Publications by authors named "Jagdeep S Sidhu"

5 Publications

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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

An Analysis of Soil Coring Strategies to Estimate Root Depth in Maize () and Common Bean ().

Plant Phenomics 2020 8;2020:3252703. Epub 2020 Nov 8.

The Pennsylvania State University, Department of Plant Science, Tyson Building, University Park, PA 16802, USA.

A soil coring protocol was developed to cooptimize the estimation of root length distribution (RLD) by depth and detection of functionally important variation in root system architecture (RSA) of maize and bean. The functional-structural model was used to perform soil coring at six locations on three different maize and bean RSA phenotypes. Results were compared to two seasons of field soil coring and one trench. Two one-sided -test (TOST) analysis of data suggests a between-row location 5 cm from plant base (location 3), best estimates whole-plot RLD/D of deep, intermediate, and shallow RSA phenotypes, for both maize and bean. Quadratic discriminant analysis indicates location 3 has ~70% categorization accuracy for bean, while an in-row location next to the plant base (location 6) has ~85% categorization accuracy in maize. Analysis of field data suggests the more representative sampling locations vary by year and species. and field studies suggest location 3 is most robust, although variation is significant among seasons, among replications within a field season, and among field soil coring, trench, and simulations. We propose that the characterization of the RLD profile as a dynamic rhizo canopy effectively describes how the RLD profile arises from interactions among an individual plant, its neighbors, and the pedosphere.
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http://dx.doi.org/10.34133/2020/3252703DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7706327PMC
November 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

Fine Mapping of the Wheat Leaf Rust Resistance Gene .

Int J Mol Sci 2019 May 17;20(10). Epub 2019 May 17.

Department of Agronomy, Horticulture & Plant Science, South Dakota State University, Brookings, SD 57006, USA.

Leaf rust caused by Eriks is one of the most problematic diseases of wheat throughout the world. The gene confers effective resistance against leaf rust at both seedling and adult plant stages. Previous studies had reported to be both recessive and dominant in hexaploid wheat; however, in diploid (TA2450), we found to be dominant by studying segregation in two independent F and their F populations. We further fine-mapped in hexaploid wheat using a KS93U50/Morocco F recombinant inbred line (RIL) population to a 3.7 cM genetic interval flanked by markers and . The 3.7 cM region physically corresponds to a 3.16 Mb genomic region on chromosome 1DS based on the Chinese Spring reference genome (RefSeq v.1.1) and a 3.5 Mb genomic interval on chromosome 1 in the reference genome. This region includes nine nucleotide-binding domain leucine-rich repeat (NLR) genes in wheat and seven in , respectively, and these are the likely candidates for . Furthermore, we developed two kompetitive allele-specific polymorphism (KASP) markers ( and ) flanking to facilitate marker-assisted selection for rust resistance in wheat breeding programs.
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http://dx.doi.org/10.3390/ijms20102445DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6567072PMC
May 2019

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
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