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The Rio Grande Valley is one of the most productive agricultural areas in the U.S and is located in the southernmost part of Texas. In October 2013, we detected an exotic plant bug, Nesidiocoris tenuis Reuter (Hemiptera: Miridae: Bryocorinae) occurring in the region. Nesidiocoris tenuis has zoophytophagous habits; however, in the absence of insect prey, it feeds on its plant hosts. After its morphological and genetic identification, this study monitored the population of N. tenuis in its introduction phase in commercial fields and corroborated its establishment in research fields for three years. Populations of N. tenuis were high during the fall and low during winter. This study found that N. tenuis populations were higher in tomato fields as compared to adjacent pepper, okra, and squash fields, indicating its host preferences during the introduction phase. Recurrent population growth patterns suggest that N. tenuis was established in Rio Grande Valley with permanent populations in tomato fields. In addition, N. tenuis populations were affected by tomato cultivar selection and by plastic mulch color. The presence of N. tenuis could establish a new trophic insect relationship for vegetable production. However, it is unknown if the presence of N. tenuis may help to control pests of economic importance, such as whiteflies in cotton, or become a pest on sesame, an emerging crop.
Gabriela Esparza-Diaz; Thiago Marconi; Carlos A. Avila; Raul T. Villanueva. Persistence of the Exotic Mirid Nesidiocoris tenuis (Hemiptera: Miridae) in South Texas. Insects 2021, 12, 715 .
AMA StyleGabriela Esparza-Diaz, Thiago Marconi, Carlos A. Avila, Raul T. Villanueva. Persistence of the Exotic Mirid Nesidiocoris tenuis (Hemiptera: Miridae) in South Texas. Insects. 2021; 12 (8):715.
Chicago/Turabian StyleGabriela Esparza-Diaz; Thiago Marconi; Carlos A. Avila; Raul T. Villanueva. 2021. "Persistence of the Exotic Mirid Nesidiocoris tenuis (Hemiptera: Miridae) in South Texas." Insects 12, no. 8: 715.
The availability of well-assembled genome sequences and reduced sequencing costs have enabled the resequencing of many additional accessions in several crops, thus facilitating the rapid discovery and development of simple sequence repeat (SSR) markers. Although the genome sequence of inbred spinach line Sp75 is available, previous efforts have resulted in a limited number of useful SSR markers. Identification of additional polymorphic SSR markers will support genetics and breeding research in spinach. This study aimed to use the available genomic resources to mine and catalog a large number of polymorphic SSR markers. A search for SSR loci on six chromosome sequences of spinach line Sp75 using GMATA identified a total of 42,155 loci with repeat motifs of two to six nucleotides in the Sp75 reference genome. Whole-genome sequences (30x) of additional 21 accessions were aligned against the chromosome sequences of the reference genome and in silico genotyped using the HipSTR program by comparing and counting repeat numbers variation across the SSR loci among the accessions. The HipSTR program generated SSR genotype data were filtered for monomorphic and high missing loci, and a final set of the 5986 polymorphic SSR loci were identified. The polymorphic SSR loci were present at a density of 12.9 SSRs/Mb and were physically mapped. Out of 36 randomly selected SSR loci for validation, two failed to amplify, while the remaining were all polymorphic in a set of 48 spinach accessions from 34 countries. Genetic diversity analysis performed using the SSRs allele score data on the 48 spinach accessions showed three main population groups. This strategy to mine and develop polymorphic SSR markers by a comparative analysis of the genome sequences of multiple accessions and computational genotyping of the candidate SSR loci eliminates the need for laborious experimental screening. Our approach increased the efficiency of discovering a large set of novel polymorphic SSR markers, as demonstrated in this report.
Gehendra Bhattarai; Ainong Shi; Devi R. Kandel; Nora Solís-Gracia; Jorge Alberto da Silva; Carlos A. Avila. Genome-wide simple sequence repeats (SSR) markers discovered from whole-genome sequence comparisons of multiple spinach accessions. Scientific Reports 2021, 11, 1 -16.
AMA StyleGehendra Bhattarai, Ainong Shi, Devi R. Kandel, Nora Solís-Gracia, Jorge Alberto da Silva, Carlos A. Avila. Genome-wide simple sequence repeats (SSR) markers discovered from whole-genome sequence comparisons of multiple spinach accessions. Scientific Reports. 2021; 11 (1):1-16.
Chicago/Turabian StyleGehendra Bhattarai; Ainong Shi; Devi R. Kandel; Nora Solís-Gracia; Jorge Alberto da Silva; Carlos A. Avila. 2021. "Genome-wide simple sequence repeats (SSR) markers discovered from whole-genome sequence comparisons of multiple spinach accessions." Scientific Reports 11, no. 1: 1-16.
The efficient acquisition and transport of nutrients by plants largely depend on the root architecture. Due to the absence of complex microbial network interactions and soil heterogeneity in a restricted soilless medium, the architecture of roots is a function of genetics defined by the soilless matrix and exogenously supplied nutrients such as nitrogen (N). The knowledge of root trait combinations that offer the optimal nitrogen use efficiency (NUE) is far from being conclusive. The objective of this study was to define the root trait(s) that best predicts and correlates with vegetative biomass under differed N treatments. We used eight image-derived root architectural traits of 202 diverse spinach lines grown in two N concentrations (high N, HN, and low N, LN) in randomized complete blocks design. Supervised random forest (RF) machine learning augmented by ranger hyperparameter grid search was used to predict the variable importance of the root traits. We also determined the broad-sense heritability (H) and genetic (r g ) and phenotypic (r p ) correlations between root traits and the vegetative biomass (shoot weight, SWt). Each root trait was assigned a predicted importance rank based on the trait’s contribution to the cumulative reduction in the mean square error (MSE) in the RF tree regression models for SWt. The root traits were further prioritized for potential selection based on the r g and SWt correlated response (CR). The predicted importance of the eight root traits showed that the number of root tips (Tips) and root length (RLength) under HN and crossings (Xsings) and root average diameter (RAvdiam) under LN were the most relevant. SWt had a highly antagonistic r g (− 0.83) to RAvdiam, but a high predicted indirect selection efficiency (− 112.8%) with RAvdiam under LN; RAvdiam showed no significant rg or rp to SWt under HN. In limited N availability, we suggest that selecting against larger RAvdiam as a secondary trait might improve biomass and, hence, NUE with no apparent yield penalty under HN.
Henry O. Awika; Amit K. Mishra; Haramrit Gill; James DiPiazza; Carlos A. Avila; Vijay Joshi. Selection of nitrogen responsive root architectural traits in spinach using machine learning and genetic correlations. Scientific Reports 2021, 11, 1 -13.
AMA StyleHenry O. Awika, Amit K. Mishra, Haramrit Gill, James DiPiazza, Carlos A. Avila, Vijay Joshi. Selection of nitrogen responsive root architectural traits in spinach using machine learning and genetic correlations. Scientific Reports. 2021; 11 (1):1-13.
Chicago/Turabian StyleHenry O. Awika; Amit K. Mishra; Haramrit Gill; James DiPiazza; Carlos A. Avila; Vijay Joshi. 2021. "Selection of nitrogen responsive root architectural traits in spinach using machine learning and genetic correlations." Scientific Reports 11, no. 1: 1-13.
A major bottleneck in identifying therapies to control citrus greening and other devastating plant diseases caused by fastidious pathogens is our inability to culture the pathogens in defined media or axenic cultures. As such, conventional approaches for antimicrobial evaluation (genetic or chemical) rely on time-consuming, low-throughput and inherently variable whole-plant assays. Here, we report that plant hairy roots support the growth of fastidious pathogens like Candidatus Liberibacter spp., the presumptive causal agents of citrus greening, potato zebra chip and tomato vein greening diseases. Importantly, we leverage the microbial hairy roots for rapid, reproducible efficacy screening of multiple therapies. We identify six antimicrobial peptides, two plant immune regulators and eight chemicals which inhibit Candidatus Liberibacter spp. in plant tissues. The antimicrobials, either singly or in combination, can be used as near- and long-term therapies to control citrus greening, potato zebra chip and tomato vein greening diseases.
Sonia Irigoyen; Manikandan Ramasamy; Shankar Pant; Prakash Niraula; Renesh Bedre; Meena Gurung; Denise Rossi; Corinne Laughlin; Zachary Gorman; Diann Achor; Amit Levy; Michael V. Kolomiets; Mamoudou Sétamou; Ismael E. Badillo-Vargas; Carlos A. Avila; Michael S. Irey; Kranthi K. Mandadi. Plant hairy roots enable high throughput identification of antimicrobials against Candidatus Liberibacter spp. Nature Communications 2020, 11, 1 -14.
AMA StyleSonia Irigoyen, Manikandan Ramasamy, Shankar Pant, Prakash Niraula, Renesh Bedre, Meena Gurung, Denise Rossi, Corinne Laughlin, Zachary Gorman, Diann Achor, Amit Levy, Michael V. Kolomiets, Mamoudou Sétamou, Ismael E. Badillo-Vargas, Carlos A. Avila, Michael S. Irey, Kranthi K. Mandadi. Plant hairy roots enable high throughput identification of antimicrobials against Candidatus Liberibacter spp. Nature Communications. 2020; 11 (1):1-14.
Chicago/Turabian StyleSonia Irigoyen; Manikandan Ramasamy; Shankar Pant; Prakash Niraula; Renesh Bedre; Meena Gurung; Denise Rossi; Corinne Laughlin; Zachary Gorman; Diann Achor; Amit Levy; Michael V. Kolomiets; Mamoudou Sétamou; Ismael E. Badillo-Vargas; Carlos A. Avila; Michael S. Irey; Kranthi K. Mandadi. 2020. "Plant hairy roots enable high throughput identification of antimicrobials against Candidatus Liberibacter spp." Nature Communications 11, no. 1: 1-14.
Tomato is an important source of health‐promoting constituents, and researchers have focused on enhancing the content. In the present study, the influence of net‐house (NH) and open‐field (OF) growing conditions on physicochemical traits of tomatoes from eight different cultivars were evaluated. The tomato fruit qualities, such as color, total soluble solids (TSS), total acidity (TA), and pH were measured. Furthermore, ultra‐performance liquid chromatography coupled to electrospray ionization high‐resolution quadrupole time‐of‐flight mass spectrometry (UPLC/ESI‐HR‐QTOFMS) was used for identification and quantification of health‐promoting compounds such as ascorbic acid, ß‐carotene, lycopene, and its isomers. In addition, in vitro bile acid binding capacity of all tomato samples was analyzed along with soluble and insoluble dietary fiber analysis as biofunctional properties. The results suggest that production systems influenced tomato fruit quality and biofunctional characteristics in a variety‐specific manner. Notably, TA and all‐trans‐ß‐carotene values were considerably influenced by production systems, and their levels were higher in the NH‐ and OF‐grown tomatoes, respectively. Our findings underline the importance of the rational choice of genotype and production system to obtain high‐quality tomatoes with enhanced desired traits for breeders and consumers. Practical Application Tomato is one of the nutritional high‐valued horticultural crops. The present study aimed to assess the impact of production systems, such as net‐house and open‐field conditions, on physicochemical traits and biofunctional properties, in vitro bile acid binding capacity of eight tomato varieties. This study supplies a good reference for the rational selection of genotype and production system to obtain high‐quality tomatoes with improved desired traits for breeders and consumers.
Jisun H.J. Lee; Guddadarangavvanahally K. Jayaprakasha; Carlos A. Avila; Kevin M. Crosby; Bhimanagouda S. Patil. Effects of genotype and production system on quality of tomato fruits and in vitro bile acids binding capacity. Journal of Food Science 2020, 85, 3806 -3814.
AMA StyleJisun H.J. Lee, Guddadarangavvanahally K. Jayaprakasha, Carlos A. Avila, Kevin M. Crosby, Bhimanagouda S. Patil. Effects of genotype and production system on quality of tomato fruits and in vitro bile acids binding capacity. Journal of Food Science. 2020; 85 (11):3806-3814.
Chicago/Turabian StyleJisun H.J. Lee; Guddadarangavvanahally K. Jayaprakasha; Carlos A. Avila; Kevin M. Crosby; Bhimanagouda S. Patil. 2020. "Effects of genotype and production system on quality of tomato fruits and in vitro bile acids binding capacity." Journal of Food Science 85, no. 11: 3806-3814.
Watermelon is the most important horticultural crop in Texas and is grown across the state under diverse environments. Our study was conducted in the southern region of Texas to understand genotype-by-environment interactions and the contribution of yield components to yield. To accomplish this, twenty genotypes were evaluated for important traits and characteristics at two locations, Uvalde and Weslaco TX, for two years, 2018 and 2019. The genotypes were evaluated for total yield, total fruit count, total soluble solids, rind thickness, fruit length, diameter and weight. Genotype-by-environment (G x E) interaction was not significant, possibly due to similarity in climatic conditions and nutrient management practices. In the grouped analysis, cultivars Crimson Diamond, Sunshade and the breeding line TAM 2 had a higher total yield. Path analysis showed a high direct effect for total fruit count and fruit diameter of 0.89 and 0.85, respectively. However, total fruit count had a high indirect effect of −0.44. Fruit weight was the only trait that showed a significant (p < 0.01) correlation towards total yield at r = 0.58. Neither of the high direct effects, total fruit count and fruit diameter, had a significant correlation. The study inferred that breeding resources could be optimized by reducing the testing location to only one representative location for measured traits in southern Texas. The indirect selection of total fruit or fruit diameter could result in better yield. The study suggested selecting for optimum total fruit and fruit diameter for higher yield.
Edgar Correa; Subas Malla; Kevin Crosby; Carlos Avila. Evaluation of Genotypes and Association of Traits in Watermelon Across Two Southern Texas Locations. Horticulturae 2020, 6, 67 .
AMA StyleEdgar Correa, Subas Malla, Kevin Crosby, Carlos Avila. Evaluation of Genotypes and Association of Traits in Watermelon Across Two Southern Texas Locations. Horticulturae. 2020; 6 (4):67.
Chicago/Turabian StyleEdgar Correa; Subas Malla; Kevin Crosby; Carlos Avila. 2020. "Evaluation of Genotypes and Association of Traits in Watermelon Across Two Southern Texas Locations." Horticulturae 6, no. 4: 67.
The bacterial pathogen ‘Candidatus Liberibacter solanacearum’ (Lso) is transmitted by the tomato potato psyllid (TPP), Bactericera cockerelli, to solanaceous crops. In the present study, the changes in metabolic profiles of insect-susceptible (cv CastleMart) and resistant (RIL LA3952) tomato plants in response to TPP vectoring Lso or not, were examined after 48 h post infestation. Non-volatile and volatile metabolites were identified and quantified using headspace solid-phase microextraction equipped with a gas chromatograph-mass spectrometry (HS-SPME/GC-MS) and ultra-high pressure liquid chromatography coupled to electrospray quadrupole time-of-flight mass spectrometry (UPLC/ESI-HR-QTOFMS), respectively. Partial least squares-discriminant analysis (PLS-DA) was used to define the major uncorrelated metabolite components assuming the treatments as the correlated predictors. Metabolic changes in various classes of metabolites, including volatiles, hormones, and phenolics, were observed in resistant and susceptible plants in response to the insects carrying the pathogen or not. The results suggest the involvement of differentially regulated and, in some cases, implicates antagonistic metabolites in plant defensive signaling. Upon validation, the identified metabolites could be used as markers to screen and select breeding lines with enhanced resistance to reduce economic losses due to the TPP-Lso vector-pathogen complex in Solanaceous crops.
Ji Sun Lee; Henry O. Awika; Guddadarangavvanahally K. Jayaprakasha; Carlos A. Avila; Kevin M. Crosby; Bhimanagouda S. Patil. Tomato Metabolic Changes in Response to Tomato-Potato Psyllid (Bactericera cockerelli) and Its Vectored Pathogen Candidatus Liberibacter solanacearum. Plants 2020, 9, 1154 .
AMA StyleJi Sun Lee, Henry O. Awika, Guddadarangavvanahally K. Jayaprakasha, Carlos A. Avila, Kevin M. Crosby, Bhimanagouda S. Patil. Tomato Metabolic Changes in Response to Tomato-Potato Psyllid (Bactericera cockerelli) and Its Vectored Pathogen Candidatus Liberibacter solanacearum. Plants. 2020; 9 (9):1154.
Chicago/Turabian StyleJi Sun Lee; Henry O. Awika; Guddadarangavvanahally K. Jayaprakasha; Carlos A. Avila; Kevin M. Crosby; Bhimanagouda S. Patil. 2020. "Tomato Metabolic Changes in Response to Tomato-Potato Psyllid (Bactericera cockerelli) and Its Vectored Pathogen Candidatus Liberibacter solanacearum." Plants 9, no. 9: 1154.
Use of high-throughput sequencing (HTS) has become indispensable in life science research. Raw HTS data contains several sequencing artifacts, and as a first step it is imperative to remove the artifacts for reliable downstream bioinformatics analysis. Although there are multiple stand-alone tools available that can perform the various quality control steps separately, availability of an integrated tool that can allow one-step, automated quality control analysis of HTS datasets will significantly enhance handling large number of samples parallelly. Here, we developed HTSeqQC, a stand-alone, flexible, and easy-to-use software for one-step quality control analysis of raw HTS data. HTSeqQC can evaluate HTS data quality and perform filtering and trimming analysis in a single run. We evaluated the performance of HTSeqQC for conducting batch analysis of HTS datasets with 322 sample datasets with an average ∼1M (paired end) sequence reads per sample. HTSeqQC accomplished the QC analysis in ∼3 hours in distributed mode and ∼31 hours in shared mode, thus underscoring its utility and robust performance. In addition to command-line execution, we integrated HTSeqQC into the free, open-source, CyVerse cyberinfrastructure resource as a GUI interface, for wider access to experimental biologists who have limited computational resources and/or programming abilities.
Renesh H Bedre; Carlos A Avila; Kranthi Mandadi. HTSeqQC: A Flexible and One-Step Quality Control Software for High-throughput Sequence Data Analysis. 2020, 1 .
AMA StyleRenesh H Bedre, Carlos A Avila, Kranthi Mandadi. HTSeqQC: A Flexible and One-Step Quality Control Software for High-throughput Sequence Data Analysis. . 2020; ():1.
Chicago/Turabian StyleRenesh H Bedre; Carlos A Avila; Kranthi Mandadi. 2020. "HTSeqQC: A Flexible and One-Step Quality Control Software for High-throughput Sequence Data Analysis." , no. : 1.
The Rio Grande Valley (RGV) of South Texas is one of the most diverse vegetable-producing regions in Texas. Traditionally, tomatoes in the RGV have been grown in open field during the spring and fall, but the production area has declined significantly due to the high pressure of pests and diseases. RGV open-field cultivation during winter is limited to cold-tolerant vegetables such spinach and cabbage due to the risk of cold days and nights. As an alternative, high tunnels offer an environment protected against pests and diseases, wind, and low temperatures. Here, we studied the feasibility of RGV high-tunnel tomato production to identify the planting date, tomato type, and cultivars best suited for producing high-quality tomatoes during winter. The high tunnel maintained temperatures above 21 °C during chilly days without providing additional heat. In addition, whitefly and thrips populations remained low during most of the cropping season, although pesticide control was required at crop establishment to lower their populations. Overall, higher yields were achieved in October compared to November planting and from determinate compared to indeterminate cultivars. Determinate tomato cultivars TAM Hot-Ty, Mykonos, and TAM HT1 transplanted in October produced up to 96.4, 129.13, and 85.98 t/ha, respectively. Among the cultivars tested, TAM Hot-Ty and TAM HT1 possessed the highest concentrations of soluble solids, with ° Brix >5 %. In an organoleptic test, fruits from high tunnel tomatoes were ranked higher than Texas supermarket tomatoes imported from other regions in terms of flavor, color, and overall characteristics. This study demonstrates that tomato high-tunnel production offers a viable alternative to open-field production in South Texas and could provide a source of high-quality locally produced tomatoes to Texas and nearby markets.
Devi R. Kandel; Thiago G. Marconi; Ismael E. Badillo-Vargas; Juan Enciso; Samuel D. Zapata; Carlos A. Lazcano; Kevin Crosby; Carlos A. Avila. Yield and fruit quality of high-tunnel tomato cultivars produced during the off-season in South Texas. Scientia Horticulturae 2020, 272, 109582 .
AMA StyleDevi R. Kandel, Thiago G. Marconi, Ismael E. Badillo-Vargas, Juan Enciso, Samuel D. Zapata, Carlos A. Lazcano, Kevin Crosby, Carlos A. Avila. Yield and fruit quality of high-tunnel tomato cultivars produced during the off-season in South Texas. Scientia Horticulturae. 2020; 272 ():109582.
Chicago/Turabian StyleDevi R. Kandel; Thiago G. Marconi; Ismael E. Badillo-Vargas; Juan Enciso; Samuel D. Zapata; Carlos A. Lazcano; Kevin Crosby; Carlos A. Avila. 2020. "Yield and fruit quality of high-tunnel tomato cultivars produced during the off-season in South Texas." Scientia Horticulturae 272, no. : 109582.
Jisun Hj Lee; Deepak M Kasote; Guddadarangavvanahally K Jayaprakasha; Carlos A Avila; Kevin M Crosby; Bhimanagouda S Patil. Effect of production system and inhibitory potential of aroma volatiles on polyphenol oxidase and peroxidase activity in tomatoes. Journal of the Science of Food and Agriculture 2020, 101, 307 -314.
AMA StyleJisun Hj Lee, Deepak M Kasote, Guddadarangavvanahally K Jayaprakasha, Carlos A Avila, Kevin M Crosby, Bhimanagouda S Patil. Effect of production system and inhibitory potential of aroma volatiles on polyphenol oxidase and peroxidase activity in tomatoes. Journal of the Science of Food and Agriculture. 2020; 101 (1):307-314.
Chicago/Turabian StyleJisun Hj Lee; Deepak M Kasote; Guddadarangavvanahally K Jayaprakasha; Carlos A Avila; Kevin M Crosby; Bhimanagouda S Patil. 2020. "Effect of production system and inhibitory potential of aroma volatiles on polyphenol oxidase and peroxidase activity in tomatoes." Journal of the Science of Food and Agriculture 101, no. 1: 307-314.
Minor alleles (MA) have been associated with disease incidence in human studies, enabling the identification of diagnostic risk factors for various diseases. However, allelic mapping has rarely been performed in plant systems. The goal of this study was to determine whether a difference in MA prevalence is a strong enough risk factor to indicate a likely significant difference in disease resistance against white rust (WR; Albugo occidentalis) in spinach (Spinacia oleracea). We used WR disease severity ratings (WR-DSRs) in a diversity panel of 267 spinach accessions to define resistant- and susceptibility-associated groups within the distribution scores and then tested the single-nucleotide polymorphism (SNP) variants to interrogate the MA prevalence in the most susceptible (MS) vs. most resistant (MR) individuals using permutation-based allelic association tests. A total of 448 minor alleles associated with WR severity were identified in the comparison between the 25% MS and the 25% MR accessions, while the MA were generally similar between the two halves of the interquartile range. The minor alleles in the MS group were distributed across all six chromosomes and made up ~71% of the markers that were also strongly associated with WR in parallel performed genome-wide association study. These results indicate that susceptibility may be highly determined by the disproportionate overrepresentation of minor alleles, which could be used to select for resistant plants. Furthermore, by focusing on the distribution tails, allelic mapping could be used to identify plant markers associated with quantitative traits on the most informative segments of the phenotypic distribution.
Henry O. Awika; Thiago G. Marconi; Renesh Bedre; Kranthi K. Mandadi; Carlos A. Avila. Minor alleles are associated with white rust (Albugo occidentalis) susceptibility in spinach (Spinacia oleracea). Horticulture Research 2019, 6, 1 -15.
AMA StyleHenry O. Awika, Thiago G. Marconi, Renesh Bedre, Kranthi K. Mandadi, Carlos A. Avila. Minor alleles are associated with white rust (Albugo occidentalis) susceptibility in spinach (Spinacia oleracea). Horticulture Research. 2019; 6 (1):1-15.
Chicago/Turabian StyleHenry O. Awika; Thiago G. Marconi; Renesh Bedre; Kranthi K. Mandadi; Carlos A. Avila. 2019. "Minor alleles are associated with white rust (Albugo occidentalis) susceptibility in spinach (Spinacia oleracea)." Horticulture Research 6, no. 1: 1-15.
Anthracnose (Colletotrichum dematium) is an important disease in spinach (Spinacia oleracea). Sources of resistance must be identified, and molecular tools must be developed to expedite cultivar development. In this study, a diverse collection of 276 spinach accessions was scored for anthracnose disease severity. We then evaluated marker identification approaches by testing how well haplotype‐based trait modelling compares to single markers in identifying strong association signals. Alleles in linkage disequilibrium were tagged in haplotype blocks, and anthracnose‐associated molecular markers were identified using single‐SNP (sSNP), pairwise haplotype (htP) and multi‐marker haplotype (htM) SNP tagging approaches. We identified 49 significantly associated markers distributed on several spinach chromosomes using all methods. The sSNP approach identified 13 markers, while htP identified 24 (~63% more) and htM 34 (~162% more). Of these markers, four were uniquely identified by the sSNP approach, nine by htP and nineteen by htM. The results indicate that resistance to anthracnose is polygenic and that haplotype‐based analysis may have more power than sSNP. Using a combination of these methods can improve the identification of molecular markers for spinach breeding.
Henry O. Awika; Kimberly Cochran; Vijay Joshi; Renesh Bedre; Kranthi K. Mandadi; Carlos A. Avila. Single‐marker and haplotype‐based association analysis of anthracnose ( Colletotrichum dematium) resistance in spinach ( Spinacia oleracea ). Plant Breeding 2019, 139, 402 -418.
AMA StyleHenry O. Awika, Kimberly Cochran, Vijay Joshi, Renesh Bedre, Kranthi K. Mandadi, Carlos A. Avila. Single‐marker and haplotype‐based association analysis of anthracnose ( Colletotrichum dematium) resistance in spinach ( Spinacia oleracea ). Plant Breeding. 2019; 139 (2):402-418.
Chicago/Turabian StyleHenry O. Awika; Kimberly Cochran; Vijay Joshi; Renesh Bedre; Kranthi K. Mandadi; Carlos A. Avila. 2019. "Single‐marker and haplotype‐based association analysis of anthracnose ( Colletotrichum dematium) resistance in spinach ( Spinacia oleracea )." Plant Breeding 139, no. 2: 402-418.
Despite advances in sequencing for genotyping, the lack of rapid, accurate, and reproducible phenotyping platforms has hampered efforts to use genetic analysis to predict traits of interest. Therefore, the use of high-throughput systems to phenotype traits related to crop growth, yield, quality, and resistance to biotic and abiotic stresses has become a major asset for breeding. Here, we assessed the efficacy of unmanned aircraft system (UAS)-based high-throughput phenotyping to obtain data for molecular marker development for spinach (Spinacia oleracea L.) improvement. We used a UAS equipped with a red–green–blue sensor to capture raw images of 284 spinach accessions throughout the crop cycle. Processed images generated orthomosaic and digital surface models for estimating canopy cover, canopy volume, and excess greenness index models. In addition, we manually recorded the number of days to bolting. Genome-wide association studies against a single-nucleotide polymorphism (SNP) panel obtained by ddRADseq identified 99 SNPs significantly associated with growth parameters. Some of these SNPs are in transcription factor and stress-response genes with possible roles in plant growth and development. The results underscore the utility of combining aerial imaging and genomic data analysis to optimize marker development. This study lays the foundation for the use of UAS-based high-throughput phenotyping for the molecular breeding of spinach. Copyright © 2019. . © 2019 The Author(s).
Henry O. Awika; Renesh Bedre; Junho Yeom; Thiago G. Marconi; Juan Enciso; Kranthi K. Mandadi; Jinha Jung; Carlos A. Avila. Developing Growth‐Associated Molecular Markers Via High‐Throughput Phenotyping in Spinach. The Plant Genome 2019, 12, 190027 -19.
AMA StyleHenry O. Awika, Renesh Bedre, Junho Yeom, Thiago G. Marconi, Juan Enciso, Kranthi K. Mandadi, Jinha Jung, Carlos A. Avila. Developing Growth‐Associated Molecular Markers Via High‐Throughput Phenotyping in Spinach. The Plant Genome. 2019; 12 (3):190027-19.
Chicago/Turabian StyleHenry O. Awika; Renesh Bedre; Junho Yeom; Thiago G. Marconi; Juan Enciso; Kranthi K. Mandadi; Jinha Jung; Carlos A. Avila. 2019. "Developing Growth‐Associated Molecular Markers Via High‐Throughput Phenotyping in Spinach." The Plant Genome 12, no. 3: 190027-19.
The tomato-potato psyllid (TPP), Bactericera cockerelli, is a vector for the phloem-limited bacterium Candidatus Liberibacter solanacearum (Lso), the causative agent of economically important diseases including tomato vein-greening and potato zebra chip. Here, we screened 11 wild tomato relatives for TPP resistance as potential resources for tomato (Solanum lycopersicum) cultivar development. Six accessions with strong TPP resistance (survival S. habrochaites, S. pennelli, S. huaylasense, S. chmielewskii, S. corneliomulleri, and S. galapagense. Two S. pennelli and S. corneliomulleri accessions also showed resistance to Lso. We evaluated recombinant inbred lines (RILs) carrying resistance from S. habrochaites accession LA1777 in the S. lycopersicum background and identified major quantitative trait loci (QTLs) responsible for adult TPP mortality and fecundity in several RILs carrying insertions in different chromosomes, indicating the polygenic nature of these traits. Analysis of a major resistance QTL in RIL LA3952 on chromosome 8 revealed that the presence of Lso is required to increase adult TPP mortality. By contrast, the reduced TPP oviposition trait in LA3952 is independent of Lso. Therefore, resistance traits are available in wild-tomato species, although their complex inheritance and modes of action require further characterisation to optimise their utilisation for tomato improvement.
Carlos A. Avila; Thiago G. Marconi; Zenaida Viloria; Julianna Kurpis; Sonia Y. Del Rio. Bactericera cockerelli resistance in the wild tomato Solanum habrochaites is polygenic and influenced by the presence of Candidatus Liberibacter solanacearum. Scientific Reports 2019, 9, 1 -11.
AMA StyleCarlos A. Avila, Thiago G. Marconi, Zenaida Viloria, Julianna Kurpis, Sonia Y. Del Rio. Bactericera cockerelli resistance in the wild tomato Solanum habrochaites is polygenic and influenced by the presence of Candidatus Liberibacter solanacearum. Scientific Reports. 2019; 9 (1):1-11.
Chicago/Turabian StyleCarlos A. Avila; Thiago G. Marconi; Zenaida Viloria; Julianna Kurpis; Sonia Y. Del Rio. 2019. "Bactericera cockerelli resistance in the wild tomato Solanum habrochaites is polygenic and influenced by the presence of Candidatus Liberibacter solanacearum." Scientific Reports 9, no. 1: 1-11.
Unmanned aerial vehicles (UAV) have been recognized as excellent tools to provide real time feedback of temporal and spatial conditions found in agricultural fields throughout the growing season. UAVs have also allowed accelerating breeding programs by screening varieties or by selecting agronomic traits that confer resistance to biotic and abiotic stresses and selecting the best management practices that optimize the management of soil and water resources. The main objectives of this study were to assess the potential use of UAVs to determine crop height, canopy cover, and NDVI during the tomato growing season for three tomato varieties; to validate tomato height obtained with a UAV; and evaluate the correlation between leaf area index and canopy cover determined with the UAV. The UAV was flown over a tomato trial planted with 90 plots that contained eight different tomato varieties; 3 roma and 5 round replicated three times per row and planted in three rows. The plots of the tomato varieties TAM-HOT, Shourouq, and Mykonos were selected for validation with the UAV. Commitment field measurements of plant height, leaf area index, and NDVI were collected weekly (from April 27 to June 22, 2017). All the tomato varieties were healthy without diseases and the NDVI values estimated with the UAV peaked between 90 and 110 days after transplanting (DAP). A coefficient of determination of 0.72 was observed between canopy cover estimated with the UAV and leaf area index measured with the ceptometer. The coefficient of correlation between the estimated and measured crop heights were 0.9845, 0.9766 and 0.9949 for the TAM-HOT, Shourouq and Mykonos, respectively. In addition, the calculated paired t test statistic showed no significant difference (P ≥ 0.05) between the estimated, the UAV and manually measured crop heights. In the future, UAV crop growth and NDVI monitoring could be improved through temporally dense data acquisition, increasing the number of ground samples and their geometric coincidence with the grids in UAV images, removal of weather effects, and other systematic errors caused from image quality and grid size.
Juan Enciso; Carlos A. Avila; Jinha Jung; Sheren Elsayed-Farag; Anjin Chang; Junho Yeom; Juan Landivar; Murilo Maeda; Jose C. Chavez. Validation of agronomic UAV and field measurements for tomato varieties. Computers and Electronics in Agriculture 2019, 158, 278 -283.
AMA StyleJuan Enciso, Carlos A. Avila, Jinha Jung, Sheren Elsayed-Farag, Anjin Chang, Junho Yeom, Juan Landivar, Murilo Maeda, Jose C. Chavez. Validation of agronomic UAV and field measurements for tomato varieties. Computers and Electronics in Agriculture. 2019; 158 ():278-283.
Chicago/Turabian StyleJuan Enciso; Carlos A. Avila; Jinha Jung; Sheren Elsayed-Farag; Anjin Chang; Junho Yeom; Juan Landivar; Murilo Maeda; Jose C. Chavez. 2019. "Validation of agronomic UAV and field measurements for tomato varieties." Computers and Electronics in Agriculture 158, no. : 278-283.
The spr2 mutation in tomato (Solanum lycopersicum), which disrupts function of FATTY ACID DESATURASE 7 (FAD7), confers resistance to the potato aphid (Macrosiphum euphorbiae) and modifies the plant’s C6 volatile profiles. To investigate whether C6 volatiles play a role in resistance, HYDROPEROXIDE LYASE (HPL), which encodes a critical enzyme in C6 volatile synthesis, was silenced in wild-type tomato plants and spr2 mutants. Silencing HPL in wild-type tomato increased potato aphid host preference and reproduction on 5-week old plants but had no influence on 3-week old plants. The spr2 mutation, in contrast, conferred strong aphid resistance at both 3 and 5 weeks, and silencing HPL in spr2 did not compromise this aphid resistance. Moreover, a mutation in the FAD7 gene in Arabidopsis thaliana also conferred resistance to the green peach aphid (Myzus persicae) in a genetic background that carries a null mutation in HPL. These results indicate that HPL contributes to certain forms of aphid resistance in tomato, but that the effects of FAD7 on aphids in tomato and Arabidopsis are distinct from and independent of HPL.
Jiamei Li; Carlos A. Avila; Denise M. Tieman; Harry J. Klee; Fiona L. Goggin. A Comparison of the Effects of FATTY ACID DESATURASE 7 and HYDROPEROXIDE LYASE on Plant–Aphid Interactions. International Journal of Molecular Sciences 2018, 19, 1077 .
AMA StyleJiamei Li, Carlos A. Avila, Denise M. Tieman, Harry J. Klee, Fiona L. Goggin. A Comparison of the Effects of FATTY ACID DESATURASE 7 and HYDROPEROXIDE LYASE on Plant–Aphid Interactions. International Journal of Molecular Sciences. 2018; 19 (4):1077.
Chicago/Turabian StyleJiamei Li; Carlos A. Avila; Denise M. Tieman; Harry J. Klee; Fiona L. Goggin. 2018. "A Comparison of the Effects of FATTY ACID DESATURASE 7 and HYDROPEROXIDE LYASE on Plant–Aphid Interactions." International Journal of Molecular Sciences 19, no. 4: 1077.
Several high-throughput molecular genetic analyses rely on high-quality genomic DNA. Copurification of other molecules can negatively impact the functionality of plant DNA preparations employed in these procedures. Isolating DNA from agronomically important crops, such as sugarcane, rice, citrus, potato and tomato is a challenge due to the presence of high fiber, polysaccharides, or secondary metabolites. We present a simplified, rapid and reproducible SDS-based method that provides high-quality and -quantity of DNA from small amounts of leaf tissue, as required by the emerging biotechnology and molecular genetic applications. We developed the TENS-CO method as a simplified SDS-based isolation procedure with sequential steps of purification to remove polysaccharides and polyphenols using 2-mercaptoethanol and potassium acetate, chloroform partitioning, and sodium acetate/ethanol precipitation to yield high-quantity and -quality DNA consistently from small amounts of tissue (0.15 g) for different plant species. The method is simplified and rapid in terms of requiring minimal manipulation, smaller extraction volume, reduced homogenization time (20 s) and DNA precipitation (one precipitation for 1 h). The method has been demonstrated to accelerate screening of large amounts of plant tissues from species that are rich in polysaccharides and secondary metabolites for Southern blot analysis of reporter gene overexpressing lines, pathogen detection by quantitative PCR, and genotyping of disease-resistant plants using marker-assisted selection. To facilitate molecular genetic studies in major agronomical crops, we have developed the TENS-CO method as a simple, rapid, reproducible and scalable protocol enabling efficient and robust isolation of high-quality and -quantity DNA from small amounts of tissue from sugarcane, rice, citrus, potato, and tomato, thereby reducing significantly the time and resources used for DNA isolation.
Kelvin T. Chiong; Mona B. Damaj; Carmen S. Padilla; Carlos A. Avila; Shankar R. Pant; Kranthi K. Mandadi; Ninfa R. Ramos; Denise V. Carvalho; T. Erik Mirkov. Reproducible genomic DNA preparation from diverse crop species for molecular genetic applications. Plant Methods 2017, 13, 1 -11.
AMA StyleKelvin T. Chiong, Mona B. Damaj, Carmen S. Padilla, Carlos A. Avila, Shankar R. Pant, Kranthi K. Mandadi, Ninfa R. Ramos, Denise V. Carvalho, T. Erik Mirkov. Reproducible genomic DNA preparation from diverse crop species for molecular genetic applications. Plant Methods. 2017; 13 (1):1-11.
Chicago/Turabian StyleKelvin T. Chiong; Mona B. Damaj; Carmen S. Padilla; Carlos A. Avila; Shankar R. Pant; Kranthi K. Mandadi; Ninfa R. Ramos; Denise V. Carvalho; T. Erik Mirkov. 2017. "Reproducible genomic DNA preparation from diverse crop species for molecular genetic applications." Plant Methods 13, no. 1: 1-11.