A guide to barley mutants

Hansson, Mats; Youssef, Helmy M.; Zakhrabekova, Shakhira; Stuart, David; Svensson, Jan T.; Dockter, Christoph; Stein, Nils; Waugh, Robbie; Lundqvist, Udda; Franckowiak, Jerome

doi:10.1186/s41065-023-00304-w

Cited by 4 publications

(1 citation statement)

References 160 publications

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“…sodium azide) treatment. Thousands of mutants that were produced are today stored in various gene banks ( Hansson et al 2024 ). These reservoirs of genetic diversity serve as a valuable asset for future plant breeding.…”

Section: Introductionmentioning

confidence: 99%

A pipeline for identification of causal mutations in barley identifies Xantha-j as the chlorophyll synthase gene

Stuart,

Zakhrabekova,

Jørgensen

et al. 2024

Plant Physiology

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Thousands of barley (Hordeum vulgare L.) mutants have been isolated over the last century, and many are stored in gene banks across various countries. In the present work, we developed a pipeline to efficiently identify causal mutations in barley. The pipeline is also efficient for mutations located in centromeric regions. Through bulked-segregant analyses using whole genome sequencing of pooled F2 seedlings, we mapped two mutations and identified a limited number of candidate genes. We applied the pipeline on F2-mapping populations made from xan-j.59 (unknown mutation) and xan-l.82 (previously known). The Xantha-j (xan-j) gene was identified as encoding chlorophyll synthase, which catalyzes the last step in the chlorophyll biosynthetic pathway: the addition of a phytol moiety to the propionate side chain of chlorophyllide. Key amino-acid residues in the active site, including the binding sites of the isoprenoid and chlorophyllide substrates, were analyzed in an AlphaFold2-generated structural model of the barley chlorophyll synthase. Three allelic mutants, xan-j.19, xan-j.59, and xan-j.64 were characterized. While xan-j.19 is a one-base pair deletion and xan-j.59 is a nonsense mutation, xan-j.64 causes an S212F substitution in chlorophyll synthase. Our analyses of xan-j.64 and treatment of growing barley with clomazone, an inhibitor of chloroplastic isoprenoid biosynthesis, suggest that binding of the isoprenoid substrate is a prerequisite for the stable maintenance of chlorophyll synthase in the plastid. We further suggest that chlorophyll synthase is a sensor for coordinating chlorophyll and isoprenoid biosynthesis.

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Section: Introductionmentioning

confidence: 99%

A pipeline for identification of causal mutations in barley identifies Xantha-j as the chlorophyll synthase gene

Stuart,

Zakhrabekova,

Jørgensen

et al. 2024

Plant Physiology

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Heat stress causes chromatin accessibility and related gene expression changes in crown tissues of barley (Hordeum vulgare)

Kiełbowicz-Matuk,

Smaczniak,

Mikołajczak

et al. 2024

Plant Mol Biol

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Plant responses to stress caused by high temperatures involve changes occurring at the molecular, metabolic, and physiological levels. Understanding the mechanisms by which plants recognize signals to activate this response is a prerequisite for identifying key genes and signaling pathways and for obtaining heat-tolerant plants. We demonstrated the first implementation of an assay for transposase-accessible chromatin to identify open chromatin regions (OCRs) in crown tissues of barley using three genotypes carrying different allelic forms of the sdw1 gene encoding gibberellin 20-oxidase subjected to elevated temperatures. In parallel, we performed gene expression analysis, which allowed us to relate changes in chromatin state to changes in transcriptional activity. The obtained data revealed that the hypersensitive chromatin regions within the genes were more repeatable than those outside the gene intervals. We observed that prolonged exposure to high temperatures increased chromatin accessibility. Genes with OCRs in their regulatory regions were involved in stress signaling and tolerance, including calcium-dependent protein kinase, mitogen-activated protein kinase (MAPK3), receptor-like cytoplasmic kinase (RLK), TIFY domain-containing transcriptional regulator, bZIP transcription factor, and regulatory protein NPR1. The effect of genotype on gene expression was not as pronounced as that of temperature. By combining results from the differential analysis of chromatin accessibility and expression profiles, we identified genes with high temperature-induced changes in chromatin accessibility associated with expression alterations. Importantly, our data revealed a relationship between the loss of chromatin accessibility in response to heat and the downregulation of genes related to gibberellin signaling.

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Cereal genetics: Novel modulators of spikelet number and flowering time

Li,

Jiao

2024

Current Biology

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A guide to barley mutants

Cited by 4 publications

References 160 publications

A pipeline for identification of causal mutations in barley identifies Xantha-j as the chlorophyll synthase gene

A pipeline for identification of causal mutations in barley identifies Xantha-j as the chlorophyll synthase gene

Heat stress causes chromatin accessibility and related gene expression changes in crown tissues of barley (Hordeum vulgare)

Cereal genetics: Novel modulators of spikelet number and flowering time

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