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Klindworth DL, Salsman E, Underdahl J, Elias EM, Green AJ, Dykes L, Faris JD, Xu SS. Linkage drag analysis in three Aegilops speltoides introgressions carrying Sr47 in modern durum and hard red spring wheat germplasm. Theor Appl Genet 2023; 136:168. [PMID: 37410182 DOI: 10.1007/s00122-023-04409-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Accepted: 06/22/2023] [Indexed: 07/07/2023]
Abstract
KEY MESSAGE Yield and quality tests of wheat lines derived from RWG35 show they carry little, or no linkage drag and are the preferred source of Sr47 for stem rust resistance. Three durum wheat (Triticum turgidum L. subsp. durum) lines, RWG35, RWG36, and RWG37 carrying slightly different Aegilops speltoides introgressions, but each carrying the Sr47 stem rust resistance gene, were backcrossed to three durum and three hard red spring (HRS) wheat (Triticum aestivum L.) cultivars to produce 18 backcross populations. Each population was backcrossed to the recurrent parent six times and prepared for yield trials to test for linkage drag. Lines carrying the introgression (S-lines) were compared to euploid sibling lines (W-lines) and their parent. Yield trials were conducted from 2018 to 2021 at three locations. Three agronomic and several quality traits were studied. In durum, lines derived from RWG35 had little or no linkage drag. Lines derived from RWG36 and RWG37 still retained linkage drag, most notably involving yield and thousand kernel weight, but also test weight, falling number, kernel hardness index, semolina extract, semolina protein content, semolina brightness, and peak height. In HRS wheat, the results were more complex, though the general result of RWG35 lines having little or no linkage drag and RWG36 and RWG37 lines retaining linkage drag still applied. But there was heterogeneity in the Glenn35S lines, and Linkert lines had problems combining with the Ae. speltoides introgressions. We concluded that introgressions derived from RWG35 either had eliminated linkage drag or any negative effects were minor in nature. We recommend that breeders who wish to incorporate Sr47 into their cultivars should work exclusively with germplasm derived from RWG35.
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Affiliation(s)
- Daryl L Klindworth
- USDA-ARS, Cereal Crops Research Unit, Edward T. Schafer Agricultural Research Centre, 1616 Albrecht Blvd, Fargo, ND, 58102-2765, USA
| | - Evan Salsman
- Department of Plant Sciences, North Dakota State University, Dep. 7670, P.O. Box 6050, Fargo, ND, 58108, USA
| | - Jesse Underdahl
- Department of Plant Sciences, North Dakota State University, Dep. 7670, P.O. Box 6050, Fargo, ND, 58108, USA
| | - Elias M Elias
- Department of Plant Sciences, North Dakota State University, Dep. 7670, P.O. Box 6050, Fargo, ND, 58108, USA
| | - Andrew J Green
- Department of Plant Sciences, North Dakota State University, Dep. 7670, P.O. Box 6050, Fargo, ND, 58108, USA
| | - Linda Dykes
- USDA-ARS, Cereal Crops Research Unit, Edward T. Schafer Agricultural Research Centre, 1616 Albrecht Blvd, Fargo, ND, 58102-2765, USA
| | - Justin D Faris
- USDA-ARS, Cereal Crops Research Unit, Edward T. Schafer Agricultural Research Centre, 1616 Albrecht Blvd, Fargo, ND, 58102-2765, USA
| | - Steven S Xu
- USDA-ARS, Crop Improvement and Genetics Research Unit, Western Regional Research Center, 800 Buchanan Street, Albany, CA, 94710, USA.
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Aoun M, Chen X, Somo M, Xu SS, Li X, Elias EM. Novel stripe rust all-stage resistance loci identified in a worldwide collection of durum wheat using genome-wide association mapping. Plant Genome 2021; 14:e20136. [PMID: 34609797 DOI: 10.1002/tpg2.20136] [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] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 06/24/2021] [Indexed: 06/13/2023]
Abstract
Durumwheat [Triticum turgidum L. ssp. durum (Desf.)] production is constrained by fungal diseases including stripe rust caused by Puccinia striiformis Westend. f. sp. tritici Erikss. (Pst). Continuous mining of germplasm for the discovery and deployment of stripe rust resistance (Yr) genes is needed to counter the impact of this disease. In this study, we evaluated a worldwide collection of 432 durum wheat accessions to seven U.S. Pst races that carry diverse virulence and avirulence combinations on wheat Yr genes. We found that 47-82% of the durum wheat accessions were susceptible to each of the tested Pst races. A total of 32 accessions were resistant to all seven races. Genome-wide association studies (GWAS) using over 97,000 single-nucleotide polymorphism markers generated from genotyping-by-sequencing of 364 accessions identified 56 quantitative trait loci (QTL) associated with all-stage stripe rust resistance located on all 14 durum wheat chromosomes. Six of these QTL were associated with resistance to 2-4 Pst races, and none were associated with resistance to all seven races. The remaining 50 QTL were race specific. Eighteen of the 56 identified QTL had relatively large effects against at least one of the races. A map-based comparison of the discovered QTL in this study with previously published Yr genes and QTL showed that 29 were previously identified, whereas the remaining 27 QTL appeared to be novel. This study reports effective sources of stripe rust resistance to contemporary races in the United States and shows that this durum wheat collection is abundant in novel resistance loci that can be transferred into adapted durum cultivars.
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Affiliation(s)
- Meriem Aoun
- Dep. of Plant Sciences, North Dakota State Univ., Fargo, ND, USA
| | - Xianming Chen
- Wheat Health, Genetics, and Quality Research Unit, USDA-ARS, Pullman, WA, USA
| | - Mohamed Somo
- Dep. of Plant Breeding and Genetics, Cornell Univ., Ithaca, NY, USA
| | - Steven S Xu
- USDA-ARS, Cereal Crops Research Unit, Fargo, ND, USA
| | - Xuehui Li
- Dep. of Plant Sciences, North Dakota State Univ., Fargo, ND, USA
| | - Elias M Elias
- Dep. of Plant Sciences, North Dakota State Univ., Fargo, ND, USA
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Cabas‐Lühmann PA, Manthey FA, Elias EM. Variations of colour, polyphenol oxidase and peroxidase activities during the production of low temperature dried pasta in various durum wheat genotypes. Int J Food Sci Technol 2021. [DOI: 10.1111/ijfs.15120] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
| | - Frank A. Manthey
- North Dakota State University Department 7670PO Box 6050 Fargo North Dakota 58108‐6050 USA
| | - Elias M. Elias
- North Dakota State University Department 7670PO Box 6050 Fargo North Dakota 58108‐6050 USA
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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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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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Gill BK, Klindworth DL, Rouse MN, Zhang J, Zhang Q, Sharma JS, Chu C, Long Y, Chao S, Olivera PD, Friesen TL, Zhong S, Jin Y, Faris JD, Fiedler JD, Elias EM, Liu S, Cai X, Xu SS. Function and evolution of allelic variations of Sr13 conferring resistance to stem rust in tetraploid wheat (Triticum turgidum L.). Plant J 2021; 106:1674-1691. [PMID: 33825238 PMCID: PMC8362117 DOI: 10.1111/tpj.15263] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 03/18/2021] [Indexed: 05/26/2023]
Abstract
The resistance gene Sr13 is one of the most important genes in durum wheat for controlling stem rust caused by Puccinia graminis f. sp. tritici (Pgt). The Sr13 functional gene CNL13 has haplotypes R1, R2 and R3. The R1/R3 and R2 haplotypes were originally designated as alleles Sr13a and Sr13b, respectively. To detect additional Sr13 alleles, we developed Kompetitive allele specific PCR (KASP™) marker KASPSr13 and four semi-thermal asymmetric reverse PCR markers, rwgsnp37-rwgsnp40, based on the CNL13 sequence. These markers were shown to detect R1, R2 and R3 haplotypes in a panel of diverse tetraploid wheat accessions. We also observed the presence of Sr13 in durum line CAT-A1, although it lacked any of the known haplotypes. Sequence analysis revealed that CNL13 of CAT-A1 differed from the susceptible haplotype S1 by a single nucleotide (C2200T) in the leucine-rich repeat region and differed from the other three R haplotypes by one or two additional nucleotides, confirming that CAT-A1 carries a new (R4) haplotype. Stem rust tests on the monogenic, transgenic and mutant lines showed that R1 differed from R3 in its susceptibility to races TCMJC and THTSC, whereas R4 differed from all other haplotypes for susceptibility to TTKSK, TPPKC and TCCJC. Based on these differences, we designate the R1, R3 and R4 haplotypes as alleles Sr13a, Sr13c and Sr13d, respectively. This study indicates that Sr13d may be the primitive functional allele originating from the S1 haplotype via a point mutation, with the other three R alleles probably being derived from Sr13d through one or two additional point mutations.
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Affiliation(s)
- Baljeet K. Gill
- Department of Plant SciencesNorth Dakota State UniversityFargoND58108USA
| | - Daryl L. Klindworth
- USDA‐ARSCereal Crops Research UnitEdward T. Schafer Agricultural Research CenterFargoND58102USA
| | | | - Jinglun Zhang
- Department of Plant SciencesNorth Dakota State UniversityFargoND58108USA
| | - Qijun Zhang
- Department of Plant SciencesNorth Dakota State UniversityFargoND58108USA
| | - Jyoti S. Sharma
- Department of Plant SciencesNorth Dakota State UniversityFargoND58108USA
| | | | - Yunming Long
- Department of Plant SciencesNorth Dakota State UniversityFargoND58108USA
| | - Shiaoman Chao
- USDA‐ARSCereal Crops Research UnitEdward T. Schafer Agricultural Research CenterFargoND58102USA
| | - Pablo D. Olivera
- Department of Plant PathologyUniversity of MinnesotaSt PaulMN55108USA
| | - Timothy L. Friesen
- USDA‐ARSCereal Crops Research UnitEdward T. Schafer Agricultural Research CenterFargoND58102USA
| | - Shaobin Zhong
- Department of Plant PathologyNorth Dakota State UniversityFargoND58108USA
| | - Yue Jin
- USDA‐ARSCereal Disease LaboratorySt PaulMN55108USA
| | - Justin D. Faris
- USDA‐ARSCereal Crops Research UnitEdward T. Schafer Agricultural Research CenterFargoND58102USA
| | - Jason D. Fiedler
- USDA‐ARSCereal Crops Research UnitEdward T. Schafer Agricultural Research CenterFargoND58102USA
| | - Elias M. Elias
- Department of Plant SciencesNorth Dakota State UniversityFargoND58108USA
| | - Shuyu Liu
- Texas A&M AgriLife ResearchAmarilloTX79106USA
| | - Xiwen Cai
- Department of Plant SciencesNorth Dakota State UniversityFargoND58108USA
| | - Steven S. Xu
- USDA‐ARSCereal Crops Research UnitEdward T. Schafer Agricultural Research CenterFargoND58102USA
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Aoun M, Rouse MN, Kolmer JA, Kumar A, Elias EM. Genome-Wide Association Studies Reveal All-Stage Rust Resistance Loci in Elite Durum Wheat Genotypes. Front Plant Sci 2021; 12:640739. [PMID: 33912208 PMCID: PMC8072158 DOI: 10.3389/fpls.2021.640739] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Accepted: 03/17/2021] [Indexed: 05/11/2023]
Abstract
Leaf rust, caused by Puccinia triticina (Pt), stripe rust caused by Puccinia striiformis f. sp. tritici (Pst), and stem rust caused by Puccinia graminis f. sp. tritici (Pgt) are major diseases to wheat production globally. Host resistance is the most suitable approach to manage these fungal pathogens. We investigated the phenotypic and genotypic structure of resistance to leaf rust, stem rust, and stripe rust pathogen races at the seedling stage in a collection of advanced durum wheat breeding lines and cultivars adapted to Upper Mid-West region of the United States. Phenotypic evaluation showed that the majority of the durum wheat genotypes were susceptible to Pt isolates adapted to durum wheat, whereas all the genotypes were resistant to common wheat type-Pt isolate. The majority of genotypes were resistant to stripe rust and stem rust pathogen races. The durum panel genotyped using Illumina iSelect 90 K wheat SNP assay was used for genome-wide association mapping (GWAS). The GWAS revealed 64 marker-trait associations (MTAs) representing six leaf rust resistance loci located on chromosome arms 2AS, 2AL, 5BS, 6AL, and 6BL. Two of these loci were identified at the positions of Lr52 and Lr64 genes, whereas the remaining loci are most likely novel. A total of 46 MTAs corresponding to four loci located on chromosome arms 1BS, 5BL, and 7BL were associated with stripe rust response. None of these loci correspond to designated stripe rust resistance genes. For stem rust, a total of 260 MTAs, representing 22 loci were identified on chromosome arms 1BL, 2BL, 3AL, 3BL, 4AL, 5AL, 5BL, 6AS, 6AL, 6BL, and 7BL. Four of these loci were located at the positions of known genes/alleles (Sr7b, Sr8155B1, Sr13a, and Sr13b). The discovery of known and novel rust resistance genes and their linked SNPs will help diversify rust resistance in durum wheat.
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Affiliation(s)
- Meriem Aoun
- Department of Plant Sciences, North Dakota State University, Fargo, ND, United States
- *Correspondence: Meriem Aoun,
| | - Matthew N. Rouse
- Cereal Disease Laboratory, United States Department of Agriculture–Agricultural Research Service, St. Paul, MN, United States
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, United States
| | - James A. Kolmer
- Cereal Disease Laboratory, United States Department of Agriculture–Agricultural Research Service, St. Paul, MN, United States
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, United States
| | - Ajay Kumar
- Department of Plant Sciences, North Dakota State University, Fargo, ND, United States
| | - Elias M. Elias
- Department of Plant Sciences, North Dakota State University, Fargo, ND, United States
- Elias M. Elias,
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Ashtari Mahini R, Kumar A, Elias EM, Fiedler JD, Porter LD, McPhee KE. Analysis and Identification of QTL for Resistance to Sclerotinia sclerotiorum in Pea ( Pisum sativum L.). Front Genet 2020; 11:587968. [PMID: 33329732 PMCID: PMC7710873 DOI: 10.3389/fgene.2020.587968] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [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: 07/27/2020] [Accepted: 10/23/2020] [Indexed: 11/13/2022] Open
Abstract
White mold caused by Sclerotinia sclerotiorum is an important constraint to field pea (Pisum sativum L.) production worldwide. To transfer white mold resistance into an adapted background, and study the genetics of the disease, two recombinant inbred line (RIL) populations (PRIL17 and PRIL19) were developed by crossing two partially resistant plant introductions with two susceptible pea cultivars. PRIL17 (Lifter × PI240515), and PRIL19 (PI169603 × Medora) were evaluated for resistance to white mold by measuring lesion expansion inhibition (LEI) and nodal transmission inhibition (NTI) at 3, 7, and 14 days post inoculation (dpi) under controlled environmental conditions. Lesion expansion inhibition percentage (LEIP), survival rate (SR), and area under disease progress curves (AUDPC) were also calculated accordingly. Because of a positive correlation between LEI and NTI with height, short and long internode individuals of each population were analyzed separately to avoid any confounding effect of height to pathogen response. A total of 22 short genotypes demonstrated partial resistance based on at least two Porter's resistance criteria. Only two pea genotypes with partial resistance to white mold (PRIL19-18 and PRIL19-124) had both semi-leafless (afila) and short internode traits. Both the RIL populations were genotyped using genotyping by sequencing (GBS). For PRIL17 and PRIL19, genetic maps were constructed from a total of 1,967 and 1,196 single nucleotide polymorphism (SNP) and spanned over 1,494 cM and 1,415 cM representing seven and nine linkage groups, respectively. A consensus map constructed using data from both populations, had 1,486 unique SNPs over 2,461 cM belonging to seven linkage groups. Inclusive composite interval mapping (ICIM) identified thirteen quantitative trait loci (QTL) associated with white mold resistance traits in both populations. Three of them were co-located with height genes (a morphological trait that reduces infection risk and acts as disease avoidance) and the other ten QTL were associated with two forms of physiological resistance (seven for LEI and three for NTI) with LOD and r2 ranging from 3.0 to 28.5 and 5.1 to 64.3, respectively. The development of resistance lines, genetic dissection and identification of markers associated will help accelerate breeding efforts for white mold resistance using molecular breeding approaches.
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Affiliation(s)
- Rahil Ashtari Mahini
- Plant Science Department, North Dakota State University, Fargo, ND, United States
| | - Ajay Kumar
- Plant Science Department, North Dakota State University, Fargo, ND, United States
| | - Elias M. Elias
- Plant Science Department, North Dakota State University, Fargo, ND, United States
| | - Jason D. Fiedler
- USDA-ARS, Cereal Crops Research Unit, Edward T. Schafer Agricultural Research Center, Fargo, ND, United States
| | - Lyndon D. Porter
- USDA-ARS, Grain Legume Genetics and Physiology Research Unit, Prosser, WA, United States
| | - Kevin E. McPhee
- Plant Sciences and Plant Pathology Department, Montana State University, Bozeman, MT, United States
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Kumar J, Rai KM, Pirseyedi S, Elias EM, Xu S, Dill-Macky R, Kianian SF. Epigenetic regulation of gene expression improves Fusarium head blight resistance in durum wheat. Sci Rep 2020; 10:17610. [PMID: 33077800 PMCID: PMC7572394 DOI: 10.1038/s41598-020-73521-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 08/14/2020] [Indexed: 12/18/2022] Open
Abstract
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 (BC1:F3) and were tested for stability and inheritance of the resistance. About, one third of the BC1:F3 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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Affiliation(s)
- Jitendra Kumar
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, USA
| | - Krishan M Rai
- Department of Microbial and Plant Genetics, University of Minnesota, St. Paul, MN, USA
| | | | - Elias M Elias
- Department of Plant Sciences, North Dakota State University, Fargo, ND, USA
| | - Steven Xu
- USDA-ARS Cereal Crops Research Unit, Edward T. Schafer Agricultural Research Center, Fargo, ND, USA
| | - Ruth Dill-Macky
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, USA
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Liu Y, Ma Y, Salsman E, Manthey FA, Elias EM, Li X, Yan C. An enrichment method for mapping ambiguous reads to the reference genome for NGS analysis. J Bioinform Comput Biol 2020; 17:1940012. [PMID: 32019414 DOI: 10.1142/s0219720019400122] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Mapping short reads to a reference genome is an essential step in many next-generation sequencing (NGS) analyses. In plants with large genomes, a large fraction of the reads can align to multiple locations of the genome with equally good alignment scores. How to map these ambiguous reads to the genome is a challenging problem with big impacts on the downstream analysis. Traditionally, the default method is to assign an ambiguous read randomly to one of the many potential locations. In this study, we explore two alternative methods that are based on the hypothesis that the possibility of an ambiguous read being generated by a location is proportional to the total number of reads produced by that location: (1) the enrichment method that assigns an ambiguous read to the location that has produced the most reads among all the potential locations, (2) the probability method that assigns an ambiguous read to a location based on a probability proportional to the number of reads the location produces. We systematically compared the performance of the proposed methods with that of the default random method. Our results showed that the enrichment method produced better results than the default random method and the probability method in the discovery of single nucleotide polymorphisms (SNPs). Not only did it produce more SNP markers, but it also produced SNP markers with better quality, which was demonstrated using multiple mainstay genomic analyses, including genome-wide association studies (GWAS), minor allele distribution, population structure, and genomic prediction.
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Affiliation(s)
- Yuan Liu
- Department of Computer Science, North Dakota State University, Fargo, North Dakota 58102, USA
| | - Yongchao Ma
- Department of Computer Science, North Dakota State University, Fargo, North Dakota 58102, USA
| | - Evan Salsman
- Department of Plant Sciences, North Dakota State University, Fargo, North Dakota 58102, USA
| | - Frank A Manthey
- Department of Plant Sciences, North Dakota State University, Fargo, North Dakota 58102, USA
| | - Elias M Elias
- Department of Plant Sciences, North Dakota State University, Fargo, North Dakota 58102, USA
| | - Xuehui Li
- Department of Plant Sciences, North Dakota State University, Fargo, North Dakota 58102, USA
| | - Changhui Yan
- Department of Computer Science, North Dakota State University, Fargo, North Dakota 58102, USA
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Kumar A, Mantovani EE, Simsek S, Jain S, Elias EM, Mergoum M. Genome wide genetic dissection of wheat quality and yield related traits and their relationship with grain shape and size traits in an elite × non-adapted bread wheat cross. PLoS One 2019; 14:e0221826. [PMID: 31532783 PMCID: PMC6750600 DOI: 10.1371/journal.pone.0221826] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Accepted: 08/15/2019] [Indexed: 12/21/2022] Open
Abstract
The genetic gain in yield and quality are two major targets of wheat breeding programs around the world. In this study, a high density genetic map consisting of 10,172 SNP markers identified a total of 43 genomic regions associated with three quality traits, three yield traits and two agronomic traits in hard red spring wheat (HRSW). When compared with six grain shape and size traits, the quality traits showed mostly independent genetic control (~18% common loci), while the yield traits showed moderate association (~53% common loci). Association of genomic regions for grain area (GA) and thousand-grain weight (TGW), with yield suggests that targeting an increase in GA may help enhancing wheat yield through an increase in TGW. Flour extraction (FE), although has a weak positive phenotypic association with grain shape and size, they do not share any common genetic loci. A major contributor to plant height was the Rht8 locus and the reduced height allele was associated with significant increase in grains per spike (GPS) and FE, and decrease in number of spikes per square meter and test weight. Stable loci were identified for almost all the traits. However, we could not find any QTL in the region of major known genes like GPC-B1, Ha, Rht-1, and Ppd-1. Epistasis also played an important role in the genetics of majority of the traits. In addition to enhancing our knowledge about the association of wheat quality and yield with grain shape and size, this study provides novel loci, genetic information and pre-breeding material (combining positive alleles from both parents) to enhance the cultivated gene pool in wheat germplasm. These resources are valuable in facilitating molecular breeding for wheat quality and yield improvement.
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Affiliation(s)
- Ajay Kumar
- Department of Plant Sciences, North Dakota State University, Fargo, ND, United States of America
| | - Eder E. Mantovani
- Department of Plant Sciences, North Dakota State University, Fargo, ND, United States of America
| | - Senay Simsek
- Department of Plant Sciences, North Dakota State University, Fargo, ND, United States of America
| | - Shalu Jain
- Department of Plant Pathology, North Dakota State University, Fargo, ND, United States of America
| | - Elias M. Elias
- Department of Plant Sciences, North Dakota State University, Fargo, ND, United States of America
| | - Mohamed Mergoum
- Department of Plant Sciences, North Dakota State University, Fargo, ND, United States of America
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Johnson M, Kumar A, Oladzad-Abbasabadi A, Salsman E, Aoun M, Manthey FA, Elias EM. Association Mapping for 24 Traits Related to Protein Content, Gluten Strength, Color, Cooking, and Milling Quality Using Balanced and Unbalanced Data in Durum Wheat [ Triticum turgidum L. var. durum (Desf).]. Front Genet 2019; 10:717. [PMID: 31475032 PMCID: PMC6706462 DOI: 10.3389/fgene.2019.00717] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [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: 02/05/2019] [Accepted: 07/08/2019] [Indexed: 12/15/2022] Open
Abstract
Durum wheat [Triticum durum (Desf).] is mostly used to produce pasta, couscous, and bulgur. The quality of the grain and end-use products determine its market value. However, quality tests are highly resource intensive and almost impossible to conduct in the early generations in the breeding program. Modern genomics-based tools provide an excellent opportunity to genetically dissect complex quality traits to expedite cultivar development using molecular breeding approaches. This study used a panel of 243 cultivars and advanced breeding lines developed during the last 20 years to identify SNPs associated with 24 traits related to nutritional value and quality. Genome-wide association study (GWAS) identified a total of 179 marker-trait associations (MTAs), located in 95 genomic regions belonging to all 14 durum wheat chromosomes. Major and stable QTLs were identified for gluten strength on chromosomes 1A and 1B, and for PPO activity on chromosomes 1A, 2B, 3A, and 3B. As a large amount of unbalance phenotypic data are generated every year on advanced lines in all the breeding programs, the applicability of such a dataset for identification of MTAs remains unclear. We observed that ∼84% of the MTAs identified using a historic unbalanced dataset (belonging to a total of 80 environments collected over a period of 16 years) were also identified in a balanced dataset. This suggests the suitability of historic unbalanced phenotypic data to identify beneficial MTAs to facilitate local-knowledge-based breeding. In addition to providing extensive knowledge about the genetics of quality traits, association mapping identified several candidate markers to assist durum wheat quality improvement through molecular breeding. The molecular markers associated with important traits could be extremely useful in the development of improved quality durum wheat cultivars using marker-assisted selection (MAS).
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Affiliation(s)
| | | | | | | | | | | | - Elias M. Elias
- Department of Plant Sciences, North Dakota State University, Fargo, ND, United States
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13
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Malalgoda M, Ohm J, Manthey FA, Elias EM, Simsek S. Quality characteristics and protein composition of durum wheat cultivars released in the last 50 years. Cereal Chem 2019. [DOI: 10.1002/cche.10151] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Maneka Malalgoda
- Department of Plant Sciences North Dakota State University Fargo North Dakota
| | - Jae‐Bom Ohm
- Red River Valley Agricultural Research Center, Cereal Crops Research Unit, Spring and Durum Wheat Quality Laboratory USDA‐ARS, North Dakota State University Fargo North Dakota
| | - Frank A. Manthey
- Department of Plant Sciences North Dakota State University Fargo North Dakota
| | - Elias M. Elias
- Department of Plant Sciences North Dakota State University Fargo North Dakota
| | - Senay Simsek
- Department of Plant Sciences North Dakota State University Fargo North Dakota
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14
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Szabo-Hever A, Zhang Q, Friesen TL, Zhong S, Elias EM, Cai X, Jin Y, Faris JD, Chao S, Xu SS. Genetic Diversity and Resistance to Fusarium Head Blight in Synthetic Hexaploid Wheat Derived From Aegilops tauschii and Diverse Triticum turgidum Subspecies. Front Plant Sci 2018; 9:1829. [PMID: 30619402 PMCID: PMC6298526 DOI: 10.3389/fpls.2018.01829] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Accepted: 11/26/2018] [Indexed: 05/18/2023]
Abstract
Synthetic hexaploid wheat (SHW) can serve as a bridge for the transfer of useful genes from Aegilops tauschii and tetraploid wheat (Triticum turgidum) into common wheat (T. aestivum). The objective of this study was to evaluate 149 SHW lines and their 74 tetraploid parents for their genetic diversity, breeding values and inter-genomic interactions for resistance to Fusarium head blight (FHB). The genetic diversity analysis was performed based on the population structure established using 4,674 and 3,330 polymorphic SNP markers among the SHW lines and tetraploid parents, respectively. The results showed that all T. carthlicum and most T. dicoccum accessions formed different clusters and subpopulations, respectively, whereas all the T. durum, T. polonicum, T. turgidum, and T. turanicum accessions were clustered together, suggesting that T. durum was more closely related to T. polonicum, T. turgidum, and T. turanicum than to T. dicoccum. The genetic diversity of the SHW lines mainly reflected that of the tetraploid parents. The SHW lines and their tetraploid parents were evaluated for reactions to FHB in two greenhouse seasons and at two field nurseries for 2 years. As expected, most of the SHW lines were more resistant than their tetraploid parents in all environments. The FHB severities of the SHW lines varied greatly depending on the Ae. tauschii and tetraploid genotypes involved. Most of the SHW lines with a high level of FHB resistance were generally derived from the tetraploid accessions with a high level of FHB resistance. Among the 149 SHW lines, 140 were developed by using three Ae. tauschii accessions CIae 26, PI 268210, and RL 5286. These SHW lines showed FHB severities reduced by 21.7%, 17.3%, and 11.5%, respectively, with an average reduction of 18.3%, as compared to the tetraploid parents, suggesting that the D genome may play a major role in reducing disease severity in the SHW lines. Thirteen SHW lines consistently showed a high level of FHB resistance compared to the resistant check, Sumai 3, in each environment. These SHW lines will be useful for the development of FHB-resistant wheat germplasm and populations for discovery of novel FHB resistance genes.
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Affiliation(s)
- Agnes Szabo-Hever
- Cereal Crops Research Unit, Edward T. Schafer Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, Fargo, ND, United States
| | - Qijun Zhang
- Department of Plant Sciences, North Dakota State University, Fargo, ND, United States
| | - Timothy L. Friesen
- Cereal Crops Research Unit, Edward T. Schafer Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, Fargo, ND, United States
| | - Shaobin Zhong
- Department of Plant Pathology, North Dakota State University, Fargo, ND, United States
| | - Elias M. Elias
- Department of Plant Sciences, North Dakota State University, Fargo, ND, United States
| | - Xiwen Cai
- Department of Plant Sciences, North Dakota State University, Fargo, ND, United States
| | - Yue Jin
- Cereal Disease Laboratory, Agricultural Research Service, United States Department of Agriculture, St. Paul, MN, United States
| | - Justin D. Faris
- Cereal Crops Research Unit, Edward T. Schafer Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, Fargo, ND, United States
| | - Shiaoman Chao
- Cereal Crops Research Unit, Edward T. Schafer Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, Fargo, ND, United States
| | - Steven S. Xu
- Cereal Crops Research Unit, Edward T. Schafer Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, Fargo, ND, United States
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Aoun M, Kolmer JA, Rouse MN, Chao S, Bulbula WD, Elias EM, Acevedo M. Inheritance and Bulked Segregant Analysis of Leaf Rust and Stem Rust Resistance in Durum Wheat Genotypes. Phytopathology 2017; 107:1496-1506. [PMID: 28745102 PMCID: PMC7779972 DOI: 10.1094/phyto-12-16-0444-r] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 07/17/2017] [Indexed: 05/25/2023]
Abstract
Leaf rust, caused by Puccinia triticina, and stem rust, caused by P. graminis f. sp. tritici, are important diseases of durum wheat. This study determined the inheritance and genomic locations of leaf rust resistance (Lr) genes to P. triticina race BBBQJ and stem rust resistance (Sr) genes to P. graminis f. sp. tritici race TTKSK in durum accessions. Eight leaf-rust-resistant genotypes were used to develop biparental populations. Accessions PI 192051 and PI 534304 were also resistant to P. graminis f. sp. tritici race TTKSK. The resulting progenies were phenotyped for leaf rust and stem rust response at seedling stage. The Lr and Sr genes were mapped in five populations using single-nucleotide polymorphisms and bulked segregant analysis. Five leaf-rust-resistant genotypes carried single dominant Lr genes whereas, in the remaining accessions, there was deviation from the expected segregation ratio of a single dominant Lr gene. Seven genotypes carried Lr genes different from those previously characterized in durum. The single dominant Lr genes in PI 209274, PI 244061, PI387263, and PI 313096 were mapped to chromosome arms 6BS, 2BS, 6BL, and 6BS, respectively. The Sr gene in PI 534304 mapped to 6AL and is most likely Sr13, while the Sr gene in PI 192051 could be uncharacterized in durum.
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Fiedler JD, Salsman E, Liu Y, Michalak de Jiménez M, Hegstad JB, Chen B, Manthey FA, Chao S, Xu S, Elias EM, Li X. Genome-Wide Association and Prediction of Grain and Semolina Quality Traits in Durum Wheat Breeding Populations. Plant Genome 2017; 10. [PMID: 29293807 DOI: 10.3835/plantgenome2017.05.0038] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Grain yield and semolina quality traits are essential selection criteria in durum wheat breeding. However, high phenotypic screening costs limit selection to relatively few breeding lines in late generations. This selection paradigm confers relatively low selection efficiency due to the advancement of undesirable lines into expensive yield trials for grain yield and quality trait testing. Marker-aided selection can enhance selection efficiency, especially for traits that are difficult or costly to phenotype. The aim of this study was to identify major quality trait quantitative trait loci (QTL) for marker-assisted selection (MAS) and to explore potential application of genomic selection (GS) in a durum wheat breeding program. In this study, genome-wide association mapping was conducted for five quality traits using 1184 lines from the North Dakota State University (NDSU) durum wheat breeding program. Several QTL associated with test weight, semolina color, and gluten strength were identified. Genomic selection models were developed and forward prediction accuracies of 0.27 to 0.66 were obtained for the five quality traits. Our results show the potential for grain and semolina quality traits to be selected more efficiently through MAS and GS with further refinement. Considerable opportunity exists to extend these techniques to other traits such as grain yield and agronomic characteristics, further improving breeding efficiency in durum cultivar development.
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17
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Affiliation(s)
- Lingzhu Deng
- Cereal Science Graduate Program, Department of Plant Sciences, North Dakota State University, NDSU Department 7670, P.O. Box 6050, Fargo, ND, 58108-6050, U.S.A
| | - Elias M. Elias
- Department of Plant Sciences, North Dakota State University, NDSU Department 7670, P.O. Box 6050, Fargo, ND, 58108-6050, U.S.A
| | - Frank A. Manthey
- Cereal Science Graduate Program, Department of Plant Sciences, North Dakota State University, NDSU Department 7670, P.O. Box 6050, Fargo, ND, 58108-6050, U.S.A
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18
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Deng L, Elias EM, Manthey FA. Relationship Between Grain, Semolina, and Whole Wheat Flour Properties and the Physical and Cooking Qualities of Whole Wheat Spaghetti. Cereal Chem 2017. [DOI: 10.1094/cchem-03-17-0064-n] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [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)
- Lingzhu Deng
- Cereal Science Graduate Program, Department of Plant Sciences, North Dakota State University, NDSU Department 7670, P.O. Box 6050, Fargo, ND 58108-6050, U.S.A
| | - Elias M. Elias
- Department of Plant Sciences, North Dakota State University, NDSU Department 7670, P.O. Box 6050, Fargo, ND 58108-6050, U.S.A
| | - Frank A. Manthey
- Cereal Science Graduate Program, Department of Plant Sciences, North Dakota State University, NDSU Department 7670, P.O. Box 6050, Fargo, ND 58108-6050, U.S.A
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Salameh JA, Elias EM, Elias CM, Al Garnawee MY, Jabbour MN, Skaf GS. Malignant phyllodes tumor of the breast with spinal metastasis: case report and review of literature. Chirurgia (Bucur) 2017. [DOI: 10.23736/s0394-9508.17.04604-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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20
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Ohm JB, Manthey F, Elias EM. Variation and Correlation of Protein Molecular Weight Distribution and Semolina Quality Parameters for Durum Genotypes Grown in North Dakota. Cereal Chem 2017. [DOI: 10.1094/cchem-07-16-0189-r] [Citation(s) in RCA: 10] [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)
- Jae-Bom Ohm
- USDA-ARS, Red River Valley Agricultural Research Center, Cereal Crops Research Unit, Hard Spring and Durum Wheat Quality Lab., Fargo, ND 58108, U.S.A. Mention of trade names or commercial products in this publication is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the U.S. Department of Agriculture. USDA is an equal opportunity provider and employer
| | - Frank Manthey
- Department of Plant Sciences, North Dakota State University, Fargo, ND 58108, U.S.A
| | - Elias M. Elias
- Department of Plant Sciences, North Dakota State University, Fargo, ND 58108, U.S.A
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21
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Kumar A, Mantovani EE, Seetan R, Soltani A, Echeverry-Solarte M, Jain S, Simsek S, Doehlert D, Alamri MS, Elias EM, Kianian SF, Mergoum M. Dissection of Genetic Factors underlying Wheat Kernel Shape and Size in an Elite × Nonadapted Cross using a High Density SNP Linkage Map. Plant Genome 2016; 9. [PMID: 27898771 DOI: 10.3835/plantgenome2015.09.0081] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Wheat kernel shape and size has been under selection since early domestication. Kernel morphology is a major consideration in wheat breeding, as it impacts grain yield and quality. A population of 160 recombinant inbred lines (RIL), developed using an elite (ND 705) and a nonadapted genotype (PI 414566), was extensively phenotyped in replicated field trials and genotyped using Infinium iSelect 90K assay to gain insight into the genetic architecture of kernel shape and size. A high density genetic map consisting of 10,172 single nucleotide polymorphism (SNP) markers, with an average marker density of 0.39 cM/marker, identified a total of 29 genomic regions associated with six grain shape and size traits; ∼80% of these regions were associated with multiple traits. The analyses showed that kernel length (KL) and width (KW) are genetically independent, while a large number (∼59%) of the quantitative trait loci (QTL) for kernel shape traits were in common with genomic regions associated with kernel size traits. The most significant QTL was identified on chromosome 4B, and could be an ortholog of major rice grain size and shape gene or . Major and stable loci also were identified on the homeologous regions of Group 5 chromosomes, and in the regions of (6A) and (7A) genes. Both parental genotypes contributed equivalent positive QTL alleles, suggesting that the nonadapted germplasm has a great potential for enhancing the gene pool for grain shape and size. This study provides new knowledge on the genetic dissection of kernel morphology, with a much higher resolution, which may aid further improvement in wheat yield and quality using genomic tools.
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22
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Klindworth DL, Hareland GA, Elias EM, Ohm JB, Puhr D, Xu SS. Interactions of Genotype and Glutenin Subunit Composition on Breadmaking Quality of Durum 1AS•1AL-1DL Translocation Lines. Cereal Chem 2014. [DOI: 10.1094/cchem-08-13-0165-r] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [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)
- Daryl L. Klindworth
- USDA-ARS Cereal Crops Research Unit, Northern Crop Science Laboratory, Fargo, ND 58102. Mention of trade names or commercial products in this article is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the U.S. Department of Agriculture. USDA is an equal opportunity provider and employer
- Corresponding author. Phone: (701) 239-1342. Fax: (701) 239-1369. E-mail:
| | - Gary A. Hareland
- USDA-ARS Cereal Crops Research Unit, Northern Crop Science Laboratory, Fargo, ND 58102. Mention of trade names or commercial products in this article is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the U.S. Department of Agriculture. USDA is an equal opportunity provider and employer
| | - Elias M. Elias
- Department of Plant Sciences, North Dakota State University, Fargo, ND 58108
| | - Jae-Bom Ohm
- USDA-ARS Cereal Crops Research Unit, Northern Crop Science Laboratory, Fargo, ND 58102. Mention of trade names or commercial products in this article is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the U.S. Department of Agriculture. USDA is an equal opportunity provider and employer
| | - Dehdra Puhr
- USDA-ARS Cereal Crops Research Unit, Northern Crop Science Laboratory, Fargo, ND 58102. Mention of trade names or commercial products in this article is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the U.S. Department of Agriculture. USDA is an equal opportunity provider and employer
| | - Steven S. Xu
- USDA-ARS Cereal Crops Research Unit, Northern Crop Science Laboratory, Fargo, ND 58102. Mention of trade names or commercial products in this article is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the U.S. Department of Agriculture. USDA is an equal opportunity provider and employer
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Kumar A, Elias EM, Ghavami F, Xu X, Jain S, Manthey FA, Mergoum M, Alamri MS, Kianian PM, Kianian SF. A major QTL for gluten strength in durum wheat (Triticum turgidum L. var. durum). J Cereal Sci 2013. [DOI: 10.1016/j.jcs.2012.09.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Chu C, Niu Z, Zhong S, Chao S, Friesen TL, Halley S, Elias EM, Dong Y, Faris JD, Xu SS. Identification and molecular mapping of two QTLs with major effects for resistance to Fusarium head blight in wheat. Theor Appl Genet 2011; 123:1107-19. [PMID: 21833554 DOI: 10.1007/s00122-011-1652-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2011] [Accepted: 06/28/2011] [Indexed: 05/23/2023]
Abstract
Fusarium head blight (FHB) is a devastating disease of wheat worldwide. Novel sources of resistance are critical for improving FHB resistance levels in wheat. From a large-scale evaluation of germplasm for reactions to FHB, we identified one wheat accession (PI 277012) that consistently showed a high level of resistance in both greenhouse and field experiments. To characterize the FHB resistance in this accession, we developed a doubled haploid (DH) mapping population consisting of 130 lines from the cross between PI 277012 and the hard red spring wheat cultivar 'Grandin'. The DH population was then evaluated for reactions to FHB in three greenhouse seasons and five field environments. Based on a linkage map that consisted of 340 SSR markers spanning 2,703 cM of genetic distance, two major quantitative trait loci (QTLs) for FHB resistance were identified on chromosome arms 5AS and 5AL, with each explaining up to 20 and 32% of the variation in FHB severity, respectively. The two QTLs also showed major effects on reducing the percentage of Fusarium damaged kernels (FDK) and deoxynivalenol (DON) accumulation in seeds. FHB resistance has not previously been reported to be associated with this particular genomic region of chromosome arm 5AL, thus indicating the novelty of FHB resistance in PI 277012. Plant maturity was not associated with FHB resistance and the effects of plant height on FHB resistance were minor. Therefore, these results suggest that PI 277012 is an excellent source for improving FHB resistance in wheat. The markers identified in this research are being used for marker-assisted introgression of the QTLs into adapted durum and hard red spring wheat cultivars.
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Affiliation(s)
- Chenggen Chu
- Department of Plant Pathology, North Dakota State University, Fargo, ND 58108, USA
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Xu SS, Chu CG, Chao S, Klindworth DL, Faris JD, Elias EM. Marker-assisted characterization of durum wheat Langdon-Golden Ball disomic substitution lines. Theor Appl Genet 2010; 120:1575-1585. [PMID: 20140662 DOI: 10.1007/s00122-010-1277-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2009] [Accepted: 01/19/2010] [Indexed: 05/28/2023]
Abstract
The durum wheat cultivar 'Golden Ball' (GB) is a source of resistance to wheat sawfly due to its superior solid stem. In the late 1980s, Dr. Leonard Joppa developed a complete set of 14 'Langdon' (LDN)-GB disomic substitution (DS) lines by using GB as the chromosome donor and LDN as the recipient. However, these substitution lines have not been previously characterized and reported in the literature. The objectives of this study were to confirm the authenticity of the substituted chromosomes and to analyze the genetic background of the 14 LDN-GB DS lines with the aid of molecular markers, and to further use the substitution lines for chromosomal localization of DNA markers and genes conferring the superior stem solidness in GB. Results from simple sequence repeat marker analysis validated the authenticity of the substituted chromosomes in 14 LDN-GB DS lines. Genome-wide scans using the target region amplification polymorphism (TRAP) marker system produced a total of 359 polymorphic fragments that were used to compare the genetic background of substitution lines with that of LDN. Among the polymorphic TRAP markers, 134 (37.3%) and 185 (51.5%) were present in LDN and GB, respectively, with only 10 (2.8%) derived from Chinese Spring. Therefore, marker analysis demonstrated that each LDN-GB DS line had a pair of chromosomes from GB with a genetic background similar to that of LDN. Of the TRAP markers generated in this study, 200 were successfully assigned to specific chromosomes based on their presence or absence in the corresponding LDN-GB DS lines. Also, evaluation of stem solidness in the substitution lines verified the presence of a major gene for stem solidness in chromosome 3B. Results from this research provides useful information for the utilization of GB and LDN-GB DS lines for genetic and genomic studies in tetraploid wheat and for the improvement of stem solidness in both durum and bread wheat.
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Affiliation(s)
- Steven S Xu
- Northern Crop Science Laboratory, USDA-ARS, 1307 18th Street North, Fargo, ND 58105-5677, USA.
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Mergoum M, Singh PK, Ali S, Elias EM, Anderson JA, Glover KD, Adhikari TB. Reaction of Elite Wheat Genotypes from the Northern Great Plains of North America to Septoria Diseases. Plant Dis 2007; 91:1310-1315. [PMID: 30780524 DOI: 10.1094/pdis-91-10-1310] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Stagonospora nodorum blotch (SNB), caused by Phaeosphaeria nodorum, and Septoria tritici blotch (STB), caused by Mycosphaerella graminicola, are the main pathogens of the Septoria disease complex of wheat (Triticum aestivum) in North America. This study was conducted to determine the disease reaction of 126 elite hard red spring, white, and durum wheat cultivars and advanced breeding lines collected from the northern Great Plains of the United States and Canada to SNB and STB. Seedlings of the 126 wheat genotypes were evaluated for resistance to SNB and STB under controlled environmental conditions. Moreover, these 126 wheat genotypes also were infiltrated with culture filtrate of P. nodorum isolate Sn2000. Based on disease reactions, three cultivars (McNeal, Dapps, and Oklee) and 12 advanced breeding lines (CA-901-580W, 97SO254-8-1, MN03291, MN03308, WA007925, MT0245, ND756, ND801, ND803, ND808, ND809, and ND811) adapted to the northern Great Plains were found to be resistant to both Septoria diseases and insensitive to the culture filtrate. Additionally, eight genetically diverse lines and cultivars, including two tetraploid wheat genotypes, were identified to be resistant to both Septoria diseases. These results suggest that the wheat genotypes contain a broad genetic base for resistance to the Septoria diseases in the northern Great Plains of the United States and Canada, and the resistant sources identified in this study may be utilized in wheat-breeding programs.
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Affiliation(s)
| | | | - S Ali
- Department of Plant Pathology
| | - E M Elias
- Department of Plant Sciences, North Dakota State University, Fargo 58105
| | - J A Anderson
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul 55108
| | - K D Glover
- Plant Science Department, South Dakota State University, Brookings 57007
| | - T B Adhikari
- Department of Plant Pathology, North Dakota State University
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Singh PK, Mergoum M, Ali S, Adhikari TB, Elias EM, Anderson JA, Glover KD, Berzonsky WA. Evaluation of Elite Wheat Germ Plasm for Resistance to Tan Spot. Plant Dis 2006; 90:1320-1325. [PMID: 30780939 DOI: 10.1094/pd-90-1320] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Tan spot, caused by Pyrenophora tritici-repentis, is a serious foliar disease of wheat (Triticum aestivum) in North America. Control of tan spot through management practices and fungicide application is possible; however, the use of resistant varieties is the most effective and economical means of controlling tan spot. This study was conducted to determine the disease reaction of 126 elite hard red spring, white, and durum wheat varieties and advanced breeding lines collected from the northern Great Plains of the United States and Canada to individual races/toxins of P. tritici-repentis. Seedling evaluation of the 126 genotypes was done under controlled environmental conditions with virulent races 2, 3, and 5 of P. tritici-repentis and toxins Ptr ToxA and Ptr ToxB. Based on disease reactions, two resistant varieties and two advanced breeding lines adapted to the northern Great Plains were found to be resistant to all the races and insensitive to the toxins tested. Additionally, six genetically diverse lines/varieties were identified to be resistant to tan spot; however, these sources may not be well adapted to the northern Great Plains. These results suggest that the wheat germ plasm contains a broad genetic base for resistance to the most prevalent races of P. tritici-repentis in North America, and the resistant sources identified in this study may be utilized in wheat breeding programs to develop tan spot resistant varieties.
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Affiliation(s)
- P K Singh
- Department of Plant Sciences, 166-Loftsgard Hall, North Dakota State University, Fargo 58105
| | - M Mergoum
- Department of Plant Sciences, 166-Loftsgard Hall, North Dakota State University, Fargo 58105
| | - S Ali
- Department of Plant Pathology, 306-Walster Hall, North Dakota State University, Fargo 58105
| | - T B Adhikari
- Department of Plant Pathology, 306-Walster Hall, North Dakota State University, Fargo 58105
| | - E M Elias
- Department of Plant Sciences, 166-Loftsgard Hall, North Dakota State University, Fargo 58105
| | - J A Anderson
- Department of Agronomy and Plant Genetics, 411-Borlaug Hall, 1991 Upper Buford Circle, University of Minnesota, St. Paul 55108
| | - K D Glover
- Plant Science Department, NPB 247 Box 2140-C, South Dakota State University, Brookings 57007
| | - W A Berzonsky
- Department of Plant Sciences, 166-Loftsgard Hall, North Dakota State University, Fargo 58105
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Singh PK, Gonzalez-Hernandez JL, Mergoum M, Ali S, Adhikari TB, Kianian SF, Elias EM, Hughes GR. Identification and Molecular Mapping of a Gene Conferring Resistance to Pyrenophora tritici-repentis Race 3 in Tetraploid Wheat. Phytopathology 2006; 96:885-9. [PMID: 18943754 DOI: 10.1094/phyto-96-0885] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
ABSTRACT Race 3 of the fungus Pyrenophora tritici-repentis, causal agent of tan spot, induces differential symptoms in tetraploid and hexaploid wheat, causing necrosis and chlorosis, respectively. This study was conducted to examine the genetic control of resistance to necrosis induced by P. tritici-repentis race 3 and to map resistance genes identified in tetraploid wheat (Triticum turgidum). A mapping population of recombinant inbred lines (RILs) was developed from a cross between the resistant genotype T. tur-gidum no. 283 (PI 352519) and the susceptible durum cv. Coulter. Based on the reactions of the Langdon-T. dicoccoides (LDN[DIC]) disomic substitution lines, chromosomal location of the resistance genes was determined and further molecular mapping of the resistance genes for race 3 was conducted in 80 RILs of the cross T. turgidum no. 283/Coulter. Plants were inoculated at the two-leaf stage and disease reaction was assessed 8 days after inoculation based on lesion type. Disease reaction of the LDN(DIC) lines and molecular mapping on the T. turgidum no. 283/Coulter population indicated that the gene, designated tsn2, conditioning resistance to race 3 is located on the long arm of chromosome 3B. Genetic analysis of the F(2) generation and of the F(4:5) and F(6:7) families indicated that a single recessive gene controlled resistance to necrosis induced by race 3 in the cross studied.
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Affiliation(s)
- Nathalie Vignaux
- Department of Plant Sciences, North Dakota State University, Fargo, ND 58105
| | - Douglas C. Doehlert
- USDA-ARS, Wheat Quality Lab, Harris Hall, North Dakota State University, Fargo, ND, 58105. Mention of firm names or trade product does not imply that they are endorsed or recommended by the U.S. Department of Agriculture over other firms or similar products not mentioned
- Corresponding author. Phone: 701-231-8069. E-mail:
| | - Elias M. Elias
- Department of Plant Sciences, North Dakota State University, Fargo, ND 58105
| | - Michael S. McMullen
- Department of Plant Sciences, North Dakota State University, Fargo, ND 58105
| | - Linda A. Grant
- USDA-ARS, Wheat Quality Lab, Harris Hall, North Dakota State University, Fargo, ND, 58105. Mention of firm names or trade product does not imply that they are endorsed or recommended by the U.S. Department of Agriculture over other firms or similar products not mentioned
| | - Shahryar F. Kianian
- Department of Plant Sciences, North Dakota State University, Fargo, ND 58105
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Vignaux N, Doehlert DC, Hegstad J, Elias EM, McMullen MS, Grant LA, Kianian SF. Grain Quality Characteristics and Milling Performance of Full and Partial Waxy Durum Lines. Cereal Chem 2004. [DOI: 10.1094/cchem.2004.81.3.377] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [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)
- Nathalie Vignaux
- Department of Plant Sciences, North Dakota State University, Fargo, ND 58105
| | - Douglas C. Doehlert
- USDA-ARS, Wheat Quality Lab. Harris Hall, 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. Phone: 701-231-8069. E-mail:
| | - Justin Hegstad
- Department of Plant Sciences, North Dakota State University, Fargo, ND 58105
| | - Elias M. Elias
- Department of Plant Sciences, North Dakota State University, Fargo, ND 58105
| | - Michael S. McMullen
- Department of Plant Sciences, North Dakota State University, Fargo, ND 58105
| | - Linda A. Grant
- USDA-ARS, Wheat Quality Lab. Harris Hall, 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
| | - Shahryar F. Kianian
- Department of Plant Sciences, North Dakota State University, Fargo, ND 58105
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Abstract
The devastating effect of Fusarium head blight (FHB) caused by Fusarium graminearum has led to significant financial losses across the Upper Midwest of the USA. These losses have spurred the need for research in biological, chemical, and genetic control methods for this disease. To date, most of the research on FHB resistance has concentrated on hexaploid wheat (Triticum aestivum L.) lines originating from China. Other sources of resistance to FHB would be desirable. One other source of resistance for both hexaploid wheat and tetraploid durum wheat (T. turgidum L. var. durum) is the wild tetraploid, T. turgidum L. var. dicoccoides (T. dicoccoides). Previous analysis of the 'Langdon'-T. dicoccoides chromosome substitution lines, LDN(Dic), indicated that the chromosome 3A substitution line expresses moderate levels of resistance to FHB. LDN(Dic-3A) recombinant inbred chromosome lines (RICL) were used to generate a linkage map of chromosome 3A with 19 molecular markers spanning a distance of 155.2 cM. The individual RICL and controls were screened for their FHB phenotype in two greenhouse seasons. Analysis of 83 RICL identified a single major quantitative trait locus, Qfhs.ndsu-3AS, that explains 37% of the phenotypic or 55% of the genetic variation for FHB resistance. A microsatellite locus, Xgwm2, is tightly linked to the highest point of the QTL peak. A region of the LDN (Dic-3A) chromosome associated with the QTL for FHB resistance encompasses a 29.3 cM region from Xmwg14 to Xbcd828.
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Affiliation(s)
- C D Otto
- Department of Plant Sciences, North Dakota State University, Fargo 58105, USA.
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