Publications by authors named "Shahryar Kianian"

68 Publications

A chromosome-level, fully phased genome assembly of the oat crown rust fungus Puccinia coronata f. sp. avenae: a resource to enable comparative genomics in the cereal rusts.

G3 (Bethesda) 2022 Jul;12(8)

Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, ACT 2601, Australia.

Advances in sequencing technologies as well as development of algorithms and workflows have made it possible to generate fully phased genome references for organisms with nonhaploid genomes such as dikaryotic rust fungi. To enable discovery of pathogen effectors and further our understanding of virulence evolution, we generated a chromosome-scale assembly for each of the 2 nuclear genomes of the oat crown rust pathogen, Puccinia coronata f. sp. avenae (Pca). This resource complements 2 previously released partially phased genome references of Pca, which display virulence traits absent in the isolate of historic race 203 (isolate Pca203) which was selected for this genome project. A fully phased, chromosome-level reference for Pca203 was generated using PacBio reads and Hi-C data and a recently developed pipeline named NuclearPhaser for phase assignment of contigs and phase switch correction. With 18 chromosomes in each haplotype and a total size of 208.10 Mbp, Pca203 has the same number of chromosomes as other cereal rust fungi such as Puccinia graminis f. sp. tritici and Puccinia triticina, the causal agents of wheat stem rust and wheat leaf rust, respectively. The Pca203 reference marks the third fully phased chromosome-level assembly of a cereal rust to date. Here, we demonstrate that the chromosomes of these 3 Puccinia species are syntenous and that chromosomal size variations are primarily due to differences in repeat element content.
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http://dx.doi.org/10.1093/g3journal/jkac149DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9339303PMC
July 2022

Genome-wide investigation of maize RAD51 binding affinity through phage display.

BMC Genomics 2022 Mar 12;23(1):199. Epub 2022 Mar 12.

School of Life Sciences, Arizona State University, 427 E Tyler Mall, Tempe, AZ, 85287, USA.

Background: RAD51 proteins, which are conserved in all eukaryotes, repair DNA double-strand breaks. This is critical to homologous chromosome pairing and recombination enabling successful reproduction. Work in Arabidopsis suggests that RAD51 also plays a role in plant defense; the Arabidopsis rad51 mutant is more susceptible to Pseudomonas syringae. However, the defense functions of RAD51 and the proteins interacting with RAD51 have not been thoroughly investigated in maize. Uncovering ligands of RAD51 would help to understand meiotic recombination and possibly the role of RAD51 in defense. This study used phage display, a tool for discovery of protein-protein interactions, to search for proteins interacting with maize RAD51A1.

Results: Maize RAD51A1 was screened against a random phage library. Eleven short peptide sequences were recovered from 15 phages which bound ZmRAD51A1 in vitro; three sequences were found in multiple successfully binding phages. Nine of these phage interactions were verified in vitro through ELISA and/or dot blotting. BLAST searches did not reveal any maize proteins which contained the exact sequence of any of the selected phage peptides, although one of the selected phages had a strong alignment (E-value = 0.079) to a binding domain of maize BRCA2. Therefore, we designed 32 additional short peptides using amino acid sequences found in the predicted maize proteome. These peptides were not contained within phages. Of these synthesized peptides, 14 bound to ZmRAD51A1 in a dot blot experiment. These 14 sequences are found in known maize proteins including transcription factors putatively involved in defense.

Conclusions: These results reveal several peptides which bind ZmRAD51A1 and support a potential role for ZmRAD51A1 in transcriptional regulation and plant defense. This study also demonstrates the applicability of phage display to basic science questions, such as the search for binding partners of a known protein, and raises the possibility of an iterated approach to test peptide sequences that closely but imperfectly align with the selected phages.
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http://dx.doi.org/10.1186/s12864-022-08419-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8917730PMC
March 2022

Study of Resistome in Response to Infection.

Life (Basel) 2021 Sep 13;11(9). Epub 2021 Sep 13.

National Agri-Food Biotechnology Institute, SAS Nagar, Mohali 140306, India.

Susceptible and resistant germplasm respond differently to pathogenic attack, including virus infections. We compared the transcriptome changes between a resistant wheat cultivar, Sonalika, and a susceptible cultivar, WL711, to understand this process in wheat against wheat dwarf India virus (WDIV) infection. A total of 2760 and 1853 genes were differentially expressed in virus-infected and mock-inoculated Sonalika, respectively, compared to WL711. The overrepresentation of genes involved in signaling, hormone metabolism, enzymes, secondary metabolites, proteolysis, and transcription factors was documented, including the overexpression of multiple PR proteins. We hypothesize that the virus resistance in Sonalika is likely due to strong intracellular surveillance via the action of multiple PR proteins (PR1, RAR1, and RPM1) and ChiB. Other genes such as PIP1, LIP1, DnaJ, defensins, oxalate oxidase, ankyrin repeat protein, serine-threonine kinase, SR proteins, beta-1,3-glucanases, and O-methyltransferases had a significant differential expression and play roles in stress tolerance, may also be contributing towards the virus resistance in Sonalika. In addition, we identified putative genes with unknown functions, which are only expressed in response to WDIV infection in Sonalika. The role of these genes could be further validated and utilized in engineering resistance in wheat and other crops.
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http://dx.doi.org/10.3390/life11090955DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8469153PMC
September 2021

Genome-Wide Association Mapping for Yield and Related Traits Under Drought Stressed and Non-stressed Environments in Wheat.

Front Genet 2021 22;12:649988. Epub 2021 Jun 22.

Institute of Plant Breeding, Genetics, and Genomics, University of Georgia, Griffin, GA, United States.

Understanding the genetics of drought tolerance in hard red spring wheat (HRSW) in northern USA is a prerequisite for developing drought-tolerant cultivars for this region. An association mapping (AM) study for drought tolerance in spring wheat in northern USA was undertaken using 361 wheat genotypes and Infinium 90K single-nucleotide polymorphism (SNP) assay. The genotypes were evaluated in nine different locations of North Dakota (ND) for plant height (PH), days to heading (DH), yield (YLD), test weight (TW), and thousand kernel weight (TKW) under rain-fed conditions. Rainfall data and soil type of the locations were used to assess drought conditions. A mixed linear model (MLM), which accounts for population structure and kinship (PC+K), was used for marker-trait association. A total of 69 consistent QTL involved with drought tolerance-related traits were identified, with ≤ 0.001. Chromosomes 1A, 3A, 3B, 4B, 4D, 5B, 6A, and 6B were identified to harbor major QTL for drought tolerance. Six potential novel QTL were identified on chromosomes 3D, 4A, 5B, 7A, and 7B. The novel QTL were identified for DH, PH, and TKW. The findings of this study can be used in marker-assisted selection (MAS) for drought-tolerance breeding in spring wheat.
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http://dx.doi.org/10.3389/fgene.2021.649988DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8258415PMC
June 2021

Identification of Main-Effect and Environmental Interaction QTL and Their Candidate Genes for Drought Tolerance in a Wheat RIL Population Between Two Elite Spring Cultivars.

Front Genet 2021 17;12:656037. Epub 2021 Jun 17.

Institute of Plant Breeding, Genetics, and Genomics, University of Georgia, Griffin, GA, United States.

Understanding the genetics of drought tolerance can expedite the development of drought-tolerant cultivars in wheat. In this study, we dissected the genetics of drought tolerance in spring wheat using a recombinant inbred line (RIL) population derived from a cross between a drought-tolerant cultivar, 'Reeder' (PI613586), and a high-yielding but drought-susceptible cultivar, 'Albany.' The RIL population was evaluated for grain yield (YLD), grain volume weight (GVW), thousand kernel weight (TKW), plant height (PH), and days to heading (DH) at nine different environments. The Infinium 90 k-based high-density genetic map was generated using 10,657 polymorphic SNP markers representing 2,057 unique loci. Quantitative trait loci (QTL) analysis detected a total of 11 consistent QTL for drought tolerance-related traits. Of these, six QTL were exclusively identified in drought-prone environments, and five were constitutive QTL (identified under both drought and normal conditions). One major QTL on chromosome 7B was identified exclusively under drought environments and explained 13.6% of the phenotypic variation (PV) for YLD. Two other major QTL were detected, one each on chromosomes 7B and 2B under drought-prone environments, and explained 14.86 and 13.94% of phenotypic variation for GVW and YLD, respectively. One novel QTL for drought tolerance was identified on chromosome 2D. expression analysis of candidate genes underlaying the exclusive QTLs associated with drought stress identified the enrichment of ribosomal and chloroplast photosynthesis-associated proteins showing the most expression variability, thus possibly contributing to stress response by modulating the glycosyltransferase () and hexosyltransferase () unique genes present in QTL 21 and 24, respectively. While both parents contributed favorable alleles to these QTL, unexpectedly, the high-yielding and less drought-tolerant parent contributed desirable alleles for drought tolerance at four out of six loci. Regardless of the origin, all QTL with significant drought tolerance could assist significantly in the development of drought-tolerant wheat cultivars, using genomics-assisted breeding approaches.
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http://dx.doi.org/10.3389/fgene.2021.656037DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8249774PMC
June 2021

Identification of Candidate Susceptibility Genes to f. sp. in Wheat.

Front Plant Sci 2021 21;12:657796. Epub 2021 Apr 21.

Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, ACT, Australia.

Wheat stem rust disease caused by f. sp. () is a global threat to wheat production. Fast evolving populations of limit the efficacy of plant genetic resistance and constrain disease management strategies. Understanding molecular mechanisms that lead to rust infection and disease susceptibility could deliver novel strategies to deploy crop resistance through genetic loss of disease susceptibility. We used comparative transcriptome-based and orthology-guided approaches to characterize gene expression changes associated with infection in susceptible and resistant genotypes as well as the non-host . We targeted our analysis to genes with differential expression in and genes suppressed or not affected in and report several processes potentially linked to susceptibility to , such as cell death suppression and impairment of photosynthesis. We complemented our approach with a gene co-expression network analysis to identify wheat targets to deliver resistance to through removal or modification of putative susceptibility genes.
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http://dx.doi.org/10.3389/fpls.2021.657796DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8097158PMC
April 2021

Increased virulence of Puccinia coronata f. sp.avenae populations through allele frequency changes at multiple putative Avr loci.

PLoS Genet 2020 12 28;16(12):e1009291. Epub 2020 Dec 28.

Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, Australia.

Pathogen populations are expected to evolve virulence traits in response to resistance deployed in agricultural settings. However, few temporal datasets have been available to characterize this process at the population level. Here, we examined two temporally separated populations of Puccinia coronata f. sp. avenae (Pca), which causes crown rust disease in oat (Avena sativa) sampled from 1990 to 2015. We show that a substantial increase in virulence occurred from 1990 to 2015 and this was associated with a genetic differentiation between populations detected by genome-wide sequencing. We found strong evidence for genetic recombination in these populations, showing the importance of the alternate host in generating genotypic variation through sexual reproduction. However, asexual expansion of some clonal lineages was also observed within years. Genome-wide association analysis identified seven Avr loci associated with virulence towards fifteen Pc resistance genes in oat and suggests that some groups of Pc genes recognize the same pathogen effectors. The temporal shift in virulence patterns in the Pca populations between 1990 and 2015 is associated with changes in allele frequency in these genomic regions. Nucleotide diversity patterns at a single Avr locus corresponding to Pc38, Pc39, Pc55, Pc63, Pc70, and Pc71 showed evidence of a selective sweep associated with the shift to virulence towards these resistance genes in all 2015 collected isolates.
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http://dx.doi.org/10.1371/journal.pgen.1009291DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7793281PMC
December 2020

Epigenetic regulation of gene expression improves Fusarium head blight resistance in durum wheat.

Sci Rep 2020 10 19;10(1):17610. Epub 2020 Oct 19.

USDA-ARS Cereal Disease Laboratory, St. Paul, MN, USA.

Eight advanced durum-breeding lines were treated with 5-methyl-azacytidine to test the feasibility of generating sources of Fusarium head blight (FHB) resistance. Of the 800 treated seeds, 415 germinated and were advanced up to four (M4) generations by selfing. Thirty-two of the resulting 415 M4 lines were selected following preliminary screening and were further tested for FHB resistance for three years at two field locations, and in the greenhouse. Five of the 32 M4 lines showed less than 30% disease severity, as compared to the parental lines and susceptible checks. Fusarium-damaged kernels and deoxynivalenol analyses supported the findings of the field and greenhouse disease assessments. Two of the most resistant M4 lines were crossed to a susceptible parent, advanced to third generation (BC:F) and were tested for stability and inheritance of the resistance. About, one third of the BC:F lines showed FHB resistance similar to their M4 parents. The overall methylation levels (%) were compared using FASTmC method, which did not show a significant difference between M4 and parental lines. However, transcriptome analysis of one M4 line revealed significant number of differentially expressed genes related to biosynthesis of secondary metabolites, MAPK signaling, photosynthesis, starch and sucrose metabolism, plant hormone signal transduction and plant-pathogen interaction pathways, which may have helped in improved FHB resistance.
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http://dx.doi.org/10.1038/s41598-020-73521-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7572394PMC
October 2020

Corrigendum: Novel Meiotic miRNAs and Indications for a Role of PhasiRNAs in Meiosis.

Front Plant Sci 2020 4;11:653. Epub 2020 Jun 4.

Department of Horticultural Science, University of Minnesota, St. Paul, MN, United States.

[This corrects the article DOI: 10.3389/fpls.2016.00762.].
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http://dx.doi.org/10.3389/fpls.2020.00653DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7290127PMC
June 2020

New Sources of Adult Plant and Seedling Resistance to Puccinia coronata f. sp. avenae Identified among Avena sativa Accessions From the National Small Grains Collection.

Plant Dis 2018 11 10;102(11):2180-2186. Epub 2018 Sep 10.

USDA-ARS, Small Grains and Potato Germplasm Research, Aberdeen, ID 83210.

Accessions of cultivated oat (Avena sativa L.) from the United States Department of Agriculture-Agricultural Research Service Small Grains Collection in Aberdeen, ID were characterized for adult plant resistance (APR) and seedling resistance to crown rust, caused by Puccinia coronata f. sp. avenae. Initially, 607 oat accessions with diverse geographic origins were evaluated in field tests in Baton Rouge, LA. Of those, 97 accessions were not fully susceptible and were tested in the field in St. Paul, MN against a diverse P. coronata f. sp. avenae population. Thirty-six accessions that had some level of resistance in both field tests and mean coefficients of infection of ≤20 were further evaluated for APR and seedling resistance. Among these, four accessions (PI 193040, PI 194201, PI 237090, and PI 247930) were resistant to eight P. coronata f. sp. avenae races as seedlings. Twenty-nine accessions had resistance to at least one of the P. coronata f. sp. avenae races. Three accessions (CIav 2272, CIav 3390, and PI 285583) were fully susceptible to all eight P. coronata f. sp. avenae races as seedlings. Further evaluation of the three seedling-susceptible accessions at the flag leaf stage in a growth chamber resulted in moderately susceptible to moderately resistant responses. The resistance sources presented here may contain genes not deployed in elite oat varieties, and may be useful for future crown rust resistance breeding. The adult and seedling resistance found in accessions of the cultivated oat species is especially valuable because it avoids problems associated with the transfer of genes from wild species to cultivated oat.
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http://dx.doi.org/10.1094/PDIS-04-18-0566-REDOI Listing
November 2018

A Novel Approach to Assess Salt Stress Tolerance in Wheat Using Hyperspectral Imaging.

Front Plant Sci 2018 24;9:1182. Epub 2018 Aug 24.

Department of Bioproducts and Biosystems Engineering, University of Minnesota, Minneapolis, MN, United States.

Salinity stress has significant adverse effects on crop productivity and yield. The primary goal of this study was to quantitatively rank salt tolerance in wheat using hyperspectral imaging. Four wheat lines were assayed in a hydroponic system with control and salt treatments (0 and 200 mM NaCl). Hyperspectral images were captured one day after salt application when there were no visual symptoms. Subsequent to necessary preprocessing tasks, two endmembers, each representing one of the treatment, were identified in each image using successive volume maximization. To simplify image analysis and interpretation, similarity of all pixels to the salt endmember was calculated by a technique proposed in this study, referred to as vector-wise similarity measurement. Using this approach allowed high-dimensional hyperspectral images to be reduced to one-dimensional gray-scale images while retaining all relevant information. Two methods were then utilized to analyze the gray-scale images: minimum difference of pair assignments and Bayesian method. The rankings of both methods were similar and consistent with the expected ranking obtained by conventional phenotyping experiments and historical evidence of salt tolerance. This research highlights the application of machine learning in hyperspectral image analysis for phenotyping of plants in a quantitative, interpretable, and non-invasive manner.
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http://dx.doi.org/10.3389/fpls.2018.01182DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6117507PMC
August 2018

Detection of Race-Specific Resistance Against Puccinia coronata f. sp. avenae in Brachypodium Species.

Phytopathology 2018 Dec 31;108(12):1443-1454. Epub 2018 Oct 31.

First, second, third, fourth, fifth, eighth, and ninth authors: Plant Pathology, University of Minnesota, St. Paul; sixth author: CSIRO Agriculture and Food, ACT, Australia; seventh author: The Sainsbury Laboratory, Norwich Research Park, Norwich NR4 7UH, U.K.; eighth author: Cereal Disease Laboratory, United States Department of Agriculture-Agricultural Research Service, St. Paul, MN, USA; and ninth author: Stakman-Borlaug Center for Sustainable Plant Health, University of Minnesota, St. Paul.

Oat crown rust caused by Puccinia coronata f. sp. avenae is the most destructive foliar disease of cultivated oat. Characterization of genetic factors controlling resistance responses to Puccinia coronata f. sp. avenae in nonhost species could provide new resources for developing disease protection strategies in oat. We examined symptom development and fungal colonization levels of a collection of Brachypodium distachyon and B. hybridum accessions infected with three North American P. coronata f. sp. avenae isolates. Our results demonstrated that colonization phenotypes are dependent on both host and pathogen genotypes, indicating a role for race-specific responses in these interactions. These responses were independent of the accumulation of reactive oxygen species. Expression analysis of several defense-related genes suggested that salicylic acid and ethylene-mediated signaling but not jasmonic acid are components of resistance reaction to P. coronata f. sp. avenae. Our findings provide the basis to conduct a genetic inheritance study to examine whether effector-triggered immunity contributes to nonhost resistance to P. coronata f. sp. avenae in Brachypodium spp.
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http://dx.doi.org/10.1094/PHYTO-03-18-0084-RDOI Listing
December 2018

High-resolution crossover mapping reveals similarities and differences of male and female recombination in maize.

Nat Commun 2018 06 18;9(1):2370. Epub 2018 Jun 18.

Section of Plant Biology, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA.

Meiotic crossovers (COs) are not uniformly distributed across the genome. Factors affecting this phenomenon are not well understood. Although many species exhibit large differences in CO numbers between sexes, sex-specific aspects of CO landscape are particularly poorly elucidated. Here, we conduct high-resolution CO mapping in maize. Our results show that CO numbers as well as their overall distribution are similar in male and female meioses. There are, nevertheless, dissimilarities at local scale. Male and female COs differ in their locations relative to transcription start sites in gene promoters and chromatin marks, including nucleosome occupancy and tri-methylation of lysine 4 of histone H3 (H3K4me3). Our data suggest that sex-specific factors not only affect male-female CO number disparities but also cause fine differences in CO positions. Differences between male and female CO landscapes indicate that recombination has distinct implications for population structure and gene evolution in male and in female meioses.
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http://dx.doi.org/10.1038/s41467-018-04562-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6006299PMC
June 2018

Comparative analysis of transcriptome in two wheat genotypes with contrasting levels of drought tolerance.

Protoplasma 2018 Sep 12;255(5):1487-1504. Epub 2018 Apr 12.

National Agri-Food Biotechnology Institute, Mohali, India.

Drought tolerance is a complex trait that is governed by multiple genes. The study presents differential transcriptome analysis between drought-tolerant (Triticum aestivum Cv. C306) and drought-sensitive (Triticum aestivum Cv. WL711) genotypes, using Affymetrix GeneChip® Wheat Genome Array. Both genotypes exhibited diverse global transcriptional responses under control and drought conditions. Pathway analysis suggested significant induction or repression of genes involved in secondary metabolism, nucleic acid synthesis, protein synthesis, and transport in C306, as compared to WL711. Significant up- and downregulation of transcripts for enzymes, hormone metabolism, and stress response pathways were observed in C306 under drought. The elevated expression of plasma membrane intrinsic protein 1 and downregulation of late embryogenesis abundant in the leaf tissues could play an important role in delayed wilting in C306. The other regulatory genes such as MT, FT, AP2, SKP1, ABA2, ARF6, WRKY6, AOS, and LOX2 are involved in defense response in C306 genotype. Additionally, transcripts with unknown functions were identified as differentially expressed, which could participate in drought responses.
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http://dx.doi.org/10.1007/s00709-018-1237-xDOI Listing
September 2018

Assembly and Phasing of Dikaryotic Genomes from Two Isolates of f. sp. , the Causal Agent of Oat Crown Rust.

mBio 2018 02 20;9(1). Epub 2018 Feb 20.

Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota, USA

Oat crown rust, caused by the fungus f. sp. , is a devastating disease that impacts worldwide oat production. For much of its life cycle, f. sp. is dikaryotic, with two separate haploid nuclei that may vary in virulence genotype, highlighting the importance of understanding haplotype diversity in this species. We generated highly contiguous genome assemblies of two f. sp. isolates, 12SD80 and 12NC29, from long-read sequences. In total, we assembled 603 primary contigs for 12SD80, for a total assembly length of 99.16 Mbp, and 777 primary contigs for 12NC29, for a total length of 105.25 Mbp; approximately 52% of each genome was assembled into alternate haplotypes. This revealed structural variation between haplotypes in each isolate equivalent to more than 2% of the genome size, in addition to about 260,000 and 380,000 heterozygous single-nucleotide polymorphisms in 12SD80 and 12NC29, respectively. Transcript-based annotation identified 26,796 and 28,801 coding sequences for isolates 12SD80 and 12NC29, respectively, including about 7,000 allele pairs in haplotype-phased regions. Furthermore, expression profiling revealed clusters of coexpressed secreted effector candidates, and the majority of orthologous effectors between isolates showed conservation of expression patterns. However, a small subset of orthologs showed divergence in expression, which may contribute to differences in virulence between 12SD80 and 12NC29. This study provides the first haplotype-phased reference genome for a dikaryotic rust fungus as a foundation for future studies into virulence mechanisms in f. sp. Disease management strategies for oat crown rust are challenged by the rapid evolution of f. sp. , which renders resistance genes in oat varieties ineffective. Despite the economic importance of understanding f. sp. , resources to study the molecular mechanisms underpinning pathogenicity and the emergence of new virulence traits are lacking. Such limitations are partly due to the obligate biotrophic lifestyle of f. sp. as well as the dikaryotic nature of the genome, features that are also shared with other important rust pathogens. This study reports the first release of a haplotype-phased genome assembly for a dikaryotic fungal species and demonstrates the amenability of using emerging technologies to investigate genetic diversity in populations of f. sp. .
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http://dx.doi.org/10.1128/mBio.01650-17DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5821079PMC
February 2018

Correction to: The transcriptome landscape of early maize meiosis.

BMC Plant Biol 2018 01 15;18(1):12. Epub 2018 Jan 15.

Department of Horticultural Science, University of Minnesota, St. Paul, MN, 55108, USA.

Correction: Following publication of the original article [1], the authors reported that the number of genes overlaying the bar graph in Fig. 3A were incorrectly counted and inserted (i.e. including a title tile, and in inverse order). The corrected numbers are below and match with the listed genes supplied in Additional File: Table S2.
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http://dx.doi.org/10.1186/s12870-017-1224-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5767970PMC
January 2018

Identification, introgression, and molecular marker genetic analysis and selection of a highly effective novel oat crown rust resistance from diploid oat, Avena strigosa.

Theor Appl Genet 2018 Mar 6;131(3):721-733. Epub 2017 Dec 6.

Department of Plant Pathology, University of Minnesota, St. Paul, MN, 55108, USA.

Key Message: Oat crown rust is one of the most damaging diseases of oat. We identified a new source of resistance and developed KASP and TaqMan markers for selection in breeding programs. A new highly effective resistance to oat crown rust (Puccinia coronata f. sp. avenae) was identified in the diploid oat Avena strigosa PI 258731 and introgressed into hexaploid cultivated oat. Young plants with this resistance show moderate susceptibility, whereas older plant tissues and adult plants are resistant with no virulent isolates encountered in over 8 years of testing. Resistance was incorporated into hexaploid oat by embryo rescue, colchicine chromosome doubling followed by backcrosses with a hexaploid parent, and selection for stable transmission of resistance. To mitigate flag leaf and panicle chlorosis/necrosis associated with the resistance, crosses were made with derived resistant lines to breeding lines of divergent parentage followed by selection. Subsequently, two F sister lines, termed MNBT1020-1 and MNBT1021-1, were identified in which the chlorosis/necrosis was reduced. These two lines performed well in replicated multi-location state trials in 2015 and 2016 out-yielding all cultivar entries. Segregating F plants resulting from crosses of MNBT lines to susceptible parents were genotyped with the oat 6K SNP array, and SNP loci with close linkage to the resistance were identified. KASP assays generated from linked SNPs showed accurate discrimination of the resistance in derivatives of the resistant MNBT lines crossed to susceptible breeding lines. A TaqMan marker was developed and correctly identified homozygous resistance in over 95% of 379 F plants when rust was scored in F plants in the field. Thus, a novel highly effective resistance and associated molecular markers are available for use in breeding, genetic analysis, and functional studies.
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http://dx.doi.org/10.1007/s00122-017-3031-0DOI Listing
March 2018

Genomic features shaping the landscape of meiotic double-strand-break hotspots in maize.

Proc Natl Acad Sci U S A 2017 11 30;114(46):12231-12236. Epub 2017 Oct 30.

School of Integrative Plant Science, Cornell University, Ithaca, NY 14853;

Meiotic recombination is the most important source of genetic variation in higher eukaryotes. It is initiated by formation of double-strand breaks (DSBs) in chromosomal DNA in early meiotic prophase. The DSBs are subsequently repaired, resulting in crossovers (COs) and noncrossovers (NCOs). Recombination events are not distributed evenly along chromosomes but cluster at recombination hotspots. How specific sites become hotspots is poorly understood. Studies in yeast and mammals linked initiation of meiotic recombination to active chromatin features present upstream from genes, such as absence of nucleosomes and presence of trimethylation of lysine 4 in histone H3 (H3K4me3). Core recombination components are conserved among eukaryotes, but it is unclear whether this conservation results in universal characteristics of recombination landscapes shared by a wide range of species. To address this question, we mapped meiotic DSBs in maize, a higher eukaryote with a large genome that is rich in repetitive DNA. We found DSBs in maize to be frequent in all chromosome regions, including sites lacking COs, such as centromeres and pericentromeric regions. Furthermore, most DSBs are formed in repetitive DNA, predominantly retrotransposons, and only one-quarter of DSB hotspots are near genes. Genic and nongenic hotspots differ in several characteristics, and only genic DSBs contribute to crossover formation. Maize hotspots overlap regions of low nucleosome occupancy but show only limited association with H3K4me3 sites. Overall, maize DSB hotspots exhibit distribution patterns and characteristics not reported previously in other species. Understanding recombination patterns in maize will shed light on mechanisms affecting dynamics of the plant genome.
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http://dx.doi.org/10.1073/pnas.1713225114DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5699076PMC
November 2017

Puccinia coronata f. sp. avenae: a threat to global oat production.

Mol Plant Pathol 2018 05 10;19(5):1047-1060. Epub 2017 Dec 10.

Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108, USA.

Puccinia coronata f. sp. avenae (Pca) causes crown rust disease in cultivated and wild oat (Avena spp.). The significant yield losses inflicted by this pathogen make crown rust the most devastating disease in the oat industry. Pca is a basidiomycete fungus with an obligate biotrophic lifestyle, and is classified as a typical macrocyclic and heteroecious fungus. The asexual phase in the life cycle of Pca occurs in oat, whereas the sexual phase takes place primarily in Rhamnus species as the alternative host. Epidemics of crown rust happens in areas with warm temperatures (20-25 °C) and high humidity. Infection by the pathogen leads to plant lodging and shrivelled grain of poor quality. Disease symptoms: Infection of susceptible oat varieties gives rise to orange-yellow round to oblong uredinia (pustules) containing newly formed urediniospores. Pustules vary in size and can be larger than 5 mm in length. Infection occurs primarily on the surfaces of leaves, although occasional symptoms develop in the oat leaf sheaths and/or floral structures, such as awns. Symptoms in resistant oat varieties vary from flecks to small pustules, typically accompanied by chlorotic halos and/or necrosis. The pycnial and aecial stages are mostly present in the leaves of Rhamnus species, but occasionally symptoms can also be observed in petioles, young stems and floral structures. Aecial structures display a characteristic hypertrophy and can differ in size, occasionally reaching more than 5 mm in diameter. Taxonomy: Pca belongs to the kingdom Fungi, phylum Basidiomycota, class Pucciniomycetes, order Pucciniales and family Pucciniaceae. Host range: Puccinia coronata sensu lato can infect 290 species of grass hosts. Pca is prevalent in all oat-growing regions and, compared with other cereal rusts, displays a broad telial host range. The most common grass hosts of Pca include cultivated hexaploid oat (Avena sativa) and wild relatives, such as bluejoint grass, perennial ryegrass and fescue. Alternative hosts include several species of Rhamnus, with R. cathartica (common buckthorn) as the most important alternative host in Europe and North America.

Control: Most crown rust management strategies involve the use of rust-resistant crop varieties and the application of fungicides. The attainment of the durability of resistance against Pca is difficult as it is a highly variable pathogen with a great propensity to overcome the genetic resistance of varieties. Thus, adult plant resistance is often exploited in oat breeding programmes to develop new crown rust-resistant varieties. Useful website: https://www.ars.usda.gov/midwest-area/st-paul-mn/cereal-disease-lab/docs/cereal-rusts/race-surveys/.
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http://dx.doi.org/10.1111/mpp.12608DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6638059PMC
May 2018

Optimization and Comparative Analysis of Plant Organellar DNA Enrichment Methods Suitable for Next-generation Sequencing.

J Vis Exp 2017 07 28(125). Epub 2017 Jul 28.

Cereal Disease Laboratory, United States Department of Agriculture-Agricultural Research Service; Department of Plant Pathology, University of Minnesota;

Plant organellar genomes contain large, repetitive elements that may undergo pairing or recombination to form complex structures and/or sub-genomic fragments. Organellar genomes also exist in admixtures within a given cell or tissue type (heteroplasmy), and an abundance of subtypes may change throughout development or when under stress (sub-stoichiometric shifting). Next-generation sequencing (NGS) technologies are required to obtain deeper understanding of organellar genome structure and function. Traditional sequencing studies use several methods to obtain organellar DNA: (1) If a large amount of starting tissue is used, it is homogenized and subjected to differential centrifugation and/or gradient purification. (2) If a smaller amount of tissue is used (i.e., if seeds, material, or space is limited), the same process is performed as in (1), followed by whole-genome amplification to obtain sufficient DNA. (3) Bioinformatics analysis can be used to sequence the total genomic DNA and to parse out organellar reads. All these methods have inherent challenges and tradeoffs. In (1), it may be difficult to obtain such a large amount of starting tissue; in (2), whole-genome amplification could introduce a sequencing bias; and in (3), homology between nuclear and organellar genomes could interfere with assembly and analysis. In plants with large nuclear genomes, it is advantageous to enrich for organellar DNA to reduce sequencing costs and sequence complexity for bioinformatics analyses. Here, we compare a traditional differential centrifugation method with a fourth method, an adapted CpG-methyl pulldown approach, to separate the total genomic DNA into nuclear and organellar fractions. Both methods yield sufficient DNA for NGS, DNA that is highly enriched for organellar sequences, albeit at different ratios in mitochondria and chloroplasts. We present the optimization of these methods for wheat leaf tissue and discuss major advantages and disadvantages of each approach in the context of sample input, protocol ease, and downstream application.
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http://dx.doi.org/10.3791/55528DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5613775PMC
July 2017

A High Resolution Radiation Hybrid Map of Wheat Chromosome 4A.

Front Plant Sci 2016 10;7:2063. Epub 2017 Jan 10.

Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research Olomouc, Czechia.

Bread wheat has a large and complex allohexaploid genome with low recombination level at chromosome centromeric and peri-centromeric regions. This significantly hampers ordering of markers, contigs of physical maps and sequence scaffolds and impedes obtaining of high-quality reference genome sequence. Here we report on the construction of high-density and high-resolution radiation hybrid (RH) map of chromosome 4A supported by high-density chromosome deletion map. A total of 119 endosperm-based RH lines of two RH panels and 15 chromosome deletion bin lines were genotyped with 90K iSelect single nucleotide polymorphism (SNP) array. A total of 2316 and 2695 markers were successfully mapped to the 4A RH and deletion maps, respectively. The chromosome deletion map was ordered in 19 bins and allowed precise identification of centromeric region and verification of the RH panel reliability. The 4A-specific RH map comprises 1080 mapping bins and spans 6550.9 cR with a resolution of 0.13 Mb/cR. Significantly higher mapping resolution in the centromeric region was observed as compared to recombination maps. Relatively even distribution of deletion frequency along the chromosome in the RH panel was observed and putative functional centromere was delimited within a region characterized by two SNP markers.
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http://dx.doi.org/10.3389/fpls.2016.02063DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5222868PMC
January 2017

Gene Evolutionary Trajectories and GC Patterns Driven by Recombination in .

Front Plant Sci 2016 22;7:1433. Epub 2016 Sep 22.

National Center for Genome Resources, Santa Fe NM, USA.

Recombination occurring during meiosis is critical for creating genetic variation and plays an essential role in plant evolution. In addition to creating novel gene combinations, recombination can affect genome structure through altering GC patterns. In maize () and other grasses, another intriguing GC pattern exists. Maize genes show a bimodal GC content distribution that has been attributed to nucleotide bias in the third, or wobble, position of the codon. Recombination may be an underlying driving force given that recombination sites are often associated with high GC content. Here we explore the relationship between recombination and genomic GC patterns by comparing GC gene content at each of the three codon positions (GC, GC, and GC, collectively termed GC) to instances of a variable GC-rich motif that underlies double strand break (DSB) hotspots and to meiocyte-specific gene expression. Surprisingly, GC bimodality in maize cannot be fully explained by the codon wobble hypothesis. High GC genes show a strong overlap with the DSB hotspot motif, possibly providing a mechanism for the high evolutionary rates seen in these genes. On the other hand, genes that are turned on in meiosis (early prophase I) are biased against both high GC genes and genes with the DSB hotspot motif, possibly allowing important meiotic genes to avoid DSBs. Our data suggests a strong link between the GC-rich motif underlying DSB hotspots and high GC genes.
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5031598PMC
http://dx.doi.org/10.3389/fpls.2016.01433DOI Listing
September 2016

Dissecting Plant Chromosomes by the Use of Ionizing Radiation.

Methods Mol Biol 2016 ;1429:91-101

USDA-ARS, Cereal Disease Laboratory, Department of Plant Pathology, University of Minnesota, 1551 Lindig Ave., St. Paul, MN, 55108, USA.

Radiation treatment of genomes is used to generate chromosome breaks for numerous applications. This protocol describes the preparation of seeds and the determination of the optimal level of irradiation dosage for the creation of a radiation hybrid (RH) population. These RH lines can be used to generate high-resolution physical maps for the assembly of sequenced genomes as well as the fine mapping of genes. This procedure can also be used for mutation breeding and forward/reverse genetics.
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http://dx.doi.org/10.1007/978-1-4939-3622-9_8DOI Listing
October 2017

Novel Meiotic miRNAs and Indications for a Role of PhasiRNAs in Meiosis.

Front Plant Sci 2016 2;7:762. Epub 2016 Jun 2.

Department of Horticultural Science, University of Minnesota, St. Paul MN, USA.

Small RNAs (sRNA) add additional layers to the regulation of gene expression, with siRNAs directing gene silencing at the DNA level by RdDM (RNA-directed DNA methylation), and micro RNAs (miRNAs) directing post-transcriptional regulation of specific target genes, mostly by mRNA cleavage. We used manually isolated male meiocytes from maize (Zea mays) to investigate sRNA and DNA methylation landscapes during zygotene, an early stage of meiosis during which steps of meiotic recombination and synapsis of paired homologous chromosomes take place. We discovered two novel miRNAs from meiocytes, zma-MIR11969 and zma-MIR11970, and identified putative target genes. Furthermore, we detected abundant phasiRNAs of 21 and 24 nt length. PhasiRNAs are phased small RNAs which occur in 21 or 24 nt intervals, at a few hundred loci, specifically in male reproductive tissues in grasses. So far, the function of phasiRNAs remained elusive. Data from isolated meiocytes now revealed elevated DNA methylation at phasiRNA loci, especially in the CHH context, suggesting a role for phasiRNAs in cis DNA methylation. In addition, we consider a role of these phasiRNAs in chromatin remodeling/dynamics during meiosis. However, this is not well supported yet and will need more additional data. Here, we only lay out the idea due to other relevant literature and our additional observation of a peculiar GC content pattern at phasiRNA loci. Chromatin remodeling is also indicated by the discovery that histone genes were enriched for sRNA of 22 nt length. Taken together, we gained clues that lead us to hypothesize sRNA-driven DNA methylation and possibly chromatin remodeling during male meiosis in the monocot maize which is in line with and extends previous knowledge.
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http://dx.doi.org/10.3389/fpls.2016.00762DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4889585PMC
June 2016

A Population of Deletion Mutants and an Integrated Mapping and Exome-seq Pipeline for Gene Discovery in Maize.

G3 (Bethesda) 2016 08 9;6(8):2385-95. Epub 2016 Aug 9.

Department of Agronomy and Horticulture, Center for Plant Science Innovation, Beadle Center for Biotechnology, University of Nebraska, Lincoln, Nebraska 68588

To better understand maize endosperm filling and maturation, we used γ-irradiation of the B73 maize reference line to generate mutants with opaque endosperm and reduced kernel fill phenotypes, and created a population of 1788 lines including 39 Mo17 × F2s showing stable, segregating, and viable kernel phenotypes. For molecular characterization of the mutants, we developed a novel functional genomics platform that combined bulked segregant RNA and exome sequencing (BSREx-seq) to map causative mutations and identify candidate genes within mapping intervals. To exemplify the utility of the mutants and provide proof-of-concept for the bioinformatics platform, we present detailed characterization of line 937, an opaque mutant harboring a 6203 bp in-frame deletion covering six exons within the Opaque-1 gene. In addition, we describe mutant line 146 which contains a 4.8 kb intragene deletion within the Sugary-1 gene and line 916 in which an 8.6 kb deletion knocks out a Cyclin A2 gene. The publically available algorithm developed in this work improves the identification of causative deletions and its corresponding gaps within mapping peaks. This study demonstrates the utility of γ-irradiation for forward genetics in large nondense genomes such as maize since deletions often affect single genes. Furthermore, we show how this classical mutagenesis method becomes applicable for functional genomics when combined with state-of-the-art genomics tools.
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http://dx.doi.org/10.1534/g3.116.030528DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4978893PMC
August 2016

The role of mitochondria in plant development and stress tolerance.

Free Radic Biol Med 2016 11 30;100:238-256. Epub 2016 Mar 30.

United States Department of Agriculture-Agricultural Research Service, Cereal Disease Laboratory, St. Paul, MN 55108, United States; Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108, United States.

Eukaryotic cells require orchestrated communication between nuclear and organellar genomes, perturbations in which are linked to stress response and disease in both animals and plants. In addition to mitochondria, which are found across eukaryotes, plant cells contain a second organelle, the plastid. Signaling both among the organelles (cytoplasmic) and between the cytoplasm and the nucleus (i.e. nuclear-cytoplasmic interactions (NCI)) is essential for proper cellular function. A deeper understanding of NCI and its impact on development, stress response, and long-term health is needed in both animal and plant systems. Here we focus on the role of plant mitochondria in development and stress response. We compare and contrast features of plant and animal mitochondrial genomes (mtDNA), particularly highlighting the large and highly dynamic nature of plant mtDNA. Plant-based tools are powerful, yet underutilized, resources for enhancing our fundamental understanding of NCI. These tools also have great potential for improving crop production. Across taxa, mitochondria are most abundant in cells that have high energy or nutrient demands as well as at key developmental time points. Although plant mitochondria act as integrators of signals involved in both development and stress response pathways, little is known about plant mtDNA diversity and its impact on these processes. In humans, there are strong correlations between particular mitotypes (and mtDNA mutations) and developmental differences (or disease). We propose that future work in plants should focus on defining mitotypes more carefully and investigating their functional implications as well as improving techniques to facilitate this research.
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http://dx.doi.org/10.1016/j.freeradbiomed.2016.03.033DOI Listing
November 2016

A whole-genome, radiation hybrid mapping resource of hexaploid wheat.

Plant J 2016 Apr;86(2):195-207

Department of Crop and Soil Science, Oregon State University, Corvallis, OR, USA.

Generating a contiguous, ordered reference sequence of a complex genome such as hexaploid wheat (2n = 6x = 42; approximately 17 GB) is a challenging task due to its large, highly repetitive, and allopolyploid genome. In wheat, ordering of whole-genome or hierarchical shotgun sequencing contigs is primarily based on recombination and comparative genomics-based approaches. However, comparative genomics approaches are limited to syntenic inference and recombination is suppressed within the pericentromeric regions of wheat chromosomes, thus, precise ordering of physical maps and sequenced contigs across the whole-genome using these approaches is nearly impossible. We developed a whole-genome radiation hybrid (WGRH) resource and tested it by genotyping a set of 115 randomly selected lines on a high-density single nucleotide polymorphism (SNP) array. At the whole-genome level, 26 299 SNP markers were mapped on the RH panel and provided an average mapping resolution of approximately 248 Kb/cR1500 with a total map length of 6866 cR1500 . The 7296 unique mapping bins provided a five- to eight-fold higher resolution than genetic maps used in similar studies. Most strikingly, the RH map had uniform bin resolution across the entire chromosome(s), including pericentromeric regions. Our research provides a valuable and low-cost resource for anchoring and ordering sequenced BAC and next generation sequencing (NGS) contigs. The WGRH developed for reference wheat line Chinese Spring (CS-WGRH), will be useful for anchoring and ordering sequenced BAC and NGS based contigs for assembling a high-quality, reference sequence of hexaploid wheat. Additionally, this study provides an excellent model for developing similar resources for other polyploid species.
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http://dx.doi.org/10.1111/tpj.13153DOI Listing
April 2016

Fast-forward genetics by radiation hybrids to saturate the locus regulating nuclear-cytoplasmic compatibility in Triticum.

Plant Biotechnol J 2016 08 24;14(8):1716-26. Epub 2016 Feb 24.

Department of Plant Sciences, North Dakota State University, Fargo, ND, USA.

The nuclear-encoded species cytoplasm specific (scs) genes control nuclear-cytoplasmic compatibility in wheat (genus Triticum). Alloplasmic cells, which have nucleus and cytoplasm derived from different species, produce vigorous and vital organisms only when the correct version of scs is present in their nucleus. In this study, bulks of in vivo radiation hybrids segregating for the scs phenotype have been genotyped by sequencing with over 1.9 million markers. The high marker saturation obtained for a critical region of chromosome 1D allowed identification of 3318 reads that mapped in close proximity of the scs. A novel in silico approach was deployed to extend these short reads to sequences of up to 70 Kb in length and identify candidate open reading frames (ORFs). Markers were developed to anchor the short contigs containing ORFs to a radiation hybrid map of 650 individuals with resolution of 288 Kb. The region containing the scs locus was narrowed to a single Bacterial Artificial Chromosome (BAC) contig of Aegilops tauschii. Its sequencing and assembly by nano-mapping allowed rapid identification of a rhomboid gene as the only ORF existing within the refined scs locus. Resequencing of this gene from multiple germplasm sources identified a single nucleotide mutation, which gives rise to a functional amino acid change. Gene expression characterization revealed that an active copy of this rhomboid exists on all homoeologous chromosomes of wheat, and depending on the specific cytoplasm each copy is preferentially expressed. Therefore, a new methodology was applied to unique genetic stocks to rapidly identify a strong candidate gene for the control of nuclear-cytoplasmic compatibility in wheat.
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http://dx.doi.org/10.1111/pbi.12532DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5067624PMC
August 2016

Novel nuclear-cytoplasmic interaction in wheat (Triticum aestivum) induces vigorous plants.

Funct Integr Genomics 2016 Mar 9;16(2):171-82. Epub 2016 Feb 9.

USDA-ARS Cereal Disease Laboratory, University of Minnesota, Saint Paul, MN, 55108, USA.

Interspecific hybridization can be considered an accelerator of evolution, otherwise a slow process, solely dependent on mutation and recombination. Upon interspecific hybridization, several novel interactions between nuclear and cytoplasmic genomes emerge which provide additional sources of diversity. The magnitude and essence of intergenomic interactions between nuclear and cytoplasmic genomes remain unknown due to the direction of many crosses. This study was conducted to address the role of nuclear-cytoplasmic interactions as a source of variation upon hybridization. Wheat (Triticum aestivum) alloplasmic lines carrying the cytoplasm of Aegilops mutica along with an integrated approach utilizing comparative quantitative trait locus (QTL) and epigenome analysis were used to dissect this interaction. The results indicate that cytoplasmic genomes can modify the magnitude of QTL controlling certain physiological traits such as dry matter weight. Furthermore, methylation profiling analysis detected eight polymorphic regions affected by the cytoplasm type. In general, these results indicate that novel nuclear-cytoplasmic interactions can potentially trigger an epigenetic modification cascade in nuclear genes which eventually change the genetic network controlling physiological traits. These modified genetic networks can serve as new sources of variation to accelerate the evolutionary process. Furthermore, this variation can synthetically be produced by breeders in their programs to develop epigenomic-segregating lines.
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http://dx.doi.org/10.1007/s10142-016-0475-2DOI Listing
March 2016

Radiation hybrid maps of the D-genome of Aegilops tauschii and their application in sequence assembly of large and complex plant genomes.

BMC Genomics 2015 Oct 16;16:800. Epub 2015 Oct 16.

Department of Plant Sciences, North Dakota State University, Fargo, ND, 58102, USA.

Background: The large and complex genome of bread wheat (Triticum aestivum L., ~17 Gb) requires high resolution genome maps with saturated marker scaffolds to anchor and orient BAC contigs/ sequence scaffolds for whole genome assembly. Radiation hybrid (RH) mapping has proven to be an excellent tool for the development of such maps for it offers much higher and more uniform marker resolution across the length of the chromosome compared to genetic mapping and does not require marker polymorphism per se, as it is based on presence (retention) vs. absence (deletion) marker assay.

Methods: In this study, a 178 line RH panel was genotyped with SSRs and DArT markers to develop the first high resolution RH maps of the entire D-genome of Ae. tauschii accession AL8/78. To confirm map order accuracy, the AL8/78-RH maps were compared with:1) a DArT consensus genetic map constructed using more than 100 bi-parental populations, 2) a RH map of the D-genome of reference hexaploid wheat 'Chinese Spring', and 3) two SNP-based genetic maps, one with anchored D-genome BAC contigs and another with anchored D-genome sequence scaffolds. Using marker sequences, the RH maps were also anchored with a BAC contig based physical map and draft sequence of the D-genome of Ae. tauschii.

Results: A total of 609 markers were mapped to 503 unique positions on the seven D-genome chromosomes, with a total map length of 14,706.7 cR. The average distance between any two marker loci was 29.2 cR which corresponds to 2.1 cM or 9.8 Mb. The average mapping resolution across the D-genome was estimated to be 0.34 Mb (Mb/cR) or 0.07 cM (cM/cR). The RH maps showed almost perfect agreement with several published maps with regard to chromosome assignments of markers. The mean rank correlations between the position of markers on AL8/78 maps and the four published maps, ranged from 0.75 to 0.92, suggesting a good agreement in marker order. With 609 mapped markers, a total of 2481 deletions for the whole D-genome were detected with an average deletion size of 42.0 Mb. A total of 520 markers were anchored to 216 Ae. tauschii sequence scaffolds, 116 of which were not anchored earlier to the D-genome.

Conclusion: This study reports the development of first high resolution RH maps for the D-genome of Ae. tauschii accession AL8/78, which were then used for the anchoring of unassigned sequence scaffolds. This study demonstrates how RH mapping, which offered high and uniform resolution across the length of the chromosome, can facilitate the complete sequence assembly of the large and complex plant genomes.
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http://dx.doi.org/10.1186/s12864-015-2030-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4609151PMC
October 2015
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