Chromosome-scale assembly of wild barley accession “OUH602”

Sato, Kazuhiro; Mascher, Martin; Himmelbach, Axel; Haberer, Georg; Spannagl, Manuel; Stein, Nils

doi:10.1093/g3journal/jkab244

Cited by 20 publications

(16 citation statements)

References 29 publications

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“…1D ). In contrast, the wild barley accessions B1K-04-12 ( 33 ) and OUH602 ( rps8 ) ( 34 ) carry a 546-kb deletion that encompasses five nonrepetitive genes: Exo70FX12 , Pur1 , CC-NB , LRR-DDE , and CC-TM ( Fig. 1, B and D ).…”

Section: Resultsmentioning

confidence: 99%

A lineage-specific Exo70 is required for receptor kinase–mediated immunity in barley

et al. 2022

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In the evolution of land plants, the plant immune system has experienced expansion in immune receptor and signaling pathways. Lineage-specific expansions have been observed in diverse gene families that are potentially involved in immunity but lack causal association. Here, we show that Rps8 -mediated resistance in barley to the pathogen Puccinia striiformis f. sp. tritici (wheat stripe rust) is conferred by a genetic module: Pur1 and Exo70FX12 , which are together necessary and sufficient. Pur1 encodes a leucine-rich repeat receptor kinase and is the ortholog of rice Xa21 , and Exo70FX12 belongs to the Poales-specific Exo70FX clade. The Exo70FX clade emerged after the divergence of the Bromeliaceae and Poaceae and comprises from 2 to 75 members in sequenced grasses. These results demonstrate the requirement of a lineage-specific Exo70FX12 in Pur1-mediated immunity and suggest that the Exo70FX clade may have evolved a specialized role in receptor kinase signaling.

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Section: Resultsmentioning

confidence: 99%

A lineage-specific Exo70 is required for receptor kinase–mediated immunity in barley

et al. 2022

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“…‘Haruna Nijo’ and the wild ancestral form of barley ( H. vulgare ssp. spontaneum ) accession ‘OUH602 (H602)’ was obtained from the Barley DB http://viewer.shigen.info/harunanijo/index.php (Sakkour et al 2022) or http://viewer.shigen.info/barley (Sato et al 2021), respectively. The locations of various cis -acting motifs in the MFT2 promoter sequences were identified using GENTYX Ver.13 software (Genetyx).…”

Section: Methodsmentioning

confidence: 99%

“…http://viewer.shigen.info/barley (Sato et al 2021), respectively. The locations of various cis-acting motifs in the MFT2 promoter sequences were identified using GENTYX Ver.13 software (Genetyx).…”

Section: ) Ormentioning

confidence: 99%

Conserved cis-acting motifs and localization of transcripts and proteins ofMFT2in barley and rice

Utsugi

Kawahigashi

Tagiri

et al. 2023

Preprint

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MFT is an important regulator of seed dormancy in flowering plants. A natural mutation in the A-box motif in the promoter of wheat (Triticum aestivum) MFT2 on chromosome 3A (TaMFT2-3A) has been used to prevent pre-harvest sprouting (PHS) in wheat cultivars in East Asia. Previous research using in situ hybridization showed that TaMFT2-3A is primarily expressed in the seed scutellum. In this study, we analyzed the localization of transcripts and encoded proteins for the TaMFT2 homologs from barley (Hordeum vulgare) and rice (Oryza sativa), HvMFT2 and OsMFT2, respectively. RNA in situ hybridization showed that, like the wheat genes, the rice and barley homologs are primarily expressed in the scutellum, indicating that these three MFT2 genes have a common expression pattern during seed development. Analysis of the cis-acting regulatory elements of their promoter sequences showed that the three MFT2 promoters share eight seed-specific cis-acting RY motifs, which are binding sites for B3-domain transcription factors of the AFL-B3 and VIVIPAROUS1/ABI3-LIKE (VAL) families. In addition, we detected tandemly repeated and partially overlapping A-box motifs in the promoters of HvMFT2, TaMFT2-3B, and TaMFT2-3D, possibly explaining why the natural allele of TaMFT2-3A has been employed in breeding. We generated transgenic rice plants expressing nuclear-localized green fluorescent protein (NLS-2xGFP) and OsMFT2-GFP under the control of a 3-kb fragment of the OsMFT2 promoter. Immunohistochemical staining using anti-GFP antibodies mainly detected GFP in the scutellum and scutellar epithelium, which is an important tissue for initiating germination upon seed hydration. We confirmed these results by confocal microscopy of GFP fluorescence in seeds. Our results suggest that MFT2 expression in rice, barley, and wheat might be regulated by a similar network of transcription factors through multi-RY motifs in the MFT2 promoters, with possible roles in scutellar epithelium development.

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“…It is now widely agreed that one or a few reference genomes are insufficient for capturing the full range of genetic diversity of a species [36]. The additional barley genomes [33,34] and pan-genome [23] recently published reveal a high degree of structural variation, including inversions, translocations, copy number variation (CNV), and presence/absence variation (PAV), which facilitates exploration of the alleles of agronomically significant genes. This approach has been used to identify 263,267 gene family members within the barley pan-genome.…”

Section: Variation Analysis Of Barley Gene Familiesmentioning

confidence: 99%

BGFD: an integrated multi-omics database of barley gene families

Bian

Tang

et al. 2022

BMC Plant Biol

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Background A gene family comprises a group of genes with similar functional domains that play various roles in plant growth, development, and responses to environmental stimuli. Barley (Hordeum vulgare L.) is the fourth most cultivated cereal crop worldwide, and it is an important model species for genetic studies. Systematic identification and annotation of gene families are key for studies of molecular function and evolutionary history. Results We constructed a multi-omics database containing 5593 genes of 77 gene families called the Barley Gene Family Database (BGFD: http://barleygfdb.com). BGFD is a free, user-friendly, and web-accessible platform that provides data on barley family genes. BGFD provides intuitive visual displays to facilitate studies of the physicochemical properties, gene structure, phylogenetic relationships, and motif organization of genes. Massive multi-omics datasets have been acquired and processed to generate an atlas of expression pattern profiles and genetic variation in BGFD. The platform offers several practical toolkits to conduct searches, browse, and employ BLAST functions, and the data are downloadable. Conclusions BGFD will aid research on the domestication and adaptive evolution of barley; it will also facilitate the screening of candidate genes and exploration of important agronomic traits in barley.

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Chromosome-scale assembly of wild barley accession “OUH602”

Cited by 20 publications

References 29 publications

A lineage-specific Exo70 is required for receptor kinase–mediated immunity in barley

A lineage-specific Exo70 is required for receptor kinase–mediated immunity in barley

Conserved cis-acting motifs and localization of transcripts and proteins ofMFT2in barley and rice

BGFD: an integrated multi-omics database of barley gene families

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