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Nguyen DT, Henningsen EC, Lewis D, Mago R, McNeil M, Suchecki R, Boden S, Sperschneider J, Kianian S, Dodds P, Figueroa M. Genotypic and resistance profile analysis of two oat crown rust differential sets urge coordination and standardisation. Phytopathology 2023. [PMID: 38114076 DOI: 10.1094/phyto-10-23-0353-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2023]
Abstract
Puccinia coronata f. sp. avenae (Pca) is the causal agent of the disease known as crown rust which represents a bottleneck in oat production worldwide. Characterisation of pathogen populations often involves race (pathotype) assignments using differential sets, which are not uniform across countries. This study compared virulence profiles of 25 Pca isolates from Australia using two host differential sets, one from Australia and one from the USA. These differential sets were also genotyped using DArT sequencing technology. Phenotypic and genotypic discrepancies were detected on eight out of 29 common lines between the two sets, indicating that pathogen race assignments based on those lines are not comparable. To further investigate molecular markers that could assist in the stacking of rust resistance genes important for Australia, four published Pc91-linked markers were validated across the differential sets and then screened across a collection of 150 oat cultivars. Drover, Aladdin, and Volta were identified as putative carriers of the Pc91 locus. This is the first report to confirm that the cultivar 'Volta' carries Pc91 and demonstrates the value of implementing molecular markers to characterise materials in breeding pools of oat. Overall, our findings highlight the necessity of examining seed stocks using pedigree and molecular markers to ensure seed uniformity and bring robustness to surveillance methodologies.
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Affiliation(s)
- Duong T Nguyen
- CSIRO, 2221, Agriculture and Food, Adelaide, South Australia, Australia;
| | - Eva Celeste Henningsen
- CSIRO, 2221, Agriculture and Food, Canberra, Australian Capital Territory, Australia
- Australian National University, 2219, Research School of Biology, Canberra, Australian Capital Territory, Australia;
| | - Dave Lewis
- CSIRO, 2221, Agriculture and Food, Canberra, Australian Capital Territory, Australia;
| | - Rohit Mago
- CSIRO, 2221, Agriculture & Food, GPO Box 1700, Canberra, Australian Capital Territory, Australia, 2601;
| | - Meredith McNeil
- CSIRO, 2221, Agriculture and Food, 306 Carmody Road, St Lucia , Queensland, Australia, 4067;
| | | | - Scott Boden
- The University of Adelaide, 1066, School of Food, Agriculture, and Wine, Adelaide, South Australia, Australia;
| | - Jana Sperschneider
- CSIRO, 2221, Agriculture and Food, Canberra, Australian Capital Territory, Australia;
| | - Shahryar Kianian
- USDA-ARS Cereal Disease Laboratory, 57840, 1551 Lindig Street, Saint Paul, Minnesota, United States, 55108;
| | - Peter Dodds
- CSIRO, 2221, Agriculture and Food, Canberra, Australian Capital Territory, Australia;
| | - Melania Figueroa
- Commonwealth Scientific and Industrial Research Organisation, 2221, Agriculture and Food, Canberra, Australian Capital Territory, Australia;
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2
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Kumar J, Alok A, Steffenson BJ, Kianian S. A geminivirus crosses the monocot-dicot boundary and acts as a viral vector for gene silencing and genome editing. J Adv Res 2023:S2090-1232(23)00262-X. [PMID: 37730118 DOI: 10.1016/j.jare.2023.09.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 08/31/2023] [Accepted: 09/17/2023] [Indexed: 09/22/2023] Open
Abstract
INTRODUCTION Members of the family Geminiviridae have been reported to infect either a monocot plant or a dicot plant, but not both. This study reports a geminivirus, Wheat Dwarf India Virus (WDIV), first identified in wheat, that is capable of infecting both monocot and dicot plants and acting as a viral vector. OBJECTIVES This study was aimed at developing a broad host range viral vector system for reverse genetics and genome editing. METHODS Here we used a wheat isolate of WDIV and Ageratum yellow leaf curl betasatellite (AYLCB) for infectivity assays and vector development. We performed Agrobacterium-mediated inoculation of WDIV and AYLCB in wheat, oat, barley, corn, soybean, and tobacco. To examine the potential of WDIV to act as a viral vector, we modified the WDIV genome and cloned DNA fragments of the phytoene desaturase (PDS) genes from wheat and tobacco, separately. For gene editing experiments, tobacco lines expressing Cas9 were infiltrated with a WDIV-based vector carrying gRNA targeting the PDS gene. RESULTS About 80 to 90% of plants inoculated with infectious clones of WDIV alone or WDIV together with AYLCB showed mild symptoms, whereas some plants showed more prominent symptoms. WDIV and AYLCB were detected in the systemically infected leaves of all the plant species. Furthermore, the inoculation of the WDIV vector carrying PDS fragments induced silencing of the PDS gene in both wheat and tobacco plants. We also observed high-efficiency genome editing in the Cas9-expressing tobacco plants that were inoculated with WDIV vector-carrying gRNA. CONCLUSION Detection of WDIV in naturally infected wheat, barley, and sugarcane in the field and its ability to systemically infect wheat, oat, barley, corn, soybean, and tobacco under laboratory conditions, provides compelling evidence that WDIV is the first geminivirus identified with the capability of infecting both monocot and dicot plant species. The wide host range of WDIV can be exploited for developing a single vector system for high-throughput genome editing in many plant species.
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Affiliation(s)
- Jitendra Kumar
- Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN 55108, United States
| | - Anshu Alok
- Department of Plant Pathology, University of Minnesota, Saint Paul, MN 55108, United States
| | - Brian J Steffenson
- Department of Plant Pathology, University of Minnesota, Saint Paul, MN 55108, United States
| | - Shahryar Kianian
- USDA-ARS Cereal Disease Laboratory, Saint Paul, MN 55108, United States.
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3
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Abdulridha J, Min A, Rouse MN, Kianian S, Isler V, Yang C. Evaluation of Stem Rust Disease in Wheat Fields by Drone Hyperspectral Imaging. Sensors (Basel) 2023; 23:s23084154. [PMID: 37112495 PMCID: PMC10141366 DOI: 10.3390/s23084154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 04/11/2023] [Accepted: 04/15/2023] [Indexed: 05/13/2023]
Abstract
Detecting plant disease severity could help growers and researchers study how the disease impacts cereal crops to make timely decisions. Advanced technology is needed to protect cereals that feed the increasing population using fewer chemicals; this may lead to reduced labor usage and cost in the field. Accurate detection of wheat stem rust, an emerging threat to wheat production, could inform growers to make management decisions and assist plant breeders in making line selections. A hyperspectral camera mounted on an unmanned aerial vehicle (UAV) was utilized in this study to evaluate the severity of wheat stem rust disease in a disease trial containing 960 plots. Quadratic discriminant analysis (QDA) and random forest classifier (RFC), decision tree classification, and support vector machine (SVM) were applied to select the wavelengths and spectral vegetation indices (SVIs). The trial plots were divided into four levels based on ground truth disease severities: class 0 (healthy, severity 0), class 1 (mildly diseased, severity 1-15), class 2 (moderately diseased, severity 16-34), and class 3 (severely diseased, highest severity observed). The RFC method achieved the highest overall classification accuracy (85%). For the spectral vegetation indices (SVIs), the highest classification rate was recorded by RFC, and the accuracy was 76%. The Green NDVI (GNDVI), Photochemical Reflectance Index (PRI), Red-Edge Vegetation Stress Index (RVS1), and Chlorophyll Green (Chl green) were selected from 14 SVIs. In addition, binary classification of mildly diseased vs. non-diseased was also conducted using the classifiers and achieved 88% classification accuracy. This highlighted that hyperspectral imaging was sensitive enough to discriminate between low levels of stem rust disease vs. no disease. The results of this study demonstrated that drone hyperspectral imaging can discriminate stem rust disease levels so that breeders can select disease-resistant varieties more efficiently. The detection of low disease severity capability of drone hyperspectral imaging can help farmers identify early disease outbreaks and enable more timely management of their fields. Based on this study, it is also possible to build a new inexpensive multispectral sensor to diagnose wheat stem rust disease accurately.
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Affiliation(s)
- Jaafar Abdulridha
- Bioproducts and Biosystems Engineering Department, University of Minnesota, 1390 Eckles Ave, St. Paul, MN 55108, USA
| | - An Min
- Bioproducts and Biosystems Engineering Department, University of Minnesota, 1390 Eckles Ave, St. Paul, MN 55108, USA
| | - Matthew N. Rouse
- U.S. Department of Agriculture, Agricultural Research Service, Cereal Disease Lab, 1551 Lindig Avenue, St. Paul, MN 55108, USA
| | - Shahryar Kianian
- U.S. Department of Agriculture, Agricultural Research Service, Cereal Disease Lab, 1551 Lindig Avenue, St. Paul, MN 55108, USA
| | - Volkan Isler
- Department of Computer Science, University of Minnesota, 100 Union St SE, Minneapolis, MN 55455, USA
| | - Ce Yang
- Bioproducts and Biosystems Engineering Department, University of Minnesota, 1390 Eckles Ave, St. Paul, MN 55108, USA
- Correspondence:
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4
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Garcia N, Yin L, Dukowic-Schulze S, Milsted C, Kianian PMA, Kianian S, Pawlowski WP, Chen C. Comparison of meiotic transcriptomes of three maize inbreds with different origins reveals differences in cell cycle and recombination. BMC Genomics 2022; 23:702. [PMID: 36224518 PMCID: PMC9554999 DOI: 10.1186/s12864-022-08922-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 09/28/2022] [Indexed: 11/21/2022] Open
Abstract
Background Cellular events during meiosis can differ between inbred lines in maize. Substantial differences in the average numbers of chiasmata and double-strand breaks (DSBs) per meiotic cell have been documented among diverse inbred lines of maize: CML228, a tropical maize inbred line, B73 and Mo17, temperate maize lines. To determine if gene expression might explain these observed differences, an RNA-Seq experiment was performed on CML228 male meiocytes which was compared to B73 and Mo17 male meiocytes, where plants were grown in the same controlled environment. Results We found that a few DSB-repair/meiotic genes which promote class I crossovers (COs) and the Zyp1 gene which limits newly formed class I COs were up-regulated, whereas Mus81 homolog 2 which promotes class II COs was down-regulated in CML228. Although we did not find enriched gene ontology (GO) categories directly related to meiosis, we found that GO categories in membrane, localization, proteolysis, energy processes were up-regulated in CML228, while chromatin remodeling, epigenetic regulation, and cell cycle related processes including meiosis related cell cycle processes were down-regulated in CML228. The degree of similarity in expression patterns between the three maize lines reflect their genetic relatedness: B73 and Mo17 had similar meiotic expressions and CML228 had a more distinct expression profile. Conclusions We found that meiotic related genes were mostly conserved among the three maize inbreds except for a few DSB-repair/meiotic genes. The findings that the molecular players in limiting class I CO formation (once CO assurance is achieved) were up-regulated and those involved in promoting class II CO formation were down-regulated in CML228 agree with the lower chiasmata number observed in CML228 previously. In addition, epigenetics such as chromatin remodeling and histone modification might play a role. Transport and energy-related processes was up-regulated and Cyclin13 was down-regulated in CML228. The direction of gene expression of these processes agree with that previously found in meiotic tissues compared with vegetative tissues. In summary, we used different natural maize inbred lines from different climatic conditions and have shown their differences in expression landscape in male meiocytes. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08922-w.
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Affiliation(s)
- Nelson Garcia
- Department of Horticultural Science, University of Minnesota, Saint Paul, MN, USA.,Present Address: Sound Agriculture, 5858 Horton St, Emeryville, CA, USA
| | - Lu Yin
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - Stefanie Dukowic-Schulze
- Department of Horticultural Science, University of Minnesota, Saint Paul, MN, USA.,Microvascular Biology and Pathobiology, University of Heidelberg, Mannheim, Germany
| | - Claire Milsted
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - Penny M A Kianian
- PepsiCo Inc., 210 Borlaug Hall, 1991 Upper Buford Circle, Saint Paul, MN, USA
| | - Shahryar Kianian
- Department of Agriculture - Agricultural Research Service, Cereal Disease Lab, U.S., Saint Paul, MN, USA
| | | | - Changbin Chen
- Department of Horticultural Science, University of Minnesota, Saint Paul, MN, USA. .,School of Life Sciences, Arizona State University, Tempe, AZ, USA.
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5
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Milsted C, Dai B, Garcia N, Yin L, He Y, Kianian S, Pawlowski W, Chen C. Genome-wide investigation of maize RAD51 binding affinity through phage display. BMC Genomics 2022; 23:199. [PMID: 35279087 PMCID: PMC8917730 DOI: 10.1186/s12864-022-08419-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2021] [Accepted: 02/18/2022] [Indexed: 11/10/2022] Open
Abstract
Abstract
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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6
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Rabbi SMHA, Kumar A, Mohajeri Naraghi S, Simsek S, Sapkota S, Solanki S, Alamri MS, Elias EM, Kianian S, Missaoui A, Mergoum M. Genome-Wide Association Mapping for Yield and Related Traits Under Drought Stressed and Non-stressed Environments in Wheat. Front Genet 2021; 12:649988. [PMID: 34239537 PMCID: PMC8258415 DOI: 10.3389/fgene.2021.649988] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 04/28/2021] [Indexed: 12/02/2022] Open
Abstract
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 p ≤ 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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Affiliation(s)
- S M Hisam A Rabbi
- Department of Plant Sciences, North Dakota State University, Fargo, ND, United States
| | - Ajay Kumar
- Department of Plant Sciences, North Dakota State University, Fargo, ND, United States
| | | | - Senay Simsek
- Department of Plant Sciences, North Dakota State University, Fargo, ND, United States
| | - Suraj Sapkota
- Institute of Plant Breeding, Genetics, and Genomics, University of Georgia, Griffin, GA, United States
| | - Shyam Solanki
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, United States
| | - Mohammed S Alamri
- Department of Food Sciences and Nutrition, King Saud University, Riyadh, Saudi Arabia
| | - Elias M Elias
- Department of Plant Sciences, North Dakota State University, Fargo, ND, United States
| | - Shahryar Kianian
- United States Department of Agriculture-The Agricultural Research Service (USDA-ARS) Cereal Disease Laboratory, University of Minnesota, St. Paul, MN, United States
| | - Ali Missaoui
- Institute of Plant Breeding, Genetics, and Genomics, University of Georgia, Griffin, GA, United States.,Department of Crop and Soil Sciences, University of Georgia, Griffin, GA, United States
| | - Mohamed Mergoum
- Institute of Plant Breeding, Genetics, and Genomics, University of Georgia, Griffin, GA, United States.,Department of Crop and Soil Sciences, University of Georgia, Griffin, GA, United States
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7
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Rabbi SMHA, Kumar A, Mohajeri Naraghi S, Sapkota S, Alamri MS, Elias EM, Kianian S, Seetan R, Missaoui A, Solanki S, Mergoum M. 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; 12:656037. [PMID: 34220939 PMCID: PMC8249774 DOI: 10.3389/fgene.2021.656037] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 05/13/2021] [Indexed: 01/22/2023] Open
Abstract
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. In silico 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 (TraesCS6A01G116400) and hexosyltransferase (TraesCS7B01G013300) 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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Affiliation(s)
- S M Hisam Al Rabbi
- Department of Plant Sciences, North Dakota State University, Fargo, ND, United States
| | - Ajay Kumar
- Department of Plant Sciences, North Dakota State University, Fargo, ND, United States
| | | | - Suraj Sapkota
- Institute of Plant Breeding, Genetics, and Genomics, University of Georgia, Griffin, GA, United States
| | - Mohammed S Alamri
- Department of Food Science and Nutrition, King Saud University, Riyadh, Saudi Arabia
| | - Elias M Elias
- Department of Plant Sciences, North Dakota State University, Fargo, ND, United States
| | - Shahryar Kianian
- USDA-ARS Cereal Disease Laboratory, University of Minnesota, St. Paul, MN, United States
| | - Raed Seetan
- Department of Computer Science, Slippery Rock University, Slippery Rock, PA, United States
| | - Ali Missaoui
- Institute of Plant Breeding, Genetics, and Genomics, University of Georgia, Griffin, GA, United States.,Department of Crop and Soil Sciences, University of Georgia, Griffin, GA, United States
| | - Shyam Solanki
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, United States
| | - Mohamed Mergoum
- Institute of Plant Breeding, Genetics, and Genomics, University of Georgia, Griffin, GA, United States.,Department of Crop and Soil Sciences, University of Georgia, Griffin, GA, United States
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8
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Dukowic-Schulze S, Sundararajan A, Ramaraj T, Kianian S, Pawlowski WP, Mudge J, Chen C. Corrigendum: Novel Meiotic miRNAs and Indications for a Role of PhasiRNAs in Meiosis. Front Plant Sci 2020; 11:653. [PMID: 32582234 PMCID: PMC7290127 DOI: 10.3389/fpls.2020.00653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 04/28/2020] [Indexed: 06/11/2023]
Abstract
[This corrects the article DOI: 10.3389/fpls.2016.00762.].
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Affiliation(s)
| | | | | | - Shahryar Kianian
- Cereal Disease Laboratory, United States Department of Agriculture - Agricultural Research Service, St. Paul, MN, United States
| | - Wojciech P. Pawlowski
- Section of Plant Biology, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States
| | - Joann Mudge
- National Center for Genome Resources, Santa Fe, NM, United States
| | - Changbin Chen
- Department of Horticultural Science, University of Minnesota, St. Paul, MN, United States
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9
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Admassu-Yimer B, Gordon T, Harrison S, Kianian S, Bockelman H, Bonman JM, Esvelt Klos K. 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; 102:2180-2186. [PMID: 30207898 DOI: 10.1094/pdis-04-18-0566-re] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
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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Affiliation(s)
| | - Tyler Gordon
- United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Small Grains and Potato Germplasm Research, Aberdeen, ID 83210
| | - Stephen Harrison
- Louisiana State University AgCenter-SPESS, Baton Rouge 70803-2110
| | | | - Harold Bockelman
- USDA-ARS, Small Grains and Potato Germplasm Research, Aberdeen, ID 83210
| | - J Michael Bonman
- USDA-ARS, Small Grains and Potato Germplasm Research, Aberdeen, ID 83210
| | - Kathy Esvelt Klos
- USDA-ARS, Small Grains and Potato Germplasm Research, Aberdeen, ID 83210
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10
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Dukowic-Schulze S, Sundararajan A, Mudge J, Ramaraj T, Farmer AD, Wang M, Sun Q, Pillardy J, Kianian S, Retzel EF, Pawlowski WP, Chen C. Correction to: The transcriptome landscape of early maize meiosis. BMC Plant Biol 2018; 18:12. [PMID: 29334940 PMCID: PMC5767970 DOI: 10.1186/s12870-017-1224-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Accepted: 12/22/2017] [Indexed: 06/07/2023]
Abstract
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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Affiliation(s)
| | | | - Joann Mudge
- National Center for Genome Resources, Santa Fe, NM, 87505, USA
| | | | - Andrew D Farmer
- National Center for Genome Resources, Santa Fe, NM, 87505, USA
| | - Minghui Wang
- Department of Plant Breeding and Genetics, Cornell University, Ithaca, NY, 14850, USA
- Computational Biology Service Unit, Cornell University, Ithaca, NY, 14850, USA
| | - Qi Sun
- Computational Biology Service Unit, Cornell University, Ithaca, NY, 14850, USA
| | - Jaroslaw Pillardy
- Computational Biology Service Unit, Cornell University, Ithaca, NY, 14850, USA
| | - Shahryar Kianian
- USDA-ARS Cereal Disease Laboratory, University of Minnesota, St. Paul, MN, 55108, USA
| | - Ernest F Retzel
- National Center for Genome Resources, Santa Fe, NM, 87505, USA
| | - Wojciech P Pawlowski
- Department of Plant Breeding and Genetics, Cornell University, Ithaca, NY, 14850, USA
| | - Changbin Chen
- Department of Horticultural Science, University of Minnesota, St. Paul, MN, 55108, USA.
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11
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Affiliation(s)
- Ali Moghimi
- Univ. of Minnesota, Twin Cities (United States)
| | - Ce Yang
- Univ. of Minnesota, Twin Cities (United States)
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12
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Tiwari VK, Heesacker A, Riera-Lizarazu O, Gunn H, Wang S, Wang Y, Gu YQ, Paux E, Koo DH, Kumar A, Luo MC, Lazo G, Zemetra R, Akhunov E, Friebe B, Poland J, Gill BS, Kianian S, Leonard JM. A whole-genome, radiation hybrid mapping resource of hexaploid wheat. Plant J 2016; 86:195-207. [PMID: 26945524 DOI: 10.1111/tpj.13153] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Revised: 02/04/2016] [Accepted: 02/22/2016] [Indexed: 06/05/2023]
Abstract
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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Affiliation(s)
- Vijay K Tiwari
- Department of Plant Pathology, Wheat Genetics Resource Center, Kansas State University, Manhattan, KS, USA
| | - Adam Heesacker
- Department of Crop and Soil Science, Oregon State University, Corvallis, OR, USA
| | | | - Hilary Gunn
- Department of Crop and Soil Science, Oregon State University, Corvallis, OR, USA
| | - Shichen Wang
- Department of Plant Pathology, Wheat Genetics Resource Center, Kansas State University, Manhattan, KS, USA
| | - Yi Wang
- Crop Improvement and Genetics Research Unit, USDA-ARS, Albany, NY, USA
| | - Young Q Gu
- Crop Improvement and Genetics Research Unit, USDA-ARS, Albany, NY, USA
| | - Etienne Paux
- Diversité et Ecophysiologie des Céréales, INRA, UMR 1095 Génétique, 5 chemin de Beaulieu, F-63039, Clermont-Ferrand, France
- Diversité et Ecophysiologie des Céréales, UMR 1095 Génétique, Université Blaise Pascal, F-63177, Aubière Cedex, France
| | - Dal-Hoe Koo
- Department of Plant Pathology, Wheat Genetics Resource Center, Kansas State University, Manhattan, KS, USA
| | - Ajay Kumar
- Department of Plant Sciences, North Dakota State University, Fargo, ND, USA
| | - Ming-Cheng Luo
- Department of Plant Sciences, University of California, Davis, CA, USA
| | - Gerard Lazo
- Crop Improvement and Genetics Research Unit, USDA-ARS, Albany, NY, USA
| | - Robert Zemetra
- Department of Crop and Soil Science, Oregon State University, Corvallis, OR, USA
| | - Eduard Akhunov
- Department of Plant Pathology, Wheat Genetics Resource Center, Kansas State University, Manhattan, KS, USA
| | - Bernd Friebe
- Department of Plant Pathology, Wheat Genetics Resource Center, Kansas State University, Manhattan, KS, USA
| | - Jesse Poland
- Department of Plant Pathology, Wheat Genetics Resource Center, Kansas State University, Manhattan, KS, USA
| | - Bikram S Gill
- Department of Plant Pathology, Wheat Genetics Resource Center, Kansas State University, Manhattan, KS, USA
| | - Shahryar Kianian
- Cereal Disease Laboratory, University of Minnesota, Saint Paul, MN, USA
| | - Jeffrey M Leonard
- Department of Crop and Soil Science, Oregon State University, Corvallis, OR, USA
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13
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Dukowic-Schulze S, Sundararajan A, Ramaraj T, Kianian S, Pawlowski WP, Mudge J, Chen C. Novel Meiotic miRNAs and Indications for a Role of PhasiRNAs in Meiosis. Front Plant Sci 2016; 7:762. [PMID: 27313591 PMCID: PMC4889585 DOI: 10.3389/fpls.2016.00762] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Accepted: 05/17/2016] [Indexed: 05/03/2023]
Abstract
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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Affiliation(s)
| | | | | | - Shahryar Kianian
- Cereal Disease Laboratory, United States Department of Agriculture – Agricultural Research Service, St. PaulMN, USA
| | - Wojciech P. Pawlowski
- Section of Plant Biology, School of Integrative Plant Science, Cornell University, IthacaNY, USA
| | - Joann Mudge
- National Center for Genome Resources, Santa FeNM, USA
| | - Changbin Chen
- Department of Horticultural Science, University of Minnesota, St. PaulMN, USA
- *Correspondence: Changbin Chen,
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Echeverry-Solarte M, Kumar A, Kianian S, Mantovani EE, McClean PE, Deckard EL, Elias E, Simsek S, Alamri MS, Hegstad J, Schatz B, Mergoum M. Genome-Wide Mapping of Spike-Related and Agronomic Traits in a Common Wheat Population Derived from a Supernumerary Spikelet Parent and an Elite Parent. Plant Genome 2015. [PMID: 33228318 DOI: 10.3835/plantgenome2014.03.0013] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
In wheat, exotic genotypes harbor a broad range of spike-related traits, and can be used as a source of new genes for germplasm enhancement in wheat breeding programs. In the present study, a population of 163 recombinant inbred lines was derived from a cross between an elite line (WCB414) and an exotic line (WCB617) with branched spike (supernumerary spikelet; SS) head morphology. The population was evaluated over four to six environments to identify quantitative trait loci (QTL) associated with nine spike-related traits and 10 agronomic traits. A genetic map consisting of 939 diversity arrays technology (DArT) markers was constructed. Composite interval mapping identified a total of 143 QTL located on 17 different wheat chromosomes and included 33 consistent and definitive QTL. The amount of phenotype variation explained (PVE) by individual QTL ranged from 0.61 to 91.8%. One major QTL for glume pubescence was located in a QTL-rich region on the short arm of chromosome 1A, where loci for other traits such as for kernels per spike (KS) and spike length (SL) were also identified. Similarly, a cluster of QTL associated with yield-related, agronomic and spike-related traits contributing up to 40.3% of PVE was found on the short arm of chromosome 2D, in the vicinity of a major QTL for SS-related traits. Consistent and major QTL identified in the present study may be useful in marker-assisted breeding programs to facilitate transfer of desirable alleles into other germplasm. Desirable QTL alleles were also contributed by the exotic line, suggesting the possibility of enriching the breeding germplasm with alleles from SS genotypes.
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Affiliation(s)
| | - Ajay Kumar
- Dep. of Plant Sciences, North Dakota State Univ., P.O. Box 6050, Fargo, ND, 58108-6050
| | - Shahryar Kianian
- USDA-ARS - Cereal Disease Laboratory, 1551 Lindig St., Univ. of Minnesota, St. Paul, Minnesota, 55108
| | - Eder E Mantovani
- Dep. of Plant Sciences, North Dakota State Univ., P.O. Box 6050, Fargo, ND, 58108-6050
| | - Phillip E McClean
- Dep. of Plant Sciences, North Dakota State Univ., P.O. Box 6050, Fargo, ND, 58108-6050
| | - Edward L Deckard
- Dep. of Plant Sciences, North Dakota State Univ., P.O. Box 6050, Fargo, ND, 58108-6050
| | - Elias Elias
- Dep. of Plant Sciences, North Dakota State Univ., P.O. Box 6050, Fargo, ND, 58108-6050
| | - Senay Simsek
- Dep. of Plant Sciences, North Dakota State Univ., P.O. Box 6050, Fargo, ND, 58108-6050
| | - Mohammed S Alamri
- Dep. of Food Sciences & Nutrition, King Saud Univ., P.O. Box 2460, Riyadh, 11451, Saudi Arabia
| | - Justin Hegstad
- Dep. of Plant Sciences, North Dakota State Univ., P.O. Box 6050, Fargo, ND, 58108-6050
| | - Blaine Schatz
- North Dakota State Univ. Carrington Research Extension Center, P.O. Box 219, Carrington, ND, 58421
| | - Mohamed Mergoum
- Dep. of Plant Sciences, North Dakota State Univ., P.O. Box 6050, Fargo, ND, 58108-6050
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15
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Echeverry-Solarte M, Kumar A, Kianian S, Mantovani EE, McClean PE, Deckard EL, Elias E, Simsek S, Alamri MS, Hegstad J, Schatz B, Mergoum M. Genome-Wide Mapping of Spike-Related and Agronomic Traits in a Common Wheat Population Derived from a Supernumerary Spikelet Parent and an Elite Parent. Plant Genome 2015; 8:eplantgenome2014.12.0089. [PMID: 33228318 DOI: 10.3835/plantgenome2014.12.0089] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Accepted: 02/02/2015] [Indexed: 05/25/2023]
Abstract
In wheat, exotic genotypes harbor a broad range of spike-related traits, and can be used as a source of new genes for germplasm enhancement in wheat breeding programs. In the present study, a population of 163 recombinant inbred lines was derived from a cross between an elite line (WCB414) and an exotic line (WCB617) with branched spike (supernumerary spikelet; SS) head morphology. The population was evaluated over four to six environments to identify quantitative trait loci (QTL) associated with nine spike-related traits and 10 agronomic traits. A genetic map consisting of 939 diversity arrays technology (DArT) markers was constructed. Composite interval mapping identified a total of 143 QTL located on 17 different wheat chromosomes and included 33 consistent and definitive QTL. The amount of phenotype variation explained (PVE) by individual QTL ranged from 0.61 to 91.8%. One major QTL for glume pubescence was located in a QTL-rich region on the short arm of chromosome 1A, where loci for other traits such as for kernels per spike (KS) and spike length (SL) were also identified. Similarly, a cluster of QTL associated with yield-related, agronomic and spike-related traits contributing up to 40.3% of PVE was found on the short arm of chromosome 2D, in the vicinity of a major QTL for SS-related traits. Consistent and major QTL identified in the present study may be useful in marker-assisted breeding programs to facilitate transfer of desirable alleles into other germplasm. Desirable QTL alleles were also contributed by the exotic line, suggesting the possibility of enriching the breeding germplasm with alleles from SS genotypes.
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Affiliation(s)
| | - Ajay Kumar
- Dep. of Plant Sciences, North Dakota State Univ., P.O. Box 6050, Fargo, ND, 58108-6050
| | - Shahryar Kianian
- USDA-ARS - Cereal Disease Laboratory, 1551 Lindig St., Univ. of Minnesota, St. Paul, Minnesota, 55108
| | - Eder E Mantovani
- Dep. of Plant Sciences, North Dakota State Univ., P.O. Box 6050, Fargo, ND, 58108-6050
| | - Phillip E McClean
- Dep. of Plant Sciences, North Dakota State Univ., P.O. Box 6050, Fargo, ND, 58108-6050
| | - Edward L Deckard
- Dep. of Plant Sciences, North Dakota State Univ., P.O. Box 6050, Fargo, ND, 58108-6050
| | - Elias Elias
- Dep. of Plant Sciences, North Dakota State Univ., P.O. Box 6050, Fargo, ND, 58108-6050
| | - Senay Simsek
- Dep. of Plant Sciences, North Dakota State Univ., P.O. Box 6050, Fargo, ND, 58108-6050
| | - Mohammed S Alamri
- Dep. of Food Sciences & Nutrition, King Saud Univ., P.O. Box 2460, Riyadh, 11451, Saudi Arabia
| | - Justin Hegstad
- Dep. of Plant Sciences, North Dakota State Univ., P.O. Box 6050, Fargo, ND, 58108-6050
| | - Blaine Schatz
- North Dakota State Univ. Carrington Research Extension Center, P.O. Box 219, Carrington, ND, 58421
| | - Mohamed Mergoum
- Dep. of Plant Sciences, North Dakota State Univ., P.O. Box 6050, Fargo, ND, 58108-6050
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16
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Echeverry-Solarte M, Kumar A, Kianian S, Simsek S, Alamri MS, Mantovani EE, McClean PE, Deckard EL, Elias E, Schatz B, Xu SS, Mergoum M. New QTL alleles for quality-related traits in spring wheat revealed by RIL population derived from supernumerary × non-supernumerary spikelet genotypes. Theor Appl Genet 2015; 128:893-912. [PMID: 25740563 DOI: 10.1007/s00122-015-2478-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2014] [Accepted: 02/04/2015] [Indexed: 06/04/2023]
Abstract
A population developed from an exotic line with supernumerary spikelets was genetically dissected for eight quality traits, discovering new genes/alleles with potential use in wheat breeding programs. Identifying new QTLs and alleles in exotic germplasm is paramount for further improvement of quality traits in wheat. In the present study, an RIL population developed from a cross of an elite wheat line (WCB414) and an exotic genotype with supernumerary spikelets (SS) was used to identify QTLs and new alleles for eight quality traits. Composite interval mapping for 1,000 kernels weight (TKW), kernel volume weight (KVW), grain protein content (GPC), percent of flour extraction (FE) and four mixograph-related traits identified a total of 69 QTLs including 19 stable QTLs. These QTLs were located on 18 different chromosomes (except 4D, 5D, and 6D). Thirteen of these QTLs explained more than 15% of phenotypic variation (PV) and were considered as major QTLs. In this study, we identified 11 QTLs for TKW (R (2) = 7.2-17.1 %), 10 for KVW (R (2) = 6.7-22.5%), 11 for GPC (R (2) = 4.7-16.9%), 6 for FE (R (2) = 4.8-19%) and 31 for mixograph-related traits (R (2) = 3.2-41.2%). In this population, several previously identified QTLs for SS, nine spike-related and ten agronomic traits were co-located with the quality QTLs, suggesting pleiotropic effects or close linkage among loci. The traits GPC and mixogram-related traits were positively correlated with SS. Indeed, several loci for quality traits were co-located with QTL for SS. The exotic parent contributed positive alleles that increased PV of the traits at 56% of loci demonstrating the suitability of germplasm with SS to improve quality traits in wheat.
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17
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Belova T, Grønvold L, Kumar A, Kianian S, He X, Lillemo M, Springer NM, Lien S, Olsen OA, Sandve SR. Utilization of deletion bins to anchor and order sequences along the wheat 7B chromosome. Theor Appl Genet 2014; 127:2029-2040. [PMID: 25134516 DOI: 10.1007/s00122-014-2358-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2014] [Accepted: 07/13/2014] [Indexed: 06/03/2023]
Abstract
A total of 3,671 sequence contigs and scaffolds were mapped to deletion bins on wheat chromosome 7B providing a foundation for developing high-resolution integrated physical map for this chromosome. Bread wheat (Triticum aestivum L.) has a large, complex and highly repetitive genome which is challenging to assemble into high quality pseudo-chromosomes. As part of the international effort to sequence the hexaploid bread wheat genome by the international wheat genome sequencing consortium (IWGSC) we are focused on assembling a reference sequence for chromosome 7B. The successful completion of the reference chromosome sequence is highly dependent on the integration of genetic and physical maps. To aid the integration of these two types of maps, we have constructed a high-density deletion bin map of chromosome 7B. Using the 270 K Nimblegen comparative genomic hybridization (CGH) array on a set of cv. Chinese spring deletion lines, a total of 3,671 sequence contigs and scaffolds (~7.8 % of chromosome 7B physical length) were mapped into nine deletion bins. Our method of genotyping deletions on chromosome 7B relied on a model-based clustering algorithm (Mclust) to accurately predict the presence or absence of a given genomic sequence in a deletion line. The bin mapping results were validated using three different approaches, viz. (a) PCR-based amplification of randomly selected bin mapped sequences (b) comparison with previously mapped ESTs and (c) comparison with a 7B genetic map developed in the present study. Validation of the bin mapping results suggested a high accuracy of the assignment of 7B sequence contigs and scaffolds to the 7B deletion bins.
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Affiliation(s)
- Tatiana Belova
- Department of Plant Sciences, Norwegian University of Life Sciences, Ås, Norway,
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18
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Dukowic-Schulze S, Sundararajan A, Mudge J, Ramaraj T, Farmer AD, Wang M, Sun Q, Pillardy J, Kianian S, Retzel EF, Pawlowski WP, Chen C. The transcriptome landscape of early maize meiosis. BMC Plant Biol 2014; 14:118. [PMID: 24885405 PMCID: PMC4032173 DOI: 10.1186/1471-2229-14-118] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2013] [Accepted: 04/28/2014] [Indexed: 05/20/2023]
Abstract
BACKGROUND A major step in the higher plant life cycle is the decision to leave the mitotic cell cycle and begin the progression through the meiotic cell cycle that leads to the formation of gametes. The molecular mechanisms that regulate this transition and early meiosis remain largely unknown. To gain insight into gene expression features during the initiation of meiotic recombination, we profiled early prophase I meiocytes from maize (Zea mays) using capillary collection to isolate meiocytes, followed by RNA-seq. RESULTS We detected ~2,000 genes as preferentially expressed during early meiotic prophase, most of them uncharacterized. Functional analysis uncovered the importance of several cellular processes in early meiosis. Processes significantly enriched in isolated meiocytes included proteolysis, protein targeting, chromatin modification and the regulation of redox homeostasis. The most significantly up-regulated processes in meiocytes were processes involved in carbohydrate metabolism. Consistent with this, many mitochondrial genes were up-regulated in meiocytes, including nuclear- and mitochondrial-encoded genes. The data were validated with real-time PCR and in situ hybridization and also used to generate a candidate maize homologue list of known meiotic genes from Arabidopsis. CONCLUSIONS Taken together, we present a high-resolution analysis of the transcriptome landscape in early meiosis of an important crop plant, providing support for choosing genes for detailed characterization of recombination initiation and regulation of early meiosis. Our data also reveal an important connection between meiotic processes and altered/increased energy production.
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Affiliation(s)
| | | | - Joann Mudge
- National Center for Genome Resources, Santa Fe, NM 87505, USA
| | | | - Andrew D Farmer
- National Center for Genome Resources, Santa Fe, NM 87505, USA
| | - Minghui Wang
- Department of Plant Breeding and Genetics, Cornell University, Ithaca, NY 14850, USA
- Computational Biology Service Unit, Cornell University, Ithaca, NY 14850, USA
| | - Qi Sun
- Computational Biology Service Unit, Cornell University, Ithaca, NY 14850, USA
| | - Jaroslaw Pillardy
- Computational Biology Service Unit, Cornell University, Ithaca, NY 14850, USA
| | - Shahryar Kianian
- USDA-ARS Cereal Disease Laboratory, University of Minnesota, St. Paul, MN 55108, USA
| | - Ernest F Retzel
- National Center for Genome Resources, Santa Fe, NM 87505, USA
| | - Wojciech P Pawlowski
- Department of Plant Breeding and Genetics, Cornell University, Ithaca, NY 14850, USA
| | - Changbin Chen
- Department of Horticultural Science, University of Minnesota, St. Paul, MN 55108, USA
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19
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Paux E, Sourdille P, Salse J, Saintenac C, Choulet F, Leroy P, Korol A, Michalak M, Kianian S, Spielmeyer W, Lagudah E, Somers D, Kilian A, Alaux M, Vautrin S, Bergès H, Eversole K, Appels R, Safar J, Simkova H, Dolezel J, Bernard M, Feuillet C. A physical map of the 1-gigabase bread wheat chromosome 3B. Science 2008; 322:101-4. [PMID: 18832645 DOI: 10.1126/science.1161847] [Citation(s) in RCA: 322] [Impact Index Per Article: 20.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
As the staple food for 35% of the world's population, wheat is one of the most important crop species. To date, sequence-based tools to accelerate wheat improvement are lacking. As part of the international effort to sequence the 17-billion-base-pair hexaploid bread wheat genome (2n = 6x = 42 chromosomes), we constructed a bacterial artificial chromosome (BAC)-based integrated physical map of the largest chromosome, 3B, that alone is 995 megabases. A chromosome-specific BAC library was used to assemble 82% of the chromosome into 1036 contigs that were anchored with 1443 molecular markers, providing a major resource for genetic and genomic studies. This physical map establishes a template for the remaining wheat chromosomes and demonstrates the feasibility of constructing physical maps in large, complex, polyploid genomes with a chromosome-based approach.
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Affiliation(s)
- Etienne Paux
- Institut National de la Recherche Agronomique, Université Blaise Pascal (INRA-UBP), UMR 1095, Genetics Diversity and Ecophysiology of Cereals, Clermont-Ferrand, France
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Friesen TL, Ali S, Kianian S, Francl LJ, Rasmussen JB. Role of Host Sensitivity to Ptr ToxA in Development of Tan Spot of Wheat. Phytopathology 2003; 93:397-401. [PMID: 18944353 DOI: 10.1094/phyto.2003.93.4.397] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
ABSTRACT Pyrenophora tritici-repentis race 2 produces Ptr ToxA, a host-selective toxin previously described as a pathogenicity factor for tan spot on wheat. The objective of this research was to evaluate the role of host sensitivity to toxin, conditioned by a single dominant gene on chromosome 5BL, in the disease development by race 2. An F(2)-derived F(6) recombinant inbred population of 108 wheat lines, produced from crosses of toxin-sensitive, disease-susceptible cv. Kulm with the toxin-insensitive, disease-resistant cv. Erik segregated 1:1 for toxin reaction. However, the population was skewed toward resistance to race 2 of the fungus. Toxin reaction accounted for 24.4% of the genetic variance for disease. Heritability estimates suggested the presence of four to five genes that influence disease reaction in the population. Toxin-insensitive mutants, previously derived Kulm, were susceptible to race 2, although disease developed more slowly on the mutants than it did on the wild-type Kulm. The data indicate that sensitivity to Ptr ToxA influences disease severity in some host genotypes without defining susceptibility.
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21
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Grant LA, Vignaux N, Doehlert DC, McMullen MS, Elias EM, Kianian S. Starch Characteristics of Waxy and Nonwaxy Tetraploid (Triticum turgidum L. var. durum) Wheats. Cereal Chem 2001. [DOI: 10.1094/cchem.2001.78.5.590] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- L. A. Grant
- USDA-ARS Hard Red Spring and Durum Wheat Quality Laboratory, North Dakota State University, Fargo, ND 58105. Names are necessary to report factually on available data; however, the USDA neither guarantees nor warrants the standard of the product, and the use of the name by the USDA implies no approval of the product to the exclusion of others that may also be suitable
- Corresponding author. Fax: 701-239-1377. E-mail:
| | - N. Vignaux
- Department of Plant Science, North Dakota State University, Fargo, ND 58105
| | - D. C. Doehlert
- USDA-ARS Hard Red Spring and Durum Wheat Quality Laboratory, North Dakota State University, Fargo, ND 58105. Names are necessary to report factually on available data; however, the USDA neither guarantees nor warrants the standard of the product, and the use of the name by the USDA implies no approval of the product to the exclusion of others that may also be suitable
| | - M. S. McMullen
- Department of Plant Science, North Dakota State University, Fargo, ND 58105
| | - E. M. Elias
- Department of Plant Science, North Dakota State University, Fargo, ND 58105
| | - S. Kianian
- Department of Plant Science, North Dakota State University, Fargo, ND 58105
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