A genome assembly of the barley ‘transformation reference’ cultivar Golden Promise

Schreiber, Miriam; Mascher, Martin; Wright, Jonathan; Padmarasu, Sudharsan; Himmelbach, Axel; Heavens, Darren; Milne, Linda; Clavijo, Bernardo; Stein, Nils; Waugh, Robbie

doi:10.1101/2020.02.12.945550

Cited by 15 publications

(21 citation statements)

References 24 publications

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“…1), reflecting the key determinants of population structure: geographical origin, row type and annual growth habit. In addition to these gene pool representatives, our panel included the reference cultivar Morex 5 , two current or former elite malting varieties (RGT Planet and Hockett), two founder lines of Chinese barley breeding (ZDM01467 and ZDM02064), Golden Promise and Igri (two genotypes with high transformation efficiency 16,17 ), Barke (a successful German variety and the parent of several mutant and mapping populations 18,19 ) and one wild barley (H. vulgare subsp. spontaneum (K. Koch) Thell.)…”

Section: Twenty Barley Reference Genomesmentioning

confidence: 99%

The barley pan-genome reveals the hidden legacy of mutation breeding

Jayakodi

Padmarasu

Haberer

et al. 2020

Nature

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408

406

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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.

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Section: Twenty Barley Reference Genomesmentioning

confidence: 99%

The barley pan-genome reveals the hidden legacy of mutation breeding

Jayakodi

Padmarasu

Haberer

et al. 2020

Nature

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408

406

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“… 24 These sequences have allowed the annotation of genes on contigs 25 or chromosome-scale genome sequences. 26 , 27 …”

Section: Genetic and Genomic Resourcesmentioning

confidence: 99%

History and future perspectives of barley genomics

Sato

2020

DNA Research

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Barley (Hordeum vulgare), one of the most widely cultivated cereal crops, possesses a large genome of 5.1 Gbp. Through various international collaborations, the genome has recently been sequenced and assembled at the chromosome level by exploiting available genetic and genomic resources. Many wild and cultivated barley accessions have been collected and preserved around the world. These accessions are crucial to obtain diverse natural and induced barley variants. The barley bioresource project aims to investigate the diversity of this crop based on purified seed and DNA samples of a large number of collected accessions. The long-term goal of this project is to analyze the genome sequences of major barley accessions worldwide. In view of technical limitations, a strategy has been employed to establish the exome structure of a selected number of accessions and to perform high-quality chromosome-scale assembly of the genomes of several major representative accessions. For the future project, an efficient annotation pipeline is essential for establishing the function of genomes and genes as well as for using this information for sequence-based digital barley breeding. In this article, I review the existing barley resources along with their applications and discuss possible future directions of research in barley genomics.

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“…More recently, a reference genome assembly for the barley cv. Golden Promise has been reported [ 48 ]. The assembled genome of seven chromosomes comprising 4.13 Gb contains 95.2% of complete and single-copy genes and will prove particularly useful for functional genomics studies, given that Golden Promise is the most readily transformable barley genotype.…”

Section: The Genomes Of Barleymentioning

confidence: 99%

Barley’s Second Spring as a Model Organism for Chloroplast Research

Rotasperti

Sansoni

Mizzotti

et al. 2020

Plants

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Barley (Hordeum vulgare) has been widely used as a model crop for studying molecular and physiological processes such as chloroplast development and photosynthesis. During the second half of the 20th century, mutants such as albostrians led to the discovery of the nuclear-encoded, plastid-localized RNA polymerase and the retrograde (chloroplast-to-nucleus) signalling communication pathway, while chlorina-f2 and xantha mutants helped to shed light on the chlorophyll biosynthetic pathway, on the light-harvesting proteins and on the organization of the photosynthetic apparatus. However, during the last 30 years, a large fraction of chloroplast research has switched to the more “user-friendly” model species Arabidopsis thaliana, the first plant species whose genome was sequenced and published at the end of 2000. Despite its many advantages, Arabidopsis has some important limitations compared to barley, including the lack of a real canopy and the absence of the proplastid-to-chloroplast developmental gradient across the leaf blade. These features, together with the availability of large collections of natural genetic diversity and mutant populations for barley, a complete genome assembly and protocols for genetic transformation and gene editing, have relaunched barley as an ideal model species for chloroplast research. In this review, we provide an update on the genomics tools now available for barley, and review the biotechnological strategies reported to increase photosynthesis efficiency in model species, which deserve to be validated in barley.

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A genome assembly of the barley ‘transformation reference’ cultivar Golden Promise

Cited by 15 publications

References 24 publications

The barley pan-genome reveals the hidden legacy of mutation breeding

The barley pan-genome reveals the hidden legacy of mutation breeding

History and future perspectives of barley genomics

Barley’s Second Spring as a Model Organism for Chloroplast Research

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