Copy number variation of chromosome 5A and its association with Q gene expression, morphological aberrations, and agronomic performance of winter wheat cultivars

Förster, Sebastian; Schümann, Erika; Baumann, Mario; Weber, Wilhelm; Pillen, Klaus

doi:10.1007/s00122-013-2192-8

Cited by 16 publications

(3 citation statements)

References 46 publications

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“…As Zeb treatment is associated with loss of DNA methylation, we anticipated that changes in phenotype should behave as a dominant, gain‐of‐function trait. Two treated plants (Z11 and Z307) had a subcompact spike (E Jean Finnegan, unpublished), similar to that seen in plants with elevated expression of the domestication gene Q (Förster, Schumann, Baumann, Weber, & Pillen, ; Greenwood, Finnegan, Watanabe, Trevaskis, & Swain, ; Simons et al, ). This phenotype was transmitted to subsequent generations of line Z11 and will be reported elsewhere.…”

Section: Resultsmentioning

confidence: 68%

Zebularine treatment is associated with deletion of FT‐B1 leading to an increase in spikelet number in bread wheat

Finnegan

Ford

Wallace

et al. 2018

Plant Cell & Environment

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The number of rachis nodes (spikelets) on a wheat spike is a component of grain yield that correlates with flowering time. The genetic basis regulating flowering in cereals is well understood, but there are reports that flowering time can be modified at a high frequency by selective breeding, suggesting that it may be regulated by both epigenetic and genetic mechanisms. We investigated the role of DNA methylation in regulating spikelet number and flowering time by treating a semi-spring wheat with the demethylating agent, Zebularine. Three lines with a heritable increase in spikelet number were identified. The molecular basis for increased spikelet number was not determined in 2 lines, but the phenotype showed non-Mendelian inheritance, suggesting that it could have an epigenetic basis. In the remaining line, the increased spikelet phenotype behaved as a Mendelian recessive trait and late flowering was associated with a deletion encompassing the floral promoter, FT-B1. Deletion of FT-B1 delayed the transition to reproductive growth, extended the duration of spike development, and increased spikelet number under different temperature regimes and photoperiod. Transiently disrupting DNA methylation can generate novel flowering behaviour in wheat, but these changes may not be sufficiently stable for use in breeding programs.

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Section: Resultsmentioning

confidence: 68%

Zebularine treatment is associated with deletion of FT‐B1 leading to an increase in spikelet number in bread wheat

Finnegan

Ford

Wallace

et al. 2018

Plant Cell & Environment

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“…Besides, gene dosage (isoform number) increase of most carotenoid biosynthetic-related genes could also accelerate the carotenoid accumulation. Previous studies revealed gene dosage balance impacts on agronomic traits in plants, and defined the linkage between quantitative trait and gene dosage variation [44,45,46]. Consequently, we might imply that the gene dosage variation and the associated changes in gene expression of these unigenes might be important for controlling the carotenoid contents in avocado during the mesocarp and seed developmental stage.…”

Section: Discussionmentioning

confidence: 91%

Transcriptome Profiling Provides Insight into the Genes in Carotenoid Biosynthesis during the Mesocarp and Seed Developmental Stages of Avocado (Persea americana)

Cheng

et al. 2019

IJMS

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Avocado (Persea americana Mill.) is an economically important crop because of its high nutritional value. However, the absence of a sequenced avocado reference genome has hindered investigations of secondary metabolism. For next-generation high-throughput transcriptome sequencing, we obtained 365,615,152 and 348,623,402 clean reads as well as 109.13 and 104.10 Gb of sequencing data for avocado mesocarp and seed, respectively, during five developmental stages. High-quality reads were assembled into 100,837 unigenes with an average length of 847.40 bp (N50 = 1725 bp). Additionally, 16,903 differentially expressed genes (DEGs) were detected, 17 of which were related to carotenoid biosynthesis. The expression levels of most of these 17 DEGs were higher in the mesocarp than in the seed during five developmental stages. In this study, the avocado mesocarp and seed transcriptome were also sequenced using single-molecule long-read sequencing to acquired 25.79 and 17.67 Gb clean data, respectively. We identified 233,014 and 238,219 consensus isoforms in avocado mesocarp and seed, respectively. Furthermore, 104 and 59 isoforms were found to correspond to the putative 11 carotenoid biosynthetic-related genes in the avocado mesocarp and seed, respectively. The isoform numbers of 10 out of the putative 11 genes involved in the carotenoid biosynthetic pathway were higher in the mesocarp than those in the seed. Besides, alpha- and beta-carotene contents in the avocado mesocarp and seed during five developmental stages were also measured, and they were higher in the mesocarp than in the seed, which validated the results of transcriptome profiling. Gene expression changes and the associated variations in gene dosage could influence carotenoid biosynthesis. These results will help to further elucidate carotenoid biosynthesis in avocado.

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“…The Q allele was the result of a spontaneous mutation in the miRNA172-binding region of the q allele in wild wheat, which increased the Q expression level [ 37 ]. The Q allele confers the free-threshing characteristic of wheat and influences several domestication-related traits, including rachis fragility, glume toughness, spike architecture, flowering time, and plant height [ 37 , 38 , 43 , 44 , 45 , 46 , 47 ]. The Q c1 allele originated from a point mutation within the miRNA172-binding region of the Q allele, which decreases the miRNA172-directed cleavage of Q c1 transcripts, thereby leading to increased expression levels and enhanced wheat bread-making quality [ 40 ].…”

Section: Discussionmentioning

confidence: 99%

The Qc5 Allele Increases Wheat Bread-Making Quality by Regulating SPA and SPR

Guo

Chen

Zhu

et al. 2022

IJMS

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Common wheat (Triticum aestivum L.) is an important food crop with a unique processing quality. The Q gene positively regulates the processing quality of wheat, but the underlying mechanism remains unclear. Here, a new Q allele (Qc5) responsible for compact spikes and good bread performance was identified. Compared with the Q allele widely distributed in modern common wheat cultivars, Qc5 had a missense mutation outside the miRNA172-binding site. This missense mutation led to a more compact messenger RNA (mRNA) secondary structure around the miRNA172-binding region, resulting in increased Qc5 expression during the spike development stage and a consequent increase in spike density. Furthermore, this missense mutation weakened the physical interaction between Qc5 and storage protein activator (SPA) in seeds and suppressed the expression of storage protein repressor (SPR). These changes increased the grain protein content and improved the bread-making quality of wheat. In conclusion, a missense mutation increases Q expression because of the resulting highly folded mRNA secondary structure around the miRNA172-binding site. Furthermore, this mutation improves the bread-making quality of wheat by repressing the expression of SPR and influencing the physical interaction between Q and SPA. These findings provide new insights into the miRNA172-directed regulation of gene expression, with implications for wheat breeding.

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Copy number variation of chromosome 5A and its association with Q gene expression, morphological aberrations, and agronomic performance of winter wheat cultivars

Cited by 16 publications

References 46 publications

Zebularine treatment is associated with deletion of FT‐B1 leading to an increase in spikelet number in bread wheat

Zebularine treatment is associated with deletion of FT‐B1 leading to an increase in spikelet number in bread wheat

Transcriptome Profiling Provides Insight into the Genes in Carotenoid Biosynthesis during the Mesocarp and Seed Developmental Stages of Avocado (Persea americana)

The Qc5 Allele Increases Wheat Bread-Making Quality by Regulating SPA and SPR

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