Genes for NUE in rice: a way forward for molecular breeding and genome editing

Abstract This chapter defines nutrient-use efficiency and the relevance of nitrogen (N) and phosphorus (P) as essential macronutrients and the molecular regulation of their metabolism in maize. The efforts towards molecular breeding of maize to improve NUE and PUE are also summarized and discussed. Plant phenotyping as one of the main and challenging components of molecular breeding and the potential of genome editing approaches to implement current findings on maize are addressed.

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Development of CRISPR_Cas9 genome editing system and its application in rice molecular breeding

In Vitro Cellular & Developmental Biology - Plant ◽

10.1007/s11627-021-10203-2 ◽

2021 ◽

Author(s):

Zengfeng Ma ◽

Minyi Wei ◽

Yuexiong Zhang ◽

Gang Qin ◽

Chi Liu ◽

...

Keyword(s):

Genome Editing ◽

Molecular Breeding

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Transgenic and genome-edited fruits: background, constraints, benefits, and commercial opportunities

Horticulture Research ◽

10.1038/s41438-021-00601-3 ◽

2021 ◽

Vol 8 (1) ◽

Author(s):

Maria Lobato-Gómez ◽

Seanna Hewitt ◽

Teresa Capell ◽

Paul Christou ◽

Amit Dhingra ◽

...

Keyword(s):

Genome Editing ◽

Molecular Breeding ◽

Genetically Engineered ◽

Socioeconomic Impact ◽

New Wave ◽

Improved Cultivars ◽

Potential Impact ◽

Commercial Introduction ◽

Breeding Techniques ◽

Insect Resistant

AbstractBreeding has been used successfully for many years in the fruit industry, giving rise to most of today’s commercial fruit cultivars. More recently, new molecular breeding techniques have addressed some of the constraints of conventional breeding. However, the development and commercial introduction of such novel fruits has been slow and limited with only five genetically engineered fruits currently produced as commercial varieties—virus-resistant papaya and squash were commercialized 25 years ago, whereas insect-resistant eggplant, non-browning apple, and pink-fleshed pineapple have been approved for commercialization within the last 6 years and production continues to increase every year. Advances in molecular genetics, particularly the new wave of genome editing technologies, provide opportunities to develop new fruit cultivars more rapidly. Our review, emphasizes the socioeconomic impact of current commercial fruit cultivars developed by genetic engineering and the potential impact of genome editing on the development of improved cultivars at an accelerated rate.

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Optimizing the CRISPR/Cas9 system for genome editing in grape by using grape promoters

Horticulture Research ◽

10.1038/s41438-021-00489-z ◽

2021 ◽

Vol 8 (1) ◽

Author(s):

Chong Ren ◽

Yanfei Liu ◽

Yuchen Guo ◽

Wei Duan ◽

Peige Fan ◽

...

Keyword(s):

Genome Editing ◽

Molecular Breeding ◽

Basic Research ◽

Phytoene Desaturase ◽

Sugar Accumulation ◽

Monosaccharide Transporter ◽

Grape Genome ◽

Tobacco Genome ◽

Sugar Levels

AbstractThe efficacy of the CRISPR/Cas9 system in grapevine (Vitis vinifera L.) has been documented, but the optimization of this system, as well as CRISPR/Cas9-mediated multiplex genome editing, has not been explored in this species. Herein, we identified four VvU3 and VvU6 promoters and two ubiquitin (UBQ) promoters in grapevine and demonstrated that the use of the identified VvU3/U6 and UBQ2 promoters could significantly increase the editing efficiency in grape by improving the expression of sgRNA and Cas9, respectively. Furthermore, we conducted multiplex genome editing using the optimized CRISPR/Cas9 vector that contained the conventional multiple sgRNA expression cassettes or the polycistronic tRNA-sgRNA cassette (PTG) by targeting the sugar-related tonoplastic monosaccharide transporter (TMT) family members TMT1 and TMT2, and the overall editing efficiencies were higher than 10%. The simultaneous editing of TMT1 and TMT2 resulted in reduced sugar levels, which indicated the role of these two genes in sugar accumulation in grapes. Moreover, the activities of the VvU3, VvU6, and UBQ2 promoters in tobacco genome editing were demonstrated by editing the phytoene desaturase (PDS) gene in Nicotiana benthamiana leaves. Our study provides materials for the optimization of the CRISPR/Cas9 system. To our knowledge, our simultaneous editing of the grape TMT family genes TMT1 and TMT2 constitutes the first example of multiplex genome editing in grape. The multiplex editing systems described in this manuscript expand the toolbox of grape genome editing, which would facilitate basic research and molecular breeding in grapevine.

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A Reliable Regeneration Method in Genome-Editable Bell Pepper ‘Dempsey’

Horticulturae ◽

10.3390/horticulturae7090317 ◽

2021 ◽

Vol 7 (9) ◽

pp. 317

Author(s):

Kang-Hee Won ◽

Sung-il Park ◽

Jisun Choi ◽

Hyun Hee Kim ◽

Byoung-Cheorl Kang ◽

...

Keyword(s):

Acetic Acid ◽

Genome Editing ◽

Molecular Breeding ◽

Cellular Level ◽

Bell Pepper ◽

Induction Medium ◽

Shoot Induction ◽

Shoot Induction Medium ◽

Indole 3 Acetic Acid ◽

Fertile Seed

A reliable regeneration technique is critical for the improvement of pepper traits in the genome editing era. Recently, we reported that peppers were successfully and specifically edited using CRISPR tools, CRISPR/Cas9 and CRISPR/Cas12a (LbCpf1). Although genome-editing tools can be applied to modify peppers at the cellular level, feasible pepper regeneration techniques have not been developed. Therefore, we studied a pepper regeneration protocol for Capsicum annuum L. ‘Dempsey’, a bell pepper species that has been proven to be genome-editable. Three explant types were used in this study, including the first leaves, cotyledons and hypocotyls of pepper seedlings. The shoot buds of the tested explants were produced using 8 mg/L 6-benzylaminopurine (BAP)- and 6 mg/L indole-3-acetic acid (IAA)-containing shoot induction medium (SIM). The first leaves of the ‘Dempsey’ seedlings showed an average shooting rate of 69.8%, whereas the hypocotyls and cotyledons had approximately 25.5% and 19.5% shooting rates, respectively. The regenerated ‘Dempsey’ plants exhibited no alterations in fruit and fertile seed phenotypes. Furthermore, the parent ‘Dempsey’ and progenies of the regenerants were cytogenetically stable with the same chromosome numbers (2n = 24). Therefore, this regeneration protocol enables the precise molecular breeding of ‘Dempsey’ peppers when coupled with CRISPR tools.

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The genome sequence of tetraploid sweet basil, Ocimum basilicum L., provides tools for advanced genome editing and molecular breeding

DNA Research ◽

10.1093/dnares/dsaa027 ◽

2020 ◽

Vol 27 (5) ◽

Author(s):

Itay Gonda ◽

Adi Faigenboim ◽

Chen Adler ◽

Renana Milavski ◽

Merrie-Jean Karp ◽

...

Keyword(s):

Genome Editing ◽

Molecular Breeding ◽

Reference Genome ◽

Ocimum Basilicum ◽

Long Terminal Repeats ◽

Protein Coding ◽

Sweet Basil ◽

A Genome ◽

Draft Version ◽

Important Pathway

Abstract Sweet basil, Ocimum basilicum L., is a well-known culinary herb grown worldwide, but its uses go beyond the kitchen to traditional medicine, cosmetics and gardening. To date, the lack of an available reference genome has limited the utilization of advanced molecular breeding methods. We present a draft version of the sweet basil genome of the cultivar ‘Perrie’, a fresh-cut Genovese-type basil. Genome sequencing showed basil to be a tetraploid organism with a genome size of 2.13 Gbp, assembled in 12,212 scaffolds, with > 90% of the assembly being composed of 107 scaffolds. About 76% of the genome is composed of repetitive elements, with the majority being long-terminal repeats. We constructed and annotated 62,067 protein-coding genes and determined their expression in different plant tissues. We analysed the currently known phenylpropanoid volatiles biosynthesis genes. We demonstrated the necessity of the reference genome for a comprehensive understanding of this important pathway in the context of tetraploidy and gene redundancy. A complete reference genome is essential to overcome this redundancy and to avoid off-targeting when designing a CRISPR: Cas9-based genome editing research. This work bears promise for developing fast and accurate breeding tools to provide better cultivars for farmers and improved products for consumers.

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Efficient genome editing with CRISPR/Cas9 in Pleurotus ostreatus

AMB Express ◽

10.1186/s13568-021-01193-w ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Tatpong Boontawon ◽

Takehito Nakazawa ◽

Chikako Inoue ◽

Keishi Osakabe ◽

Moriyuki Kawauchi ◽

...

Keyword(s):

Genome Editing ◽

Pleurotus Ostreatus ◽

Molecular Breeding ◽

Heterologous Gene Expression ◽

Homology Directed Repair ◽

Guide Rnas ◽

Efficient Gene ◽

Fungal Protoplasts ◽

Resistant Strains ◽

Drug Resistant Strains

AbstractPleurotus ostreatus is one of the most commercially produced edible mushrooms worldwide. Improved cultivated strains with more useful traits have been obtained using classical breeding, which is laborious and time-consuming. Here, we attempted efficient gene mutagenesis using plasmid-based CRISPR/Cas9 as the first step for non-genetically modified (non-GM) P. ostreatus generation. Plasmids harboring expression cassettes of Cas9 and different single guide RNAs targeting fcy1 and pyrG were individually transferred into fungal protoplasts of the PC9 strain, which generated some strains exhibiting resistance to 5-fluorocytosine and 5-fluoroorotic acid, respectively. Genomic PCR followed by sequencing revealed small insertions/deletions or insertion of a fragment from the plasmid at the target site in some of the drug-resistant strains. The results demonstrated efficient CRISPR/Cas9-assisted genome editing in P. ostreatus, which could contribute to the molecular breeding of non-GM cultivated strains in the future. Furthermore, a mutation in fcy1 via homology-directed repair using this CRISPR/Cas9 system was also efficiently introduced, which could be applied not only for precise gene disruption, but also for insertions leading to heterologous gene expression in this fungus.

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Conventional Breeding, Molecular Breeding and Speed Breeding; Brave Approaches to Revamp the Production of Cereal Crops

10.20944/preprints202011.0667.v1 ◽

2020 ◽

Author(s):

Muhammad Haroon ◽

Muhammad Mubashar Zafar ◽

Muhammad Awais Farooq ◽

Rabail Afzal ◽

Maria Batool ◽

...

Keyword(s):

Genome Editing ◽

Molecular Breeding ◽

Epigenetic Modification ◽

Genomic Variation ◽

Cereal Crops ◽

Breeding Methods ◽

Breeding Method ◽

Base Editing ◽

Increase Food Production ◽

Crop Cycle

Conventional plant breeding methods exploit already existing genomic variation in plants to develop a variety in 8 to 10 years, which can decrease the genetic variability of the plant’s genome. The ever-increasing food demand for cereals crops cannot be met by traditional breeding methods. In order to increase food production in less time, there is a dire need to improve breeding methods. Several conventional and molecular breeding methods are being used to improve the crops traits. Molecular researchers have developed new genome editing tools like CRISPR/Cas9, CRISPR/Cpf1, prime editing, base editing, dcas9 epigenetic modification, and several other transgene-free genomes editing approaches. These genome editing tools can improve the desired traits precisely and efficiently. Moreover, a newly developed breeding method “Speed Breeding” has revolutionized the agriculture by shortening the crop cycle. It can produce 5-6 generations of cereals in a year. In this review, we have summarized all these conventional and molecular breeding approaches to improve cereal crops.

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Genome editing: Wollen wir das wirklich?

Lernen und Lernstörungen ◽

10.1024/2235-0977/a000184 ◽

2017 ◽

Vol 6 (3) ◽

pp. 162-162

Author(s):

Liane Kaufmann ◽

Michael von Aster

Keyword(s):

Genome Editing

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