Creating novel <i>Wx</i> alleles with fine‐tuned amylose levels and improved grain quality in rice by promoter editing using CRISPR/Cas9 system

Huang, Li‐Chun; Li, Qianfeng; Zhang, Changquan; Chu, Rui; Gu, Zhengwen; Tan, Hongyan; Zhao, Dongsheng; Fan, Xiaolei

doi:10.1111/pbi.13391

Cited by 133 publications

(79 citation statements)

References 12 publications

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“…Recent studies have generated a series of glutinous rice mutants by editing the Wx coding sequence using CRISPR/Cas9 (Ma et al, 2015; Zhang et al, 2018). Likewise, we have created a series of rice lines with fine‐turned AC levels by editing the Wx promoter core regions via CRISPR/Cas9 editing (Huang et al, 2020).…”

Section: Discussionmentioning

confidence: 99%

A rare Waxy allele coordinately improves rice eating and cooking quality and grain transparency

Zhang

Yang

Chen

et al. 2020

JIPB

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In rice (Oryza sativa), amylose content (AC) is the major factor that determines eating and cooking quality (ECQ). The diversity in AC is largely attributed to natural allelic variation at the Waxy (Wx) locus. Here we identified a rare Wx allele, Wxmw, which combines a favorable AC, improved ECQ and grain transparency. Based on a phylogenetic analysis of Wx genomic sequences from 370 rice accessions, we speculated that Wxmw may have derived from recombination between two important natural Wx alleles, Wxin and Wxb. We validated the effects of Wxmw on rice grain quality using both transgenic lines and near‐isogenic lines (NILs). When introgressed into the japonica Nipponbare (NIP) background, Wxmw resulted in a moderate AC that was intermediate between that of NILs carrying the Wxb allele and NILs with the Wxmp allele. Notably, mature grains of NILs fixed for Wxmw had an improved transparent endosperm relative to soft rice. Further, we introduced Wxmw into a high‐yielding japonica cultivar via molecular marker‐assisted selection: the introgressed lines exhibited clear improvements in ECQ and endosperm transparency. Our results suggest that Wxmw is a promising allele to improve grain quality, especially ECQ and grain transparency of high‐yielding japonica cultivars, in rice breeding programs.

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Section: Discussionmentioning

confidence: 99%

A rare Waxy allele coordinately improves rice eating and cooking quality and grain transparency

Zhang

Yang

Chen

et al. 2020

JIPB

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“…Over the past decade, a new genome editing technology called CRISPR/Cas9 has emerged, providing a simple and more accurate tool for creating targeted mutations (Mussolino and Cathomen 2013;Chen et al 2019;Manghwar et al 2019). This system has been applied to create new alleles for rice improvement (Shen et al 2017;Huang et al 2020;Li et al 2020b;Zeng et al 2020).…”

Section: Electronic Supplementary Materialsmentioning

confidence: 99%

Identification through fine mapping and verification using CRISPR/Cas9-targeted mutagenesis for a minor QTL controlling grain weight in rice

et al. 2020

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Key message A minor QTL for grain weight in rice, qTGW1.2b, was fine-mapped. Its casual gene OsVQ4 was confirmed through CRISPR/Cas9-targeted mutagenesis, exhibiting an effect that was larger than the original QTL effect. Abstract The CRISPR/Cas system exhibits a great potential for rice improvement, but the application was severely hindered due to insufficient target genes, especial the lack of validated genes underlying quantitative trait loci having small effects. In this study, a minor QTL for grain weight, qTGW1.2b, was fine-mapped into a 44.0 kb region using seven sets of near isogenic lines (NILs) developed from the indica rice cross (Zhenshan 97)3/Milyang 46, followed by validation of the causal gene using CRISPR/Cas9-targeted mutagenesis. In the NIL populations, 1000-grain weight of the Zhenshan 97 homozygous lines decreased by 0.9–2.0% compared with the Milyang 46 homozygous lines. A gene encoding VQ-motif protein, OsVQ4, was identified as the candidate gene based on parental sequence differences. The effect of OsVQ4 was confirmed by creating CRISPR/Cas9 knockout lines, whose 1000-grain weight decreased by 2.8–9.8% compared with the wild-type transgenic line and the recipient. These results indicate that applying genome editing system could create novel alleles with large phenotypic variation at minor QTLs, which is an effective way to validate causal genes of minor QTLs. Our study establishes a strategy for cloning minor QTLs, which could also be used to identify a large number of potential target genes for the application of CRISPR/Cas system.

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“…Interestingly, the morphologies of different Arabidopsis gi mutants differ drastically, implying that different parts of the GI protein are involved in diverse biological functions, and mutations in different parts of this protein could thus lead to quite different phenotypes (Mishra and Panigrahi, 2015). Based on this information, strategic modifications of GmGIa by genome editing may result in other possible changes to soybean as what researchers have done on the rice waxy gene (Chen and Mas, 2019;Huang et al, 2020). Although we have gained some knowledge of the soybean circadian clock components, in that they have crucial impacts on growth and development, the mechanisms of their actual involvement in the clock is still largely unknown.…”

Section: Discussionmentioning

confidence: 98%

The Modification of Circadian Clock Components in Soybean During Domestication and Improvement

Lam

2020

Front. Genet.

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Agricultural production is greatly dependent on daylength, which is determined by latitude. Living organisms align their physiology to daylength through the circadian clock, which is made up of input sensors, core and peripheral clock components, and output. The light/dark cycle is the major input signal, moderated by temperature fluctuations and metabolic changes. The core clock in plants functions mainly through a number of transcription feedback loops. It is known that the circadian clock is not essential for survival. However, alterations in the clock components can lead to substantial changes in physiology. Thus, these clock components have become the de facto targets of artificial selection for crop improvement during domestication. Soybean was domesticated around 5,000 years ago. Although the circadian clock itself is not of particular interest to soybean breeders, specific alleles of the circadian clock components that affect agronomic traits, such as plant architecture, sensitivity to light/dark cycle, flowering time, maturation time, and yield, are. Consequently, compared to their wild relatives, cultivated soybeans have been bred to be more adaptive and productive at different latitudes and habitats for acreage expansion, even though the selection processes were made without any prior knowledge of the circadian clock. Now with the advances in comparative genomics, known modifications in the circadian clock component genes in cultivated soybean have been found, supporting the hypothesis that modifications of the clock are important for crop improvement. In this review, we will summarize the known modifications in soybean circadian clock components as a result of domestication and improvement. In addition to the well-studied effects on developmental timing, we will also discuss the potential of circadian clock modifications for improving other aspects of soybean productivity.

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Creating novel Wx alleles with fine‐tuned amylose levels and improved grain quality in rice by promoter editing using CRISPR/Cas9 system

Cited by 133 publications

References 12 publications

A rare Waxy allele coordinately improves rice eating and cooking quality and grain transparency

A rare Waxy allele coordinately improves rice eating and cooking quality and grain transparency

Identification through fine mapping and verification using CRISPR/Cas9-targeted mutagenesis for a minor QTL controlling grain weight in rice

The Modification of Circadian Clock Components in Soybean During Domestication and Improvement

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