RESUMO
Increasing the proportion of locally produced plant protein in currently meat-rich diets could substantially reduce greenhouse gas emissions and loss of biodiversity1. However, plant protein production is hampered by the lack of a cool-season legume equivalent to soybean in agronomic value2. Faba bean (Vicia faba L.) has a high yield potential and is well suited for cultivation in temperate regions, but genomic resources are scarce. Here, we report a high-quality chromosome-scale assembly of the faba bean genome and show that it has expanded to a massive 13 Gb in size through an imbalance between the rates of amplification and elimination of retrotransposons and satellite repeats. Genes and recombination events are evenly dispersed across chromosomes and the gene space is remarkably compact considering the genome size, although with substantial copy number variation driven by tandem duplication. Demonstrating practical application of the genome sequence, we develop a targeted genotyping assay and use high-resolution genome-wide association analysis to dissect the genetic basis of seed size and hilum colour. The resources presented constitute a genomics-based breeding platform for faba bean, enabling breeders and geneticists to accelerate the improvement of sustainable protein production across the Mediterranean, subtropical and northern temperate agroecological zones.
Assuntos
Produtos Agrícolas , Diploide , Variação Genética , Genoma de Planta , Genômica , Melhoramento Vegetal , Proteínas de Plantas , Vicia faba , Cromossomos de Plantas/genética , Produtos Agrícolas/genética , Produtos Agrícolas/metabolismo , Variações do Número de Cópias de DNA/genética , DNA Satélite/genética , Amplificação de Genes/genética , Genes de Plantas/genética , Variação Genética/genética , Genoma de Planta/genética , Estudo de Associação Genômica Ampla , Geografia , Melhoramento Vegetal/métodos , Proteínas de Plantas/genética , Proteínas de Plantas/metabolismo , Recombinação Genética , Retroelementos/genética , Sementes/anatomia & histologia , Sementes/genética , Vicia faba/anatomia & histologia , Vicia faba/genética , Vicia faba/metabolismoRESUMO
Genetic diversity is key to crop improvement. Owing to pervasive genomic structural variation, a single reference genome assembly cannot capture the full complement of sequence diversity of a crop species (known as the 'pan-genome'1). Multiple high-quality sequence assemblies are an indispensable component of a pan-genome infrastructure. Barley (Hordeum vulgare L.) is an important cereal crop with a long history of cultivation that is adapted to a wide range of agro-climatic conditions2. Here we report the construction of chromosome-scale sequence assemblies for the genotypes of 20 varieties of barley-comprising landraces, cultivars and a wild barley-that were selected as representatives of global barley diversity. We catalogued genomic presence/absence variants and explored the use of structural variants for quantitative genetic analysis through whole-genome shotgun sequencing of 300 gene bank accessions. We discovered abundant large inversion polymorphisms and analysed in detail two inversions that are frequently found in current elite barley germplasm; one is probably the product of mutation breeding and the other is tightly linked to a locus that is involved in the expansion of geographical range. This first-generation barley pan-genome makes previously hidden genetic variation accessible to genetic studies and breeding.
Assuntos
Cromossomos de Plantas/genética , Genoma de Planta/genética , Hordeum/genética , Internacionalidade , Mutação , Melhoramento Vegetal , Inversão Cromossômica/genética , Mapeamento Cromossômico , Loci Gênicos/genética , Genótipo , Hordeum/classificação , Polimorfismo Genético/genética , Padrões de Referência , Banco de Sementes , Inversão de Sequência , Sequenciamento Completo do GenomaRESUMO
Eggplant (Solanum melongena L.) is an important horticultural crop and one of the most widely grown vegetables from the Solanaceae family. It was domesticated from a wild, prickly progenitor carrying small, round, non-anthocyanic fruits. We obtained a novel, highly contiguous genome assembly of the eggplant '67/3' reference line, by Hi-C retrofitting of a previously released short read- and optical mapping-based assembly. The sizes of the 12 chromosomes and the fraction of anchored genes in the improved assembly were comparable to those of a chromosome-level assembly. We resequenced 23 accessions of S. melongena representative of the worldwide phenotypic, geographic, and genetic diversity of the species, and one each from the closely related species Solanum insanum and Solanum incanum. The eggplant pan-genome contained approximately 51.5 additional megabases and 816 additional genes compared with the reference genome, while the pan-plastome showed little genetic variation. We identified 53 selective sweeps related to fruit color, prickliness, and fruit shape in the nuclear genome, highlighting selection leading to the emergence of present-day S. melongena cultivars from its wild ancestors. Candidate genes underlying the selective sweeps included a MYBL1 repressor and CHALCONE ISOMERASE (for fruit color), homologs of Arabidopsis GLABRA1 and GLABROUS INFLORESCENCE STEMS2 (for prickliness), and orthologs of tomato FW2.2, OVATE, LOCULE NUMBER/WUSCHEL, SUPPRESSOR OF OVATE, and CELL SIZE REGULATOR (for fruit size/shape), further suggesting that selection for the latter trait relied on a common set of orthologous genes in tomato and eggplant.
Assuntos
Domesticação , Genoma de Planta/genética , Melhoramento Vegetal , Solanum melongena/genética , Mapeamento Cromossômico , Genes de Plantas/genética , Variação Genética , Polimorfismo de Nucleotídeo Único/genética , Característica Quantitativa Herdável , Solanum melongena/crescimento & desenvolvimento , Sequenciamento Completo do GenomaRESUMO
A resistance gene atlas is an integral component of the breeder's arsenal in the fight against evolving pathogens. Thanks to high-throughput sequencing, catalogues of resistance genes can be assembled even in crop species with large and polyploid genomes. Here, we report on capture sequencing and assembly of resistance gene homologs in a diversity panel of 907 winter wheat genotypes comprising ex situ genebank accessions and current elite cultivars. In addition, we use accurate long-read sequencing and chromosome conformation capture sequencing to construct a chromosome-scale genome sequence assembly of cv. Attraktion, an elite variety representative of European winter wheat. We illustrate the value of our resource for breeders and geneticists by (i) comparing the resistance gene complements in plant genetic resources and elite varieties and (ii) conducting genome-wide associations scans (GWAS) for the fungal diseases yellow rust and leaf rust using reference-based and reference-free GWAS approaches. The gene content under GWAS peaks was scrutinized in the assembly of cv. Attraktion.
Assuntos
Basidiomycota , Triticum , Basidiomycota/genética , Mapeamento Cromossômico , Cromossomos , Resistência à Doença/genética , Doenças das Plantas/genética , Doenças das Plantas/microbiologia , Polimorfismo de Nucleotídeo Único , Locos de Características Quantitativas , Triticum/genética , Triticum/microbiologiaRESUMO
Bread wheat is a major crop that has long been the focus of basic and breeding research. Assembly of its genome has been difficult because of its large size and allohexaploid nature (AABBDD genome). Following the first reported assembly of the genome of the experimental strain Chinese Spring (CS), the 10+ Wheat Genomes Project was launched to produce multiple assemblies of worldwide modern cultivars. The only Asian cultivar in the project is Norin 61, a representative Japanese cultivar adapted to grow across a broad latitudinal range, mostly characterized by a wet climate and a short growing season. Here, we characterize the key aspects of its chromosome-scale genome assembly spanning 15 Gb with a raw scaffold N50 of 22 Mb. Analysis of the repetitive elements identified chromosomal regions unique to Norin 61 that encompass a tandem array of the pathogenesis-related 13 family. We report novel copy-number variations in the B homeolog of the florigen gene FT1/VRN3, pseudogenization of its D homeolog and the association of its A homeologous alleles with the spring/winter growth habit. Furthermore, the Norin 61 genome carries typical East Asian functional variants different from CS, ranging from a single nucleotide to multi-Mb scale. Examples of such variation are the Fhb1 locus, which confers Fusarium head-blight resistance, Ppd-D1a, which confers early flowering, Glu-D1f for Asian noodle quality and Rht-D1b, which introduced semi-dwarfism during the green revolution. The adoption of Norin 61 as a reference assembly for functional and evolutionary studies will enable comprehensive characterization of the underexploited Asian bread wheat diversity.
Assuntos
Resistência à Doença/genética , Flores/crescimento & desenvolvimento , Genes de Plantas/genética , Genoma de Planta/genética , Triticum/genética , Mapeamento Cromossômico , Cromossomos de Plantas/genética , Citogenética , Ásia Oriental , Flores/genética , Fusarium , Genes de Plantas/fisiologia , Estudos de Associação Genética , Variação Genética/genética , Variação Genética/fisiologia , Genoma de Planta/fisiologia , Genótipo , Filogenia , Alinhamento de Sequência , Análise de Sequência de DNA , Triticum/crescimento & desenvolvimento , Triticum/imunologia , Triticum/fisiologiaRESUMO
Rye (Secale cereale L.) is an exceptionally climate-resilient cereal crop, used extensively to produce improved wheat varieties via introgressive hybridization and possessing the entire repertoire of genes necessary to enable hybrid breeding. Rye is allogamous and only recently domesticated, thus giving cultivated ryes access to a diverse and exploitable wild gene pool. To further enhance the agronomic potential of rye, we produced a chromosome-scale annotated assembly of the 7.9-gigabase rye genome and extensively validated its quality by using a suite of molecular genetic resources. We demonstrate applications of this resource with a broad range of investigations. We present findings on cultivated rye's incomplete genetic isolation from wild relatives, mechanisms of genome structural evolution, pathogen resistance, low-temperature tolerance, fertility control systems for hybrid breeding and the yield benefits of rye-wheat introgressions.
Assuntos
Mapeamento Cromossômico/métodos , Genoma de Planta , Melhoramento Vegetal/métodos , Proteínas de Plantas/genética , Secale/genética , Triticum/genética , Adaptação Fisiológica/genética , Produtos Agrícolas/genética , Produtos Agrícolas/imunologia , Regulação da Expressão Gênica de Plantas , Introgressão Genética , Cariótipo , Imunidade Vegetal/genética , Proteínas de Plantas/metabolismo , Secale/imunologia , Estresse FisiológicoRESUMO
Recently, long noncoding RNAs (lncRNAs) are shown to be implicating nuclear domain organization and gene regulation by mediating long-range chromatin interactions. Chromosome conformation capture (3C) is a method used to study such long-range interaction between two different loci in the 3D nuclear space. Through successive improvement in resolution and throughput, 3C, chromosome conformation capture on chip (4C), and chromosome conformation capture carbon copy (5C) to Hi-C methods were developed to study interactions between loci from one versus one scale to an unprecedented genome-wide resolution. In situ Hi-C is a variant of Hi-C in which proximity ligation is performed at the intact nuclei to improve the signal-to-noise ratio and throughput of the experiment to provide useful genome-wide contact frequency matrix/maps. The contact frequency maps obtained could be used for physical ordering of scaffolds in complex genome assembly projects, in deducing the nuclear domain organization in high resolution and in identifying specific long-range interactions between genomic regions of interest. In this chapter, we describe in detail a protocol for in situ Hi-C used on crops like barley, wheat, rye, oat, and evening primrose.
Assuntos
Cromatina/metabolismo , Cromossomos de Plantas , Biologia Computacional/métodos , Regulação da Expressão Gênica de Plantas , Genoma de Planta , Hordeum/metabolismo , Triticum/metabolismo , Núcleo Celular/genética , Cromatina/genética , Mapeamento Cromossômico , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Hordeum/genética , Triticum/genéticaRESUMO
Chromosome-scale genome sequence assemblies underpin pan-genomic studies. Recent genome assembly efforts in the large-genome Triticeae crops wheat and barley have relied on the commercial closed-source assembly algorithm DeNovoMagic. We present TRITEX, an open-source computational workflow that combines paired-end, mate-pair, 10X Genomics linked-read with chromosome conformation capture sequencing data to construct sequence scaffolds with megabase-scale contiguity ordered into chromosomal pseudomolecules. We evaluate the performance of TRITEX on publicly available sequence data of tetraploid wild emmer and hexaploid bread wheat, and construct an improved annotated reference genome sequence assembly of the barley cultivar Morex as a community resource.