals. their widespread adoption, tallness limited structural failure. allele (Rht1) Norin 10, originally variety Daruma, Gonjiro Inazuka Japan 1935. took 10 introgression, pleiotropic Rht nitrogen [28.Reynolds Borlaug N.E. international collaborative improvement.J. Agric. 2006; 144: 3-17Crossref (109) spearheaded Revolution tripling saving estimated 1 lives famine aforementioned examples systematic, demand-driven shy away logistical challenges. Five challenging that, tackled systematically, likely open bottlenecks discussed herein, discussion used CGMs. exhaustive cannot presented here, nor bottlenecks, emerge improves. were broadly agreed authors colleagues sectors. complementary each existing 2). opinion colleagues, 'best bets' achieving step changes roles increasing sink strength carbon assimilation meiotic harness diversity. reviewed: exploration prebreeding Illuminating 'black boxes' simulation modelling. authorship represents stakeholders sectors, topics priorities 'precompetitive space' defined companies exercise; words, general neglected, potentially hold industry. aid foraging, responsive abiotic biotic signals local highly adaptable behavior, termed 'developmental plasticity', offers breeders 'customized' architecture (RSA) adapted forage heterogenous conditions [29.Hodge plastic plant: responses heterogeneous supplies nutrients.New Phytol. 2004; 162: 9-24Crossref (1052) (N) form nitrate (NO3–) particular challenge capture, mobile leaches deeper layers. N exploit steeper angle brace crown [30.Trachsel S. al.Maize angles become low conditions.Field 2013; 140: 18-31Crossref (56) elongation lateral seminal [31.Gioia al.Impact domestication phenotypic durum fertilization.J. 66: 5519-5530Crossref reduced length density near surface axial [32.Zhan Lynch J.P. Reduced frequency branching improves low-N soils maize.J. 2055-2065Crossref (81) serve layers abundant. contrast, phosphate (P) available inorganic immobile concentrated topsoil [33.Rubio G. al.Topsoil foraging competitiveness phosphorus bean.Crop 2003; 43: 598-607Crossref P increased lengths patches availability [34.Flavel R.J. al.Quantifying (Triticum aestivum L) Oxisol.Plant 385: 303-310Crossref (7) shallower hairs [35.Bates T.R. Root confer competitive advantage availability.Plant 2001; 236: 243-250Crossref (125) cluster formation [36.Shane M.W. Lambers Cluster roots: curiosity context.Plant 2005; 274: 101-125Crossref (255) sorghum, [37.Singh V. variability sorghum.Crop 2011; 51: 2011-2020Crossref (36) enables × Skip row systems expressing angles, past decade, remain, following:•Given change, urgent determine RSA controlled signals, often mediated aerial temperature. Whilst heat impairs any developmental stage, rooting depth appear reduce [38.Lopes M.S. Partitioning assimilates cooler canopies wheat.Funct. 2010; 37: 147Crossref Scholar].•How carbon/biomass should invest resource sustainability, yet minimize yield? Surprisingly, detailed CGM simulations (validated reference data) predict 'less more,' lower longer [39.Postma optimal depends Physiol. 166: 590-602Crossref (160) addition RSA, anatomical scale cortical aerenchyma 50% [40.Zhu al.Root (Zea mays L.).Plant Cell Environ. 33: 740-749PubMed enabling reinvest C organs.•Despite recognition microbiome vice versa [41.de la Fuente C.C. al.An extended phenotype: rhizosphere, fitness.Plant 103: 951-964Crossref (9) multibillion-dollar industry selling microbiome-based coatings mechanisms integrating signaling. Studying arguably relevant, poses Indirect approaches canopy measurements determining extraction profiles electrical electromagnetic inductance methods infer traits, currently coarse resolution [42.Whalley W.R. al.Methods estimate activity field.Plant 415: 407-422Crossref (22) Invasive coring 'shovelomics' greatly facilitated throughput [43.Trachsel al.Shovelomics: L.) 341: 75-87Crossref (338) destructive techniques result loss finer-scale features roots), give snapshot development. Nondestructive imaging techniques, agar plates, rhizotrons, paper-based hydro-/aeroponic systems, temporal observed throughout possible transparent gels [44.Clark R.T. al.Three-dimensional software platform.Plant 156: 455-465Crossref (274) non–soil-based helps decrease experimental reducing heterogeneity microbial populations, results difficult extrapolate conditions. experiments [45.Messina al.Reproductive resilience underpin L.).bioRxiv. (Published online October 1, 2020. https://doi.org/10.1101/2020.09.30.320937)Google Magnetic resonance X-ray computed successfully noninvasively [46.Mairhofer al.Extracting multiple interacting microcomputed tomography.Plant 84: 1034-1043Crossref (19) Scholar,47.van Dusschoten al.Quantitative magnetic imaging.Plant 2016; 170: 1176-1188Crossref Nevertheless, expensive, throughput, deployable field. Understanding stresses vital develop [48.Lynch phenotypes nutrient capture: underexploited opportunity agriculture.New 223: 548-564Crossref (72) dries, vertical gradient availability. Roots experiencing reach [49.Uga Y. al.Control DEEPER ROOTING increases conditions.Nat. 45: 1097-1102Crossref (619) Water upper suppresses different [50.Sebastian al.Grasses suppress shoot-borne conserve drought.Proc. Natl. Acad. U. 113: 8861-8866Crossref (43) Scholar,51.Gao Y.Z. acquisition L.).J. 67: 4545-4557Crossref (84) few long ideotype suggested stress, saved extend profiles. indeed tuned based fundamental [52.Cooper gap productivity.Crop 582-604Crossref (10) colonizing

Language: Английский

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Next-Generation Breeding Strategies for Climate-Ready Crops

Frontiers in Plant Science, Journal Year: 2021, Volume and Issue: 12

Published: July 21, 2021

Climate change is a threat to global food security due the reduction of crop productivity around globe. Food matter concern for stakeholders and policymakers as population predicted bypass 10 billion in coming years. Crop improvement via modern breeding techniques along with efficient agronomic practices innovations microbiome applications, exploiting natural variations underutilized crops an excellent way forward fulfill future requirements. In this review, we describe next-generation tools that can be used increase production by developing climate-resilient superior genotypes cope challenges security. Recent genomic-assisted (GAB) strategies allow construction highly annotated pan-genomes give snapshot full landscape genetic diversity (GD) recapture lost gene repertoire species. Pan-genomes provide new platforms exploit these unique genes or variation optimizing programs. The advent clustered regularly interspaced short palindromic repeat/CRISPR-associated (CRISPR/Cas) systems, such prime editing, base de nova domestication, has institutionalized idea genome editing revamped improvement. Also, availability versatile Cas orthologs, including Cas9, Cas12, Cas13, Cas14, improved efficiency. Now, CRISPR/Cas systems have numerous applications research successfully edit major develop resistance against abiotic biotic stress. By adopting high-throughput phenotyping approaches big data analytics like artificial intelligence (AI) machine learning (ML), agriculture heading toward automation digitalization. integration speed genomic phenomic rapid identifications ultimately accelerate addition, multidisciplinary open exciting avenues climate-ready

Language: Английский

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