Publications by authors named "Sumit Pradhan"

7 Publications

  • Page 1 of 1

Genetics of Fusarium head blight resistance in soft red winter wheat using a genome-wide association study.

Plant Genome 2022 May 28:e20222. Epub 2022 May 28.

Dep. of Plant Pathology, Univ. of Georgia, Griffin Campus, Griffin, GA, 30223, USA.

Host resistance is an effective and sustainable approach to manage the negative impact of Fusarium head blight (FHB) on wheat (Triticum aestivum L.) grain yield and quality. The objective of this study was to characterize the phenotypic responses and identify quantitative trait loci (QTL) conditioning different FHB resistance types using a panel of 236 elite soft red winter wheat (SRWW) lines in a genome-wide association study (GWAS). The panel was phenotyped for five FHB and three morphological traits under two field and two greenhouse environments in 2018-2019 and 2019-2020. We identified 160 significant marker-trait associations (MTAs) for FHB traits and 11 MTAs for plant height. Eleven QTL showed major effects and explained >10% phenotypic variation (PV) for FHB resistance. Among these major loci, three QTL were stable and five QTL exhibited a pleiotropic effect. The QTL QFhb-3BL, QFhb-5AS, QFhb-5BL, QFhb-7AS.1, QFhb-7AS.2, and QFhb-7BS are presumed to be novel. Pyramiding multiple resistance alleles from all the major-effect QTL resulted in a significant reduction in FHB incidence, severity, index, deoxynivalenol (DON), and Fusarium-damaged kernel (FDK) by 17, 43, 45, 55, and 25%, respectively. Further validation of these QTL could potentially facilitate successful introgression of these resistance loci in new cultivars for improved FHB resistance in breeding programs.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1002/tpg2.20222DOI Listing
May 2022

Multi-trait genomic prediction using in-season physiological parameters increases prediction accuracy of complex traits in US wheat.

BMC Genomics 2022 Apr 12;23(1):298. Epub 2022 Apr 12.

Department of Agronomy, 3105 McCarty Hall B, Gainesville, FL, 32611, USA.

Background: Recently genomic selection (GS) has emerged as an important tool for plant breeders to select superior genotypes. Multi-trait (MT) prediction model provides an opportunity to improve the predictive ability of expensive and labor-intensive traits. In this study, we assessed the potential use of a MT genomic prediction model by incorporating two physiological traits (canopy temperature, CT and normalized difference vegetation index, NDVI) to predict 5 complex primary traits (harvest index, HI; grain yield, GY; grain number, GN; spike partitioning index, SPI; fruiting efiiciency, FE) using two cross-validation schemes CV1 and CV2.

Results: In this study, we evaluated 236 wheat genotypes in two locations in 2 years. The wheat genotypes were genotyped with genotyping by sequencing approach which generated 27,466 SNPs. MT-CV2 (multi-trait cross validation 2) model improved predictive ability by 4.8 to 138.5% compared to ST-CV1(single-trait cross validation 1). However, the predictive ability of MT-CV1 was not significantly different compared to the ST-CV1 model.

Conclusions: The study showed that the genomic prediction of complex traits such as HI, GN, and GY can be improved when correlated secondary traits (cheaper and easier phenotyping) are used. MT genomic selection could accelerate breeding cycles and improve genetic gain for complex traits in wheat and other crops.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12864-022-08487-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9004054PMC
April 2022

Multi-Trait Genomic Prediction of Yield-Related Traits in US Soft Wheat under Variable Water Regimes.

Genes (Basel) 2020 10 28;11(11). Epub 2020 Oct 28.

Department of Agronomy, University of Florida, Gainesville, FL 32611, USA.

The performance of genomic prediction (GP) on genetically correlated traits can be improved through an interdependence multi-trait model under a multi-environment context. In this study, a panel of 237 soft facultative wheat ( L.) lines was evaluated to compare single- and multi-trait models for predicting grain yield (GY), harvest index (HI), spike fertility (SF), and thousand grain weight (TGW). The panel was phenotyped in two locations and two years in Florida under drought and moderately drought stress conditions, while the genotyping was performed using 27,957 genotyping-by-sequencing (GBS) single nucleotide polymorphism (SNP) makers. Five predictive models including Multi-environment Genomic Best Linear Unbiased Predictor (MGBLUP), Bayesian Multi-trait Multi-environment (BMTME), Bayesian Multi-output Regressor Stacking (BMORS), Single-trait Multi-environment Deep Learning (SMDL), and Multi-trait Multi-environment Deep Learning (MMDL) were compared. Across environments, the multi-trait statistical model (BMTME) was superior to the multi-trait DL model for prediction accuracy in most scenarios, but the DL models were comparable to the statistical models for response to selection. The multi-trait model also showed 5 to 22% more genetic gain compared to the single-trait model across environment reflected by the response to selection. Overall, these results suggest that multi-trait genomic prediction can be an efficient strategy for economically important yield component related traits in soft wheat.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3390/genes11111270DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7716228PMC
October 2020

Increased Prediction Accuracy Using Combined Genomic Information and Physiological Traits in A Soft Wheat Panel Evaluated in Multi-Environments.

Sci Rep 2020 04 27;10(1):7023. Epub 2020 Apr 27.

Department of Agronomy, University of Florida, Gainesville, FL, USA.

An integration of field-based phenotypic and genomic data can potentially increase the genetic gain in wheat breeding for complex traits such as grain and biomass yield. To validate this hypothesis in empirical field experiments, we compared the prediction accuracy between multi-kernel physiological and genomic best linear unbiased prediction (BLUP) model to a single-kernel physiological or genomic BLUP model for grain yield (GY) using a soft wheat population that was evaluated in four environments. The physiological data including canopy temperature (CT), SPAD chlorophyll content (SPAD), membrane thermostability (MT), rate of senescence (RS), stay green trait (SGT), and NDVI values were collected at four environments (2016, 2017, and 2018 at Citra, FL; 2017 at Quincy, FL). Using a genotyping-by-sequencing (GBS) approach, a total of 19,353 SNPs were generated and used to estimate prediction model accuracy. Prediction accuracies of grain yield evaluated in four environments improved when physiological traits and/or interaction effects (genotype × environment or physiology × environment) were included in the model compared to models with only genomic data. The proposed multi-kernel models that combined physiological and genomic data showed 35 to 169% increase in prediction accuracy compared to models with only genomic data included when heading date was used as a covariate. In general, higher response to selection was captured by the model combing effects of physiological and genotype × environment interaction compared to other models. The results of this study support the integration of field-based physiological data into GY prediction to improve genetic gain from selection in soft wheat under a multi-environment context.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41598-020-63919-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7184575PMC
April 2020

Genetic dissection of heat-responsive physiological traits to improve adaptation and increase yield potential in soft winter wheat.

BMC Genomics 2020 Apr 20;21(1):315. Epub 2020 Apr 20.

Department of Plant Pathology, University of Wisconsin-Madison, Madison, WI, USA.

Background: Climate change, including higher temperatures (HT) has a detrimental impact on wheat productivity and modeling studies predict more frequent heat waves in the future. Wheat growth can be impaired by high daytime and nighttime temperature at any developmental stage, especially during the grain filling stage. Leaf chlorophyll content, leaf greenness, cell membrane thermostability, and canopy temperature have been proposed as candidate traits to improve crop adaptation and yield potential of wheat under HT. Nonetheless, a significant gap exists in knowledge of genetic backgrounds associated with these physiological traits. Identifying genetic loci associated with these traits can facilitate physiological breeding for increased yield potential under high temperature stress condition in wheat.

Results: We conducted genome-wide association study (GWAS) on a 236 elite soft wheat association mapping panel using 27,466 high quality single nucleotide polymorphism markers. The panel was phenotyped for three years in two locations where heat shock was common. GWAS identified 500 significant marker-trait associations (MTAs) (p ≤ 9.99 × 10). Ten MTAs with pleiotropic effects detected on chromosomes 1D, 2B, 3A, 3B, 6A, 7B, and 7D are potentially important targets for selection. Five MTAs associated with physiological traits had pleiotropic effects on grain yield and yield-related traits. Seventy-five MTAs were consistently expressed over several environments indicating stability and more than half of these stable MTAs were found in genes encoding different types of proteins associated with heat stress.

Conclusions: We identified 500 significant MTAs in soft winter wheat under HT stress. We found several stable loci across environments and pleiotropic markers controlling physiological and agronomic traits. After further validation, these MTAs can be used in marker-assisted selection and breeding to develop varieties with high stability for grain yield under high temperature.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12864-020-6717-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7171738PMC
April 2020

Understanding the Genetic Basis of Spike Fertility to Improve Grain Number, Harvest Index, and Grain Yield in Wheat Under High Temperature Stress Environments.

Front Plant Sci 2019 29;10:1481. Epub 2019 Nov 29.

Department of Plant Pathology, Kansas State University, Manhattan, KS, United States.

Moderate heat stress accompanied by short episodes of extreme heat during the post-anthesis stage is common in most US wheat growing areas and causes substantial yield losses. Sink strength (grain number) is a key yield limiting factor in modern wheat varieties. Increasing spike fertility (SF) and improving the partitioning of assimilates can optimize sink strength which is essential to improve wheat yield potential under a hot and humid environment. A genome-wide association study (GWAS) allows identification of novel quantitative trait loci (QTLs) associated with SF and other partitioning traits that can assist in marker assisted breeding. In this study, GWAS was performed on a soft wheat association mapping panel (SWAMP) comprised of 236 elite lines using 27,466 single nucleotide polymorphisms (SNPs). The panel was phenotyped in two heat stress locations over 3 years. GWAS identified 109 significant marker-trait associations (MTAs) (p ≤ 9.99 x 10-5) related to eight phenotypic traits including SF (a major component of grain number) and spike harvest index (SHI, a major component of grain weight). MTAs detected on chromosomes 1B, 3A, 3B, and 5A were associated with multiple traits and are potentially important targets for selection. More than half of the significant MTAs (60 out of 109) were found in genes encoding different types of proteins related to metabolism, disease, and abiotic stress including heat stress. These MTAs could be potential targets for further validation study and may be used in marker-assisted breeding for improving wheat grain yield under post-anthesis heat stress conditions. This is the first study to identify novel QTLs associated with SF and SHI which represent the major components of grain number and grain weight, respectively, in wheat.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3389/fpls.2019.01481DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6895025PMC
November 2019

Hormetic Effects of Thiophanate-Methyl in Multiple Isolates of Sclerotinia homoeocarpa.

Plant Dis 2019 Jan 6;103(1):89-94. Epub 2018 Nov 6.

Department of Entomology and Plant Pathology, Oklahoma State University, Stillwater, and GIMA Research Group, Department of Live Sciences and Agriculture, Universidad de las Fuerzas Armadas-ESPE, Sangolquí, Ecuador.

Twenty-eight isolates of Sclerotinia homoeocarpa, causal agent of dollar spot disease in turf, were assessed for fungicide hormesis at sublethal concentrations of thiophanate-methyl (T-methyl). Each isolate was grown in corn meal agar amended with 11 concentrations of T-methyl (30,500 to 0.047 µg/liter), and the area of mycelial growth was determined relative to the control. Three replicates were used per concentration, and the experiment was repeated three to five times for each isolate. Reference isolates (EC > 20 µg/liter), with no prior history of T-methyl exposure, were highly sensitive and not stimulated by low doses. Likewise, no stimulation was observed in two highly sensitive isolates (EC > 30 µg/liter) that had been preconditioned by exposure to T-methyl, or in four T-methyl-tolerant isolates. Seventeen (81%) preconditioned T-methyl-tolerant isolates (EC = 294 to1,550 µg/liter) had statistically significant growth stimulation, in the range of 2.8 to 19.7% relative to the control. These results support that hormesis (low-dose stimulation, high-dose inhibition) is a common dose response in preconditioned S. homoeocarpa, particularly in response to subtoxic doses of T-methyl.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1094/PDIS-05-18-0872-REDOI Listing
January 2019
-->