Browsing by Author "Dorrance, Anne E."

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    Diallel analysis of diplopodia ear rot resistance in maize and an assessment of the genetic variability of Stenocarpella maydis through isozyme analysis
    Dorrance, Anne E. (Virginia Tech, 1995-12-05)
    Diplodia ear rot (DER) of maize (Zea mays L.) caused by the fungus, Stenocarpella maydis (Berk.) Sutton has increased in incidence in localized fields over the past decade. My research focused on screening for resistance by examining the development of DER following inoculations prior to flowering, analyzing a diallel cross for DER resistance, and examining the genetic variability of the fungus from isolates collected from the U.S. and the Republic of South Africa. DER developed in maize following inoculations with a spore suspension prior to flowering in both greenhouse and field evaluations. A spore suspension gave a better differentiation of resistance responses than dried preparations of colonized millet, colonized ground popcorn, or kernels from a diseased maize ear, all applied in the whorl 10 to 15 days prior to flowering (V12 for inbreds), and natural occurrence of disease. General combining ability was significant for both 1994 and 1995 growing seasons in an analysis of the F₁ of the diallel cross, indicating that additive gene action may be responsible for resistance and could be introduced into commercial cultivars. Specific combining ability was significant in 1995 and indicates that dominant gene action or epistasis may play role in DER resistance. There were minimal numbers of isozyme polymorphisms found in my S. maydis collection. Two isolates were polymorphic for esterase, two isolates were polymorphic for hexokinase and malate dehydrogenase and one isolate was polymorphic for hexose kinase. Fungi that have limited isozyme polymorphisms often are biotrophs or fungi with formae speciales which are usually limited to one host. These groups of fungi usually have races and this may indicate that a gene-for-gene interaction exists. These findings suggest that i) the whorl inoculation separates genotypes into resistant, intermediate, and susceptible groupings; ii) additive gene action is predominant form of inheritance, and iii) there are few isozyme polymorphisms in the population of S. maydis sampled.
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    Genetic variants in root architecture-related genes in a Glycine soja accession, a potential resource to improve cultivated soybean
    Prince, Silvas J.; Li, Song; Qiu, Dan; Maldonado dos Santos, Joao V.; Chai, Chenglin; Joshi, Trupti; Patil, Gunvant; Valliyodan, Babu; Vuong, Tri D.; Murphy, Mackensie; Krampis, Konstantinos; Tucker, Dominic M.; Biyashev, Ruslan M.; Dorrance, Anne E.; Saghai-Maroof, Mohammad A.; Xu, Dong; Shannon, J. Grover; Nguyen, Henry T. (2015-02-25)
    Background Root system architecture is important for water acquisition and nutrient acquisition for all crops. In soybean breeding programs, wild soybean alleles have been used successfully to enhance yield and seed composition traits, but have never been investigated to improve root system architecture. Therefore, in this study, high-density single-feature polymorphic markers and simple sequence repeats were used to map quantitative trait loci (QTLs) governing root system architecture in an inter-specific soybean mapping population developed from a cross between Glycine max and Glycine soja. Results Wild and cultivated soybean both contributed alleles towards significant additive large effect QTLs on chromosome 6 and 7 for a longer total root length and root distribution, respectively. Epistatic effect QTLs were also identified for taproot length, average diameter, and root distribution. These root traits will influence the water and nutrient uptake in soybean. Two cell division-related genes (D type cyclin and auxin efflux carrier protein) with insertion/deletion variations might contribute to the shorter root phenotypes observed in G. soja compared with cultivated soybean. Based on the location of the QTLs and sequence information from a second G. soja accession, three genes (slow anion channel associated 1 like, Auxin responsive NEDD8-activating complex and peroxidase), each with a non-synonymous single nucleotide polymorphism mutation were identified, which may also contribute to changes in root architecture in the cultivated soybean. In addition, Apoptosis inhibitor 5-like on chromosome 7 and slow anion channel associated 1-like on chromosome 15 had epistatic interactions for taproot length QTLs in soybean. Conclusion Rare alleles from a G. soja accession are expected to enhance our understanding of the genetic components involved in root architecture traits, and could be combined to improve root system and drought adaptation in soybean.
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    Identification of Quantitative Disease Resistance Loci Toward Four Pythium Species in Soybean
    Clevinger, Elizabeth M.; Biyashev, Ruslan M.; Lerch-Olson, Elizabeth; Yu, Haipeng; Quigley, Charles; Song, Qijian; Dorrance, Anne E.; Robertson, Alison E.; Saghai-Maroof, Mohammad A. (Frontiers, 2021-03-30)
    In this study, four recombinant inbred line (RIL) soybean populations were screened for their response to infection by Pythium sylvaticum, Pythium irregulare, Pythium oopapillum, and Pythium torulosum. The parents, PI 424237A, PI 424237B, PI 408097, and PI 408029, had higher levels of resistance to these species in a preliminary screening and were crossed with “Williams,” a susceptible cultivar. A modified seed rot assay was used to evaluate RIL populations for their response to specific Pythium species selected for a particular population based on preliminary screenings. Over 2500 single-nucleotide polymorphism (SNP) markers were used to construct chromosomal maps to identify regions associated with resistance to Pythium species. Several minor and large effect quantitative disease resistance loci (QDRL) were identified including one large effect QDRL on chromosome 8 in the population of PI 408097 × Williams. It was identified by two different disease reaction traits in P. sylvaticum, P. irregulare, and P. torulosum. Another large effect QDRL was identified on chromosome 6 in the population of PI 408029 × Williams, and conferred resistance to P. sylvaticum and P. irregulare. These large effect QDRL will contribute toward the development of improved soybean cultivars with higher levels of resistance to these common soil-borne pathogens.
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    Infection and genotype remodel the entire soybean transcriptome
    Zhou, Lecong; Mideros, Santiago X.; Bao, Lei; Hanlon, Regina; Arredondo, Felipe D.; Tripathy, Sucheta; Krampis, Konstantinos; Jerauld, Adam; Evans, Clive; St Martin, Steven K.; Saghai-Maroof, Mohammad A.; Hoeschele, Ina; Dorrance, Anne E.; Tyler, Brett M. (2009-01-26)
    Background High throughput methods, such as high density oligonucleotide microarray measurements of mRNA levels, are popular and critical to genome scale analysis and systems biology. However understanding the results of these analyses and in particular understanding the very wide range of levels of transcriptional changes observed is still a significant challenge. Many researchers still use an arbitrary cut off such as two-fold in order to identify changes that may be biologically significant. We have used a very large-scale microarray experiment involving 72 biological replicates to analyze the response of soybean plants to infection by the pathogen Phytophthora sojae and to analyze transcriptional modulation as a result of genotypic variation. Results With the unprecedented level of statistical sensitivity provided by the high degree of replication, we show unambiguously that almost the entire plant genome (97 to 99% of all detectable genes) undergoes transcriptional modulation in response to infection and genetic variation. The majority of the transcriptional differences are less than two-fold in magnitude. We show that low amplitude modulation of gene expression (less than two-fold changes) is highly statistically significant and consistent across biological replicates, even for modulations of less than 20%. Our results are consistent through two different normalization methods and two different statistical analysis procedures. Conclusion Our findings demonstrate that the entire plant genome undergoes transcriptional modulation in response to infection and genetic variation. The pervasive low-magnitude remodeling of the transcriptome may be an integral component of physiological adaptation in soybean, and in all eukaryotes.
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    Mining germplasm panels and phenotypic datasets to identify loci for resistance to Phytophthora sojae in soybean
    Van, Kyujung; Rolling, William; Biyashev, Ruslan M.; Matthiesen, Rashelle L.; Abeysekara, Nilwala S.; Robertson, Alison E.; Veney, Deloris J.; Dorrance, Anne E.; McHale, Leah K.; Saghai-Maroof, Mohammad A. (Wiley, 2020-11-16)
    Phytophthora sojae causes Phytophthora root and stem rot of soybean and has been primarily managed through deployment of qualitative Resistance to P. sojae genes (Rps genes). The effectiveness of each individual or combination of Rps gene(s) depends on the diversity and pathotypes of the P. sojae populations present. Due to the complex nature of P. sojae populations, identification of more novel Rps genes is needed. In this study, phenotypic data from previous studies of 16 panels of plant introductions (PIs) were analyzed. Panels 1 and 2 consisted of 448 Glycine max and 520 G. soja, which had been evaluated for Rps gene response with a combination of P. sojae isolates. Panels 3 and 4 consisted of 429 and 460 G. max PIs, respectively, which had been evaluated using individual P. sojae isolates with complex virulence pathotypes. Finally, Panels 5–16 (376 G. max PIs) consisted of data deposited in the USDA Soybean Germplasm Collection from evaluations with 12 races of P. sojae. Using these panels, genome-wide association (GWA) analyses were carried out by combining phenotypic and SoySNP50K genotypic data. GWA models identified two, two, six, and seven novel Rps loci with Panels 1, 2, 3, and 4, respectively. A total of 58 novel Rps loci were identified using Panels 5–16. Genetic and phenotypic dissection of these loci may lead to the characterization of novel Rps genes that can be effectively deployed in new soybean cultivars against diverse P. sojae populations.