The Wheat 660K SNP array demonstrates great potential for marker‐assisted selection in polyploid wheat

Plant Biotechnology Journal, Journal Year: 2020, Volume and Issue: 18(6), P. 1354 - 1360

Published: Feb. 17, 2020

Abstract The rapid development and application of molecular marker assays have facilitated genomic selection genome‐wide linkage association studies in wheat breeding. Although PCR‐based markers (e.g. simple sequence repeats functional markers) genotyping by sequencing contributed greatly to gene discovery marker‐assisted selection, the release a more accurate complete bread reference genome has resulted design single‐nucleotide polymorphism (SNP) arrays based on different densities or targets. Here, we evaluated seven types SNP terms their number, distribution, density, associated genes, heterozygosity application. results suggested that Wheat 660K array contained highest percentage (99.05%) genome‐specific SNPs with reliable physical positions. density analysis indicated were almost evenly distributed across whole genome. In addition, 229 266 located 66 834 annotated promoter intervals. genes revealed covered all 35K (97.44%), 55K (99.73%), 90K (86.9%) 820K (85.3%) arrays. Therefore, could act as substitute for other 6 shows promise wide range possible applications. summary, is cost‐effective may be best choice targeted genetic improvement.

Language: Английский

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Fast-Forwarding Genetic Gain

Trends in Plant Science, Journal Year: 2018, Volume and Issue: 23(3), P. 184 - 186

Published: Feb. 7, 2018

'Speed breeding' enables scientists to exploit gene bank accessions and mutant collections for an unparalleled rapid discovery deployment. Combining speed breeding other leading-edge plant technologies with strategic global partnerships, has the potential achieve genetic gain targets required deliver our future crops.

Language: Английский

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Genomic Selection in Aquaculture: Application, Limitations and Opportunities With Special Reference to Marine Shrimp and Pearl Oysters

Frontiers in Genetics, Journal Year: 2019, Volume and Issue: 9

Published: Jan. 23, 2019

Within aquaculture industries, selection based on genomic information (genomic selection) has the profound potential to change genetic improvement programs and production systems. Genomic exploits use of realized relationships among individuals, from genome-wide markers in close linkage disequilibrium with genes biological economic importance. We discuss technical advances, practical requirements commercial applications that have made feasible a range particular focus molluscs (pearl oysters, Pinctada maxima) marine shrimp (Litopeneaus vannamei Penaeus monodon). The low-cost genome sequencing enabled cost-effective genotyping large-scale is value for species without reference or access arrays. highlight pitfalls offer solutions by approach, building appropriate resources undertake first-hand experience. describe capture phenotypes image analysis artificial intelligence through machine learning, as inputs calculation breeding values. application over traditional aquatic offers significant advantages being able accurately predict complex polygenic traits including disease resistance; increasing rates gain; minimizing inbreeding; negating limiting effects genotype environment interactions. Further selection, communal mating rearing systems are highlighted, well presenting rate-limiting steps which impact attaining maximum benefits adopting selection. now at tipping point where can be readily adopted short long-term sustainable profitable industries.

Language: Английский

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5Gs for crop genetic improvement

Current Opinion in Plant Biology, Journal Year: 2020, Volume and Issue: 56, P. 190 - 196

Published: Jan. 28, 2020

Here we propose a 5G breeding approach for bringing much-needed disruptive changes to crop improvement. These 5Gs are Genome assembly, Germplasm characterization, Gene function identification, Genomic (GB), and editing (GE). In our view, it is important have genome assemblies available each deep collection of germplasm characterized at sequencing agronomic levels identification marker-trait associations superior haplotypes. Systems biology sequencing-based mapping approaches can be used identify genes involved in pathways leading the expression trait, thereby providing diagnostic markers target traits. genes, markers, haplotypes, genome-wide data may utilized GB GE methodologies combination with rapid cycle strategy.

Language: Английский

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Toward the sequence-based breeding in legumes in the post-genome sequencing era

Theoretical and Applied Genetics, Journal Year: 2018, Volume and Issue: 132(3), P. 797 - 816

Published: Dec. 17, 2018

Efficiency of breeding programs legume crops such as chickpea, pigeonpea and groundnut has been considerably improved over the past decade through deployment modern genomic tools technologies. For instance, next-generation sequencing technologies have facilitated availability genome sequence assemblies, re-sequencing several hundred lines, development HapMaps, high-density genetic maps, a range marker genotyping platforms identification markers associated with number agronomic traits in these crops. Although marker-assisted backcrossing selection approaches used to develop superior lines cases, it is need hour for continuous population improvement after every cycle accelerate gain programs. In this context, we propose sequence-based approach which includes use independent or combination parental selection, enhancing diversity programs, forward early generation using sequencing/genotyping Also, adoption speed technology by generating 4-6 generations per year will be contributing gain. While see huge potential revolutionize crop legumes, anticipate challenges especially high-quality precise phenotyping at affordable costs, data analysis management related improving operation efficiency. Finally, integration seed systems better packages varieties ensure higher gains farmers' fields.

Language: Английский

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Back to the future: revisiting MAS as a tool for modern plant breeding

Theoretical and Applied Genetics, Journal Year: 2018, Volume and Issue: 132(3), P. 647 - 667

Published: Dec. 17, 2018

New models for integration of major gene MAS with modern breeding approaches stand to greatly enhance the reliability and efficiency breeding, facilitating leveraging traditional genetic diversity. Genetic diversity is well recognised as contributing essential variation crop processes, marker-assisted selection cited primary tool bring this into programs without associated drag from otherwise poor-quality genomes donor varieties. However, implementation techniques remains a challenge in many worldwide. Many factors contribute lack adoption, such uncertainty how integrate confidence tool, expense process. developments genomics tools, locus validation techniques, new utilise QTLs address these issues. Marker-assisted forward needs be enabled through identification robust QTLs, design reliable marker systems select delivery elite genomic backgrounds enable their use drag. To adoption effectiveness MAS, rice used an example processes coherent, efficient strategy utilising variation. When are instituted issues, genes can rolled out program rapidly completely minimum expense.

Language: Английский

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Genetic architecture underpinning yield component traits in wheat

Theoretical and Applied Genetics, Journal Year: 2020, Volume and Issue: 133(6), P. 1811 - 1823

Published: Feb. 15, 2020

Language: Английский

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History and Current Status of Sugarcane Breeding, Germplasm Development and Molecular Genetics in Brazil

Sugar Tech, Journal Year: 2021, Volume and Issue: 24(1), P. 112 - 133

Published: Feb. 16, 2021

Abstract Brazil is the world’s largest producer of sugarcane and one leading suppliers sugar ethanol worldwide. In 2019–2020 crop season, country produced 642.7 million tons in a harvest area 8.44 hectares. Historically, breeding has contributed continuously to increasing yields by regularly releasing superior cultivars for use Brazilian industry. last 40 years, an average annual increase 155.7 kg ha −1 yield been reported, about half which may be attributed programs. However, due size country, intensive expansion low-fertility soils few especially degraded pasture areas, widespread adoption mechanization, new challenges have imposed on national This review covers current situation with main advances that allowed maintain world leadership developing Additionally, history breeding, institutions, germplasm development, key objectives, selection stages methodologies are summarized. An overview also presented biotechnological approaches become tools improving traditional The strategies yield, aiming consolidate production food energy matrix, discussed.

Language: Английский

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Photosynthetic Metabolism under Stressful Growth Conditions as a Bases for Crop Breeding and Yield Improvement

Plants, Journal Year: 2020, Volume and Issue: 9(1), P. 88 - 88

Published: Jan. 10, 2020

Increased periods of water shortage and higher temperatures, together with a reduction in nutrient availability, have been proposed as major factors that negatively impact plant development. Photosynthetic CO2 assimilation is the basis crop production for animal human food, this reason, it has selected primary target phenotyping/breeding studies. Within context, knowledge mechanisms involved response acclimation photosynthetic to multiple changing environmental conditions (including nutrients, rising temperature) matter great concern understanding behavior under stress conditions, development new strategies tools enhancing growth future. The current review aims analyze, from multi-perspective approach (ranging across breeding, gas exchange, genomics, etc.) on performance apparatus and, consequently, growth.

Language: Английский

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Fast-forward breeding for a food-secure world

Trends in Genetics, Journal Year: 2021, Volume and Issue: 37(12), P. 1124 - 1136

Published: Sept. 14, 2021

The rapid advances in plant genome sequencing and phenotyping have enhanced trait mapping gene discovery crops.Increasing adoption of machine learning algorithms is crucial to derive meaningful inferences from complex multidimensional data.Emerging breeding approaches like optimal contribution selection, alone or combination with genomic will enhance the genetic base programs while accelerating gain.Integrating speed new-age technologies holds promise relieve long-standing bottleneck lengthy crop cycles.Haplotype-based breeding, prediction, editing hasten targeted assembly superior alleles future cultivars for sustainable agricultural development long-term food security. Crop production systems need expand their outputs sustainably feed a burgeoning human population. Advances combined efficient procedures accelerate availability beneficial research. Enhanced interoperability between different omics platforms, leveraged by evolving tools, help provide mechanistic explanations traits. Targeted using optimized strategies precise techniques could deliver ideal crops future. Realizing desired productivity gains field imperative securing an adequate supply 10 billion people. Safeguarding person's right nutritious requires intensive research efforts innovative solutions breed improved resilience [1.Siddique K.H.M. et al.Re-discovering Asia's forgotten fight chronic hidden hunger.Nat. Plants. 2021; 7: 116-122Crossref PubMed Scopus (10) Google Scholar]. However, major challenge uneven distribution resources, resulting huge gap demand food. harvest are access modern infrastructure technologies, including varieties, agronomic practices, machinery farm preparation, harvest, processing, marketing. Regions high populations low should be studied address these challenges equitable opportunities. Lessons learned pandemic highlight self-sustainability, less dependence on imports, especially agriculture. For instance, vast portion entire global population resides low-income deficit countries (32.23%), least developed (12%), net food-importing developing (20.15%)i,ii. Therefore, enhancing addressing worldwide zero hunger nutrition security through infrastructure, soil improvement remains essential. A high-quality reference (see Glossary) prerequisite genomics studies given attain accurate results performance [2.Varshney R.K. al.5Gs improvement.Curr. Opin. Plant Biol. 2020; 56: 190-196Crossref (46) High-confidence variant calling facilitated genome, such as manipulation. 'Democratization' concert advanced informatics tools has contiguity completeness existing assemblies. Since single cannot capture all variations species, increased number gold- platinum-standard genomes become available several crops. Long-read linked-read PacBio, 10X Chromium, Oxford Nanopore, supplemented short reads next-generation (NGS), allow long contigs base-to-base precision (Figure 1). Hi-C [3.Belton J.M. al.Hi-C: comprehensive technique conformation genomes.Methods. 2012; 58: 268-276Crossref (418) Scholar] Bionano Genomics Optical Mapping [4.Pendleton M. al.Assembly diploid architecture individual via single-molecule technologies.Nat. Methods. 2015; 12: 780-786Crossref (310) assemblies greater dramatically improving haplotype phasing scaffolding, polyploid [5.Zhuang W. al.The cultivated peanut provides insight into legume karyotypes, evolution domestication.Nat. Genet. 2019; 51: 865-876Crossref (174) Due reduction costs, high-density genotyping now affordable assaying large samples [6.Huang B.E. al.MAGIC crops: current status prospects.Theor. Appl. 128: 999-1017Crossref (136) suite platforms (e.g., Affymetrix Axiom, GeneChip, Illumina Infinium BeadChip) varying nucleotide polymorphisms (SNPs) most species [7.Rasheed A. al.Crop chips platforms: progress, challenges, perspectives.Mol. Plant. 2017; 10: 1047-1064Abstract Full Text PDF (206) Several genome-wide integrating deep reduced representation methods, genotyping-by-sequencing, restriction site associated DNA sequencing, double-digest RAD, fragment led innovations marker various Compared array-based NGS whole resequencing can simultaneously detect known uncatalogued SNPs structural (SVs), presence/absence (PAVs) copy (CNVs). Concurrent driven mainly image sensor cost- time-efficient acquisition massive spatial temporal data, predictive phenomics [8.Mir R.R. al.Integrated genomics, physiology drought tolerance crops.Theor. 125: 625-645Crossref (274) Automated equipped plant-to-sensor sensor-to-plant modes monitor dynamic response at organ, plant, scales 3D imaging applications, X-ray computed tomography, situ root system architecture, alleviating underground bottlenecks. growing nondestructively real world fully automated field-based facilities. In contrast, aerial include unmanned vehicles, manned satellites levels payload capacity resolution 1) [9.Jin X. al.High-throughput estimation traits: review ground platforms.IEEE Trans. Geosci. Remote Sens. 9: 200-231Crossref (54) Fewer than 20% mechanized established infrastructures [10.Yang high-throughput phenotyping: past decades, 13: 187-214Abstract (159) African countries, instead specialized facilities, setting up stations surveying local pathogens regional, opposed international foundation, needs considered. Fast-tracking mining resources (PGRs), wild relatives landraces conserved genebanks, ensuring supplies. Current accumulated traits suitable agriculture consumption human-mediated domestication species. dissection, range populations, biparental multiple parental multi-parent generation inter-cross (MAGIC) nested association been many Scholar,11.Scott M.F. al.Multi-parent toolbox breeding.Heredity. 396-416Crossref (38) With new sequencing/genotyping PGRs assayed evaluated environments seasons Superior genes/alleles interest identified pangenomics (Box (GWAS) (Table S1 supplemental information online, Figure Concerning modernizing addressed identify conserve germplasm undertake improvement.Box 1Pangenomics bring genes back pastSequencing popularized 'pangenome' set present within core individuals dispensable absent one individual. literature provided strong evidence SVs, evolutionary processes that shaped adaptive diversity plants. plants, PAVs 7.8% rice [80.Schatz M.C. al.Whole de novo three divergent strains rice, Oryza sativa, document novel space aus indica.Genome 2014; 15: 506PubMed 40% wheat [81.Montenegro J.D. pangenome hexaploid bread wheat.Plant J. 90: 1007-1013Crossref (170) Scholar], plants having ~30–50% variable [82.Gao L. tomato pan-genome uncovers rare allele regulating fruit flavor.Nat. 1044-1051Crossref (190) De accessions enabled called 'super-pangenome' [83.Khan A.W. al.Super-pangenome side accelerated improvement.Trends Sci. 25: 148-158Abstract (70) Scholar].Gene environmental adaptation, domestication, [84.Tan S. al.Variation among Arabidopsis populations.BMC Evol. 86Crossref (31) annotations pangenomes often enriched traits, biotic abiotic stress. Many lost during bottlenecks; identifying characterizing support reintroduction programs. Calling across domesticated lines helps retrace impact pangenome; negative effects decrease frequency those benefits increase effective size ineffective recombination, may drift bottlenecks.Knowledge enables us fine-tune outcomes constructing content variety. This building species-wide even genus-wide super-pangenomes representing allelic variants next Pangenomes teach which haplotypes combine produce combinations, enabling breeders shift useful when planning important selective elite varieties. knowledge quickly phenotypic attributes simply backcrossing Alternatively, GE molecular modify key drivers domestication; alta (CCDD) was achieved six agronomically [85.Yu H. al.A route allotetraploid rice.Cell. 184: 1156-1170Abstract (65) Sequencing Gene Knowledge Transcriptomics, proteomics, metabolomics, epigenomics windows variation beyond actual interpretable they contain [12.Weckwerth al.PANOMICS meets germplasm.Plant Biotechnol. 18: 1507-1525Crossref (25) Scholar,13.Pazhamala L.T. al.Systems biology improvement: prospects challenges.Plant Genome. 14e20098Crossref (12) These closer phenotype, narrow phenome divide, independent sets markers complement 2). Associative transcriptomics examines correlations both sequence transcript abundance [14.Harper A.L. al.Associative Brassica napus.Nat. 30: 798-802Crossref (219) maize, cis expression QTLs (eQTLs) contribute adaptation [15.Lemmon Z.H. role regulatory maize domestication.PLoS 10e1004745Crossref (79) Expression read depth GWAS transcriptome-wide test associations mRNA [16.Lin al.Substantial transcription factors revealed eRD-GWAS.Genome 192Crossref (27) Scholar,17.Kremling K.A.G. al.Transcriptome-wide supplements Zea mays.G3 (Bethesda). 3023-3033Crossref (29) Unlike variants, linkage disequilibrium genome; methods insights mechanisms enable better prioritization causal candidate [17.Kremling Proteomics also used ways refining underlying 2).Box 2Proteomics refine traitsProteomics, based mass spectrometry identification peptides matching them translated sequences, resolving ways:1.Reference proteomes compared predicted evaluate genotype-specific protein differences orthology [86.Ghatak al.Proteomics survey Solanaceae family: ahead.J. Proteome. 169: 41-57Crossref Scholar,87.Hooper C.M. al.CropPAL discovering subcellular location divergence breeding.Plant 104: 812-827Crossref (4) INDELS (missing additional proteins) genotypes.2.Quantitative proteomics same way discoveries specific [88.Hoehenwarter al.MAPA distinguishes variability highly similar isoforms potato tuber.J. Proteome Res. 2011; 2979-2991Crossref not other means because difficult structure due post-transcriptional modification [89.Millar A.H. scope, functions, dynamics posttranslational modifications.Annu. Rev. 70: 119-151Crossref (76) Scholar].3.Major proteomics-based protein–protein interaction maps coexpression link products functional units responses [90.Duncan O. al.Resource: Triticum aestivum proteome.Plant 89: 601-616Crossref (32) reduce solution resolve underlie QTL fail reach statistical significance its own [91.Weckwerth al.Differential metabolic networks unravel silent phenotypes.Proc. Natl Acad. USA. 2004; 101: 7809-7814Crossref (306) Scholar].4.Specific traditionally poorly accessible analysis postharvest seed germination traits) sought proteome tissues critical timing [92.Vanderschuren model species: status, limitations strategic improvement.J. 2013; 93: 5-19Crossref (56) Scholar].5.Traits involving post-translational processes, cascades activation/deactivation kinases/phosphatases degradation studies, usually resolved loci alone, needing direct phosphopeptides [93.Chen Y. Weckwerth Mass untangles membrane signaling networks.Trends 930-944Abstract (14) turnover [94.Nelson C.J. Millar Protein biology.Nat. 1: 15017Crossref (49) Such analyses potential maintaining target stabilizing protein, overexpression protein) altering (phosphomimic alterations), breeding.6.Proteomics offers data-independent hundreds thousands [e.g., sequential window theoretical ion spectra (SWATH) multiple-reaction monitoring (MRM)] directly assess line selection cycles Jacoby al. [95.Jacoby R.P. al.Application selected reaction field-grown dissection stress tolerance.Front. 4: 20Crossref (16) Scholar]). Proteomics, Alterations attributed heritable epigenetic changes do involve methylation, histone modification, noncoding RNAs [18.Hu al.Prediction height thaliana methylation data.Genetics. 201: 779-793Crossref (40) Recent NGS-based protocols, methylated immunoprecipitation bisulfite large-scale levels, common form polymorphisms. there modifications regulation. High-throughput screen cycles, metabolomics reached technical standard application studies. Specific metabolomic gas chromatography liquid chromatography, coupled mas

Language: Английский

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