River Falls, WI, United States
River Falls, WI, United States

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Breeze M.L.,Monsanto Corporation | Leyva-Guerrero E.,Monsanto Corporation | Yeaman G.R.,Monsanto Corporation | Dudin Y.,Monsanto Corporation | And 14 more authors.
JAOCS, Journal of the American Oil Chemists' Society | Year: 2015

Soybean agglutinin (SBA) protein, also known as soybean lectin, is regarded as an anti-nutrient due to its negative effect on the ability of monogastric animals to gain weight following consumption of raw soybean seed. Historically, SBA has been measured using a time-consuming and cumbersome hemagglutination procedure. The objective of our research was to obtain a validated methodology that is precise and accurate in the measurement of SBA while allowing minimally equipped laboratories to effectively conduct the analysis, thus our focus was on evaluating an existing commercially available ELISA, an enzyme-linked-lectin-assay (ELLA), and a hybrid ELISA/ELLA. A new ELLA technique that can detect and quantify lectins was chosen and modified specifically for the quantitation of SBA in soybean seed. The proposed ELLA methodology is similar to a standard sandwich ELISA, and uses polyacrylamide-linked N-acetylgalactosamine (Gal-NAc-PAA) for a capture phase and the biotinylated version (Gal-NAc-PAA-Biotin) for detection. Based upon the validation data, the ELLA method can precisely and accurately determine soybean lectin levels in soybean seed. The validated ELLA method was used to quantify SBA in nine commercial soybean varieties introduced between 1972 and 2008 and demonstrated that the natural variability of SBA is subject to the effects of genotype and environment. © 2015 AOCS.


Chandra-Shekara A.C.,BioDiagnostics Inc | Chandra-Shekara A.C.,Dow AgroSciences | Pegadaraju V.,BioDiagnostics Inc | Thompson M.,BioDiagnostics Inc | And 3 more authors.
Molecular Breeding | Year: 2011

Perennial ryegrass (Lolium perenne L.) is a preferred choice for the turf grass industry due to its ability to provide a durable turf cover. Genetic or physical contamination of annual (L. multiflorum Lam.) or intermediate (L. hybridum) ryegrass species in perennial ryegrass is one of the major problems affecting the grass seed industry. At present, seedling root fluorescence (SRF), a biochemical marker, is used for the detection of annual ryegrass contamination. Due to the unreliability of the SRF test, the seed industry is seeking an alternative, more reliable and accurate detection method. Currently, there are no DNA tests available in ryegrass for detecting contamination with annual and intermediate ryegrass types. We developed a novel quantitative polymerase chain reaction (Q-PCR)-based DNA test for the detection of annual and/or intermediate ryegrass types in perennial ryegrass. This DNA test was designed using an insertion/deletion (InDel) site in the LpVRN2_2 (Vernalization 2) gene, which is one of the several genes controlling vernalization in ryegrass. The new DNA test is more reliable, accurate and cost-effective in detecting contamination, with a high sensitivity of 0.04% in a sample size of 5,000 seeds. Use of larger sample sizes (12.5-fold higher compared to SRF test) provided additional accuracy in detecting the level of contamination. The method has produced consistent results in 68 perennial, 26 annual and 14 intermediate ryegrass lines. © 2010 Springer Science+Business Media B.V.


Nimmakayala P.,West Virginia State University | Abburi V.L.,West Virginia State University | Bhandary A.,West Virginia State University | Abburi L.,West Virginia State University | And 10 more authors.
Molecular Breeding | Year: 2014

Watermelon (Citrullus lanatus var. lanatus) is one of the most important vegetable crops in the world. Molecular markers have become the tools of choice for resolving watermelon taxonomic relationships and evolution. Increased numbers of single nucleotide polymorphism (SNP) markers together with simple sequence repeat (SSR) markers would be useful for phylogenetic analyses of germplasm accessions and for linkage mapping for marker-assisted breeding with quantitative trait loci and single genes. We aimed to construct a genetic map based on SNPs (generated by Illumina Veracode multiplex assays for genotyping) and SSR markers and evaluate relationships inferred from SNP genotypes between 130 watermelon accessions collected throughout the world. We incorporated 282 markers (232 SNPs and 50 SSRs) into the linkage map. The genetic map consisted of 11 linkage groups spanning 924.72 cM with an average distance of 3.28 cM between markers. Because all of the SNP-containing sequences were assembled with the whole-genome sequence draft for watermelon, chromosome numbers could be readily assigned for all the linkage groups. We found that 134 SNPs were polymorphic in 130 watermelon accessions chosen for diversity studies. The current 384-plex SNP set is a powerful tool for characterizing genetic relatedness and for developing medium-resolution genetic maps. © 2014 Springer Science+Business Media Dordrecht.


Talukder Z.I.,North Dakota State University | Hulke B.S.,U.S. Department of Agriculture | Qi L.,U.S. Department of Agriculture | Scheffler B.E.,U.S. Department of Agriculture | And 3 more authors.
Theoretical and Applied Genetics | Year: 2014

Key message: Functional markers for Sclerotinia basal stalk rot resistance in sunflower were obtained using gene-level information from the model species Arabidopsis thaliana. Sclerotinia stalk rot, caused by Sclerotinia sclerotiorum, is one of the most destructive diseases of sunflower (Helianthus annuus L.) worldwide. Markers for genes controlling resistance to S. sclerotiorum will enable efficient marker-assisted selection (MAS). We sequenced eight candidate genes homologous to Arabidopsis thaliana defense genes known to be associated with Sclerotinia disease resistance in a sunflower association mapping population evaluated for Sclerotinia stalk rot resistance. The total candidate gene sequence regions covered a concatenated length of 3,791 bp per individual. A total of 187 polymorphic sites were detected for all candidate gene sequences, 149 of which were single nucleotide polymorphisms (SNPs) and 38 were insertions/deletions. Eight SNPs in the coding regions led to changes in amino acid codons. Linkage disequilibrium decay throughout the candidate gene regions declined on average to an r 2 = 0.2 for genetic intervals of 120 bp, but extended up to 350 bp with r 2 = 0.1. A general linear model with modification to account for population structure was found the best fitting model for this population and was used for association mapping. Both HaCOI1-1 and HaCOI1-2 were found to be strongly associated with Sclerotinia stalk rot resistance and explained 7.4 % of phenotypic variation in this population. These SNP markers associated with Sclerotinia stalk rot resistance can potentially be applied to the selection of favorable genotypes, which will significantly improve the efficiency of MAS during the development of stalk rot resistant cultivars. © 2013 Springer-Verlag Berlin Heidelberg (outside the USA).


Pegadaraju V.,BioDiagnostics Inc | Nipper R.,Floragenex Inc. | Hulke B.,U.S. Department of Agriculture | Qi L.,U.S. Department of Agriculture | Schultz Q.,BioDiagnostics Inc
BMC Genomics | Year: 2013

Background: Application of Single Nucleotide Polymorphism (SNP) marker technology as a tool in sunflower breeding programs offers enormous potential to improve sunflower genetics, and facilitate faster release of sunflower hybrids to the market place. Through a National Sunflower Association (NSA) funded initiative, we report on the process of SNP discovery through reductive genome sequencing and local assembly of six diverse sunflower inbred lines that represent oil as well as confection types.Results: A combination of Restriction site Associated DNA Sequencing (RAD-Seq) protocols and Illumina paired-end sequencing chemistry generated high quality 89.4 M paired end reads from the six lines which represent 5.3 GB of the sequencing data. Raw reads from the sunflower line, RHA 464 were assembled de novo to serve as a framework reference genome. About 15.2 Mb of sunflower genome distributed over 42,267 contigs were obtained upon assembly of RHA 464 sequencing data, the contig lengths ranged from 200 to 950 bp with an N50 length of 393 bp. SNP calling was performed by aligning sequencing data from the six sunflower lines to the assembled reference RHA 464. On average, 1 SNP was located every 143 bp of the sunflower genome sequence. Based on several filtering criteria, a final set of 16,467 putative sequence variants with characteristics favorable for Illumina Infinium Genotyping Technology (IGT) were mined from the sequence data generated across six diverse sunflower lines.Conclusion: Here we report the molecular and computational methodology involved in SNP development for a complex genome like sunflower lacking reference assembly, offering an attractive tool for molecular breeding purposes in sunflower. © 2013 Pegadaraju et al.; licensee BioMed Central Ltd.


Talukder Z.I.,North Dakota State University | Gong L.,North Dakota State University | Hulke B.S.,U.S. Department of Agriculture | Pegadaraju V.,BioDiagnostics Inc. | And 3 more authors.
PLoS ONE | Year: 2014

A high-resolution genetic map of sunflower was constructed by integrating SNP data from three F2 mapping populations (HA 89/RHA 464, B-line/RHA 464, and CR 29/RHA 468). The consensus map spanned a total length of 1443.84 cM, and consisted of 5,019 SNP markers derived from RAD tag sequencing and 118 publicly available SSR markers distributed in 17 linkage groups, corresponding to the haploid chromosome number of sunflower. The maximum interval between markers in the consensus map is 12.37 cM and the average distance is 0.28 cM between adjacent markers. Despite a few short-distance inversions in marker order, the consensus map showed high levels of collinearity among individual maps with an average Spearman's rank correlation coefficient of 0.972 across the genome. The order of the SSR markers on the consensus map was also in agreement with the order of the individual map and with previously published sunflower maps. Three individual and one consensus maps revealed the uneven distribution of markers across the genome. Additionally, we performed fine mapping and marker validation of the rust resistance gene R12, providing closely linked SNP markers for marker-assisted selection of this gene in sunflower breeding programs. This high resolution consensus map will serve as a valuable tool to the sunflower community for studying marker-trait association of important agronomic traits, marker assisted breeding, map-based gene cloning, and comparative mapping.


PubMed | BioDiagnostics Inc., U.S. Department of Agriculture and North Dakota State University
Type: Journal Article | Journal: PloS one | Year: 2014

A high-resolution genetic map of sunflower was constructed by integrating SNP data from three F2 mapping populations (HA 89/RHA 464, B-line/RHA 464, and CR 29/RHA 468). The consensus map spanned a total length of 1443.84 cM, and consisted of 5,019 SNP markers derived from RAD tag sequencing and 118 publicly available SSR markers distributed in 17 linkage groups, corresponding to the haploid chromosome number of sunflower. The maximum interval between markers in the consensus map is 12.37 cM and the average distance is 0.28 cM between adjacent markers. Despite a few short-distance inversions in marker order, the consensus map showed high levels of collinearity among individual maps with an average Spearmans rank correlation coefficient of 0.972 across the genome. The order of the SSR markers on the consensus map was also in agreement with the order of the individual map and with previously published sunflower maps. Three individual and one consensus maps revealed the uneven distribution of markers across the genome. Additionally, we performed fine mapping and marker validation of the rust resistance gene R12, providing closely linked SNP markers for marker-assisted selection of this gene in sunflower breeding programs. This high resolution consensus map will serve as a valuable tool to the sunflower community for studying marker-trait association of important agronomic traits, marker assisted breeding, map-based gene cloning, and comparative mapping.


Basirnia A.,Urmia University | Maleki H.H.,Islamic Azad University at Maragheh | Darvishzadeh R.,Urmia University | Ghavami F.,Dakota State University | Ghavami F.,BioDiagnostics Inc.
Journal of Plant Interactions | Year: 2014

Chloride is an essential micronutrient in tobacco (Nicotiana tabaccum L.) cultivation. However, large amounts of it have many adverse effects on burning quality of tobacco leaves. The objective of this study was to evaluate the genetic variability among 70 oriental-type tobacco genotypes and determine the genomic regions associated with chloride accumulation rate using mixed linear model (MLM) procedure. A total number of 66 alleles were detected by 26 simple sequence repeat (SSR) loci with an average of 2.53 alleles per locus. A model-based Bayesian approach subdivided 70 tobacco genotypes into the three subgroups. Almost 5.85% of the 325 marker pairs showed a significant level of linkage disequilibrium (P ≤ 0.01). Using MLM procedure, 1 SSR locus (pt30027) from linkage group 13 was identified to be associated with the gene(s) controlling low chloride accumulation in oriental tobacco genotypes. Identified markers could be of great interest in marker-assisted selection in tobacco breeding programs. © 2014 The Author(s).

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