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Genome editing in Wheat

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https://www.readbyqxmd.com/read/30029701/food-processing-and-breeding-strategies-for-coeliac-safe-and-healthy-wheat-products
#1
Aurélie Jouanin, Luud J W J Gilissen, Lesley A Boyd, James Cockram, Fiona J Leigh, Emma J Wallington, Hetty C van den Broeck, Ingrid M van der Meer, Jan G Schaart, Richard G F Visser, Marinus J M Smulders
A strict gluten-free diet is currently the only treatment for the 1-2% of the world population who suffer from coeliac disease (CD). However, due to the presence of wheat and wheat derivatives in many food products, avoiding gluten consumption is difficult. Gluten-free products, made without wheat, barley or rye, typically require the inclusion of numerous additives, resulting in products that are often less healthy than gluten-based equivalents. Here, we present and discuss two broad approaches to decrease wheat gluten immunogenicity for CD patients...
August 2018: Food Research International
https://www.readbyqxmd.com/read/29959543/advancing-agrobacterium-based-crop-transformation-and-genome-modification-technology-for-agricultural-biotechnology
#2
Ajith Anand, Todd J Jones
The last decade has seen significant strides in Agrobacterium-mediated plant transformation technology. This has not only expanded the number of crop species that can be transformed by Agrobacterium, but has also made it possible to routinely transform several recalcitrant crop species including cereals (e.g., maize, sorghum, and wheat). However, the technology is limited by the random nature of DNA insertions, genotype dependency, low frequency of quality events, and variation in gene expression arising from genomic insertion sites...
June 30, 2018: Current Topics in Microbiology and Immunology
https://www.readbyqxmd.com/read/29734518/zinc-finger-nuclease-mediated-precision-genome-editing-of-an-endogenous-gene-in-hexaploid-bread-wheat-triticum-aestivum-using-a-dna-repair-template
#3
Yidong Ran, Nicola Patron, Pippa Kay, Debbie Wong, Margaret Buchanan, Ying-Ying Cao, Tim Sawbridge, John P Davies, John Mason, Steven R Webb, German Spangenberg, William M Ainley, Terence A Walsh, Matthew J Hayden
Sequence-specific nucleases have been used to engineer targeted genome modifications in various plants. While targeted gene knockouts resulting in loss of function have been reported with relatively high rates of success, targeted gene editing using an exogenously supplied DNA repair template and site-specific transgene integration has been more challenging. Here, we report the first application of zinc finger nuclease (ZFN)-mediated, nonhomologous end-joining (NHEJ)-directed editing of a native gene in allohexaploid bread wheat to introduce, via a supplied DNA repair template, a specific single amino acid change into the coding sequence of acetohydroxyacid synthase (AHAS) to confer resistance to imidazolinone herbicides...
May 7, 2018: Plant Biotechnology Journal
https://www.readbyqxmd.com/read/29723918/genotyping-genome-edited-mutations-in-plants-using-crispr-ribonucleoprotein-complexes
#4
Zhen Liang, Kunling Chen, Yan Yan, Yi Zhang, Caixia Gao
Despite the great achievements in genome editing, accurately detecting mutations induced by sequence-specific nucleases is still a challenge in plants, especially in polyploidy plants. An efficient detection method is particularly vital when the mutation frequency is low or when a large population needs to be screened. Here, we applied purified CRISPR ribonucleoprotein complexes to cleave PCR products for genome-edited mutation detection in hexaploid wheat and diploid rice. We show that this mutation detection method is more sensitive than Sanger sequencing and more applicable than PCR/RE method without the requirement for restriction enzyme site...
May 3, 2018: Plant Biotechnology Journal
https://www.readbyqxmd.com/read/29722792/alphamate-a-program-for-optimising-selection-maintenance-of-diversity-and-mate-allocation-in-breeding-programs
#5
Gregor Gorjanc, John M Hickey
Summary: AlphaMate is a flexible program that optimises selection, maintenance of genetic diversity, and mate allocation in breeding programs. It can be used in animal and cross- and self-pollinating plant populations. These populations can be subject to selective breeding or conservation management. The problem is formulated as a multi-objective optimisation of a valid mating plan that is solved with an evolutionary algorithm. A valid mating plan is defined by a combination of mating constraints (the number of matings, the maximal number of parents, the minimal/equal/maximal number of contributions per parent, or allowance for selfing) that are gender specific or generic...
May 2, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29710373/transforming-plant-biology-and-breeding-with-crispr-cas9-cas12-and-cas13
#6
REVIEW
Patrick Schindele, Felix Wolter, Holger Puchta
Currently, biology is revolutionized by ever growing applications of the CRISPR/Cas system. As discussed in this Review, new avenues have opened up for plant research and breeding by the use of the sequence-specific DNases Cas9 and Cas12 (formerly named Cpf1) and, more recently, the RNase Cas13 (formerly named C2c2). Although double strand break-induced gene editing based on error-prone nonhomologous end joining has been applied to obtain new traits, such as powdery mildew resistance in wheat or improved pathogen resistance and increased yield in tomato, improved technologies based on CRISPR/Cas for programmed change in plant genomes via homologous recombination have recently been developed...
June 2018: FEBS Letters
https://www.readbyqxmd.com/read/29695804/targeted-mutagenesis-in-wheat-microspores-using-crispr-cas9
#7
Pankaj Bhowmik, Evan Ellison, Brittany Polley, Venkatesh Bollina, Manoj Kulkarni, Kaveh Ghanbarnia, Halim Song, Caixia Gao, Daniel F Voytas, Sateesh Kagale
CRISPR/Cas9 genome editing is a transformative technology that will facilitate the development of crops to meet future demands. However, application of gene editing is hindered by the long life cycle of many crop species and because desired genotypes generally require multiple generations to achieve. Single-celled microspores are haploid cells that can develop into double haploid plants and have been widely used as a breeding tool to generate homozygous plants within a generation. In this study, we combined the CRISPR/Cas9 system with microspore technology and developed an optimized haploid mutagenesis system to induce genetic modifications in the wheat genome...
April 25, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29559984/rnai-mediated-downregulation-of-inositol-pentakisphosphate-kinase-ipk1-in-wheat-grains-decreases-phytic-acid-levels-and-increases-fe-and-zn-accumulation
#8
Sipla Aggarwal, Anil Kumar, Kaushal K Bhati, Gazaldeep Kaur, Vishnu Shukla, Siddharth Tiwari, Ajay K Pandey
Enhancement of micronutrient bioavailability is crucial to address the malnutrition in the developing countries. Various approaches employed to address the micronutrient bioavailability are showing promising signs, especially in cereal crops. Phytic acid (PA) is considered as a major antinutrient due to its ability to chelate important micronutrients and thereby restricting their bioavailability. Therefore, manipulating PA biosynthesis pathway has largely been explored to overcome the pleiotropic effect in different crop species...
2018: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29516116/tilling-the-next-generation
#9
Bradley J Till, Sneha Datta, Joanna Jankowicz-Cieslak
Gene space: the final frontier in plant functional genomics. These are the voyages of TILLING, the reverse-genetics strategy that sought to boldly go where no-one had gone before by combining high-density chemical mutagenesis with high-throughput mutation discovery. Its 18-year mission has been to explore new technologies such as next generation sequencing and to seek out new strategies like in silico databases of catalogued EMS-induced mutations from entire mutant plant populations. This chapter is a clip show highlighting key milestones in the development of TILLING...
March 8, 2018: Advances in Biochemical Engineering/biotechnology
https://www.readbyqxmd.com/read/29472693/a-new-allele-of-the-brachytic2-gene-in-maize-can-efficiently-modify-plant-architecture
#10
Lai Wei, Xuan Zhang, Zhihai Zhang, Huanhuan Liu, Zhongwei Lin
The applications of semi-dwarf genes such as sd1 and Rht1 in rice and wheat resulted in the first "green revolution" in the 1960s. However, such semi-dwarf genes that can efficiently reduce plant stature and have few negative yield traits have not yet been identified in maize. In this study, a new allele of Brachytic2 gene (qpa1) encoding P-glycoprotein was rapidly fine-mapped using a modified method. The qpa1, containing a 241-bp deletion in the last exon, had no negative effect on yield, but greatly modified the plant architecture including significantly reduced plant height and ear height, increased stalk diameter and erected leaf...
July 2018: Heredity
https://www.readbyqxmd.com/read/29388938/genome-editing-of-bread-wheat-using-biolistic-delivery-of-crispr-cas9-in-vitro-transcripts-or-ribonucleoproteins
#11
Zhen Liang, Kunling Chen, Yi Zhang, Jinxing Liu, Kangquan Yin, Jin-Long Qiu, Caixia Gao
This protocol is an extension to: Nat. Protoc. 9, 2395-2410 (2014); doi:10.1038/nprot.2014.157; published online 18 September 2014In recent years, CRISPR/Cas9 has emerged as a powerful tool for improving crop traits. Conventional plant genome editing mainly relies on plasmid-carrying cassettes delivered by Agrobacterium or particle bombardment. Here, we describe DNA-free editing of bread wheat by delivering in vitro transcripts (IVTs) or ribonucleoprotein complexes (RNPs) of CRISPR/Cas9 by particle bombardment...
March 2018: Nature Protocols
https://www.readbyqxmd.com/read/29259968/drought-response-in-wheat-key-genes-and-regulatory-mechanisms-controlling-root-system-architecture-and-transpiration-efficiency
#12
REVIEW
Manoj Kulkarni, Raju Soolanayakanahally, Satoshi Ogawa, Yusaku Uga, Michael G Selvaraj, Sateesh Kagale
Abiotic stresses such as, drought, heat, salinity, and flooding threaten global food security. Crop genetic improvement with increased resilience to abiotic stresses is a critical component of crop breeding strategies. Wheat is an important cereal crop and a staple food source globally. Enhanced drought tolerance in wheat is critical for sustainable food production and global food security. Recent advances in drought tolerance research have uncovered many key genes and transcription regulators governing morpho-physiological traits...
2017: Frontiers in Chemistry
https://www.readbyqxmd.com/read/29240874/wheat-genetic-resources-in-the-post-genomics-era-promise-and-challenges
#13
Awais Rasheed, Abdul Mujeeb-Kazi, Francis Chuks Ogbonnaya, Zhonghu He, Sanjaya Rajaram
Background: Wheat genetic resources have been used for genetic improvement since 1876, when Stephen Wilson (Transactions and Proceedings of the Botanical Society of Edinburgh 12: 286) consciously made the first wide hybrid involving wheat and rye in Scotland. Wide crossing continued with sporadic attempts in the first half of 19th century and became a sophisticated scientific discipline during the last few decades with considerable impact in farmers' fields. However, a large diversity of untapped genetic resources could contribute in meeting future wheat production challenges...
March 14, 2018: Annals of Botany
https://www.readbyqxmd.com/read/29158641/development-of-an-efficient-and-reproducible-regeneration-system-in-wheat-triticum-aestivum-l
#14
Rakesh Kumar, Harohalli Masthigowda Mamrutha, Amandeep Kaur, Karnam Venkatesh, Anita Grewal, Raj Kumar, Vinod Tiwari
The availability of reproducible regeneration system through tissue culture is a major bottleneck in wheat improvement program. The present study has considered to develop an efficient callus induction and regeneration system using mature and immature embryos as explants in recently released agronomically superior spring wheat varieties. An efficient sterilization process was standardized using 0.1% HgCl2 and 70% ethanol for both seeds and embryos. The maximum possible combinations of plant growth regulators (PGRs) were evaluated for their effect on different wheat regeneration processes through tissue culture starting from callus to root induction...
October 2017: Physiology and Molecular Biology of Plants: An International Journal of Functional Plant Biology
https://www.readbyqxmd.com/read/29102241/from-genetic-stock-to-genome-editing-gene-exploitation-in-wheat
#15
REVIEW
Meng Wang, Shubin Wang, Zhen Liang, Weiming Shi, Caixia Gao, Guangmin Xia
Bread wheat (Triticum aestivum) ranks as one of our most important staple crops. However, its hexaploid nature has complicated our understanding of the genetic bases underlying many of its traits. Historically, functional genetic studies in wheat have focused on identifying natural variations and have contributed to assembling and enriching its genetic stock. Recently, mold-breaking advances in whole genome sequencing, exome-capture based mutant libraries, and genome editing have revolutionized strategies for genetic research in wheat...
February 2018: Trends in Biotechnology
https://www.readbyqxmd.com/read/28934591/combining-traditional-mutagenesis-with-new-high-throughput-sequencing-and-genome-editing-to-reveal-hidden-variation-in-polyploid-wheat
#16
REVIEW
Cristobal Uauy, Brande B H Wulff, Jorge Dubcovsky
Induced mutations have been used to generate novel variation for breeding purposes since the early 1900s. However, the combination of this old technology with the new capabilities of high-throughput sequencing has resulted in powerful reverse genetic approaches in polyploid crops. Sequencing genomes or exomes of large mutant populations can generate extensive databases of mutations for most genes. These mutant collections, together with genome editing, are being used in polyploid species to combine mutations in all copies of a gene (homoeologs), and to expose phenotypic variation that was previously hidden by functional redundancy among homoeologs...
November 27, 2017: Annual Review of Genetics
https://www.readbyqxmd.com/read/28918562/crispr-cas9-genome-editing-in-wheat
#17
Dongjin Kim, Burcu Alptekin, Hikmet Budak
Genome editing has been a long-term challenge for molecular biology research, particularly for plants possess complex genome. The recently discovered Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) system is a versatile tool for genome editing which enables editing of multiple genes based on the guidance of small RNAs. Even though the efficiency of CRISPR/Cas9 system has been shown with several studies from diploid plants, its application remains a challenge for plants with polyploid and complex genome...
January 2018: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/28913791/enabling-molecular-technologies-for-trait-improvement-in-wheat
#18
REVIEW
Prem L Bhalla, Akanksha Sharma, Mohan B Singh
Wheat is the major staple food crop and a source of calories for humans worldwide. A steady increase in the wheat production is essential to meet the demands of an ever-increasing global population and to achieve food security. The large size and structurally intricate genome of polyploid wheat had hindered the genomic analysis. However, with the advent of new genomic technologies such as next generation sequencing has led to genome drafts for bread wheat and its progenitors and has paved the way to design new strategies for crop improvement...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28871543/respiration-traits-as-novel-markers-for-plant-robustness-under-the-threat-of-climate-change-a-protocol-for-validation
#19
Birgit Arnholdt-Schmitt
Respiration traits allow calculating temperature-dependent carbon use efficiency and prediction of growth rates. This protocol aims (1) to enable validation of respiration traits as non-DNA biomarkers for breeding on robust plants in support of sustainable and healthy plant production; (2) to provide an efficient, novel way to identify and predict functionality of DNA-based markers (genes, polymorphisms, edited genes, transgenes, genomes, and hologenomes), and (3) to directly help farmers select robust material appropriate for a specified region...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28827167/breeding-major-cereal-grains-through-the-lens-of-nutrition-sensitivity
#20
REVIEW
Shu Yu, Li Tian
Cereal grains are the common food staples that collectively provide over 50% of dietary calories and proteins for the world's population. Although the Green Revolution has greatly increased the yield of commercial cereal crops, they often lack nutrients essential for human health in the edible tissues. In developing nutrition-sensitive agriculture, the nutritional quality of cereal grains has been a major target for improvement using breeding and biotechnology approaches. This review examines recent progress on biofortification of micronutrients (provitamin A and folates) and an essential amino acid (lysine) in three major cereal grains, wheat, rice, and maize, through plant breeding...
January 8, 2018: Molecular Plant
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