Publications by authors named "Brent Turnipseed"

8 Publications

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Multi-Trait Multi-Environment Genomic Prediction of Agronomic Traits in Advanced Breeding Lines of Winter Wheat.

Front Plant Sci 2021 18;12:709545. Epub 2021 Aug 18.

Department of Agronomy, Horticulture & Plant Science, South Dakota State University, Brookings, SD, United States.

Genomic prediction is a promising approach for accelerating the genetic gain of complex traits in wheat breeding. However, increasing the prediction accuracy (PA) of genomic prediction (GP) models remains a challenge in the successful implementation of this approach. Multivariate models have shown promise when evaluated using diverse panels of unrelated accessions; however, limited information is available on their performance in advanced breeding trials. Here, we used multivariate GP models to predict multiple agronomic traits using 314 advanced and elite breeding lines of winter wheat evaluated in 10 site-year environments. We evaluated a multi-trait (MT) model with two cross-validation schemes representing different breeding scenarios (CV1, prediction of completely unphenotyped lines; and CV2, prediction of partially phenotyped lines for correlated traits). Moreover, extensive data from multi-environment trials (METs) were used to cross-validate a Bayesian multi-trait multi-environment (MTME) model that integrates the analysis of multiple-traits, such as G × E interaction. The MT-CV2 model outperformed all the other models for predicting grain yield with significant improvement in PA over the single-trait (ST-CV1) model. The MTME model performed better for all traits, with average improvement over the ST-CV1 reaching up to 19, 71, 17, 48, and 51% for grain yield, grain protein content, test weight, plant height, and days to heading, respectively. Overall, the empirical analyses elucidate the potential of both the MT-CV2 and MTME models when advanced breeding lines are used as a training population to predict related preliminary breeding lines. Further, we evaluated the practical application of the MTME model in the breeding program to reduce phenotyping cost using a sparse testing design. This showed that complementing METs with GP can substantially enhance resource efficiency. Our results demonstrate that multivariate GS models have a great potential in implementing GS in breeding programs.
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http://dx.doi.org/10.3389/fpls.2021.709545DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8416538PMC
August 2021

Genome-wide association analysis permits characterization of Stagonospora nodorum blotch (SNB) resistance in hard winter wheat.

Sci Rep 2021 Jun 15;11(1):12570. Epub 2021 Jun 15.

Department of Agronomy, Horticulture and Plant Science, South Dakota State University, Brookings, SD, 57007, USA.

Stagonospora nodorum blotch (SNB) is an economically important wheat disease caused by the necrotrophic fungus Parastagonospora nodorum. SNB resistance in wheat is controlled by several quantitative trait loci (QTLs). Thus, identifying novel resistance/susceptibility QTLs is crucial for continuous improvement of the SNB resistance. Here, the hard winter wheat association mapping panel (HWWAMP) comprising accessions from breeding programs in the Great Plains region of the US, was evaluated for SNB resistance and necrotrophic effectors (NEs) sensitivity at the seedling stage. A genome-wide association study (GWAS) was performed to identify single-nucleotide polymorphism (SNP) markers associated with SNB resistance and effectors sensitivity. We found seven significant associations for SNB resistance/susceptibility distributed over chromosomes 1B, 2AL, 2DS, 4AL, 5BL, 6BS, and 7AL. Two new QTLs for SNB resistance/susceptibility at the seedling stage were identified on chromosomes 6BS and 7AL, whereas five QTLs previously reported in diverse germplasms were validated. Allele stacking analysis at seven QTLs explained the additive and complex nature of SNB resistance. We identified accessions ('Pioneer-2180' and 'Shocker') with favorable alleles at five of the seven identified loci, exhibiting a high level of resistance against SNB. Further, GWAS for sensitivity to NEs uncovered significant associations for SnToxA and SnTox3, co-locating with previously identified host sensitivity genes (Tsn1 and Snn3). Candidate region analysis for SNB resistance revealed 35 genes of putative interest with plant defense response-related functions. The QTLs identified and validated in this study could be easily employed in breeding programs using the associated markers to enhance the SNB resistance in hard winter wheat.
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http://dx.doi.org/10.1038/s41598-021-91515-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8206080PMC
June 2021

Genome-Wide Association Study Uncovers Novel Genomic Regions Associated With Coleoptile Length in Hard Winter Wheat.

Front Genet 2019 5;10:1345. Epub 2020 Feb 5.

Department of Agronomy, Horticulture & Plant Science, South Dakota State University, Brookings, SD, United States.

Successful seedling establishment depends on the optimum depth of seed placement especially in drought-prone conditions, providing an opportunity to exploit subsoil water and increase winter survival in winter wheat. Coleoptile length is a key determinant for the appropriate depth at which seed can be sown. Thus, understanding the genetic basis of coleoptile length is necessary and important for wheat breeding. We conducted a genome-wide association study (GWAS) using a diverse panel of 298 winter wheat genotypes to dissect the genetic architecture of coleoptile length. We identified nine genomic regions associated with the coleoptile length on seven different chromosomes. Of the nine genomic regions, five have been previously reported in various studies, including one mapped to previously known region. Three novel quantitative trait loci (QTLs), , , and were identified in our study. has a large substitution effect which is comparable to 's effect and could be used to compensate for the negative effect of on coleoptile length. In total, the nine QTLs explained 59% of the total phenotypic variation. Cultivars 'Agate' and 'MT06103' have the longest coleoptile length and interestingly, have favorable alleles at nine and eight coleoptile loci, respectively. These lines could be a valuable germplasm for longer coleoptile breeding. Gene annotations in the candidate regions revealed several putative proteins of specific interest including cytochrome P450-like, expansins, and phytochrome A. The QTLs for coleoptile length linked to single-nucleotide polymorphism (SNP) markers reported in this study could be employed in marker-assisted breeding for longer coleoptile in wheat. Thus, our study provides valuable insights into the genetic and molecular regulation of the coleoptile length in winter wheat.
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http://dx.doi.org/10.3389/fgene.2019.01345DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7025573PMC
February 2020

Mining and genomic characterization of resistance to tan spot, Stagonospora nodorum blotch (SNB), and Fusarium head blight in Watkins core collection of wheat landraces.

BMC Plant Biol 2019 Nov 8;19(1):480. Epub 2019 Nov 8.

Department of Agronomy, Horticulture & Plant Science, South Dakota State University, Brookings, SD, 57007, USA.

Background: In the late 1920s, A. E. Watkins collected about 7000 landrace cultivars (LCs) of bread wheat (Triticum aestivum L.) from 32 different countries around the world. Among which 826 LCs remain viable and could be a valuable source of superior/favorable alleles to enhance disease resistance in wheat. In the present study, a core set of 121 LCs, which captures the majority of the genetic diversity of Watkins collection, was evaluated for identifying novel sources of resistance against tan spot, Stagonospora nodorum blotch (SNB), and Fusarium Head Blight (FHB).

Results: A diverse response was observed in 121 LCs for all three diseases. The majority of LCs were moderately susceptible to susceptible to tan spot Ptr race 1 (84%) and FHB (96%) whereas a large number of LCs were resistant or moderately resistant against tan spot Ptr race 5 (95%) and SNB (54%). Thirteen LCs were identified in this study could be a valuable source for multiple resistance to tan spot Ptr races 1 and 5, and SNB, and another five LCs could be a potential source for FHB resistance. GWAS analysis was carried out using disease phenotyping score and 8807 SNPs data of 118 LCs, which identified 30 significant marker-trait associations (MTAs) with -log10 (p-value) > 3.0. Ten, five, and five genomic regions were found to be associated with resistance to tan spot Ptr race 1, race 5, and SNB, respectively in this study. In addition to Tsn1, several novel genomic regions Q.Ts1.sdsu-4BS and Q.Ts1.sdsu-5BS (tan spot Ptr race 1) and Q.Ts5.sdsu-1BL, Q.Ts5.sdsu-2DL, Q.Ts5.sdsu-3AL, and Q.Ts5.sdsu-6BL (tan spot Ptr race 5) were also identified. Our results indicate that these putative genomic regions contain several genes that play an important role in plant defense mechanisms.

Conclusion: Our results suggest the existence of valuable resistant alleles against leaf spot diseases in Watkins LCs. The single-nucleotide polymorphism (SNP) markers linked to the quantitative trait loci (QTLs) for tan spot and SNB resistance along with LCs harboring multiple disease resistance could be useful for future wheat breeding.
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http://dx.doi.org/10.1186/s12870-019-2093-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6839225PMC
November 2019

Ketamine Assisted Psychotherapy (KAP): Patient Demographics, Clinical Data and Outcomes in Three Large Practices Administering Ketamine with Psychotherapy.

J Psychoactive Drugs 2019 Apr-Jun;51(2):189-198. Epub 2019 Mar 27.

c Center for Transformational Psychotherapy , San Anselmo , CA.

Currently, ketamine is the only legal psychedelic medicine available to mental health providers for the treatment of emotional suffering. Over the past several years, ketamine has come into psychiatric use as an intervention for treatment resistant depression (TRD), administered intravenously without a psychotherapeutic component. In these settings, ketamine's psychedelic effects are viewed as undesirable "side effects." In contrast, we believe ketamine can benefit patients with a wide variety of diagnoses when administered with psychotherapy and using its psychedelic properties without need for intravenous (IV) access. Its proven safety over decades of use makes it ideal for office and supervised at-home use. The unique experience that ketamine facilitates with its biological, experiential, and psychological impacts has been tailored to optimize office-based treatment evolving into a method that we call Ketamine Assisted Psychotherapy (KAP). This article is the first to explore KAP within an analytical framework examining three distinct practices that use similar methods. Here, we present demographic and outcome data from 235 patients. Our findings suggest that KAP is an effective method for decreasing depression and anxiety in a private practice setting, especially for older patients and those with severe symptom burden.
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http://dx.doi.org/10.1080/02791072.2019.1587556DOI Listing
May 2020

Genome-Wide Association Study for Spot Blotch Resistance in Hard Winter Wheat.

Front Plant Sci 2018 6;9:926. Epub 2018 Jul 6.

Department of Agronomy, Horticulture, and Plant Science, South Dakota State University, Brookings, SD, United States.

Spot blotch (SB) caused by (anamorph: ) is an economically important disease of wheat worldwide. Under a severe epidemic condition, the disease can cause yield losses up to 70%. Previous approaches like bi-parental mapping for identifying SB resistant genes/QTLs exploited only a limited portion of the available genetic diversity with a lower capacity to detect polygenic traits, and had a lower marker density. In this study, we performed genome-wide association study (GWAS) for SB resistance in hard winter wheat association mapping panel (HWWAMP) of 294 genotypes. The HWWAMP was evaluated for response to (isolate SD40), and a range of reactions was observed with 10 resistant, 38 moderately resistant, 120 moderately resistant- moderately susceptible, 111 moderately susceptible, and 15 susceptible genotypes. GWAS using 15,590 high-quality SNPs and 294 genotypes we identified six QTLs ( = <0.001) on chromosomes 2D, 3A, 4A, 4B, 5A, and 7B that collectively explained 30% of the total variation for SB resistance. Highly associated SNPs were identified for all six QTLs, (SNP: Kukri_c31121_1460, = 4%), (SNP: Excalibur_c46082_440, = 4%), 1 (SNP: IWA8475, = 5.5%), (SNP: Excalibur_rep_c79414_306, = 4%), (SNP: Kukri_rep_c104877_2166, = 6%), and (SNP: TA005844-0160, = 6%). Our study not only validates three (2D, 5A, and 7B) genomic regions identified in previous studies but also provides highly associated SNP markers for marker assisted selection. In addition, we identified three novel QTLs (, 1, and ) for SB resistance in wheat. Gene annotation analysis of the candidate regions identified nine NBS-LRR and 38 other plant defense-related protein families across multiple QTLs, and these could be used for fine mapping and further characterization of SB resistance in wheat. Comparative analysis with barley indicated the SB resistance locus on wheat chromosomes 2D, 3A, 5A, and 7B identified in our study are syntenic to the previously identified SB resistance locus on chromosomes 2H, 3H, 5H, and 7H in barley. The 10 highly resistant genotypes and SNP markers identified in our study could be very useful resources for breeding of SB resistance in wheat.
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http://dx.doi.org/10.3389/fpls.2018.00926DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6043670PMC
July 2018

Insights into Tan Spot and Stem Rust Resistance and Susceptibility by Studying the Pre-Green Revolution Global Collection of Wheat.

Plant Pathol J 2017 Apr 1;33(2):125-132. Epub 2017 Apr 1.

Department of Agronomy, Horticulture and Plant Science, South Dakota State University, Brookings, SD 57007, USA.

Tan spot (TS), caused by the fungus (Died) Drechs, is an important foliar disease of wheat and has become a threat to world wheat production since the 1970s. In this study a globally diverse pre-1940s collection of 247 wheat genotypes was evaluated against Ptr ToxA, race 1, and stem rust to determine if; (i) acquisition of Ptr ToxA by the from led to increased pathogen virulence or (ii) incorporation of TS susceptibility during development stem rust resistant cultivars led to an increase in TS epidemics globally. Most genotypes were susceptible to stem rust; however, a range of reactions to TS and Ptr ToxA were observed. Four combinations of disease-toxin reactions were observed among the genotypes; TS susceptible-Ptr ToxA sensitive, TS susceptible-Ptr ToxA insensitive, TS resistant-Ptr ToxA insensitive, and TS resistant-Ptr ToxA toxin sensitive. A weak correlation (r = 0.14 for bread wheat and -0.082 for durum) was observed between stem rust susceptibility and TS resistance. Even though there were no reported epidemics in the pre-1940s, TS sensitive genotypes were widely grown in that period, suggesting that Ptr ToxA may not be an important factor responsible for enhanced prevalence of TS.
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http://dx.doi.org/10.5423/PPJ.OA.07.2016.0157DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5378433PMC
April 2017

The qSD12 locus controls offspring tissue-imposed seed dormancy in rice.

Genetics 2008 Aug;179(4):2263-73

Plant Science Department, South Dakota State University, Brookings, South Dakota 57007, USA.

Seed component structures were grouped into maternal and offspring (embryo and endosperm) tissues to characterize a dormancy quantitative trait locus (QTL) for tissue-specific function using a marker-assisted genetic approach. The approach was devised to test if genotypic/allelic frequencies of a marker tightly linked to the QTL deviate from Mendelian expectations in germinated and nongerminated subpopulations derived from a segregation population of partially after-ripened seeds and was applied to the dormancy QTL qSD12 and qSD7-1 in a nearly isogenic background of rice. Experimental results unambiguously demonstrated that qSD12 functions in the offspring tissue(s) and suggested that qSD7-1 may control dormancy through the maternal tissues. These experiments also provide the first solid evidence that an offspring tissue-imposed dormancy gene contributes to the segregation distortion in a mapping population developed from partially after-ripened seeds and, in part, to the germination heterogeneity of seeds from hybrid plants. Offspring and maternal tissue-imposed dormancy genes express in very early and late stages of the life cycle, respectively, and interact to provide the species with complementary adaptation strategies. The qSD12 locus was narrowed to the region of approximately 600 kbp on a high-resolution map to facilitate cloning and marker-assisted selection of the major dormancy gene.
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http://dx.doi.org/10.1534/genetics.108.092007DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2516096PMC
August 2008
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