Genome-Wide Sequencing of 41 Rice (Oryza sativa L.) Mutated Lines Reveals Diverse Mutations Induced by Fast-Neutron Irradiation

Li, Guotian; Chern, Mawsheng; Jain, Rashmi; Martin, Joel; Schackwitz, Wendy; Jiang, Liangrong; Vega‐Sánchez, Miguel E.; Lipzen, Anna; Barry, Kerrie; Schmutz, Jeremy; Ronald, Pamela C.

doi:10.1016/j.molp.2016.03.009

Cited by 80 publications

(124 citation statements)

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“…The positive transgenic lines were then transferred to greenhouses under the conditions described above. Genomic DNA was isolated from young leaves using the CTAB method [55]. The ubiquiin gene was used as the DNA quality control and the primers were Ubi/QF (5′-agaagcgcaagaagaagacg-3′) and Ubi/QR (5′-ccaccttgtagaactggagca-3′).…”

Section: Methodsmentioning

confidence: 99%

Overexpression of a rice BAHD acyltransferase gene in switchgrass (Panicum virgatum L.) enhances saccharification

Jones

Eudes

et al. 2018

BMC Biotechnol

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BackgroundSwitchgrass (Panicum virgatum L.) is a promising bioenergy feedstock because it can be grown on marginal land and produces abundant biomass. Recalcitrance of the lignocellulosic components of the switchgrass cell wall to enzymatic degradation into simple sugars impedes efficient biofuel production. We previously demonstrated that overexpression of OsAT10, a BAHD acyltransferase gene, enhances saccharification efficiency in rice.ResultsHere we show that overexpression of the rice OsAT10 gene in switchgrass decreased the levels of cell wall-bound ferulic acid (FA) in green leaf tissues and to a lesser extent in senesced tissues, and significantly increased levels of cell wall-bound p-coumaric acid (p-CA) in green leaves but decreased its level in senesced tissues of the T0 plants under greenhouse conditions. The engineered switchgrass lines exhibit an approximate 40% increase in saccharification efficiency in green tissues and a 30% increase in senesced tissues.ConclusionOur study demonstrates that overexpression of OsAT10, a rice BAHD acyltransferase gene, enhances saccharification of lignocellulosic biomass in switchgrass.Electronic supplementary materialThe online version of this article (10.1186/s12896-018-0464-8) contains supplementary material, which is available to authorized users.

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Section: Methodsmentioning

confidence: 99%

Overexpression of a rice BAHD acyltransferase gene in switchgrass (Panicum virgatum L.) enhances saccharification

Jones

Eudes

et al. 2018

BMC Biotechnol

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“…Hence, massive numbers of new genes have been identified, and functional analysis is required to decipher related biological traits and explore potential applications of these genes. A widely used approach in functional analysis is to generate mutations using chemical or physical agents (Kodym and Afza, 2003; Belfield et al, 2012; Hanafy and Mohamed, 2014; Serrat et al, 2014; Dhaliwal et al, 2015; Li et al, 2016; Zhang et al, 2016), T-DNA insertion (Weigel et al, 2000; Alonso et al, 2003), RNA interference (RNAi) (Kusaba, 2004; Mahmood-ur-Rahman et al, 2008; Wang et al, 2008, 2013), or genome editing (Shan et al, 2013; Wang et al, 2014; Kumar and Jain, 2015). However, those techniques often generate large numbers of mutants, and require tedious screening or genetic transformation procedures.…”

Section: Introductionmentioning

confidence: 99%

Vacuum and Co-cultivation Agroinfiltration of (Germinated) Seeds Results in Tobacco Rattle Virus (TRV) Mediated Whole-Plant Virus-Induced Gene Silencing (VIGS) in Wheat and Maize

Zhang

et al. 2017

Front. Plant Sci.

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Tobacco rattle virus (TRV)-mediated virus-induced gene silencing (VIGS) has been frequently used in dicots. Here we show that it can also be used in monocots, by presenting a system involving use of a novel infiltration solution (containing acetosyringone, cysteine, and Tween 20) that enables whole-plant level VIGS of (germinated) seeds in wheat and maize. Using the established system, phytoene desaturase (PDS) genes were successfully silenced, resulting in typical photo-bleaching symptoms in the leaves of treated wheat and maize. In addition, three wheat homoeoalleles of MLO, a key gene repressing defense responses to powdery mildew in wheat, were simultaneously silenced in susceptible wheat with this system, resulting in it becoming resistant to powdery mildew. The system has the advantages generally associated with TRV-mediated VIGS systems (e.g., high-efficiency, mild virus infection symptoms, and effectiveness in different organs). However, it also has the following further advantages: (germinated) seed-stage agroinfiltration; greater rapidity and convenience; whole-plant level gene silencing; adequately stable transformation; and suitability for studying functions of genes involved in seed germination and early plant development stages.

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“…Henry and L. Comai, unpublished). In contrast to what is emerging from gamma irradiation, whole-genome sequencing studies of fast neutronirradiated rice suggest a broader spectrum of mutations (Li et al 2016). The presence of large genomic deletions may make the task of cloning much easier.…”

Section: Cloning Mutant Alleles Causative For Improved Traitsmentioning

confidence: 92%

Mutagenesis for Crop Breeding and Functional Genomics

Jankowicz-Cieślak

Chikelu

Till

2016

Biotechnologies for Plant Mutation Breeding

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Genetic variation is a source of phenotypic diversity and is a major driver of evolutionary diversification. Heritable variation was observed and used thousands of years ago in the domestication of plants and animals. The mechanisms that govern the inheritance of traits were later described by Mendel. In the early decades of the twentieth century, scientists showed that the relatively slow rate of natural mutation could be increased by several orders of magnitude by treating Drosophila and cereals with X-rays. What is striking about these achievements is that they came in advance of experimental evidence that DNA is the heritable material. This highlights one major advantage of induced mutations for crop breeding: prior knowledge of genes or gene function is not required to successfully create plants with improved traits and to release new varieties. Indeed, mutation induction has been an important tool for crop breeding since the release of the first mutant variety of tobacco in the 1930s. In addition to plant mutation breeding, induced mutations have been used extensively for functional genomics in model organisms and crops. Novel reverse-genetic strategies, such as Targeting Induced Local Lesions IN Genomes (TILLING), are being used for the production of stable genetic stocks of mutant plant populations such as Arabidopsis, barley, soybean, tomato and wheat. These can be kept for many years and screened repeatedly for different traits. Robust and efficient methods are required for the seamless integration of induced mutations in breeding and functional genomics studies. This chapter provides an overview of the principles and methodologies that underpin the set of protocols and guidelines for the use of induced mutations to improve crops.

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Genome-Wide Sequencing of 41 Rice (Oryza sativa L.) Mutated Lines Reveals Diverse Mutations Induced by Fast-Neutron Irradiation

Abstract: for assistance with genomic DNA isolation and seed organization, and Dr. Catherine Nelson for critical reading of the manuscript. No conflict of interest declared.

Cited by 80 publications

References 12 publications

Overexpression of a rice BAHD acyltransferase gene in switchgrass (Panicum virgatum L.) enhances saccharification

Overexpression of a rice BAHD acyltransferase gene in switchgrass (Panicum virgatum L.) enhances saccharification

Vacuum and Co-cultivation Agroinfiltration of (Germinated) Seeds Results in Tobacco Rattle Virus (TRV) Mediated Whole-Plant Virus-Induced Gene Silencing (VIGS) in Wheat and Maize

Mutagenesis for Crop Breeding and Functional Genomics

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