Multiple wheat genomes reveal global variation in modern breeding

Nature, Journal Year: 2020, Volume and Issue: 588(7837), P. 277 - 283

Published: Nov. 25, 2020

Abstract Advances in genomics have expedited the improvement of several agriculturally important crops but similar efforts wheat ( Triticum spp.) been more challenging. This is largely owing to size and complexity genome 1 , lack genome-assembly data for multiple lines 2,3 . Here we generated ten chromosome pseudomolecule five scaffold assemblies hexaploid explore genomic diversity among from global breeding programs. Comparative analysis revealed extensive structural rearrangements, introgressions wild relatives differences gene content resulting complex histories aimed at improving adaptation diverse environments, grain yield quality, resistance stresses 4,5 We provide examples outlining utility these genomes, including a detailed multi-genome-derived nucleotide-binding leucine-rich repeat protein repertoire involved disease characterization Sm1 6 associated with insect resistance. These will basis functional discovery deliver next generation modern cultivars.

Language: Английский

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Designing Future Crops: Genomics-Assisted Breeding Comes of Age

Trends in Plant Science, Journal Year: 2021, Volume and Issue: 26(6), P. 631 - 649

Published: April 21, 2021

Availability of reference genomes and genome-wide surveys on comprehensive diversity panels pave the way to associate allelic variation with phenotypes.Methods are now available evaluate genetic worth vast resources archived in gene banks streamline application these crop improvement programs.Precise genome editing technologies concert enhanced trait architectures enable innovative solutions engineer complex variation.High-throughput phenotyping methods beginning alleviate challenge accurate, precise, large-scale measurements plant performance.Optimized speed breeding protocols remain crucial accelerating advance when applied genomic approaches.Sustaining gains from seeks fast-tracking exploitation minor effect alleles, accumulation favorable purging deleterious alleles. Over past decade, genomics-assisted (GAB) has been instrumental harnessing potential modern characterizing exploiting for germplasm enhancement cultivar development. Sustaining GAB future (GAB 2.0) will rely upon a suite new approaches that fast-track targeted manipulation creating novel facilitate their rapid efficient incorporation programs. Genomic strategies optimize beneficial alleles be indispensable designing crops. In coming decades, 2.0 is expected play role more climate-smart cultivars higher nutritional value cost-effective timely manner. Ensuring sustainable increase global food production finite an increasing human population great challenge. wake enormous advances, 15 years back we proposed concept [1.Varshney R.K. et al.Genomics-assisted improvement.Trends Plant Sci. 2005; 10: 621-630Abstract Full Text PDF PubMed Scopus (392) Google Scholar]. Interestingly, proposition coincided release high-quality sequence assembly rice (Oryza sativa), representing first any [2.International Rice Genome Sequencing Project The map-based genome.Nature. 436: 793-800Crossref (2692) Subsequently, array tools have become applications (Table 1). Parallel advancements technologies, designs based multi-parent synthetic populations were implemented discovery impart benefits both association mapping linkage analysis, such as diversity, controlled structure, greater power quantitative locus (QTL) detection improved accuracy [3.Kover P.X. al.A multiparent advanced generation inter-cross fine-map traits Arabidopsis thaliana.PLoS Genet. 2009; 5e1000551Crossref (361) Scholar,4.Yu J. al.Genetic design statistical nested maize.Genetics. 2008; 178: 539-551Crossref (627) Scholar].Table 1Genome Resources Ten Topmost Food CropsaAbbreviation: n.d., no data.CropArea (mha)bSource: http://www.fao.org/faostat/en/#data/QC.Production (mmt)bSource: http://www.fao.org/faostat/en/#data/QC.Assembled (Mb)SNP arrayGenomic databasesGene expression atlasPan-genomeWheat(Triticum aestivum)215.9765.714 500[61.International Wheat Consortium (IWGSC) Shifting limits wheat research using fully annotated genome.Science. 2018; 361eaar7191Crossref (891) Scholar]Wheat 9K iSelect [62.Cavanagh C.R. al.Genome-wide comparative uncovers multiple targets selection hexaploid landraces cultivars.Proc. 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B73 maize genome: complexity, dynamics.Science. 326: 1112-1115Crossref (2568) Scholar]MaizeSNP50 BeadChip (llumina Infinium 50K) [70.Ganal M.W. large (Zea mays L.) array: development genotyping, compare genome.PLoS One. 2011; 6e28334Crossref Scholar]Subset MaizeSNP50 (Illumina 3K) [71.Rousselle al.Study essential derivation maize: III. Selection evaluation panel single nucleotide polymorphism loci use European North American germplasm.Crop 55: 1170-1180Crossref (3) Scholar]Axiom 600K [72.Unterseer powerful tool analysis high density 600 K array.BMC Genomics. 823Crossref 55K [73.Xu C. al.Development 55 coverage molecular breeding.Mol. Breed. 37: Scholar]MaizeSNPDB [74.Zhou W. al.MaizeSNPDB: retrieve SNPs among 1210 lines.Comput. 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Rep. 5: 11600Crossref (34) Affymetrix GeneChip (44K) [81.Tung platform dissecting phenotype genotype associations spp.).Rice. 3: 205-217Crossref Scholar]SNP-Seek [82.Alexandrov al.SNP-Seek derived 3000 genomes.Nucleic Acids Res. 43: D1023-D1027Crossref (188) Scholar][83.Wang L. dynamic covering entire life cycle 61: 752-766Crossref (248) Scholar,84.Cao P. Oligonucleotide Array Database: expression.Rice. 2012; 17Crossref Scholar]66 Accessions [85.Zhao Q. al.Pan-genome highlights extent cultivated wild rice.Nat. 50: 278-284Crossref (149) Scholar]Soybean(Glycine max)120.5333.7973[86.Schmutz al.Genome palaeopolyploid soybean.Nature. 463: 7278Crossref (2570) Scholar]SoySNP50K [87.Song SoySNP50K, high-density soybean.PLoS 8e54985Crossref (292) Scholar]SoyaSNP180K [88.Lee Y.G. al.Development, validation soybean array.Plant 81: 625-636Crossref (30) Scholar]SoyKB [89.Joshi T. al.Soybean knowledge base (SoyKB): web resource integration translational genomics breeding.Nucleic 42: D1245-D1252Crossref Scholar]55 616 [90.Libault M. transcriptome model Glycine max, plants.Plant 63: 86-99PubMed Scholar]26 [91.Liu soybeans.Cell. 182: 162-176Abstract (42) Scholar]Barley(Hordeum vulgare)51.1158.94980 [92.International Barley A physical, functional barley 491: 711-716Crossref (978) Scholar]; 4790 [93.Mascher chromosome conformation capture ordered 544: 427-433Crossref (553) Scholar]9K Illumina Custom Genotyping [94.Comadr`an al.Natural homolog Antirrhinum CENTRORADIALIS contributed spring growth habit environmental adaptation barley.Nat. 44: 1388-1392Crossref (284) 50K [95.Bayer M.M. 50k array.Front. 8: 1792Crossref (74) Scholar]BarleyVarDB [96.Tan al.BarleyVarDB: variation.Database. 2020baaa091Crossref (1) Scholar]21 439 [97.Druka seed through development.Funct. Integr. 2006; 6: 202-211Crossref Scholar]20 [98.Jayakodi hidden legacy mutation breeding.Nature. 588: 284-289Crossref (6) Scholar]Sorghum(Sorghum bicolor)4057.9739 [99.Paterson A.H. Sorghum bicolor diversification grasses.Nature. 457: 551-556Crossref (1906) Scholar]3K [100.Bekele W.A. al.High-throughput sorghum: resequencing screening 11: 1112-1125Crossref (37) Scholar]SorGSD [101.Luo al.SorGSD: sorghum database.Biotechnol. Biofuels. 9: 6Crossref (21) Scholar]27 577 [102.Shakoor genotype-specific profiles vegetative tissues grain, sweet bioenergy sorghums.BMC 35Crossref (45) Scholar]n.d.Rapeseed(Brassica napus)3470.5849.7 [103.Chalhoub B. al.Early allopolyploid evolution post-Neolithic Brassica napus oilseed 345: 950-953Crossref (1027) Scholar]International (60K) [104.Clarke W.E. ancestral diploid species optimised markers allotetraploid genome.Theor. Appl. 129: 1887-1899Crossref Scholar]BnaGVD [105.Yan al.BnaGVD: rapeseed (Brassica napus).Plant Cell Physiol. 2021; (Published online January 5, 2021. https://doi.org/10.1093/pcp/pcaa169)Crossref Scholar]101 040 [106.Chao al.BrassicaEDB: crops.Int. Mol. 21: 5831Crossref (2) Scholar]8 [107.Song J.M. al.Eight reveal architecture ecotype differentiation napus.Nat. Plants. 34-45Crossref (61) Scholar]Dry beans(Phaseolus vulgaris)3328.9473 [108.Schmutz common bean dual domestications.Nat. 707-713Crossref (602) Scholar]BARCBean6K_1, BARCBean6K_2, BARCBean6K_3 [109.Song al.SNP assay map construction, anchoring sequence, other bean.G3 (Bethesda). 2285-2290Crossref (73) Scholar]PhaseolusGenes (http://phaseolusgenes.bioinformatics.ucdavis.edu/)[110.O'Rourke J.A. RNA-Seq bean.BMC 866Crossref (68) Scholar]n.d.Groundnut(Arachis hypogaea)29.648.82540 [111.Bertioli D.J. sequences Arachis duranensis ipaensis, ancestors peanut.Nat. 48: 438-446Crossref (372) 2540 [112.Zhuang peanut provides insight legume karyotypes, domestication.Nat. 51: 865-876Crossref (64) Scholar]'Axiom_Arachis' 58K [113.Pandey M.K. Axiom_Arachis 58 genetics groundnut.Sci. 7: 40577Crossref Scholar]n.d.57 344 Transcripts [114.Sinha al.Arachis hypogaea fastigiata subspecies groundnut accelerate applications.Plant 18: 2187-2200Crossref Scholar]n.d.Sugarcane(Saccharum officinarum)26.71949.3800–900 (Monoploid)76K [115.Yang X. al.Mining variations representative sugarcane accessions.BMC 594Crossref (17) 84K [116.Balsalobre T.W.A. al.GBS-based dosage QTL allow mining yield-related sugarcane.BMC 72Crossref Sugarcane100K [117.You construction identification.Theor. 13: 2829-2845Crossref Scholar]n.d.n.d.n.d.a Abbreviation: data.b Source: http://www.fao.org/faostat/en/#data/QC. Open table tab characterization underlying important agronomic processes. this article, discuss products delivered opportunities latest innovations offer sustain recent decades [i.e., or (GB)]. We highlight broad create selection. years, expedited timelines progress across range species, than 130 publicly bred different crops [5.Vogel Marker-Assisted Selection: Biotechnology Breeding Without Genetic Engineering. Greenpeace International, 2014Google majority noteworthy by variety programs include having elevated levels against diseases bacterial blight blast rust aestivum). Among biotic stresses, tolerance submergence, salinity, drought remained key target GAB. similar impact witnessed quality several (Box 1).Box 1Key Products Delivered Genomics-Assisted Some CropsGAB Biotic Stress ResistanceSimply inherited under influence strong-effect QTL, disease resistance, most preferred introgression approaches. 'Improved Samba Mahsuri' (ISM) carrying (BB) (Xanthomonas oryzae pv. oryzae) genes (Xa21, xa13, xa5) [132.Sundaram R.M. al.Marker assisted Mahsuri, elite indica variety.Euphytica. 160: 411-422Crossref Two major (Magnaporthe (Pi-2 Pi-54) BB (Xa38) further stacked 'ISM' [133.Madhavi K.R. background elite, resistant variety, Mahsuri.Euphytica. 212: 331-342Crossref (8) Scholar,134.Yugander al.Incorporation Xa38 Improved Mahsuri.PLoS 13e0198260Crossref (14) 'Pusa Basmati 1' pyramided two (Pi2+Pi5) (Pi54+Pi1+Pita) [135.Khanna near-isogenic gene(s) rice.Theor. 128: 1243-1259Crossref (57) version 1121' 6' (Pi2 Pi54) (xa13 Xa21) others [136.Ellur al.Improvement varieties marker backcross breeding.Plant 242: 330-341Crossref Scholar].A DNA improving stress response quality-related (http://maswheat.ucdavis.edu/protocols/index.htm). Examples versions hard red winter (HRWW) 'Jagger' 'Overley' Yr40/Lr57 Lr58, respectively [137.Kuraparthy V. PCR marker-assisted transfer leaf stripe Lr57 Yr40 wheats.Crop 49: 120-126Crossref 'HUW510' Lr34 [138.Vasistha al.Molecular validates spot blotch wheat.Euphytica. 213: 262Crossref (4) pearl millet, 'HHB 67-improved' represented downy mildew 67', which was released commercial cultivation India 2005 (see Rai al. [139.Rai K.N. al.Adaptation germplasm-derived parent millet.Plant Resour. Newsl. 154: 20-24Google Scholar]). Other success stories demonstrating cereal included eyespot (Rhizoctonia cerealis) Pch1, recessive rym4/ rym5 yellow mosaic viruses, mlo (Blumeria graminis f. sp. hordei).Unlike cereals, grain lagged behind terms product delivery; however, genotyping-based selections increasingly embraced For instance, pyramiding cyst nematode (Heterodera glycines) races (2, 3, 14) at USDA-ARS led registration high-yielding genotypes 'JTN 5503', 5303', 'DS 880', 5109' [140.Arelli al.Registration yielding JTN5503.Crop 2723-2724Crossref Scholar, 141.Arelli conventional JTN-4307 nematodes fungal diseases.J. Regist. 192-199Crossref 142.Arelli P.R. Young L.D. Inheritance PI 567516C LY1 infecting cv. Hartwig.Euphytica. 165: 1-4Crossref (19) 143.Smith USDA, ARS, National Program. Germplasm Information Network, 2010Google Similarly, Varshney [144.Varshney al.Marker-assisted region improve popular (Arachis L.).Theor. 127: 1771-1781Crossref (93) obtained set 20 hypogaea) showing yield increased (Puccinia arachidis) transferring susceptible ('ICGV 91114', 'JL 24', 'TAG 24'). chickpea, simultaneous wilt (Fusarium oxysporum ciceris) (Ascochyta rabiei) shown chickpea C 214 [145.Varshney backcrossing introgress Fusarium race 1 Ascochyta 214, chickpea.Plant Genome. 1-11Crossref (77) Scholar].GAB Abiotic ToleranceThe immense utility abiotic exemplified controlling submergence (sub1), salt (Saltol), introgressed them. Sub1 'Swarna', India, within short span 2 [146.Neeraja approach developing submergence-tolerant cultivars.Theor. 2007; 115: 767-776Crossref (276) Vietnam, nearly ten cross OM1490/IR64-Sub1 90–99% revival field conditions [147.Lang N.T. (MAB) Mekong delta.Omonrice. 11-21Google Higher survival rates mega-varieties, including 'Samba (BPT 5204), 'CR 1009' 'Thadokkham (TDK1) Laos, 'BR 11' Bangladesh also evident following QTL-introgression Hasan [148.Hasan backcrossing: useful method improvement.Biotechnol. Equip. 29: 237-254Crossref Scholar]).The Saltol various countries, candidate 1121', 6', 'AS 996', 'BT 7', 'Bacthom 'Q5DB', 'BRRI-Dhan 49' Waziri [149.Waziri al.Saltol salinity rice.Austin. Bioeng. 1-5Google Successful Sub1, Saltol, (Pi2, Pi9), gall midge (Orseolia (Gm1, Gm4) Tapaswini', pyramid (Xa 4, xa5, highly 'Tapaswini', demonstrated [150.Das G. al.Improved Tapaswini four six genes/QTLs, resistance/tolerance stresses 2413Crossref Scholar].Similar above-mentioned examples tolerance, major-effect QTLs 'Sabitri' (a yet drought-susceptible Nepal) yielded variants good type rain-fed areas Nepal countries South Asia [151.Dixit develop drought-tolerant Sabitri, Nepal.Euphytica. 184Crossref (11) availability stable effects facilitated well. 'QTL hotspot' 372' pulse 10216' (https://icar.org.in/content/development-two-superior-chickpea-varieties-genomics-assisted-breeding).GAB Quality TraitsOne breakthroughs plants involves introduction Gpc-B1 (grain protein content) tetra caused creation GPC viz. USA ('Farnum', 'Lassik', 'Westmore', 'Desert King-High Protein'), Canada ('Lillian', 'Somerset', 'Burnside'), Australia (improved 'Wyalkatchem', 'Gladius', 'VR 1128') Mitrofanova Khakimova [152.Mitrofanova O.P. A.G. New content.Russ. 477-487Crossref references therein). variant badh2 Wx basmati 'Manawthukha' (an Myanmar) resulted fragrance intermediate amylose content [153.Yi cooking Myanmar Manawthukha.Field Crops 113: 178-186Crossref By reducing cycles up 3 Chu [154.Chu oleic peanut.Plant 4: 110-117Crossref developed 'Tifguard High O/L' acid resistance. More recently, oil combined late (Phaeoisariopsis personata Berk. & Curtis) [155.Janila fatty desaturase mutant (ahFAD2A ahFAD2B) enhances low containing genotypes.Plant 203-213Crossref (66) Scholar,156.Yaduru Indian foliar SSR backcrossing.Crop 1-15Crossref (5) Resistance Simply bl

Language: Английский

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Genome sequences of five Sitopsis species of Aegilops and the origin of polyploid wheat B subgenome

Molecular Plant, Journal Year: 2022, Volume and Issue: 15(3), P. 488 - 503

Published: Jan. 1, 2022

Common wheat (Triticum aestivum, BBAADD) is a major staple food crop worldwide. The diploid progenitors of the A and D subgenomes have been unequivocally identified; that B, however, remains ambiguous controversial but suspected to be related species Aegilops, section Sitopsis. Here, we report assembly chromosome-level genome sequences all five Sitopsis species, namely Aegilops bicornis, Ae. longissima, searsii, sharonensis, speltoides, as well partial Amblyopyrum muticum (synonym mutica) for phylogenetic analysis. Our results reveal donor common B subgenome distinct, most probably extinct, diverged from an ancestral progenitor lineage which still extant speltoides Am. belong. In addition, identified interspecific genetic introgressions throughout evolution Triticum/Aegilops complex. various assembled sizes (4.11–5.89 Gb) with high proportions repetitive (85.99%–89.81%); nonetheless, they retain collinearity other genomes or in Differences size were primarily due independent post-speciation amplification transposons. We also set genes pertinent important agronomic traits can harnessed breeding. These newly resources provide new roadmap evolutionary studies complex, improvement.

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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Modern plant biotechnology as a strategy in addressing climate change and attaining food security

Agriculture & Food Security, Journal Year: 2022, Volume and Issue: 11(1)

Published: April 3, 2022

Abstract Global warming causes a range of negative impacts on plants especially due to rapid changes in temperatures, alterations rainfall patterns, floods or drought conditions, and outbreaks pests diseases. These, turn, affect crop production reducing the quality quantity agricultural produce. Climatic extremes high population growth significantly increase world’s food demand. Therefore, fulfilling goal attaining security for present future generations is prime importance. Biotechnology enables creating dramatic crops withstand stress which difficult attain using conventional breeding approaches. It viable tool used improve production. The development biotechnological approaches such as genetic engineering, genome editing, RNA-mediated gene silencing armored with next-generation sequencing, mapping have paved way precise faster modifications plants. Such intensive efforts are currently underway desirable cultivars meet demand support sustainable productivity climate change adaptation.

Language: Английский

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Genome sequences of three Aegilops species of the section Sitopsis reveal phylogenetic relationships and provide resources for wheat improvement

The Plant Journal, Journal Year: 2022, Volume and Issue: 110(1), P. 179 - 192

Published: Jan. 8, 2022

SUMMARY Aegilops is a close relative of wheat ( Triticum spp.), and species in the section Sitopsis represent rich reservoir genetic diversity for improvement wheat. To understand their advance utilization, we produced whole‐genome assemblies longissima speltoides . Whole‐genome comparative analysis, along with recently sequenced sharonensis genome, showed that Ae. genomes are highly similar most closely related to D subgenome. By contrast, genome more B Haplotype block analysis supported idea closest subgenome, highlighted variable genomic regions between three Genome‐wide nucleotide‐binding leucine‐rich repeat NLR ) genes revealed species‐specific lineage‐specific variants, demonstrating potential improvement.

Language: Английский

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Harnessing landrace diversity empowers wheat breeding

Nature, Journal Year: 2024, Volume and Issue: 632(8026), P. 823 - 831

Published: June 17, 2024

Abstract Harnessing genetic diversity in major staple crops through the development of new breeding capabilities is essential to ensure food security 1 . Here we examined and phenotypic A. E. Watkins landrace collection 2 bread wheat ( Triticum aestivum ), a global cereal, by whole-genome re-sequencing 827 landraces 208 modern cultivars in-depth field evaluation spanning decade. We found that are derived from two seven ancestral groups maintain very long-range haplotype integrity. The remaining five represent untapped sources, providing access landrace-specific alleles haplotypes for breeding. Linkage disequilibrium-based association genetics analyses link genomes thousands identified high-resolution quantitative trait loci significant marker–trait associations. Using these structured germplasm, genotyping informatics resources, revealed many Watkins-unique beneficial can confer superior traits wheat. Furthermore, assessed effects 44,338 haplotypes, introgressed 143 prioritized context cultivars, bridging gap between current This study establishes framework systematically utilizing crop improvement achieve sustainable security.

Language: Английский

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Climate Change—The Rise of Climate-Resilient Crops

Plants, Journal Year: 2024, Volume and Issue: 13(4), P. 490 - 490

Published: Feb. 8, 2024

Climate change disrupts food production in many regions of the world. The accompanying extreme weather events, such as droughts, floods, heat waves, and cold snaps, pose threats to crops. concentration carbon dioxide also increases atmosphere. United Nations is implementing climate-smart agriculture initiative ensure security. An element this project involves breeding climate-resilient crops or plant cultivars with enhanced resistance unfavorable environmental conditions. Modern agriculture, which currently homogeneous, needs diversify species cultivated plants. Plant programs should extensively incorporate new molecular technologies, supported by development field phenotyping techniques. Breeders closely cooperate scientists from various fields science.

Language: Английский

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Computational methods for chromosome-scale haplotype reconstruction

Genome biology, Journal Year: 2021, Volume and Issue: 22(1)

Published: April 12, 2021

Abstract High-quality chromosome-scale haplotype sequences of diploid genomes, polyploid and metagenomes provide important insights into genetic variation associated with disease biodiversity. However, whole-genome short read sequencing does not yield information spanning whole chromosomes directly. Computational assembly shorter fragments is required for reconstruction, which can be challenging owing to limited fragment lengths high repeat variability across genomes. Recent advancements in long-read technologies, alongside computational innovations, are improving the reconstruction haplotypes at level chromosomes. Here, we review recent discuss methodological progress perspectives these areas.

Language: Английский

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Rewilding crops for climate resilience: economic analysis and de novo domestication strategies

Journal of Experimental Botany, Journal Year: 2021, Volume and Issue: 72(18), P. 6123 - 6139

Published: June 10, 2021

To match predicted population growth, annual food production should be doubled by 2050. This is not achievable current agronomical and breeding practices, due to the impact of climate changes associated abiotic stresses on agricultural systems. Here, we analyze global trends crop productivity show that overall loss in from climate-driven may exceed US$170 billion year-1 represents a major threat security. We also stress tolerance had been present wild progenitors modern crops but was lost during their domestication. argue for shift our paradigm breeding, focusing resilience, call broader use relatives as tool this process. that, while molecular tools are currently place harness potential climate-resilient genes relatives, complex polygenic nature traits remains bottleneck Future research efforts focused only finding appropriate development efficient cell-based high-throughput phenotyping platforms allowing assessment planta operation key genes.

Language: Английский

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