Molecular Genetics, Genomics and Biotechnology of Crop Plants Breeding - Series Ⅱ

A special issue of Agronomy (ISSN 2073-4395). This special issue belongs to the section "Crop Breeding and Genetics".

Deadline for manuscript submissions: closed (31 March 2021) | Viewed by 49540

Special Issue Editor

Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Copenhagen, Denmark
Interests: mutational breeding; genome-wide association studies; quality traits; grain crops; molecular plant breeding
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Breeding crop plants for end-product use is greatly facilitated by DNA molecular markers. Quality traits of the top 10 grain crops that feed the world have to be maintained during breeding programmes to fulfil consumer expectations. Cost-efficient sequence technologies are available that allow markers to be developed even for orphan crops. Marker-assisted selection also facilitates the introgression of new site-directed mutation developed in a pre-breeding line into elite cultivars. Molecular markers make it possible to monitor F1 hybrid seed production and authenticity of plant-based products.

We welcome research papers and reviews on the use of molecular marker technologies, genomics selection, site-directed mutagenesis, gene-discovery by genome-wide association studies, and biotechnology in crop plants.

Prof. Søren Kjærsgaard Rasmussen
Guest Editor

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Keywords

  • Molecular markers technology
  • Reverse breeding
  • Genotyping-by-sequencing
  • Oligo-directed mutagenesis
  • Crispr/cas9 mutagenesis
  • Genome-wide association scan
  • Genomic selection and prediction
  • Genetic modification

Published Papers (12 papers)

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Editorial

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2 pages, 186 KiB  
Editorial
Molecular Genetics, Genomics and Biotechnology in Crop Plant Breeding, Series II
by Søren K. Rasmussen
Agronomy 2021, 11(8), 1577; https://doi.org/10.3390/agronomy11081577 - 09 Aug 2021
Viewed by 1716
Abstract
This second volume of this series of Special Issues provides research papers and reviews on the use of molecular marker technologies, genomics selection, site-directed mutagenesis, gene-discovery by genome-wide association studies and biotechnology in important grain crops, tubers, fruit bearing shrub and small fruit [...] Read more.
This second volume of this series of Special Issues provides research papers and reviews on the use of molecular marker technologies, genomics selection, site-directed mutagenesis, gene-discovery by genome-wide association studies and biotechnology in important grain crops, tubers, fruit bearing shrub and small fruit crops [...] Full article

Research

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16 pages, 5653 KiB  
Article
The Development of the Genic SSR Markers for Analysis of Genetic Diversity in Gooseberry Cultivars
by Elena O. Vidyagina, Vadim G. Lebedev, Natalya M. Subbotina, Ella I. Treschevskaya, Tatyana N. Lebedeva and Konstantin A. Shestibratov
Agronomy 2021, 11(6), 1050; https://0-doi-org.brum.beds.ac.uk/10.3390/agronomy11061050 - 24 May 2021
Cited by 5 | Viewed by 1974
Abstract
Gooseberry is one of the most promising and underrated small fruit crops. There is a need to improve and genotype the existing cultivars, and this work requires the use of new efficient DNA marking techniques. Marker-assisted selection (MAS) is a modern approach for [...] Read more.
Gooseberry is one of the most promising and underrated small fruit crops. There is a need to improve and genotype the existing cultivars, and this work requires the use of new efficient DNA marking techniques. Marker-assisted selection (MAS) is a modern approach for work with genetic resources. However, the genetic determinants of key qualitative traits are poorly studied. Therefore, we developed SSR markers located in flavonoid biosynthesis genes that can affect the resistance of plants to biotic and abiotic stresses to study the genetic diversity of gooseberry cultivars grown in the Russian Federation and varying in genetic and geographical origin. We have genotyped 22 gooseberry cultivars using a set of 19 of our original microsatellite markers and two neutral previously published ones. A total of 53 alleles were found. Nine of the 21 analyzed loci were polymorphic. The most polymorphic loci of flavonoid biosynthesis were found in the DFR gene (RucDFR1-2, RucDFR1-3, RucDFR2-1), their mean PIC (polymorphism information content) being 0.65, comparable to the PIC values of neutral markers. Our set of gene-targeted SSR markers showed that most of all the studied gooseberry cultivars differed in origin, based on which they were divided into three groups: European cultivars, Russian cultivars, and interspecies hybrids. Thus, the polymorphic markers can be used for cultivar identification and certification as well as for the marker-assisted selection of gooseberry plants having different origins and phenotypic traits. Full article
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11 pages, 5853 KiB  
Article
Genetic Diversity and Population Structure of Soybean Lines Adapted to Sub-Saharan Africa Using Single Nucleotide Polymorphism (SNP) Markers
by Subhash Chander, Ana Luísa Garcia-Oliveira, Melaku Gedil, Trushar Shah, Gbemisola Oluwayemisi Otusanya, Robert Asiedu and Godfree Chigeza
Agronomy 2021, 11(3), 604; https://0-doi-org.brum.beds.ac.uk/10.3390/agronomy11030604 - 22 Mar 2021
Cited by 17 | Viewed by 3536
Abstract
Soybean productivity in sub-Saharan Africa (SSA) is less than half of the global average yield. To plug the productivity gap, further improvement in grain yield must be attained by enhancing the genetic potential of new cultivars that depends on the genetic diversity of [...] Read more.
Soybean productivity in sub-Saharan Africa (SSA) is less than half of the global average yield. To plug the productivity gap, further improvement in grain yield must be attained by enhancing the genetic potential of new cultivars that depends on the genetic diversity of the parents. Hence, our aim was to assess genetic diversity and population structure of elite soybean genotypes, mainly released cultivars and advanced selections in SSA. In this study, a set of 165 lines was genotyped with high-throughput single nucleotide polymorphism (SNP) markers covering the complete genome of soybean. The genetic diversity (0.414) was high considering the bi-allelic nature of SNP markers. The polymorphic information content (PIC) varied from 0.079 to 0.375, with an average of 0.324 and about 49% of the markers had a PIC value above 0.350. Cluster analysis grouped all the genotypes into three major clusters. The model-based STRUCTURE and discriminant analysis of principal components (DAPC) exhibited high consistency in the allocation of lines in subpopulations or groups. Nonetheless, they presented some discrepancy and identified the presence of six and five subpopulations or groups, respectively. Principal coordinate analysis revealed more consistency with subgroups suggested by DAPC analysis. Our results clearly revealed the broad genetic base of TGx (Tropical Glycine max) lines that soybean breeders may select parents for crossing, testing and selection of future cultivars with desirable traits for SSA. Full article
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14 pages, 4821 KiB  
Article
Genome-Wide Identification of the NHX Gene Family in Punica granatum L. and Their Expressional Patterns under Salt Stress
by Jianmei Dong, Cuiyu Liu, Yuying Wang, Yujie Zhao, Dapeng Ge and Zhaohe Yuan
Agronomy 2021, 11(2), 264; https://0-doi-org.brum.beds.ac.uk/10.3390/agronomy11020264 - 30 Jan 2021
Cited by 17 | Viewed by 3410
Abstract
Most cultivated lands are suffering from soil salinization, which is a global problem affecting agricultural development and economy. High NaCl concentrations in the soil result in the accumulation of toxic Cl and Na+ in plants. Na+/H+ antiporter (NHX) [...] Read more.
Most cultivated lands are suffering from soil salinization, which is a global problem affecting agricultural development and economy. High NaCl concentrations in the soil result in the accumulation of toxic Cl and Na+ in plants. Na+/H+ antiporter (NHX) can regulate Na+ compartmentalization or efflux to reduce Na+ toxicity. This study aims to identify the NHX genes in pomegranate (Punica granatum L.) from the genome sequences and investigate their expression patterns under different concentrations of NaCl stress. In this study, we used the sequences of PgNHXs to analyze the physicochemical properties, phylogenetic evolution, conserved motifs, gene structures, cis-acting elements, protein tertiary structure and expression pattern. A total of 10 PgNHX genes were identified, and divided into three clades. Conserved motifs and gene structures showed that most of them had an amiloride-binding site (FFI/LY/FLLPPI), except for the members of clade III. There were multiple cis-acting elements involved in abiotic stress in PgNHX genes. Additionally, protein-protein interaction network analysis suggested that PgNHXs might play crucial roles in keeping a balance of Na+ in cells. The qRT-PCR analysis suggested that PgNHXs had tissue-specific expressional patterns under salt stress. Overall, our findings indicated that the PgNHXs could play significant roles in response to salt stress. The theoretical foundation was established in the present study for the further functional characterization of the NHX gene family in pomegranate. Full article
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24 pages, 3499 KiB  
Article
Genome-Wide Association Mapping of Freezing Tolerance Loci in Canola (Brassica napus L.)
by Wun S. Chao, David P. Horvath, Michael J. Stamm and James V. Anderson
Agronomy 2021, 11(2), 233; https://0-doi-org.brum.beds.ac.uk/10.3390/agronomy11020233 - 27 Jan 2021
Cited by 6 | Viewed by 2396
Abstract
Winter canola generally produces greater yields than spring canola. However, its range is limited due to its inability to withstand the harsh winter conditions that occur in many northern regions of the U.S.A. To identify loci associated with freezing tolerance in canola, we [...] Read more.
Winter canola generally produces greater yields than spring canola. However, its range is limited due to its inability to withstand the harsh winter conditions that occur in many northern regions of the U.S.A. To identify loci associated with freezing tolerance in canola, we conducted a genome-wide association study (GWAS) using a genotyped diversity panel containing 399 accessions consisting primarily of winter canola. One-month-old greenhouse grown plants were subsequently cold-acclimated for two months in an environmental growth chamber prior to phenotyping for freezing survival using a visual damage scale and chlorophyll fluorescence (Fv/Fo). There was reasonable correlation observed between visual damage and chlorophyll fluorescence ratings among the top associated loci; the results indicated that some loci contributed to both freezing damage/tolerance and photosynthetic efficiency. The resulting numerical values for phenotypes were used for association analyses with the identified SNPs. Thirteen significant markers were identified on nine chromosomes for the phenotypes scored, with several showing significance for multiple phenotypes. Twenty-five candidate genes were identified as previously associated with freezing tolerance, photosynthesis, or cold-responsive in canola or Arabidopsis. Full article
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9 pages, 279 KiB  
Article
Identification of Associations between SSR Markers and Quantitative Traits of Maize (Zea mays L.)
by Jan Bocianowski, Kamila Nowosad, Barbara Wróbel and Piotr Szulc
Agronomy 2021, 11(1), 182; https://0-doi-org.brum.beds.ac.uk/10.3390/agronomy11010182 - 19 Jan 2021
Cited by 11 | Viewed by 2890
Abstract
Microsatellite or simple sequence repeat (SSR) markers have wide applicability for genetic analysis in crop plant improvement strategies. Marker-assisted selection is an important tool for plant breeders to increase the efficiency of a breeding process, especially for multigenic traits, highly influenced by the [...] Read more.
Microsatellite or simple sequence repeat (SSR) markers have wide applicability for genetic analysis in crop plant improvement strategies. Marker-assisted selection is an important tool for plant breeders to increase the efficiency of a breeding process, especially for multigenic traits, highly influenced by the environment. In this paper, the relationships between SSR markers and 26 quantitative traits of hybrid maize varieties (Zea mays L.) were analyzed. Association analyses were performed based on 30 SSR primers in a set of thirteen hybrid maize varieties. A total of 112 SSR markers were detected in these genotypes. The number of alleles per locus ranged from 1 to 17, with the average number of alleles per locus equal to 3.7. The number of molecular markers associated with observed traits ranged from 1 (for the number of kernels in row, ears weight and fresh weight of one plant) to 14 (for damage of maize caused by P. nubilalis) in 2016 as well as from 1 (for soil plant analysis development—SPAD, the number of grains in ear and fresh weight of one plant) to 12 (for carotenoids content) in 2017. The sum of statistically significant associations between SSR markers and at least one trait was equal to one hundred sixty in 2016 as well as one hundred twenty-five in 2017. Marker trait associations (MTAs) were found on the basis of regression analysis. The proportion of the total phenotypic variances of individual traits explained by the marker ranged from 24.4% to 77.7% in the first year of study and from 24.3% to 77.9% in 2017. Twenty-two SSR markers performed a significant effect on at least one tested trait in both years of experiment. The three markers (phi021/4, phi036/3, and phi061/2) can be a good tool in marker-assisted selection because they allow simultaneous selection for multiple traits in both years of study, such as the number of kernels in row and the number of grains in ear (phi021/4), the number of plant after germination, the number of plants before harvest, and the number of ears (phi036/3), as well as moisture of grain and length of ears (phi061/2). Full article
17 pages, 2443 KiB  
Article
Mapping of the Waxy Bloom Gene in ‘Black Jewel’ in a Parental Linkage Map of ‘Black Jewel’ × ‘Glen Ample’ (Rubus) Interspecific Population
by Dora Pinczinger, Marcel von Reth, Jens Keilwagen, Thomas Berner, Andreas Peil, Henryk Flachowsky and Ofere Francis Emeriewen
Agronomy 2020, 10(10), 1579; https://0-doi-org.brum.beds.ac.uk/10.3390/agronomy10101579 - 16 Oct 2020
Cited by 6 | Viewed by 2267
Abstract
Black and red raspberries (Rubus occidentalis L. and Rubus idaeus L.) are the prominent members of the genus Rubus (Rosaceae family). Breeding programs coupled with the low costs of high-throughput sequencing have led to a reservoir of data that have improved our [...] Read more.
Black and red raspberries (Rubus occidentalis L. and Rubus idaeus L.) are the prominent members of the genus Rubus (Rosaceae family). Breeding programs coupled with the low costs of high-throughput sequencing have led to a reservoir of data that have improved our understanding of various characteristics of Rubus and facilitated the mapping of different traits. Gene B controls the waxy bloom, a clearly visible epicuticular wax on canes. The potential effects of this trait on resistance/susceptibility to cane diseases in conjunction with other morphological factors are not fully studied. Previous studies suggested that gene H, which controls cane pubescence, is closely associated with gene B. Here, we used tunable genotyping-by-sequencing technology to identify the de novo SNPs of R. occidentalis and R. idaeus using an interspecific population that segregates for the waxy bloom phenotype. We created linkage maps of both species and mapped the identified SNPs to the seven chromosomes (Ro01–Ro07) of Rubus. Importantly, we report, for the first time, the mapping of gene B to chromosome 2 of R. occidentalis using a genetic map consisting of 443 markers spanning 479.76 cM. We observed the poor transferability of R. idaeus SSRs to R. occidentalis and discrepancies in their previously reported chromosome locations. Full article
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13 pages, 2454 KiB  
Communication
Plant Sex Prediction Using Genetic Markers in Cultivated Yams (Dioscorea rotundata Poir.) in Benin
by Narcisse Denadi, Christophe Gandonou, Antoine Abel Missihoun, Jeanne Zoundjihékpon and Muriel Quinet
Agronomy 2020, 10(10), 1521; https://0-doi-org.brum.beds.ac.uk/10.3390/agronomy10101521 - 06 Oct 2020
Cited by 6 | Viewed by 2198
Abstract
Dioscorea rotundata Poir. is mainly dioecious but it also produces monoecious individuals. Recently two genetic markers were proposed to determine the sex in this species. We tested them in 119 individuals from 101 different cultivars of the national collection of Benin to verify [...] Read more.
Dioscorea rotundata Poir. is mainly dioecious but it also produces monoecious individuals. Recently two genetic markers were proposed to determine the sex in this species. We tested them in 119 individuals from 101 different cultivars of the national collection of Benin to verify whether they can predict the sex observed in the field. Among the analyzed individuals, 72 were male, 37 were female, 7 were monoecious and 3 were non-flowering. Our results showed that the marker sp16, associated with the W allele (female allele), was present in all female individuals but also in more than 42% of male individuals. Thus, while the absence of sp16 confirmed the male sex of the individuals, its presence did not allow sex discrimination. The marker sp1 allowed the identification of four genotypes (AA, AB, BB and AC) in the analyzed individuals with AA and AB being the most represented. Although AA was observed in 62.16% of female individuals and AB in 83.33% of male individuals, we did not observe a clear correlation between sp1 genotypes and sex identity. We concluded that the tested markers did not allow a clear sex discrimination in Beninese Dioscorea rotundata cultivars. Our results also suggest that Beninese D. rotundata cultivars have adopted a male XX/XY heterogametic system that is undergoing reorganization. Full article
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15 pages, 730 KiB  
Article
Genetic Diversity among Lathyrus ssp. Based on Agronomic Traits and Molecular Markers
by Meriem Miyassa Aci, Antonio Lupini, Giuseppe Badagliacca, Antonio Mauceri, Emilio Lo Presti and Giovanni Preiti
Agronomy 2020, 10(8), 1182; https://0-doi-org.brum.beds.ac.uk/10.3390/agronomy10081182 - 12 Aug 2020
Cited by 10 | Viewed by 2587
Abstract
Grasspea (Lathyrus sativus L.) and its relatives are considered resilient legumes due to their high ability to cope with different stresses. In this study, the genetic diversity of three Lathyrus species (L. sativus, L cicera and L. ochrus) was [...] Read more.
Grasspea (Lathyrus sativus L.) and its relatives are considered resilient legumes due to their high ability to cope with different stresses. In this study, the genetic diversity of three Lathyrus species (L. sativus, L cicera and L. ochrus) was assessed by agronomic traits and molecular markers (Simple Sequence Repeat-SSR) in order to detect accessions useful for future breeding strategies. Phenotypic traits showed a high significant variation in which 1000 seed weight (1000 SW) and protein content appeared the most discriminant, as observed by principal component analysis (PCA). SSR analysis was able to detect forty-eight different alleles with an average of 9.6 allele per locus, and a Polymorphic Information Content (PIC) and a gene diversity of 0.745 and 0.784, respectively. Cluster analysis based on agronomic traits as well as molecular data grouped accessions by species but not by geographical origin. This result was confirmed by Principal Coordinates Analysis (PCoA) and Structure Analysis as well. Moreover, genetic structure analysis revealed a high genetic differentiation between L. ochrus and the other species. Analysis of MOlecular Variance (AMOVA) displayed a greater genetic diversity within species (77%) than among them (23%). Finally, a significant positive correlation was observed between agronomic and genetic distances (Mantel’s test). In conclusion, the variability detected within accessions in each species and the differences among species may be useful to plan next breeding programs, focusing on biomass production as well as protein content. Full article
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22 pages, 2918 KiB  
Article
SNP in DFR1 Coding Sequence Is Tightly Associated with Anthocyanin Accumulation in Cabbage (B. oleracea var. capitata f. alba) at Low Temperature
by Hayoung Song, Jong-In Park, Byung-Ho Hwang, Hankuil Yi, HyeRan Kim and Yoonkang Hur
Agronomy 2020, 10(4), 602; https://0-doi-org.brum.beds.ac.uk/10.3390/agronomy10040602 - 23 Apr 2020
Cited by 6 | Viewed by 3010
Abstract
Keeping green leaf color at the time of harvest is one of the important traits for breeding of Brassica oleracea var. capitata f. alba, and this trait is related to low anthocyanin contents. To understand the differential accumulation of anthocyanins in cabbage, [...] Read more.
Keeping green leaf color at the time of harvest is one of the important traits for breeding of Brassica oleracea var. capitata f. alba, and this trait is related to low anthocyanin contents. To understand the differential accumulation of anthocyanins in cabbage, we selected high anthocyanin accumulators (HAAs) and low anthocyanin accumulator (LAAs) of cabbages and examined the anthocyanin content and the expression of anthocyanin biosynthesis-related genes. Among many genes investigated, BoDFR1 was found to be closely related to anthocyanin accumulation, even under low temperature (LT) conditions. BoDFR1 sequence analyses between HAAs and LAAs revealed that there is a single nucleotide polymorphism (SNP) (1118T/A) in the coding sequence, which substitutes one amino acid from Leu261 to His261; we named BoDFR1 with His261 substitution as BoDFR1v. This amino acid substitution did not affect dihydroflavonol 4-reductase (DFR) activity and substrate specificity, but the polymorphism showed tight association to the BoDFR1 expression, i.e., high level expression of BoDFR1 and low level expression of BoDFR1v under LT conditions. The high levels of BoDFR1 expression were due to the high levels of BoMYB114 and BobHLH expressions combined with low level expression of BoMYBL2, a repressor MYB. On the other hand, low levels of BoDFR1v expression seemed to be related to very low level expressions of BoMYB114 and BobHLH combined with a high level expression of BoMYBL2. It seems that different expression levels of these regulatory genes for MBW (MYB-bHLH-WD40) complex between HAAs and LAAs regulate BoDFR expression and anthocyanin accumulation. Using a single nucleotide polymorphism (SNP) between BoDFR1 and BoDFR1v, molecular markers for PCR and high resolution melt analyses were developed and validated to distinguish between HAAs and LAAs. Combined use of the BoDFR1 SNP marker with other stress markers, such as a cold tolerant marker, will greatly improve cabbage breeding. Full article
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Review

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28 pages, 2265 KiB  
Review
Modern Approaches for the Genetic Improvement of Rice, Wheat and Maize for Abiotic Constraints-Related Traits: A Comparative Overview
by Elena Benavente and Estela Giménez
Agronomy 2021, 11(2), 376; https://0-doi-org.brum.beds.ac.uk/10.3390/agronomy11020376 - 20 Feb 2021
Cited by 17 | Viewed by 5224
Abstract
After a basic description of the different sets of genetic tools and genomic approaches most relevant for modern crop breeding (e. g., QTL mapping, GWAS and genomic selection; transcriptomics, qPCR and RNA-seq; transgenesis and gene editing), this review paper describes their history and [...] Read more.
After a basic description of the different sets of genetic tools and genomic approaches most relevant for modern crop breeding (e. g., QTL mapping, GWAS and genomic selection; transcriptomics, qPCR and RNA-seq; transgenesis and gene editing), this review paper describes their history and the main achievements in rice, wheat and maize research, with a further focus on crop traits related to the improvement of plant responses to face major abiotic constrains, including nutritional limitations, drought and heat tolerance, and nitrogen-use efficiency (NUE). Remarkable differences have been evidenced regarding the timing and degree of development of some genetic approaches among these major crops. The underlying reasons related to their distinct genome complexity, are also considered. Based on bibliographic records, drought tolerance and related topics (i.e., water-use efficiency) are by far the most abundantly addressed by molecular tools among the breeding objectives considered. Heat tolerance is usually more relevant than NUE in rice and wheat, while the opposite is true for maize. Full article
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41 pages, 4999 KiB  
Review
CRISPR-Cas9 System for Plant Genome Editing: Current Approaches and Emerging Developments
by Jake Adolf V. Montecillo, Luan Luong Chu and Hanhong Bae
Agronomy 2020, 10(7), 1033; https://0-doi-org.brum.beds.ac.uk/10.3390/agronomy10071033 - 17 Jul 2020
Cited by 47 | Viewed by 17286
Abstract
Targeted genome editing using CRISPR-Cas9 has been widely adopted as a genetic engineering tool in various biological systems. This editing technology has been in the limelight due to its simplicity and versatility compared to other previously known genome editing platforms. Several modifications of [...] Read more.
Targeted genome editing using CRISPR-Cas9 has been widely adopted as a genetic engineering tool in various biological systems. This editing technology has been in the limelight due to its simplicity and versatility compared to other previously known genome editing platforms. Several modifications of this editing system have been established for adoption in a variety of plants, as well as for its improved efficiency and portability, bringing new opportunities for the development of transgene-free improved varieties of economically important crops. This review presents an overview of CRISPR-Cas9 and its application in plant genome editing. A catalog of the current and emerging approaches for the implementation of the system in plants is also presented with details on the existing gaps and limitations. Strategies for the establishment of the CRISPR-Cas9 molecular construct such as the selection of sgRNAs, PAM compatibility, choice of promoters, vector architecture, and multiplexing approaches are emphasized. Progress in the delivery and transgene detection methods, together with optimization approaches for improved on-target efficiency are also detailed in this review. The information laid out here will provide options useful for the effective and efficient exploitation of the system for plant genome editing and will serve as a baseline for further developments of the system. Future combinations and fine-tuning of the known parameters or factors that contribute to the editing efficiency, fidelity, and portability of CRISPR-Cas9 will indeed open avenues for new technological advancements of the system for targeted gene editing in plants. Full article
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