Browsing by Author "Burow, Mark D. (TTU)"
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Item A Proof-of-Principle Study of Non-invasive Identification of Peanut Genotypes and Nematode Resistance Using Raman Spectroscopy(2022) Payne, William Z.; Dou, Tianyi; Cason, John M.; Simpson, Charles E.; McCutchen, Bill; Burow, Mark D. (TTU); Kurouski, DmitryIdentification of peanut cultivars for distinct phenotypic or genotypic traits whether using visual characterization or laboratory analysis requires substantial expertise, time, and resources. A less subjective and more precise method is needed for identification of peanut germplasm throughout the value chain. In this proof-of-principle study, the accuracy of Raman spectroscopy (RS), a non-invasive, non-destructive technique, in peanut phenotyping and identification is explored. We show that RS can be used for highly accurate peanut phenotyping via surface scans of peanut leaves and the resulting chemometric analysis: On average 94% accuracy in identification of peanut cultivars and breeding lines was achieved. Our results also suggest that RS can be used for highly accurate determination of nematode resistance and susceptibility of those breeding lines and cultivars. Specifically, nematode-resistant peanut cultivars can be identified with 92% accuracy, whereas susceptible breeding lines were identified with 81% accuracy. Finally, RS revealed substantial differences in biochemical composition between resistant and susceptible peanut cultivars. We found that resistant cultivars exhibit substantially higher carotenoid content compared to the susceptible breeding lines. The results of this study show that RS can be used for quick, accurate, and non-invasive identification of genotype, nematode resistance, and nutrient content. Armed with this knowledge, the peanut industry can utilize Raman spectroscopy for expedited breeding to increase yields, nutrition, and maintaining purity levels of cultivars following release.Item Comparisons of de novo transcriptome assemblers in diploid and polyploid species using peanut (Arachis spp.) RNA-Seq data(2014) Chopra, Ratan (TTU); Burow, Gloria; Farmer, Andrew; Mudge, Joann; Simpson, Charles E.; Burow, Mark D. (TTU)The narrow genetic base and limited genetic information on Arachis species have hindered the process of marker-assisted selection of peanut cultivars. However, recent developments in sequencing technologies have expanded opportunities to exploit genetic resources, and at lower cost. To use the genetic information for Arachis species available at the transcriptome level, it is important to have a good quality reference transcriptome. The available Tifrunner 454 FLEX transcriptome sequences have an assembly with 37,000 contigs and low N50 values of 500-751bp. Therefore, we generated de novo transcriptome assemblies, with about 38 million reads in the tetraploid cultivar OLin, and 16 million reads in each of the diploids, A. duranensis K38901 and A. ipaënsis KGBSPSc30076 using three different de novo assemblers, Trinity, SOAPdenovo-Trans and TransAByss. All these assemblers can use single kmer analysis, and the latter two also permit multiple kmer analysis. Assemblies generated for all three samples had N50 values ranging from 1278-1641 bp in Arachis hypogaea (AABB), 1401-1492 bp in Arachis duranensis (AA), and 1107-1342 bp in Arachis ipaënsis (BB). Comparison with legume ESTs and protein databases suggests that assemblies generated had more than 40% full length transcripts with good continuity. Also, on mapping the raw reads to each of the assemblies generated, Trinity had a high success rate in assembling sequences compared to both TransAByss and SOAPdenovo-Trans. De novo assembly of OLin had a greater number of contigs (67,098) and longer contig length (N50=1,641) compared to the Tifrunner TSA. Despite having shorter read length (2 × 50) than the Tifrunner 454FLEX TSA, de novo assembly of OLin proved superior in comparison. Assemblies generated to represent different genome combinations may serve as a valuable resource for the peanut research community.Item Effect of elevated CO2 on peanut performance in a semi-arid production region(2021) Laza, Haydee (TTU); Baker, Jeffrey T.; Yates, Charles; Mahan, James R.; Burow, Mark D. (TTU); Puppala, Naveen; Gitz, Dennis C. III; Emendack, Yves; Layland, Nancy; Ritchie, Glen L. (TTU); Chen, Junping; Rowland, Diane; Tissue, David T.; Payton, PaxtonWith the intensification and frequency of heat waves and periods of water deficit stress, along with rising atmospheric carbon dioxide [CO2], understanding the seasonal leaf-gas-exchange responses to combined abiotic factors will be important in predicting crop performance in semi-arid production systems. In peanut (Arachis hypogaea L.), the availability of developmental stage physiological data on the response to repeated water deficit stress periods in an elevated [CO2] (EC) environment is limited and necessary to improve crop model predictions. Here, we investigated the effects of season-long EC (650 µmol CO2 m−2 s−1) on the physiology and productivity of peanut in a semi-arid environment. This study was conducted over two-growing seasons using field-based growth chambers to maintain EC conditions, and impose water-stress at three critical developmental stages. Our results showed that relative to ambient [CO2] (AC), long-term EC during water-stress episodes, increased leaf-level light-saturated CO2 assimilation (Asat), transpiration efficiency (TE), vegetative biomass, and pod yield by 58%, 73%, 58%, and 39%, respectively. Although leaf nitrogen content was reduced by 16%, there was 41% increase in maximum Rubisco carboxylation efficiency in EC, indicating that there was minimal photosynthetic down-regulation. Furthermore, long-term EC modified the short-term physiological response (Asat) to rapid changes in [CO2] during the water-stress episodes, generating a much greater change in EC (54%) compared to AC (10%). Additionally, long-term EC generated a 23% greater Asat compared to the short-term EC during the water-stress episodes. These findings indicate high levels of physiological adjustment in EC, which may increase drought resilience. We concluded that EC may reduce the negative impacts of repeated water-stress events at critical developmental stages on rain-fed peanut in semi-arid regions. These results can inform current models to improve the projections of peanut response to future climates.Item Evaluation and selection of interspecific lines of groundnut (Arachis hypogaea l.) for resistance to leaf spot disease and for yield improvement(2021) Denwar, Nicholas N. (TTU); Simpson, Charles E.; Starr, James L.; Wheeler, Terry A.; Burow, Mark D. (TTU)Early and late leaf spot are two devastating diseases of peanut (Arachis hypogaea L.) worldwide. The development of a fertile, cross-compatible synthetic amphidiploid, TxAG-6 ([A. batizocoi x (A. cardenasii x A. diogoi)]4x ), opened novel opportunities for the introgression of wild alleles for disease and pest resistance into commercial cultivars. Twenty-seven interspecific lines selected from prior evaluation of an advanced backcross population were evaluated for resistance to early and late leaf spot, and for yield in two locations in Ghana in 2006 and 2007. Several interspecific lines had early leaf spot scores significantly lower than the susceptible parent, indicating that resistance to leaf spot had been successfully introgressed and retained after three cycles of backcrossing. Time to appearance of early leaf spot symptoms was less in the introgression lines than in susceptible check cultivars, but the opposite was true for late leaf spot. Selected lines from families 43-08, 43-09, 50-04, and 60-02 had significantly reduced leaf spot scores, while lines from families 43-09, 44-10, and 63-06 had high pod yields. One line combined both resistance to leaf spot and high pod yield, and several other useful lines were also identified. Results suggest that it is possible to break linkage drag for low yield that accompanies resistance. However, results also suggest that resistance was diluted in many of the breeding lines, likely a result of the multigenic nature of resistance. Future QTL analysis may be useful to identify alleles for resistance and allow recombination and pyramiding of resistance alleles while reducing linkage drag.Item Evaluation of the U.S. Peanut Germplasm Mini-Core Collection in the Virginia-Carolina Region Using Traditional and New High-Throughput Methods(2022) Sarkar, Sayantan; Oakes, Joseph; Cazenave, Alexandre Brice; Burow, Mark D. (TTU); Bennett, Rebecca S.; Chamberlin, Kelly D.; Wang, Ning; White, Melanie; Payton, Paxton; Mahan, James; Chagoya, Jennifer; Sung, Cheng Jung (TTU); McCall, David S.; Thomason, Wade E.; Balota, MariaPeanut (Arachis hypogaea L.) is an important food crop for the U.S. and the world. The Virginia-Carolina (VC) region (Virginia, North Carolina, and South Carolina) is an important peanut-growing region of the U.S and is affected by numerous biotic and abiotic stresses. Identification of stress-resistant germplasm, along with improved phenotyping methods, are important steps toward developing improved cultivars. Our objective in 2017 and 2018 was to assess the U.S. mini-core collection for desirable traits, a valuable source for resistant germplasm under limited water conditions. Accessions were evaluated using traditional and high-throughput phenotyping (HTP) techniques, and the suitability of HTP methods as indirect selection tools was assessed. Traditional phenotyping methods included stand count, plant height, lateral branch growth, normalized difference vegetation index (NDVI), canopy temperature depression (CTD), leaf wilting, fungal and viral disease, thrips rating, post-digging in-shell sprouting, and pod yield. The HTP method included 48 aerial vegetation indices (VIs), which were derived using red, blue, green, and near-infrared reflectance; color space indices were collected using an octocopter drone at the same time, with traditional phenotyping. Both phenotypings were done 10 times between 4 and 16 weeks after planting. Accessions had yields comparable to high yielding checks. Correlation coefficients up to 0.8 were identified for several Vis, with yield indicating their suitability for indirect phenotyping. Broad-sense heritability (H2) was further calculated to assess the suitability of particular VIs to enable genetic gains. VIs could be used successfully as surrogates for the physiological and agronomic trait selection in peanuts. Further, this study indicates that UAV-based sensors have potential for measuring physiologic and agronomic characteristics measured for peanut breeding, variable rate input application, real time decision making, and precision agriculture applications.Item Lipid modulation contributes to heat stress adaptation in peanut(2023) Spivey, William W.; Rustgi, Sachin; Welti, Ruth; Roth, Mary R.; Burow, Mark D. (TTU); Bridges, William C.; Narayanan, SruthiAt the cellular level, membrane damage is a fundamental cause of yield loss at high temperatures (HT). We report our investigations on a subset of a peanut (Arachis hypogaea) recombinant inbred line population, demonstrating that the membrane lipid remodeling occurring at HT is consistent with homeoviscous adaptation to maintain membrane fluidity. A major alteration in the leaf lipidome at HT was the reduction in the unsaturation levels, primarily through reductions of 18:3 fatty acid chains, of the plastidic and extra-plastidic diacyl membrane lipids. In contrast, levels of 18:3-containing triacylglycerols (TGs) increased at HT, consistent with a role for TGs in sequestering fatty acids when membrane lipids undergo remodeling during plant stress. Polyunsaturated acyl chains from membrane diacyl lipids were also sequestered as sterol esters (SEs). The removal of 18:3 chains from the membrane lipids decreased the availability of susceptible molecules for oxidation, thereby minimizing oxidative damage in membranes. Our results suggest that transferring 18:3 chains from membrane diacyl lipids to TGs and SEs is a key feature of lipid remodeling for HT adaptation in peanut. Finally, QTL-seq allowed the identification of a genomic region associated with heat-adaptive lipid remodeling, which would be useful for identifying molecular markers for heat tolerance.Item Peanut Seed Coat Acts as a Physical and Biochemical Barrier against Aspergillus flavus Infection(2021) Commey, Leslie (TTU); Tengey, Theophilus K. (TTU); Cobos, Christopher J. (TTU); Dampanaboina, Lavanya (TTU); Dhillon, Kamalpreet K. (TTU); Pandey, Manish K.; Sudini, Hari Kishan; Falalou, Hamidou; Varshney, Rajeev K.; Burow, Mark D. (TTU); Mendu, Vengopal (TTU)Aflatoxin contamination is a global menace that adversely affects food crops and human health. Peanut seed coat is the outer layer protecting the cotyledon both at pre- and post-harvest stages from biotic and abiotic stresses. The aim of the present study is to investigate the role of seed coat against A. flavus infection. In-vitro seed colonization (IVSC) with and without seed coat showed that the seed coat acts as a physical barrier, and the developmental series of peanut seed coat showed the formation of a robust multilayered protective seed coat. Radial growth bioassay revealed that both insoluble and soluble seed coat extracts from 55-437 line (resistant) showed higher A. flavus inhibition compared to TMV-2 line (susceptible). Further analysis of seed coat biochemicals showed that hydroxycinnamic and hydroxybenzoic acid derivatives are the predominant phenolic compounds, and addition of these compounds to the media inhibited A. flavus growth. Gene expression analysis showed that genes involved in lignin monomer, proanthocyanidin, and flavonoid biosynthesis are highly abundant in 55-437 compared to TMV-2 seed coats. Overall, the present study showed that the seed coat acts as a physical and biochemical barrier against A. flavus infection and its potential use in mitigating the aflatoxin contamination.Item PeanutMap: An online genome database for comparative molecular maps of peanut(2006) Jesubatham, Arun M. (TTU); Burow, Mark D. (TTU)Background: Molecular maps have been developed for many species, and are of particular importance for varietal development and comparative genomics. However, despite the existence of multiple sets of linkage maps, databases of these data are lacking for many species, including peanut. Description: PeanutMap http://peanutgenetics.tamu.edu/cmap provides a web-based interface for viewing specific linkage groups of a map set PeanutMap can display and compare multiple maps of a set based upon marker or trait correspondences, which is particularly important as cultivated peanut is a disomic tetraploid. The database can also compare linkage groups among multiple map sets, allowing identification of corresponding linkage groups from results of different research projects. Data from the two published peanut genome map sets, and also from three maps sets of phenotypic traits are present in the database. Data from PeanutMap have been incorporated into the Legume Information System website http://www.comparative-legumes.org to allow peanut map data to be used for cross-species comparisons. Conclusion: The utility of the database is expected to increase as several SSR-based maps are being developed currently, and expanded efforts for comparative mapping of legumes are underway. Optimal use of these data will benefit from the development of tools to facilitate comparative analysis. © 2006 Jesubatham and Burow; licensee BioMed Central Ltd.Item Phenotyping Peanut Drought Stress with Aerial Remote-Sensing and Crop Index Data(2024) Balota, Maria; Sarkar, Sayantan; Bennett, Rebecca S.; Burow, Mark D. (TTU)Peanut (Arachis hypogaea L.) plants respond to drought stress through changes in morpho-physiological and agronomic characteristics that breeders can use to improve the drought tolerance of this crop. Although agronomic traits, such as plant height, lateral growth, and yield, are easily measured, they may have low heritability due to environmental dependencies, including the soil type and rainfall distribution. Morpho-physiological characteristics, which may have high heritability, allow for optimal genetic gain. However, they are challenging to measure accurately at the field scale, hindering the confident selection of drought-tolerant genotypes. To this end, aerial imagery collected from unmanned aerial vehicles (UAVs) may provide confident phenotyping of drought tolerance. We selected a subset of 28 accessions from the U.S. peanut mini-core germplasm collection for in-depth evaluation under well-watered (rainfed) and water-restricted conditions in 2018 and 2019. We measured morpho-physiological and agronomic characteristics manually and estimated them from aerially collected vegetation indices. The peanut genotype and water regime significantly (p < 0.05) affected all the plant characteristics (RCC, SLA, yield, etc.). Manual and aerial measurements correlated with r values ranging from 0.02 to 0.94 (p < 0.05), but aerially estimated traits had a higher broad sense heritability (H2) than manual measurements. In particular, CO2 assimilation, stomatal conductance, and transpiration rates were efficiently estimated (R2 ranging from 0.76 to 0.86) from the vegetation indices, indicating that UAVs can be used to phenotype drought tolerance for genetic gains in peanut plants.Item The genome sequences of Arachis duranensis and Arachis ipaensis, the diploid ancestors of cultivated peanut(2016) Bertioli, David John; Cannon, Steven B.; Froenicke, Lutz; Huang, Guodong; Farmer, Andrew D.; Cannon, Ethalinda K.S.; Liu, Xin; Gao, Dongying; Clevenger, Josh; Dash, Sudhansu; Ren, Longhui; Moretzsohn, Mrcio C.; Shirasawa, Kenta; Huang, Wei; Vidigal, Bruna; Abernathy, Brian; Chu, Ye; Niederhuth, Chad E.; Umale, Pooja; Arajo, Ana Cludia G.; Kozik, Alexander; Do Kim, Kyung; Burow, Mark D. (TTU); Varshney, Rajeev K.; Wang, Xingjun; Zhang, Xinyou; Barkley, Noelle; Guimares, Patrcia M.; Isobe, Sachiko; Guo, Baozhu; Liao, Boshou; Stalker, H. Thomas; Schmitz, Robert J.; Scheffler, Brian E.; Leal-Bertioli, Soraya C.M.; Xun, Xu; Jackson, Scott A.; Michelmore, Richard; Ozias-Akins, PeggyCultivated peanut (Arachis hypogaea) is an allotetraploid with closely related subgenomes of a total size of ∼2.7 Gb. This makes the assembly of chromosomal pseudomolecules very challenging. As a foundation to understanding the genome of cultivated peanut, we report the genome sequences of its diploid ancestors (Arachis duranensis and Arachis ipaensis). We show that these genomes are similar to cultivated peanut's A and B subgenomes and use them to identify candidate disease resistance genes, to guide tetraploid transcript assemblies and to detect genetic exchange between cultivated peanut's subgenomes. On the basis of remarkably high DNA identity of the A. ipaensis genome and the B subgenome of cultivated peanut and biogeographic evidence, we conclude that A. ipaensis may be a direct descendant of the same population that contributed the B subgenome to cultivated peanut.Item Thresholding analysis and feature extraction from 3D ground penetrating radar data for noninvasive assessment of peanut yield(2021) Dobreva, Iliyana D.; Ruiz-Guzman, Henry A.; Barrios-Perez, Ilse; Adams, Tyler; Teare, Brody L.; Payton, Paxton (TTU); Everett, Mark E.; Burow, Mark D. (TTU); Hays, Dirk B.This study explores the efficacy of utilizing a novel ground penetrating radar (GPR) acquisition platform and data analysis methods to quantify peanut yield for breeding selection, agronomic research, and producer management and harvest applications. Sixty plots comprising different peanut market types were scanned with a multichannel, air-launched GPR antenna. Image thresholding analysis was performed on 3D GPR data from four of the channels to extract features that were correlated to peanut yield with the objective of developing a noninvasive high-throughput peanut phenotyping and yield-monitoring methodology. Plot-level GPR data were summarized using mean, standard deviation, sum, and the number of nonzero values (counts) below or above different percentile threshold values. Best results were obtained for data below the percentile threshold for mean, standard deviation and sum. Data both below and above the percentile threshold generated good correlations for count. Correlating individual GPR features to yield generated correlations of up to 39% explained variability, while combining GPR features in multiple linear regression models generated up to 51% explained variability. The correlations increased when regression models were developed separately for each peanut type. This research demonstrates that a systematic search of thresholding range, analysis window size, and data summary statistics is necessary for successful application of this type of analysis. The results also establish that thresholding analysis of GPR data is an appropriate methodology for noninvasive assessment of peanut yield, which could be further developed for high-throughput phenotyping and yield-monitoring, adding a new sensor and new capabilities to the growing set of digital agriculture technologies.Item Use of targeted amplicon sequencing in peanut to generate allele information on allotetraploid sub-genomes(2020) Kulkarni, Roshan (TTU); Chopra, Ratan; Chagoya, Jennifer; Simpson, Charles E.; Baring, Michael R.; Hillhouse, Andrew; Puppala, Naveen; Chamberlin, Kelly; Burow, Mark D. (TTU)The use of molecular markers in plant breeding has become a routine practice, but the cost per accession can be a hindrance to the routine use of Quantitative Trait Loci (QTL) identification in breeding programs. In this study, we demonstrate the use of targeted re-sequencing as a proof of concept of a cost-effective approach to retrieve highly informative allele information, as well as develop a bioinformatics strategy to capture the genome-specific information of a polyploid species. SNPs were identified from alignment of raw transcriptome reads (2 × 50 bp) to a synthetic tetraploid genome using BWA followed by a GATK pipeline. Regions containing high polymorphic SNPs in both A genome and B genomes were selected as targets for the resequencing study. Targets were amplified using multiplex PCR followed by sequencing on an Illumina HiSeq. Eighty-one percent of the SNP calls in diploids and 68% of the SNP calls in tetraploids were confirmed. These results were also confirmed by KASP validation. Based on this study, we find that targeted resequencing technologies have potential for obtaining maximum allele information in allopolyploids at reduced cost.