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The harvesting of sweet cherry (Prunus avium L.) fruit is a labor-intensive process. The mechanical harvesting of sweet cherry fruit is feasible; however, it is dependent on the formation of an abscission zone at the fruit–pedicel junction. The natural propensity for pedicel-–fruit abscission zone (PFAZ) activation varies by cultivar, and the general molecular basis for PFAZ activation is not well characterized. In this study, ethylene-inducible change in pedicel fruit retention force (PFRF) was recorded in a developmental time-course with a concomitant analysis of the PFAZ transcriptome from three sweet cherry cultivars. In ‘Skeena’, mean PFRF for both control and treatment fruit dropped below the 0.40 kg-force (3.92 N) threshold for mechanical harvesting, indicating the activation of a discrete PFAZ. In ‘Bing’, mean PFRF for both control and treatment groups decreased over time. However, a mean PFRF conducive to mechanical harvesting was achieved only in the ethylene-treated fruit. While in ‘Chelan’ the mean PFRF of the control and treatment groups did not meet the threshold required for efficient mechanical harvesting. Transcriptome analysis of the PFAZ region followed by the functional annotation, differential expression analysis, and gene ontology (GO) enrichment analyses of the data facilitated the identification of phytohormone-responsive and abscission-related transcripts, as well as processes that exhibited differential expression and enrichment in a cultivar-dependent manner over the developmental time-course. Additionally, read alignment-based variant calling revealed several short variants in differentially expressed genes, associated with enriched gene ontologies and associated metabolic processes, lending potential insight into the genetic basis for different abscission responses between the cultivars. These results provide genetic targets for the induction or inhibition of PFAZ activation, depending on the desire to harvest the fruit with or without the stem attached. Understanding the genetic mechanisms underlying the development of the PFAZ will inform future cultivar development while laying a foundation for mechanized sweet cherry harvest.
SeAnna Hewitt; Benjamin Kilian; Tyson Koepke; Jonathan Abarca; Matthew Whiting; Amit Dhingra. Transcriptome Analysis Reveals Potential Mechanisms for Ethylene-Inducible Pedicel–Fruit Abscission Zone Activation in Non-Climacteric Sweet Cherry (Prunus avium L.). Horticulturae 2021, 7, 270 .
AMA StyleSeAnna Hewitt, Benjamin Kilian, Tyson Koepke, Jonathan Abarca, Matthew Whiting, Amit Dhingra. Transcriptome Analysis Reveals Potential Mechanisms for Ethylene-Inducible Pedicel–Fruit Abscission Zone Activation in Non-Climacteric Sweet Cherry (Prunus avium L.). Horticulturae. 2021; 7 (9):270.
Chicago/Turabian StyleSeAnna Hewitt; Benjamin Kilian; Tyson Koepke; Jonathan Abarca; Matthew Whiting; Amit Dhingra. 2021. "Transcriptome Analysis Reveals Potential Mechanisms for Ethylene-Inducible Pedicel–Fruit Abscission Zone Activation in Non-Climacteric Sweet Cherry (Prunus avium L.)." Horticulturae 7, no. 9: 270.
Pisum sativum (pea) yields in the United States have declined significantly over the last decades, predominantly due to susceptibility to root rot diseases. One of the main causal agents of root rot is the fungus Fusarium solani f. sp. pisi (Fsp), leading to yield losses ranging from 15 to 60%. Determining and subsequently incorporating the genetic basis for resistance in new cultivars offers one of the best solutions to control this pathogen; however, no green-seeded pea cultivars with complete resistance to Fsp have been identified. To date, only partial levels of resistance to Fsp has been identified among pea genotypes. SNPs mined from Fsp-responsive differentially expressed genes (DEGs) identified in a preceding study were utilized to identify QTLs associated with Fsp resistance using composite interval mapping in two recombinant inbred line (RIL) populations segregating for partial root rot resistance. A total of 769 DEGs with single nucleotide polymorphisms (SNPs) were identified, and the putative SNPs were evaluated for being polymorphic across four partially resistant and four susceptible P. sativum genotypes. The SNPs with validated polymorphisms were used to screen two RIL populations using two phenotypic criteria: root disease severity and plant height. One QTL, WB.Fsp-Ps 5.1 that mapped to chromosome 5 explained 14.8% of the variance with a confidence interval of 10.4 cM. The other four QTLs located on chromosomes 2, 3, and 5, explained 5.3–8.1% of the variance. The use of SNPs derived from Fsp-responsive DEGs for QTL mapping proved to be an efficient way to identify molecular markers associated with Fsp resistance in pea. These QTLs are potential candidates for marker-assisted selection and gene pyramiding to obtain high levels of partial resistance in pea cultivars to combat root rot caused by Fsp.
Bruce A. Williamson-Benavides; Richard M. Sharpe; Grant Nelson; Eliane T. Bodah; Lyndon D. Porter; Amit Dhingra. Identification of Root Rot Resistance QTLs in Pea Using Fusarium solani f. sp. pisi-Responsive Differentially Expressed Genes. Frontiers in Genetics 2021, 12, 1 .
AMA StyleBruce A. Williamson-Benavides, Richard M. Sharpe, Grant Nelson, Eliane T. Bodah, Lyndon D. Porter, Amit Dhingra. Identification of Root Rot Resistance QTLs in Pea Using Fusarium solani f. sp. pisi-Responsive Differentially Expressed Genes. Frontiers in Genetics. 2021; 12 ():1.
Chicago/Turabian StyleBruce A. Williamson-Benavides; Richard M. Sharpe; Grant Nelson; Eliane T. Bodah; Lyndon D. Porter; Amit Dhingra. 2021. "Identification of Root Rot Resistance QTLs in Pea Using Fusarium solani f. sp. pisi-Responsive Differentially Expressed Genes." Frontiers in Genetics 12, no. : 1.
Breeding 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.
Maria Lobato-Gómez; SeAnna Hewitt; Teresa Capell; Paul Christou; Amit Dhingra; Patricia Sarai Girón-Calva. Transgenic and genome-edited fruits: background, constraints, benefits, and commercial opportunities. Horticulture Research 2021, 8, 1 -16.
AMA StyleMaria Lobato-Gómez, SeAnna Hewitt, Teresa Capell, Paul Christou, Amit Dhingra, Patricia Sarai Girón-Calva. Transgenic and genome-edited fruits: background, constraints, benefits, and commercial opportunities. Horticulture Research. 2021; 8 (1):1-16.
Chicago/Turabian StyleMaria Lobato-Gómez; SeAnna Hewitt; Teresa Capell; Paul Christou; Amit Dhingra; Patricia Sarai Girón-Calva. 2021. "Transgenic and genome-edited fruits: background, constraints, benefits, and commercial opportunities." Horticulture Research 8, no. 1: 1-16.
The advent of genome editing has opened new avenues for targeted trait enhancement in fruit, ornamental, industrial, and all specialty crops. In particular, CRISPR-based editing systems, derived from bacterial immune systems, have quickly become routinely used tools for research groups across the world seeking to edit plant genomes with a greater level of precision, higher efficiency, reduced off-target effects, and overall ease-of-use compared to ZFNs and TALENs. CRISPR systems have been applied successfully to a number of horticultural and industrial crops to enhance fruit ripening, increase stress tolerance, modify plant architecture, control the timing of flower development, and enhance the accumulation of desired metabolites, among other commercially-important traits. As editing technologies continue to advance, so too does the ability to generate improved crop varieties with non-transgenic modifications; in some crops, direct transgene-free edits have already been achieved, while in others, T-DNAs have successfully been segregated out through crossing. In addition to the potential to produce non-transgenic edited crops, and thereby circumvent regulatory impediments to the release of new, improved crop varieties, targeted gene editing can speed up trait improvement in crops with long juvenile phases, reducing inputs resulting in faster market introduction to the market. While many challenges remain regarding optimization of genome editing in ornamental, fruit, and industrial crops, the ongoing discovery of novel nucleases with niche specialties for engineering applications may form the basis for additional and potentially crop-specific editing strategies.
Fabiola Ramirez-Torres; Rishikesh Ghogare; Evan Stowe; Pedro Cerdá-Bennasser; Maria Lobato-Gómez; Bruce A Williamson-Benavides; Patricia Sarai Giron-Calva; SeAnna Hewitt; Paul Christou; Amit Dhingra. Genome editing in fruit, ornamental, and industrial crops. Transgenic Research 2021, 30, 499 -528.
AMA StyleFabiola Ramirez-Torres, Rishikesh Ghogare, Evan Stowe, Pedro Cerdá-Bennasser, Maria Lobato-Gómez, Bruce A Williamson-Benavides, Patricia Sarai Giron-Calva, SeAnna Hewitt, Paul Christou, Amit Dhingra. Genome editing in fruit, ornamental, and industrial crops. Transgenic Research. 2021; 30 (4):499-528.
Chicago/Turabian StyleFabiola Ramirez-Torres; Rishikesh Ghogare; Evan Stowe; Pedro Cerdá-Bennasser; Maria Lobato-Gómez; Bruce A Williamson-Benavides; Patricia Sarai Giron-Calva; SeAnna Hewitt; Paul Christou; Amit Dhingra. 2021. "Genome editing in fruit, ornamental, and industrial crops." Transgenic Research 30, no. 4: 499-528.
Genome editing holds the potential for rapid crop improvement to meet the challenge of feeding the planet in a changing climate. The delivery of gene editing reagents into the plant cells has been dominated by plasmid vectors delivered using agrobacterium or particle bombardment. This approach involves the production of genetically engineered plants, which need to undergo regulatory approvals. There are various reagent delivery approaches available that have enabled the delivery of DNA-free editing reagents. They invariably involve the use of ribonucleoproteins (RNPs), especially in the case of CRISPR/Cas9-mediated gene editing. The explant of choice for most of the non-DNA approaches utilizes protoplasts as the recipient explant. While the editing efficiency is high in protoplasts, the ability to regenerate individual plants from edited protoplasts remains a challenge. There are various innovative delivery approaches being utilized to perform in planta edits that can be incorporated in the germline cells or inherited via seed. With the modification and adoption of various novel approaches currently being used in animal systems, it seems likely that non-transgenic genome editing will become routine in higher plants.
Rishikesh Ghogare; Yvonne Ludwig; Gela Myan Bueno; Inez H. Slamet-Loedin; Amit Dhingra. Genome editing reagent delivery in plants. Transgenic Research 2021, 30, 321 -335.
AMA StyleRishikesh Ghogare, Yvonne Ludwig, Gela Myan Bueno, Inez H. Slamet-Loedin, Amit Dhingra. Genome editing reagent delivery in plants. Transgenic Research. 2021; 30 (4):321-335.
Chicago/Turabian StyleRishikesh Ghogare; Yvonne Ludwig; Gela Myan Bueno; Inez H. Slamet-Loedin; Amit Dhingra. 2021. "Genome editing reagent delivery in plants." Transgenic Research 30, no. 4: 321-335.
Root rot diseases remain a major global threat to the productivity of agricultural crops. They are usually caused by more than one type of pathogen and are thus often referred to as a root rot complex. Fungal and oomycete species are the predominant participants in the complex, while bacteria and viruses are also known to cause root rot. Incorporating genetic resistance in cultivated crops is considered the most efficient and sustainable solution to counter root rot, however, resistance is often quantitative in nature. Several genetics studies in various crops have identified the quantitative trait loci associated with resistance. With access to whole genome sequences, the identity of the genes within the reported loci is becoming available. Several of the identified genes have been implicated in pathogen responses. However, it is becoming apparent that at the molecular level, each pathogen engages a unique set of proteins to either infest the host successfully or be defeated or contained in attempting so. In this review, a comprehensive summary of the genes and the potential mechanisms underlying resistance or susceptibility against the most investigated root rots of important agricultural crops is presented.
Bruce Williamson-Benavides; Amit Dhingra. Understanding Root Rot Disease in Agricultural Crops. Horticulturae 2021, 7, 33 .
AMA StyleBruce Williamson-Benavides, Amit Dhingra. Understanding Root Rot Disease in Agricultural Crops. Horticulturae. 2021; 7 (2):33.
Chicago/Turabian StyleBruce Williamson-Benavides; Amit Dhingra. 2021. "Understanding Root Rot Disease in Agricultural Crops." Horticulturae 7, no. 2: 33.
The conventional breeding of fruits and fruit trees has led to the improvement of consumer-driven traits such as fruit size, yield, nutritional properties, aroma and taste, as well as the introduction of agronomic properties such as disease resistance. However, even with the assistance of modern molecular approaches such as marker-assisted selection, the improvement of fruit varieties by conventional breeding takes considerable time and effort. The advent of genetic engineering led to the rapid development of new varieties by allowing the direct introduction of genes into elite lines. In this review article, we discuss three such case studies: the Arctic® apple, the Pinkglow pineapple and the SunUp/Rainbow papaya. We consider these events in the light of global regulations for the commercialization of genetically modified organisms (GMOs), focusing on the differences between product-related systems (the USA/Canada comparative safety assessment) and process-related systems (the EU “precautionary principle” model). More recently, genome editing has provided an efficient way to introduce precise mutations in plants, including fruits and fruit trees, replicating conventional breeding outcomes without the extensive backcrossing and selection typically necessary to introgress new traits. Some jurisdictions have reacted by amending the regulations governing GMOs to provide exemptions for crops that would be indistinguishable from conventional varieties based on product comparison. This has revealed the deficiencies of current process-related regulatory frameworks, particularly in the EU, which now stands against the rest of the world as a unique example of inflexible and dogmatic governance based on political expediency and activism rather than rigorous scientific evidence.
Derry Alvarez; Pedro Cerda-Bennasser; Evan Stowe; Fabiola Ramirez-Torres; Teresa Capell; Amit Dhingra; Paul Christou. Fruit crops in the era of genome editing: closing the regulatory gap. Plant Cell Reports 2021, 40, 915 -930.
AMA StyleDerry Alvarez, Pedro Cerda-Bennasser, Evan Stowe, Fabiola Ramirez-Torres, Teresa Capell, Amit Dhingra, Paul Christou. Fruit crops in the era of genome editing: closing the regulatory gap. Plant Cell Reports. 2021; 40 (6):915-930.
Chicago/Turabian StyleDerry Alvarez; Pedro Cerda-Bennasser; Evan Stowe; Fabiola Ramirez-Torres; Teresa Capell; Amit Dhingra; Paul Christou. 2021. "Fruit crops in the era of genome editing: closing the regulatory gap." Plant Cell Reports 40, no. 6: 915-930.
Pisum sativum (pea) yields have declined significantly over the last decades, predominantly due to susceptibility to root rot diseases. One of the main causal agents of root rot is the fungus Fusarium solani f. sp. pisi (Fsp), leading to yield losses ranging from 15 to 60%. Determining and subsequently incorporating the genetic basis for resistance in new cultivars offers one of the best solutions to control this pathogen; however, no green-seeded pea cultivars with complete resistance to Fsp have been identified. To date, only partial levels of resistance to Fsp has been identified among pea genotypes. SNPs mined from Fsp-responsive differentially expressed genes (DEGs) identified in a preceding study were utilized to identify QTLs associated with Fsp resistance using composite interval mapping in two recombinant inbred line (RIL) populations segregating for partial root rot resistance. A total of 769 DEGs with single nucleotide polymorphisms (SNPs) were identified, and the putative SNPs were evaluated for being polymorphic across four partially resistant and four susceptible P. sativum genotypes. The SNPs with validated polymorphisms were used to screen two RIL populations using two phenotypic criteria: root disease severity and plant height. One QTL, WB.Fsp-Ps 5.1 that mapped to chromosome V explained 14.76 % of the variance with a confidence interval of 10.36 cM. The other four QTLs located on chromosomes II, III, and V, explained 5.26–8.05 % of the variance. The use of SNPs derived from Fsp-responsive DEGs for QTL mapping proved to be an efficient way to identify molecular markers associated with Fsp resistance in pea. These QTLs are potential candidates for marker-assisted selection and gene pyramiding to obtain high levels of partial resistance in pea cultivars to combat root rot caused by Fsp.
Bruce A. Williamson-Benavides; Richard Sharpe; Grant Nelson; Eliane T. Bodah; Lyndon D. Porter; Amit Dhingra. Identification of root rot resistance QTLs in pea using Fusarium solani f. sp. pisi-responsive differentially expressed genes. 2020, 1 .
AMA StyleBruce A. Williamson-Benavides, Richard Sharpe, Grant Nelson, Eliane T. Bodah, Lyndon D. Porter, Amit Dhingra. Identification of root rot resistance QTLs in pea using Fusarium solani f. sp. pisi-responsive differentially expressed genes. . 2020; ():1.
Chicago/Turabian StyleBruce A. Williamson-Benavides; Richard Sharpe; Grant Nelson; Eliane T. Bodah; Lyndon D. Porter; Amit Dhingra. 2020. "Identification of root rot resistance QTLs in pea using Fusarium solani f. sp. pisi-responsive differentially expressed genes." , no. : 1.
Climacteric fruits are characterized by a dramatic increase in autocatalytic ethylene production that is accompanied by a spike in respiration at the onset of ripening. The change in the mode of ethylene production from autoinhibitory to autostimulatory is known as the System 1 (S1) to System 2 (S2) transition. Existing physiological models explain the basic and overarching genetic, hormonal, and transcriptional regulatory mechanisms governing the S1 to S2 transition of climacteric fruit. However, the links between ethylene and respiration, the two main factors that characterize the respiratory climacteric, have not been examined in detail at the molecular level. Results of recent studies indicate that the alternative oxidase (AOX) respiratory pathway may play an essential role in mediating cross-talk between ethylene response, carbon metabolism, ATP production, and ROS signaling during climacteric ripening. New genomic, metabolic, and epigenetic information sheds light on the interconnectedness of ripening metabolic pathways, necessitating an expansion of the current, ethylene-centric physiological models. Understanding points at which ripening responses can be manipulated may reveal key, species- and cultivar-specific targets for regulation of ripening, enabling superior strategies for reducing postharvest wastage.
SeAnna Hewitt; Amit Dhingra. Beyond Ethylene: New Insights Regarding the Role of Alternative Oxidase in the Respiratory Climacteric. Frontiers in Plant Science 2020, 11, 543958 .
AMA StyleSeAnna Hewitt, Amit Dhingra. Beyond Ethylene: New Insights Regarding the Role of Alternative Oxidase in the Respiratory Climacteric. Frontiers in Plant Science. 2020; 11 ():543958.
Chicago/Turabian StyleSeAnna Hewitt; Amit Dhingra. 2020. "Beyond Ethylene: New Insights Regarding the Role of Alternative Oxidase in the Respiratory Climacteric." Frontiers in Plant Science 11, no. : 543958.
Harvesting of sweet cherry (Prunus avium L.) fruit is a labor-intensive process. Mechanical harvesting of sweet cherry fruit is feasible; however, it is dependent on the formation of an abscission zone at the fruit-pedicel junction. The natural propensity for pedicel-fruit abscission zone (PFAZ) formation varies by cultivar, and the general molecular basis for PFAZ formation is not well characterized. In this study, ethylene-inducible change in pedicel fruit retention force (PFRF) was recorded in a developmental time course with a concomitant analysis of the PFAZ transcriptome from three sweet cherry cultivars. In ‘Skeena’, mean PFRF for both control and treatment fruit dropped below the 0.40kg-force (3.92N) threshold for mechanical harvesting and indicating the formation of a discrete PFAZ. In ‘Bing’, mean PFRF for both control and treatment groups decreased over time. However, a mean PFRF conducive to mechanical harvesting was achieved only in the ethylene-treated fruit. While in ‘Chelan’ the mean PFRF of the control and treatment groups did not meet the threshold required for efficient mechanical harvesting. Transcriptome analysis of the PFAZ followed by the functional annotation, differential expression analysis, and gene ontology (GO) enrichment analyses of the data facilitated the identification of phytohormone-responsive and abscission-related transcripts as well as processes that exhibited differential expression and enrichment in a cultivar-dependent manner over the developmental time-course. Additionally, read alignment-based variant calling revealed several short variants in differentially expressed genes, associated with enriched gene ontologies and associated metabolic processes, lending potential insight into the genetic basis for different abscission responses between the cultivars. These results provide genetic targets for induction or inhibition of PFAZ formation, depending on the desire to harvest the fruit with or without the stem attached. Understanding the genetic mechanisms underlying the development of the PFAZ will inform future cultivar development while laying a foundation for mechanized sweet cherry harvest.
Seanna L Hewitt; Benjamin Kilian; Tyson Koepke; Jonathan Abarca; Matthew Whiting; Amit Dhingra. Characterization of ethylene-inducible pedicel-fruit abscission zone formation in non-climacteric sweet cherry (Prunus avium L.). 2020, 1 .
AMA StyleSeanna L Hewitt, Benjamin Kilian, Tyson Koepke, Jonathan Abarca, Matthew Whiting, Amit Dhingra. Characterization of ethylene-inducible pedicel-fruit abscission zone formation in non-climacteric sweet cherry (Prunus avium L.). . 2020; ():1.
Chicago/Turabian StyleSeanna L Hewitt; Benjamin Kilian; Tyson Koepke; Jonathan Abarca; Matthew Whiting; Amit Dhingra. 2020. "Characterization of ethylene-inducible pedicel-fruit abscission zone formation in non-climacteric sweet cherry (Prunus avium L.)." , no. : 1.
Chloroplast genome information is critical to understanding forms of photosynthesis in the plant kingdom. During the evolutionary process, plants have developed different photosynthetic strategies that are accompanied by complementary biochemical and anatomical features. Members of family Chenopodiaceae have species with C3 photosynthesis, and variations of C4 photosynthesis in which photorespiration is reduced by concentrating CO2 around Rubisco through dual coordinated functioning of dimorphic chloroplasts. Among dicots, the family has the largest number of C4 species, and greatest structural and biochemical diversity in forms of C4 including the canonical dual-cell Kranz anatomy, and the recently identified single cell C4 with the presence of dimorphic chloroplasts separated by a vacuole. This is the first comparative analysis of chloroplast genomes in species representative of photosynthetic types in the family. Methodology with high throughput sequencing complemented with Sanger sequencing of selected loci provided high quality and complete chloroplast genomes of seven species in the family and one species in the closely related Amaranthaceae family, representing C3, Kranz type C4 and single cell C4 (SSC4) photosynthesis six of the eight chloroplast genomes are new, while two are improved versions of previously published genomes. The depth of coverage obtained using high-throughput sequencing complemented with targeted resequencing of certain loci enabled superior resolution of the border junctions, directionality and repeat region sequences. Comparison of the chloroplast genomes with previously sequenced plastid genomes revealed similar genome organization, gene order and content with a few revisions. High-quality complete chloroplast genome sequences resulted in correcting the orientation the LSC region of the published Bienertia sinuspersici chloroplast genome, identification of stop codons in the rpl23 gene in B. sinuspersici and B. cycloptera, and identifying an instance of IR expansion in the Haloxylon ammodendron inverted repeat sequence. The rare observation of a mitochondria-to-chloroplast inter-organellar gene transfer event was identified in family Chenopodiaceae. This study reports complete chloroplast genomes from seven Chenopodiaceae and one Amaranthaceae species. The depth of coverage obtained using high-throughput sequencing complemented with targeted resequencing of certain loci enabled superior resolution of the border junctions, directionality, and repeat region sequences. Therefore, the use of high throughput and Sanger sequencing, in a hybrid method, reaffirms to be rapid, efficient, and reliable for chloroplast genome sequencing.
Richard M. Sharpe; Bruce Williamson-Benavides; Gerald E. Edwards; Amit Dhingra. Methods of analysis of chloroplast genomes of C3, Kranz type C4 and Single Cell C4 photosynthetic members of Chenopodiaceae. Plant Methods 2020, 16, 1 -14.
AMA StyleRichard M. Sharpe, Bruce Williamson-Benavides, Gerald E. Edwards, Amit Dhingra. Methods of analysis of chloroplast genomes of C3, Kranz type C4 and Single Cell C4 photosynthetic members of Chenopodiaceae. Plant Methods. 2020; 16 (1):1-14.
Chicago/Turabian StyleRichard M. Sharpe; Bruce Williamson-Benavides; Gerald E. Edwards; Amit Dhingra. 2020. "Methods of analysis of chloroplast genomes of C3, Kranz type C4 and Single Cell C4 photosynthetic members of Chenopodiaceae." Plant Methods 16, no. 1: 1-14.
Subcellular relocalization of proteins determines an organism’s metabolic repertoire and thereby its survival in unique evolutionary niches. In plants, the plastid and its various morphotypes import a large and varied number of nuclear-encoded proteins to orchestrate vital biochemical reactions in a spatiotemporal context. Recent comparative genomics analysis and high-throughput shotgun proteomics data indicate that there are a large number of plastid-targeted proteins that are either semi-conserved or non-conserved across different lineages. This implies that homologs are differentially targeted across different species, which is feasible only if proteins have gained or lost plastid targeting peptides during evolution. In this study, a broad, multi-genome analysis of 15 phylogenetically diverse genera and in-depth analyses of pangenomes from Arabidopsis and Brachypodium were performed to address the question of how proteins acquire or lose plastid targeting peptides. The analysis revealed that random insertions or deletions were the dominant mechanism by which novel transit peptides are gained by proteins. While gene duplication was not a strict requirement for the acquisition of novel subcellular targeting, 40% of novel plastid-targeted genes were found to be most closely related to a sequence within the same genome, and of these, 30.5% resulted from alternative transcription or translation initiation sites. Interestingly, analysis of the distribution of amino acids in the transit peptides of known and predicted chloroplast-targeted proteins revealed monocot and eudicot-specific preferences in residue distribution.
Ryan W. Christian; Seanna L. Hewitt; Grant Nelson; Eric H. Roalson; Amit Dhingra. Plastid transit peptides—where do they come from and where do they all belong? Multi-genome and pan-genomic assessment of chloroplast transit peptide evolution. PeerJ 2020, 8, e9772 .
AMA StyleRyan W. Christian, Seanna L. Hewitt, Grant Nelson, Eric H. Roalson, Amit Dhingra. Plastid transit peptides—where do they come from and where do they all belong? Multi-genome and pan-genomic assessment of chloroplast transit peptide evolution. PeerJ. 2020; 8 ():e9772.
Chicago/Turabian StyleRyan W. Christian; Seanna L. Hewitt; Grant Nelson; Eric H. Roalson; Amit Dhingra. 2020. "Plastid transit peptides—where do they come from and where do they all belong? Multi-genome and pan-genomic assessment of chloroplast transit peptide evolution." PeerJ 8, no. : e9772.
Pisum sativum (pea) is rapidly emerging as an inexpensive and significant contributor to the plant-derived protein market. Due to its nitrogen-fixation capability, short life cycle, and low water usage, pea is a useful cover-and-break crop that requires minimal external inputs. It is critical for sustainable agriculture and indispensable for future food security. Root rot in pea, caused by the fungal pathogen Fusarium solani f. sp. pisi (Fsp), can result in a 15–60% reduction in yield. It is urgent to understand the molecular basis of Fsp interaction in pea to develop root rot tolerant cultivars. A complementary genetics and gene expression approach was undertaken in this study to identify Fsp-responsive genes in four tolerant and four susceptible pea genotypes. Time course RNAseq was performed on both sets of genotypes after the Fsp challenge. Analysis of the transcriptome data resulted in the identification of 42,905 differentially expressed contigs (DECs). Interestingly, the vast majority of DECs were overexpressed in the susceptible genotypes at all sampling time points, rather than in the tolerant genotypes. Gene expression and GO enrichment analyses revealed genes coding for receptor-mediated endocytosis, sugar transporters, salicylic acid synthesis, and signaling, and cell death were overexpressed in the susceptible genotypes. In the tolerant genotypes, genes involved in exocytosis, and secretion by cell, the anthocyanin synthesis pathway, as well as the DRR230 gene, a pathogenesis-related (PR) gene, were overexpressed. The complementary genetic and RNAseq approach has yielded a set of potential genes that could be targeted for improved tolerance against root rot in P. sativum. Fsp challenge produced a futile transcriptomic response in the susceptible genotypes. This type of response is hypothesized to be related to the speed at which the pathogen infestation advances in the susceptible genotypes and the preexisting level of disease-preparedness in the tolerant genotypes.
Bruce A. Williamson-Benavides; Richard M. Sharpe; Grant Nelson; Eliane T. Bodah; Lyndon D. Porter; Amit Dhingra. Identification of Fusarium solani f. sp. pisi (Fsp) Responsive Genes in Pisum sativum. Frontiers in Genetics 2020, 11, 1 .
AMA StyleBruce A. Williamson-Benavides, Richard M. Sharpe, Grant Nelson, Eliane T. Bodah, Lyndon D. Porter, Amit Dhingra. Identification of Fusarium solani f. sp. pisi (Fsp) Responsive Genes in Pisum sativum. Frontiers in Genetics. 2020; 11 ():1.
Chicago/Turabian StyleBruce A. Williamson-Benavides; Richard M. Sharpe; Grant Nelson; Eliane T. Bodah; Lyndon D. Porter; Amit Dhingra. 2020. "Identification of Fusarium solani f. sp. pisi (Fsp) Responsive Genes in Pisum sativum." Frontiers in Genetics 11, no. : 1.
Background Chloroplast genome information is critical to understanding forms of photosynthesis in the plant kingdom. During the evolutionary process, plants have developed different photosynthetic strategies that are accompanied by complementary biochemical and anatomical features. Members of family Chenopodiaceae have species with C 3 photosynthesis, and variations of C 4 photosynthesis in which photorespiration is reduced by concentrating CO 2 around Rubisco through dual coordinated functioning of dimorphic chloroplasts. Among dicots, the family has the largest number of C 4 species, and greatest structural and biochemical diversity in forms of C 4 including the canonical dual-cell Kranz anatomy, and the recently identified single cell C 4 with the presence of dimorphic chloroplasts separated by a vacuole. This is the first comparative analysis of chloroplast genomes in species representative of photosynthetic types in the family. Results Methodology with high throughput sequencing complemented with Sanger sequencing of selected loci provided high quality and complete chloroplast genomes of seven species in the family and one species in the closely related Amaranthaceae family, representing C 3 , Kranz type C 4 and single cell C 4 (SSC 4 ) photosynthesis Six of the eight chloroplast genomes are new, while two are improved versions of previously published genomes. The depth of coverage obtained using high-throughput sequencing complemented with targeted resequencing of certain loci enabled superior resolution of the border junctions, directionality and repeat region sequences. Comparison of the chloroplast genomes with previously sequenced plastid genomes revealed similar genome organization, gene order and content with a few revisions. High-quality complete chloroplast genome sequences resulted in correcting the orientation the LSC region of the published Bienertia sinuspersici chloroplast genome, identification of stop codons in the rpl23 gene in B. sinuspersici and B. cycloptera , and identifying an instance of IR expansion in the Haloxylon ammodendron inverted repeat sequence. The rare observation of a mitochondria-to-chloroplast inter-organellar gene transfer event was identified in family Chenopodiaceae. Conclusions This study reports complete chloroplast genomes from seven Chenopodiaceae and one Amaranthaceae species. The depth of coverage obtained using high-throughput sequencing complemented with targeted resequencing of certain loci enabled superior resolution of the border junctions, directionality, and repeat region sequences. Therefore, the use of high throughput and Sanger sequencing, in a hybrid method, reaffirms to be rapid, efficient, and reliable for chloroplast genome sequencing.
Richard Sharpe; Bruce Andreas Williamson-Benavides; Gerry Edwards; Amit Dhingra. Methods of analysis of Chloroplast Genomes of C3, Kranz type C4 and Single Cell C4 photosynthetic members of Chenopodiaceae. 2020, 1 .
AMA StyleRichard Sharpe, Bruce Andreas Williamson-Benavides, Gerry Edwards, Amit Dhingra. Methods of analysis of Chloroplast Genomes of C3, Kranz type C4 and Single Cell C4 photosynthetic members of Chenopodiaceae. . 2020; ():1.
Chicago/Turabian StyleRichard Sharpe; Bruce Andreas Williamson-Benavides; Gerry Edwards; Amit Dhingra. 2020. "Methods of analysis of Chloroplast Genomes of C3, Kranz type C4 and Single Cell C4 photosynthetic members of Chenopodiaceae." , no. : 1.
The sustainable production of food faces formidable challenges. Foremost is the availability of arable soils, which have been ravaged by the overuse of fertilizers and detrimental soil management techniques. The maintenance of soil quality and reclamation of marginal soils are urgent priorities. The use of biochar, a carbon-rich, porous material thought to improve various soil properties, is gaining interest. Biochar (BC) is produced through the thermochemical decomposition of organic matter in a process known as pyrolysis. Importantly, the source of organic material, or ‘feedstock’, used in this process and different parameters of pyrolysis determine the chemical and physical properties of biochar. The incorporation of BC impacts soil–water relations and soil health, and it has been shown to have an overall positive impact on crop yield; however, pre-existing physical, chemical, and biological soil properties influence the outcome. The effects of long-term field application of BC and how it influences the soil microcosm also need to be understood. This literature review, including a focused meta-analysis, summarizes the key outcomes of BC studies and identifies critical research areas for future investigations. This knowledge will facilitate the predictable enhancement of crop productivity and meaningful carbon sequestration.
Elvir Tenic; Rishikesh Ghogare; Amit Dhingra. Biochar—A Panacea for Agriculture or Just Carbon? Horticulturae 2020, 6, 37 .
AMA StyleElvir Tenic, Rishikesh Ghogare, Amit Dhingra. Biochar—A Panacea for Agriculture or Just Carbon? Horticulturae. 2020; 6 (3):37.
Chicago/Turabian StyleElvir Tenic; Rishikesh Ghogare; Amit Dhingra. 2020. "Biochar—A Panacea for Agriculture or Just Carbon?" Horticulturae 6, no. 3: 37.
Background: Intensive agricultural practices have reduced soil health thereby negatively impacting crop yields. There is a need to maintain healthy soils and restore marginal lands to ensure efficient food production. Biochar, a porous carbon-rich material generated from pyrolysis of various feedstock sources is receiving attention as a soil amendment that has the potential to restore soil organic carbon content and also enhance crop yields. However, the physical and chemical properties of biochar are influenced by pyrolysis parameters. These in turn determine its interaction with the soil, thereby influencing its biological properties in terms of impact on soil microcosm and plant productivity. While most studies report the evaluation of one biochar and a single plant cultivar, the role of the genetic background of a plant in responding to biochar as a soil amendment remains unanswered. The impact of six distinct biochars on agronomic performance and fruit quality of three genetically diverse tomatoes (Solanum lycopersicum) cultivars was evaluated to test the hypotheses that 1) biochars derived from different feedstock sources would produce unique phenotypes in a single cultivar of tomato, and 2) single feedstock-derived BC would produce different phenotypes in each of the three tomato cultivars. Results: Different biochars impacted shoot dry weight, total fruit weight, and yield per plant in each cultivar differently. Both positive and negative effects were observed depending on the biochar-cultivar combination. In Oregon Spring, Ryegrass straw and CoolTerra biochar enhanced yield. In Heinz, an increase in fruit weight and citric acid was observed with several of the biochars. In Cobra, improved yields were accompanied by the reduction in fruit quality parameters. Both hypotheses were supported by the data.
Elvir Tenic; Daylen Isaac; Rishikesh Ghogare; Amit Dhingra. Variability in Fruit Yield and Quality of Genetically Diverse Tomato Cultivars in Response to Different Biochars. 2020, 1 .
AMA StyleElvir Tenic, Daylen Isaac, Rishikesh Ghogare, Amit Dhingra. Variability in Fruit Yield and Quality of Genetically Diverse Tomato Cultivars in Response to Different Biochars. . 2020; ():1.
Chicago/Turabian StyleElvir Tenic; Daylen Isaac; Rishikesh Ghogare; Amit Dhingra. 2020. "Variability in Fruit Yield and Quality of Genetically Diverse Tomato Cultivars in Response to Different Biochars." , no. : 1.
European pear (Pyrus communis L.) cultivars require a genetically pre-determined duration of cold-temperature exposure to induce autocatalytic system 2 ethylene biosynthesis and subsequent fruit ripening. The physiological responses of pear to cold-temperature-induced ripening have been well characterized, but the molecular mechanisms underlying this phenomenon continue to be elucidated. This study employed previously established cold temperature conditioning treatments for ripening of two pear cultivars, ‘D’Anjou’ and ‘Bartlett’. Using a time-course transcriptomics approach, global gene expression responses of each cultivar were assessed at four stages of developmental during the cold conditioning process. Differential expression, functional annotation, and gene ontology enrichment analyses were performed. Interestingly, evidence for the involvement of cold-induced, vernalization-related genes and repressors of endodormancy release was found. These genes have not previously been described to play a role in fruit during the ripening transition. The resulting data provide insight into cultivar-specific mechanisms of cold-induced transcriptional regulation of ripening in European pear, as well as a unique comparative analysis of the two cultivars with very different cold conditioning requirements.
SeAnna Hewitt; Christopher A. Hendrickson; Amit Dhingra. Evidence for the Involvement of Vernalization-related Genes in the Regulation of Cold-induced Ripening in ‘D’Anjou’ and ‘Bartlett’ Pear Fruit. Scientific Reports 2020, 10, 1 .
AMA StyleSeAnna Hewitt, Christopher A. Hendrickson, Amit Dhingra. Evidence for the Involvement of Vernalization-related Genes in the Regulation of Cold-induced Ripening in ‘D’Anjou’ and ‘Bartlett’ Pear Fruit. Scientific Reports. 2020; 10 (1):1.
Chicago/Turabian StyleSeAnna Hewitt; Christopher A. Hendrickson; Amit Dhingra. 2020. "Evidence for the Involvement of Vernalization-related Genes in the Regulation of Cold-induced Ripening in ‘D’Anjou’ and ‘Bartlett’ Pear Fruit." Scientific Reports 10, no. 1: 1.
The sustainable production of food faces formidable challenges. Foremost is the availability of arable soils, which have been ravaged by the overuse of fertilizers and detrimental soil management techniques. As such, maintenance of soil quality, and reclamation of marginal soils, has become an increasingly important endeavor. Recently, there has been emerging interest in the use of biochar, a carbon rich, porous material thought to improve various aspects of soil performance. Biochar (BC) is produced through the thermochemical decomposition of organic matter at high temperature in an oxygen limited environment, in a process known as pyrolysis. Importantly, the source of organic material, or ‘feedstock,’ used in this process and different parameters of pyrolysis, especially temperature, determine the chemical and physical properties of biochar. Incorporation of BC impacts soil-water relations, tilth and nutrient status, pH, soil organic matter (SOM), and microbial activity. Soil amendment with BC has been shown to have an overall positive impact on soil health and crop productivity; however, initial soil properties need to be considered prior to the application of BC. There is an urgent need to understand the effects of long-term field application of BC and how it influences the soil microcosm. This knowledge will facilitate predictable enhancement of crop productivity and meaningful carbon sequestration.
Elvir Tenic; Rishikesh Ghogare; Amit Dhingra. Biochar - A Panacea for Agriculture or Just Carbon? 2020, 1 .
AMA StyleElvir Tenic, Rishikesh Ghogare, Amit Dhingra. Biochar - A Panacea for Agriculture or Just Carbon? . 2020; ():1.
Chicago/Turabian StyleElvir Tenic; Rishikesh Ghogare; Amit Dhingra. 2020. "Biochar - A Panacea for Agriculture or Just Carbon?" , no. : 1.
Plastids are morphologically and functionally diverse organelles that are dependent on nuclear-encoded, plastid-targeted proteins for all biochemical and regulatory functions. However, how plastid proteomes vary temporally, spatially, and taxonomically has been historically difficult to analyze at a genome-wide scale using experimental methods. A bioinformatics workflow was developed and evaluated using a combination of fast and user-friendly subcellular prediction programs to maximize performance and accuracy for chloroplast transit peptides and demonstrate this technique on the predicted proteomes of 15 sequenced plant genomes. Gene family grouping was then performed in parallel using modified approaches of reciprocal best BLAST hits (RBH) and UCLUST. A total of 628 protein families were found to have conserved plastid targeting across angiosperm species using RBH, and 828 using UCLUST. However, thousands of clusters were also detected where only one species had predicted plastid targeting, most notably in Panicum virgatum which had 1,458 proteins with species-unique targeting. An average of 45% overlap was found in plastid-targeted protein-coding gene families compared with Arabidopsis, but an additional 20% of proteins matched against the full Arabidopsis proteome, indicating a unique evolution of plastid targeting. Neofunctionalization through subcellular relocalization is known to impart novel biological functions but has not been described before on a genome-wide scale for the plastid proteome. Further work to correlate these predicted novel plastid-targeted proteins to transcript abundance and high-throughput proteomics will uncover unique aspects of plastid biology and shed light on how the plastid proteome has evolved to influence plastid morphology and biochemistry.
Ryan W. Christian; SeAnna Hewitt; Eric Roalson; Amit Dhingra. Genome-Scale Characterization of Predicted Plastid-Targeted Proteomes in Higher Plants. Scientific Reports 2020, 10, 1 -22.
AMA StyleRyan W. Christian, SeAnna Hewitt, Eric Roalson, Amit Dhingra. Genome-Scale Characterization of Predicted Plastid-Targeted Proteomes in Higher Plants. Scientific Reports. 2020; 10 (1):1-22.
Chicago/Turabian StyleRyan W. Christian; SeAnna Hewitt; Eric Roalson; Amit Dhingra. 2020. "Genome-Scale Characterization of Predicted Plastid-Targeted Proteomes in Higher Plants." Scientific Reports 10, no. 1: 1-22.
Background Chloroplast genome information is critical to understanding taxonomic relationships in the plant kingdom. During the evolutionary process, plants have developed different photosynthetic strategies that are accompanied by complementary biochemical and anatomical features. Members of family Chenopodiaceae have species with C3 photosynthesis and variations of C4 photosynthesis in which photorespiration is reduced by concentrating CO2 around Rubisco through dual coordinated functioning of dimorphic chloroplasts. Among dicots, the family has a large number of C4 species, and greatest structural and biochemical diversity in forms of C4 including the canonical dual-cell Kranz anatomy, and the recently identified single-cell C4 with the presence of dimorphic chloroplasts separated by a vacuole. This is the first comparative analysis of chloroplast genomes in species representative of photosynthetic types in the family. Results High quality and complete chloroplast genomes of eight species representing C3, Kranz type C4, and single-cell C4 (SSC4) photosynthesis were obtained using high throughput sequencing complemented with Sanger sequencing of selected loci. Six of the eight chloroplast genome sequences are new, while two represent corrected versions of previously published chloroplast genomes. Comparative genomic analysis with previously sequenced plastid genomes revealed a similar genome organization, gene order, and content with a few revisions. High-quality complete chloroplast genome sequences resulted in correcting the orientation of the LSC region of the published Bienertia sinuspersici chloroplast genome, identification of stop codons in the rpl23 gene in B. sinuspersici and B. cycloptera, and identifying an instance of IR expansion in the Haloxylon ammodendron inverted repeat sequence. The rare observation of a mitochondria-to-chloroplast inter-organellar gene transfer event was identified in family Chenopodiaceae. Conclusions This study reports complete chloroplast genomes from seven Chenopodiaceae and one Amaranthaceae species. The depth of coverage obtained using high-throughput sequencing complemented with targeted resequencing of certain loci enabled superior resolution of the border junctions, directionality, and repeat region sequences. Therefore, the use of high throughput and Sanger sequencing, in a hybrid method, reaffirms to be rapid, efficient, and reliable for chloroplast genome sequencing.
Richard Sharpe; Bruce Andreas Williamson-Benavides; Gerry Edwards; Amit Dhingra. Comparative Chloroplast Genomics of C3, Kranz type C4 and Single Cell C4 photosynthetic members of Chenopodiaceae. 2020, 1 .
AMA StyleRichard Sharpe, Bruce Andreas Williamson-Benavides, Gerry Edwards, Amit Dhingra. Comparative Chloroplast Genomics of C3, Kranz type C4 and Single Cell C4 photosynthetic members of Chenopodiaceae. . 2020; ():1.
Chicago/Turabian StyleRichard Sharpe; Bruce Andreas Williamson-Benavides; Gerry Edwards; Amit Dhingra. 2020. "Comparative Chloroplast Genomics of C3, Kranz type C4 and Single Cell C4 photosynthetic members of Chenopodiaceae." , no. : 1.