Genomic mechanisms of climate adaptation in polyploid bioenergy switchgrass

Nature, Journal Year: 2021, Volume and Issue: 590(7846), P. 438 - 444

Published: Jan. 27, 2021

Long-term climate change and periodic environmental extremes threaten food fuel security1 global crop productivity2-4. Although molecular adaptive breeding strategies can buffer the effects of climatic stress improve resilience5, these approaches require sufficient knowledge genes that underlie productivity adaptation6-knowledge has been limited to a small number well-studied model systems. Here we present assembly annotation large complex genome polyploid bioenergy switchgrass (Panicum virgatum). Analysis biomass survival among 732 resequenced genotypes, which were grown across 10 common gardens span 1,800 km latitude, jointly revealed extensive genomic evidence adaptation. Climate-gene-biomass associations abundant but varied considerably deeply diverged gene pools. Furthermore, found flow accelerated adaptation during postglacial colonization northern habitats through introgression alleles from pre-adapted pool. The nature also enhanced potential fractionation function, as there was an increased level heritable genetic diversity on nondominant subgenome. In addition investigating patterns adaptation, resources gene-trait developed here provide breeders with necessary tools increase yield for sustainable production bioenergy.

Language: Английский

---

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

---

The NLR-Annotator Tool Enables Annotation of the Intracellular Immune Receptor Repertoire

PLANT PHYSIOLOGY, Journal Year: 2020, Volume and Issue: 183(2), P. 468 - 482

Published: March 17, 2020

Disease resistance genes encoding nucleotide-binding and leucine-rich repeat (NLR) intracellular immune receptor proteins detect pathogens by the presence of pathogen effectors. Plant genomes typically contain hundreds NLR-encoding genes. The availability hexaploid wheat (Triticum aestivum) cultivar Chinese Spring reference genome allows a detailed study its NLR complement. However, low expression high intrafamily sequence homology hinder their accurate annotation. Here, we developed NLR-Annotator, software tool for in silico identification independent transcript support. Although wheat, demonstrate universal applicability NLR-Annotator across diverse plant taxa. We applied our to combined it with transcript-validated subset from gene annotation characterize structure, phylogeny, profile family. detected 3,400 full-length loci, which 1,560 were confirmed as expressed intact open reading frames. NLRs integrated domains mostly group specific subclades. Members another subclade predominantly locate close physical proximity carrying domains, suggesting paired helper function. Most (88%) display basal (in lower 10 percentile transcripts). In young leaves subjected biotic stress, found up-regulation 266 To illustrate utility positional cloning genes, estimated number within intervals mapped rust Our will support functional accelerate breeding engineering disease-resistant varieties.

Language: Английский

---

High-Resolution Genome-wide Association Study Identifies Genomic Regions and Candidate Genes for Important Agronomic Traits in Wheat

Molecular Plant, Journal Year: 2020, Volume and Issue: 13(9), P. 1311 - 1327

Published: July 20, 2020

Language: Английский

---

Current Strategies of Polyploid Plant Genome Sequence Assembly

Frontiers in Plant Science, Journal Year: 2018, Volume and Issue: 9

Published: Nov. 21, 2018

Polyploidy or duplication of an entire genome occurs in the majority angiosperms. The understanding polyploid genomes is important for improvement those crops, which humans rely on sustenance and basic nutrition. As climate change continues to pose a potential threat agricultural production, there will increasingly be demand plant cultivars that can resist biotic abiotic stresses also provide needed improved In past decade, Next Generation Sequencing (NGS) has fundamentally changed genomics landscape by providing tools exploration genomes. Here, we review challenges assembly genomes, present recent advances genomic resources functional molecular genetics breeding. diploid less heterozygous progenitor species are available, discuss lack complexity these currently available reference as they relate crops. Finally, approaches haplotyping phasing impact third generation technologies assembly.

Language: Английский

---

A chickpea genetic variation map based on the sequencing of 3,366 genomes

Nature, Journal Year: 2021, Volume and Issue: 599(7886), P. 622 - 627

Published: Nov. 10, 2021

Abstract Zero hunger and good health could be realized by 2030 through effective conservation, characterization utilization of germplasm resources 1 . So far, few chickpea ( Cicer arietinum ) accessions have been characterized at the genome sequence level 2 Here we present a detailed map variation in 3,171 cultivated 195 wild to provide publicly available for genomics research breeding. We constructed pan-genome describe genomic diversity across its progenitor accessions. A divergence tree using genes around 80% individuals one species allowed us estimate over last 21 million years. Our analysis found chromosomal segments that show signatures selection during domestication, migration improvement. The locations deleterious mutations responsible limited genetic decreased fitness were identified elite germplasm. superior haplotypes improvement-related traits landraces can introgressed into breeding lines haplotype-based breeding, targets purging alleles genomics-assisted and/or gene editing. Finally, propose three crop strategies based on prediction enhance productivity 16 while avoiding erosion optimal contribution (OCS)-based pre-breeding. predicted performance 100-seed weight, an important yield-related trait, increased up 23% 12% with OCS- approaches, respectively.

Language: Английский

---

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

---

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

---

Features and applications of haplotypes in crop breeding

Communications Biology, Journal Year: 2021, Volume and Issue: 4(1)

Published: Nov. 4, 2021

Abstract Climate change with altered pest-disease dynamics and rising abiotic stresses threatens resource-constrained agricultural production systems worldwide. Genomics-assisted breeding (GAB) approaches have greatly contributed to enhancing crop efficiency delivering better varieties. Fast-growing capacity affordability of DNA sequencing has motivated large-scale germplasm projects, thus opening exciting avenues for mining haplotypes applications. This review article highlights ways mine apply them complex trait dissection in GAB including haplotype-GWAS, haplotype-based breeding, haplotype-assisted genomic selection. Improvement strategies that efficiently deploy superior hasten progress will be key safeguarding global food security.

Language: Английский

---

Improved pea reference genome and pan-genome highlight genomic features and evolutionary characteristics

Nature Genetics, Journal Year: 2022, Volume and Issue: 54(10), P. 1553 - 1563

Published: Sept. 22, 2022

Abstract Complete and accurate reference genomes annotations provide fundamental resources for functional genomics crop breeding. Here we report a de novo assembly annotation of pea cultivar ZW6 with contig N50 8.98 Mb, which features 243-fold increase in length evident improvements the continuity quality sequence complex repeat regions compared existing one. Genome diversity 118 cultivated wild demonstrated that Pisum abyssinicum is separate species different from P. fulvum sativum within . Quantitative trait locus analyses uncovered two known Mendel’s genes related to stem ( Le/le ) seed shape R/r as well some candidate pod form studied by Mendel. A pan-genome 116 accessions was constructed, pan-genes preferred showed distinct enrichment, indicating potential value them breeding future.

Language: Английский

---