Late blight disease of potato and tomato, caused by Phytophthora infestans, results in serious lo... more Late blight disease of potato and tomato, caused by Phytophthora infestans, results in serious losses to Egyptian and global potato and tomato production. To understand the structure and dynamics of the Egyptian population of P. infestans, 205 isolates were collected from potato and tomato plants during three growing seasons in 2010–2012. The characterization was achieved by mating-type assay, metalaxyl sensitivity assay, and virulence pattern. Additionally, genotyping of 85 Egyptian isolates and 15 reference UK isolates was performed using 12 highly informative microsatellite (SSR) markers David E. L. Cooke and five effector (RxLR) genes. Mating-type testing showed that 58% (118 of 205) of the isolates belonged to mating type A1, 35% (71 isolates) to mating type A2, and the rest 8% (16 isolates) were self-fertile. The phenotype of metalaxyl response was represented as 45% resistant, 43% sensitive, and 12% as intermediate. Structure analysis grouped the 85 identified genotypes into ...
A genome represents an organelle’s complete DNA repertoire and it is the starting point of geneti... more A genome represents an organelle’s complete DNA repertoire and it is the starting point of genetic studies and genome mapping. Since the advent of genome mapping techniques, researchers have devoted concerted efforts to link phenotype to genotype. Initially, efforts were made to accomplish genotyping by isozymes, followed by the execution of various kinds of molecular markers such as simple sequence repeats (SSR), single nucleotide polymorphism (SNP), and random amplified polymorphic DNA (RAPD). Nonetheless, genome mapping was dramatically revolutionized as next-generation sequencing (NGS) technologies emerged. NGS technologies have produced a deluge of genome sequencing. The analysis of such sequencing data is only possible through highly sophisticated computational tools. Presently, the low-cost sequencing technologies and highly sophisticated computational tools are of great significance in unraveling the complexity of plant genomes. Date palm (Phoenix dactylifera L.) is a socioeconomically important plant. Cultivar identification mostly relied on phenotypic traits rather than genotyping. Still, limited information is available on date palm genotyping and genome mapping. Nonetheless, advancements in whole-genome sequencing and genome assembly computational tools hold a substantial advantage to boost the identification of date palm cultivars, genome variants, and gene/genome annotation. In this chapter, advancements in date palm genome mapping are categorized into two main types: date palm genetic mapping in the pre-NGS and post-NGS eras. Various computational tools that hold an unparalleled advantage to conduct genome-wide association mapping, genome prediction, and selection, and with higher prediction accuracy of SNPs and other variations in date palm genomes are discussed. In addition, various databases related to date palm genomes are discussed, these databases encompass important information about the whole genome of certain date palm cultivars, molecular markers such as SNPs and SSR, and phylogenetic relationship of different date palm cultivars.
Fruit trees provide essential nutrients to humans by contributing to major agricultural outputs a... more Fruit trees provide essential nutrients to humans by contributing to major agricultural outputs and economic growth globally. However, major constraints to sustainable agricultural productivity are the uncontrolled proliferation of the population, and biotic and abiotic stresses. Tree mutation breeding has been substantially improved using different physical and chemical mutagens. Nonetheless, tree plant breeding has certain crucial bottlenecks including a long life cycle, ploidy level, occurrence of sequence polymorphisms, nature of parthenocarpic fruit development and linkage. Genetic engineering of trees has focused on boosting quality traits such as productivity, wood quality, and resistance to biotic and abiotic stresses. Recent technological advances in genome editing provide a unique opportunity for the genetic improvement of woody plants. This review examines application of the CRISPR-Cas system to reduce disease susceptibility, alter plant architecture, enhance fruit qualit...
In recent years, next-generation sequencing (NGS) and contemporary Clustered Regularly Interspace... more In recent years, next-generation sequencing (NGS) and contemporary Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-CRISPR-associated (Cas) technologies have revolutionized the life sciences and the field of plant virology. Both these technologies offer an unparalleled platform for sequencing and deciphering viral metagenomes promptly. Over the past two decades, NGS technologies have improved enormously and have impacted plant virology. NGS has enabled the detection of plant viruses that were previously undetectable by conventional approaches, such as quarantine and archeological plant samples, and has helped to track the evolutionary footprints of viral pathogens. The CRISPR-Cas-based genome editing (GE) and detection techniques have enabled the development of effective approaches to virus resistance. Different versions of CRISPR-Cas have been employed to successfully confer resistance against diverse plant viruses by directly targeting the virus genome or indirec...
Advances in Plant Breeding Strategies: Vegetable Crops, 2021
Potato (Solanum tuberosum L.), with approximately 388 million mt annual world production, is rank... more Potato (Solanum tuberosum L.), with approximately 388 million mt annual world production, is ranked fourth among food crops after rice, wheat and corn. However, substantial potato production is vulnerable due to the susceptibility of potato crop to different devastating pathogens especially RNA viruses. The present potato breeding approaches are laborious, intensive and require a protracted time-consuming procedure to develop new resistant and elite cultivars with desired traits. On the other hand, the rapid ability of potato pathogens to evolve has enabled them to cope with the host defense; therefore, a quick technique having a fine-tuned, broad-spectrum and durable mechanism of resistance is required. In addition, such techniques should meet GMO guidelines to win public acceptance. The disclosures of CRISPR-Cas variants, especially Cas13a as a programmable RNA-guided RNase ability, could be reprogramed to target the potato infecting pathogens. Successful execution of a CRISPR-Cas13a system against different pathogens and obtaining transgene-free plants have been described in recent ongoing investigations. The present chapter features the plausible implication of CRISPR-Cas systems to accelerate potato breeding programs. Besides, a multiplexed CRISPR-Cas13a based theoretical model is discussed to combat the menacing worldwide spread of the pathogen potato virus Y (PVY).
Pumpkin ( Cucurbita maxima ) plants showing begomovirus-like yellowing, curling and stunting symp... more Pumpkin ( Cucurbita maxima ) plants showing begomovirus-like yellowing, curling and stunting symptoms were observed in the Barka Governate, Oman in December 2016. Cloning and sequencing of rolling circle amplified circular DNA molecules showed the plants to be infected with watermelon chlorotic stunt virus (WmCSV); a bipartite Old World begomovirus that is a serious pathogen of cucurbit crops across the Middle East, Arabian Peninsula and North Africa. Although not known to interact with satellites, the risk of WmCSV possibly interacting with betasatellites and alphasatellites to agriculture in Oman, and beyond, was assessed. Tomato leaf curl betasatellite (ToLCB) and Ageratum enation alphasatellite (AEA) are commonly associated with other begomoviruses in Oman. A cognate pair of WmCSV DNA-A and DNA-B clones was highly infectious to Nicotiana benthamiana by Agrobacterium -mediated inoculation, inducing severe leaf curling and crumpling symptoms. Inoculation of only the DNA-A component with ToLCB or AEA did not result in symptoms or significant levels of the DNA-A or satellites in plants. Inoculation of both DNA-A and DNA-B with ToLCB or AEA resulted in a slight change in symptom phenotype and reduced DNA-A and DNA-B titers. Although ToLCB DNA levels in co-infected plants were low, the levels of AEA were high. This is the first identification of WmCSV infecting pumpkin in Oman and the isolates identified were typical of the virus previously identified in Oman, being distinct from the isolates occurring in the western Arabian Peninsula. Additionally the infectivity analyses suggest that WmCSV interaction with satellites, in contrast to some other bipartite begomoviruses, is unlikely to result in more serious disease in the field.
Cotton crop has been severely affected by multiple begomoviruses in Pakistan and India. In our pr... more Cotton crop has been severely affected by multiple begomoviruses in Pakistan and India. In our previous study, we found okra enation leaf curl virus (OELCuV), cotton leaf curl Multan betasatellite (CLCuMuB) and cotton leaf curl Multan alphasatellite (CLCuMuA) infecting cotton in Pakistan. The current study was designed to investigate the infectivity of OELCuV and its ability to trans-replicate non-cognate CLCuMuB. Agro-infectious clones containing the partial tandem repeats of OELCuV and CLCuMuB were constructed and the infectivity assays were carried out through Agrobacterium mediated transformation in the model host species Nicotiana benthamiana under controlled conditions. The results showed that in the inoculated plants OELCuV alone can cause downward curling and yellowing of leaves with thickened veins. However, when co-inoculated with the non-cognate CLCuMuB it could functionally trans-replicate CLCuMuB resulting in a more severe phenotype. The expression of Pre-coat/V2 protei...
Cotton leaf curl disease (CLCuD), the most complex disease of cotton, is a major limiting biotic ... more Cotton leaf curl disease (CLCuD), the most complex disease of cotton, is a major limiting biotic factor to worldwide cotton productivity. Several whitefly-transmitted monopartite begomoviruses causing CLCuD have been characterized and designated as CLCuD-associated begomoviruses. Despite of being reported over 100 years ago in Africa, CLCuD became economically pandemic causing massive losses to cotton production in Pakistan and India during past couple of decades. In Asia, cotton has faced two major epidemics during this period viz. "Multan epidemic" and "Burewala epidemic." The "Multan epidemic" era was 1988-1999 after which the virus remained calm until 2002 when "Burewala epidemic" broke into the cotton fields in Indo-Pak subcontinent, till 2013-2014. However, both the epidemics were…
Late blight disease of potato and tomato, caused by Phytophthora infestans, results in serious lo... more Late blight disease of potato and tomato, caused by Phytophthora infestans, results in serious losses to Egyptian and global potato and tomato production. To understand the structure and dynamics of the Egyptian population of P. infestans, 205 isolates were collected from potato and tomato plants during three growing seasons in 2010–2012. The characterization was achieved by mating-type assay, metalaxyl sensitivity assay, and virulence pattern. Additionally, genotyping of 85 Egyptian isolates and 15 reference UK isolates was performed using 12 highly informative microsatellite (SSR) markers David E. L. Cooke and five effector (RxLR) genes. Mating-type testing showed that 58% (118 of 205) of the isolates belonged to mating type A1, 35% (71 isolates) to mating type A2, and the rest 8% (16 isolates) were self-fertile. The phenotype of metalaxyl response was represented as 45% resistant, 43% sensitive, and 12% as intermediate. Structure analysis grouped the 85 identified genotypes into ...
A genome represents an organelle’s complete DNA repertoire and it is the starting point of geneti... more A genome represents an organelle’s complete DNA repertoire and it is the starting point of genetic studies and genome mapping. Since the advent of genome mapping techniques, researchers have devoted concerted efforts to link phenotype to genotype. Initially, efforts were made to accomplish genotyping by isozymes, followed by the execution of various kinds of molecular markers such as simple sequence repeats (SSR), single nucleotide polymorphism (SNP), and random amplified polymorphic DNA (RAPD). Nonetheless, genome mapping was dramatically revolutionized as next-generation sequencing (NGS) technologies emerged. NGS technologies have produced a deluge of genome sequencing. The analysis of such sequencing data is only possible through highly sophisticated computational tools. Presently, the low-cost sequencing technologies and highly sophisticated computational tools are of great significance in unraveling the complexity of plant genomes. Date palm (Phoenix dactylifera L.) is a socioeconomically important plant. Cultivar identification mostly relied on phenotypic traits rather than genotyping. Still, limited information is available on date palm genotyping and genome mapping. Nonetheless, advancements in whole-genome sequencing and genome assembly computational tools hold a substantial advantage to boost the identification of date palm cultivars, genome variants, and gene/genome annotation. In this chapter, advancements in date palm genome mapping are categorized into two main types: date palm genetic mapping in the pre-NGS and post-NGS eras. Various computational tools that hold an unparalleled advantage to conduct genome-wide association mapping, genome prediction, and selection, and with higher prediction accuracy of SNPs and other variations in date palm genomes are discussed. In addition, various databases related to date palm genomes are discussed, these databases encompass important information about the whole genome of certain date palm cultivars, molecular markers such as SNPs and SSR, and phylogenetic relationship of different date palm cultivars.
Fruit trees provide essential nutrients to humans by contributing to major agricultural outputs a... more Fruit trees provide essential nutrients to humans by contributing to major agricultural outputs and economic growth globally. However, major constraints to sustainable agricultural productivity are the uncontrolled proliferation of the population, and biotic and abiotic stresses. Tree mutation breeding has been substantially improved using different physical and chemical mutagens. Nonetheless, tree plant breeding has certain crucial bottlenecks including a long life cycle, ploidy level, occurrence of sequence polymorphisms, nature of parthenocarpic fruit development and linkage. Genetic engineering of trees has focused on boosting quality traits such as productivity, wood quality, and resistance to biotic and abiotic stresses. Recent technological advances in genome editing provide a unique opportunity for the genetic improvement of woody plants. This review examines application of the CRISPR-Cas system to reduce disease susceptibility, alter plant architecture, enhance fruit qualit...
In recent years, next-generation sequencing (NGS) and contemporary Clustered Regularly Interspace... more In recent years, next-generation sequencing (NGS) and contemporary Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-CRISPR-associated (Cas) technologies have revolutionized the life sciences and the field of plant virology. Both these technologies offer an unparalleled platform for sequencing and deciphering viral metagenomes promptly. Over the past two decades, NGS technologies have improved enormously and have impacted plant virology. NGS has enabled the detection of plant viruses that were previously undetectable by conventional approaches, such as quarantine and archeological plant samples, and has helped to track the evolutionary footprints of viral pathogens. The CRISPR-Cas-based genome editing (GE) and detection techniques have enabled the development of effective approaches to virus resistance. Different versions of CRISPR-Cas have been employed to successfully confer resistance against diverse plant viruses by directly targeting the virus genome or indirec...
Advances in Plant Breeding Strategies: Vegetable Crops, 2021
Potato (Solanum tuberosum L.), with approximately 388 million mt annual world production, is rank... more Potato (Solanum tuberosum L.), with approximately 388 million mt annual world production, is ranked fourth among food crops after rice, wheat and corn. However, substantial potato production is vulnerable due to the susceptibility of potato crop to different devastating pathogens especially RNA viruses. The present potato breeding approaches are laborious, intensive and require a protracted time-consuming procedure to develop new resistant and elite cultivars with desired traits. On the other hand, the rapid ability of potato pathogens to evolve has enabled them to cope with the host defense; therefore, a quick technique having a fine-tuned, broad-spectrum and durable mechanism of resistance is required. In addition, such techniques should meet GMO guidelines to win public acceptance. The disclosures of CRISPR-Cas variants, especially Cas13a as a programmable RNA-guided RNase ability, could be reprogramed to target the potato infecting pathogens. Successful execution of a CRISPR-Cas13a system against different pathogens and obtaining transgene-free plants have been described in recent ongoing investigations. The present chapter features the plausible implication of CRISPR-Cas systems to accelerate potato breeding programs. Besides, a multiplexed CRISPR-Cas13a based theoretical model is discussed to combat the menacing worldwide spread of the pathogen potato virus Y (PVY).
Pumpkin ( Cucurbita maxima ) plants showing begomovirus-like yellowing, curling and stunting symp... more Pumpkin ( Cucurbita maxima ) plants showing begomovirus-like yellowing, curling and stunting symptoms were observed in the Barka Governate, Oman in December 2016. Cloning and sequencing of rolling circle amplified circular DNA molecules showed the plants to be infected with watermelon chlorotic stunt virus (WmCSV); a bipartite Old World begomovirus that is a serious pathogen of cucurbit crops across the Middle East, Arabian Peninsula and North Africa. Although not known to interact with satellites, the risk of WmCSV possibly interacting with betasatellites and alphasatellites to agriculture in Oman, and beyond, was assessed. Tomato leaf curl betasatellite (ToLCB) and Ageratum enation alphasatellite (AEA) are commonly associated with other begomoviruses in Oman. A cognate pair of WmCSV DNA-A and DNA-B clones was highly infectious to Nicotiana benthamiana by Agrobacterium -mediated inoculation, inducing severe leaf curling and crumpling symptoms. Inoculation of only the DNA-A component with ToLCB or AEA did not result in symptoms or significant levels of the DNA-A or satellites in plants. Inoculation of both DNA-A and DNA-B with ToLCB or AEA resulted in a slight change in symptom phenotype and reduced DNA-A and DNA-B titers. Although ToLCB DNA levels in co-infected plants were low, the levels of AEA were high. This is the first identification of WmCSV infecting pumpkin in Oman and the isolates identified were typical of the virus previously identified in Oman, being distinct from the isolates occurring in the western Arabian Peninsula. Additionally the infectivity analyses suggest that WmCSV interaction with satellites, in contrast to some other bipartite begomoviruses, is unlikely to result in more serious disease in the field.
Cotton crop has been severely affected by multiple begomoviruses in Pakistan and India. In our pr... more Cotton crop has been severely affected by multiple begomoviruses in Pakistan and India. In our previous study, we found okra enation leaf curl virus (OELCuV), cotton leaf curl Multan betasatellite (CLCuMuB) and cotton leaf curl Multan alphasatellite (CLCuMuA) infecting cotton in Pakistan. The current study was designed to investigate the infectivity of OELCuV and its ability to trans-replicate non-cognate CLCuMuB. Agro-infectious clones containing the partial tandem repeats of OELCuV and CLCuMuB were constructed and the infectivity assays were carried out through Agrobacterium mediated transformation in the model host species Nicotiana benthamiana under controlled conditions. The results showed that in the inoculated plants OELCuV alone can cause downward curling and yellowing of leaves with thickened veins. However, when co-inoculated with the non-cognate CLCuMuB it could functionally trans-replicate CLCuMuB resulting in a more severe phenotype. The expression of Pre-coat/V2 protei...
Cotton leaf curl disease (CLCuD), the most complex disease of cotton, is a major limiting biotic ... more Cotton leaf curl disease (CLCuD), the most complex disease of cotton, is a major limiting biotic factor to worldwide cotton productivity. Several whitefly-transmitted monopartite begomoviruses causing CLCuD have been characterized and designated as CLCuD-associated begomoviruses. Despite of being reported over 100 years ago in Africa, CLCuD became economically pandemic causing massive losses to cotton production in Pakistan and India during past couple of decades. In Asia, cotton has faced two major epidemics during this period viz. "Multan epidemic" and "Burewala epidemic." The "Multan epidemic" era was 1988-1999 after which the virus remained calm until 2002 when "Burewala epidemic" broke into the cotton fields in Indo-Pak subcontinent, till 2013-2014. However, both the epidemics were…
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