1
|
Yu Z, Yunusbaev U, Fritz A, Tilley M, Akhunova A, Trick H, Akhunov E. CRISPR-based editing of the ω- and γ-gliadin gene clusters reduces wheat immunoreactivity without affecting grain protein quality. Plant Biotechnol J 2024; 22:892-903. [PMID: 37975410 PMCID: PMC10955484 DOI: 10.1111/pbi.14231] [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] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Revised: 10/17/2023] [Accepted: 10/30/2023] [Indexed: 11/19/2023]
Abstract
Wheat immunotoxicity is associated with abnormal reaction to gluten-derived peptides. Attempts to reduce immunotoxicity using breeding and biotechnology often affect dough quality. Here, the multiplexed CRISPR-Cas9 editing of cultivar Fielder was used to modify gluten-encoding genes, specifically focusing on ω- and γ-gliadin gene copies, which were identified to be abundant in immunoreactive peptides based on the analysis of wheat genomes assembled using the long-read sequencing technologies. The whole-genome sequencing of an edited line showed mutation or deletion of nearly all ω-gliadin and half of the γ-gliadin gene copies and confirmed the lack of editing in the α/β-gliadin genes. The estimated 75% and 64% reduction in ω- and γ-gliadin content, respectively, had no negative impact on the end-use quality characteristics of grain protein and dough. A 47-fold immunoreactivity reduction compared to a non-edited line was demonstrated using antibodies against immunotoxic peptides. Our results indicate that the targeted CRISPR-based modification of the ω- and γ-gliadin gene copies determined to be abundant in immunoreactive peptides by analysing high-quality genome assemblies is an effective mean for reducing immunotoxicity of wheat cultivars while minimizing the impact of editing on protein quality.
Collapse
Affiliation(s)
- Zitong Yu
- Wheat Genetic Resources CenterKansas State UniversityManhattanKSUSA
- Department of Plant PathologyKansas State UniversityManhattanKSUSA
| | - Ural Yunusbaev
- Wheat Genetic Resources CenterKansas State UniversityManhattanKSUSA
- Department of Plant PathologyKansas State UniversityManhattanKSUSA
| | - Allan Fritz
- Department of AgronomyKansas State UniversityManhattanKSUSA
| | - Michael Tilley
- USDA‐ARSGrain Quality and Structure Research UnitManhattanKSUSA
| | - Alina Akhunova
- Department of Plant PathologyKansas State UniversityManhattanKSUSA
- Integrated Genomic FacilityKansas State UniversityManhattanKSUSA
| | - Harold Trick
- Department of Plant PathologyKansas State UniversityManhattanKSUSA
| | - Eduard Akhunov
- Wheat Genetic Resources CenterKansas State UniversityManhattanKSUSA
- Department of Plant PathologyKansas State UniversityManhattanKSUSA
| |
Collapse
|
2
|
Coombes B, Lux T, Akhunov E, Hall A. Introgressions lead to reference bias in wheat RNA-seq analysis. BMC Biol 2024; 22:56. [PMID: 38454464 PMCID: PMC10921782 DOI: 10.1186/s12915-024-01853-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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 02/21/2024] [Indexed: 03/09/2024] Open
Abstract
BACKGROUND RNA-seq is a fundamental technique in genomics, yet reference bias, where transcripts derived from non-reference alleles are quantified less accurately, can undermine the accuracy of RNA-seq quantification and thus the conclusions made downstream. Reference bias in RNA-seq analysis has yet to be explored in complex polyploid genomes despite evidence that they are often a complex mosaic of wild relative introgressions, which introduce blocks of highly divergent genes. RESULTS Here we use hexaploid wheat as a model complex polyploid, using both simulated and experimental data to show that RNA-seq alignment in wheat suffers from widespread reference bias which is largely driven by divergent introgressed genes. This leads to underestimation of gene expression and incorrect assessment of homoeologue expression balance. By incorporating gene models from ten wheat genome assemblies into a pantranscriptome reference, we present a novel method to reduce reference bias, which can be readily scaled to capture more variation as new genome and transcriptome data becomes available. CONCLUSIONS This study shows that the presence of introgressions can lead to reference bias in wheat RNA-seq analysis. Caution should be exercised by researchers using non-sample reference genomes for RNA-seq alignment and novel methods, such as the one presented here, should be considered.
Collapse
Affiliation(s)
| | - Thomas Lux
- Plant Genome and Systems Biology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Eduard Akhunov
- Department of Plant Pathology, Kansas State University, Manhattan, KS, USA
| | - Anthony Hall
- Earlham Institute, Norwich, Norfolk, NR4 7UZ, UK.
| |
Collapse
|
3
|
Peirce ES, Evers B, Winn ZJ, Raupp WJ, Guttieri M, Fritz AK, Poland J, Akhunov E, Haley S, Mason E, Nachappa P. Identifying novel sources of resistance to wheat stem sawfly in five wild wheat species. Pest Manag Sci 2024. [PMID: 38318926 DOI: 10.1002/ps.8008] [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] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 01/12/2024] [Accepted: 01/30/2024] [Indexed: 02/07/2024]
Abstract
BACKGROUND The wheat stem sawfly (WSS, Cephus cinctus) is a major pest of wheat (Triticum aestivum) and can cause significant yield losses. WSS damage results from stem boring and/or cutting, leading to the lodging of wheat plants. While solid-stem wheat genotypes can effectively reduce larval survival, they may have lower yields than hollow-stem genotypes and show inconsistent solidness expression. Due to limited resistance sources to WSS, evaluating diverse wheat germplasm for novel resistance genes is crucial. We evaluated 91 accessions across five wild wheat species (Triticum monococcum, T. urartu, T. turgidum, T. timopheevii, and Aegilops tauschii) and common wheat cultivars (T. aestivum) for antixenosis (host selection) and antibiosis (host suitability) to WSS. Host selection was measured as the number of eggs after adult oviposition, and host suitability was determined by examining the presence or absence of larval infestation within the stem. The plants were grown in the greenhouse and brought to the field for WSS infestation. In addition, a phylogenetic analysis was performed to determine the relationship between the WSS traits and phylogenetic clustering. RESULTS Overall, Ae. tauschii, T. turgidum, and T. urartu had lower egg counts and larval infestation than T. monococcum, and T. timopheevii. T. monococcum, T. timopheevii, T. turgidum, and T. urartu had lower larval weights compared to T. aestivum. CONCLUSION This study shows that wild relatives of wheat could be a valuable source of alleles for enhancing resistance to WSS and identifies specific germplasm resources that may be useful for breeding.
Collapse
Affiliation(s)
- Erika S Peirce
- Rangeland Resources and Systems Research Unit, USDA-ARS, Fort Collins, Colorado, USA
- Department of Agricultural Biology, Colorado State University, 307 University Ave, Fort Collins, Colorado, USA
| | | | - Zachary J Winn
- Department of Soil and Crop Sciences, Colorado State University, 307 University Ave, Fort Collins, Colorado, USA
| | - W John Raupp
- Wheat Genetics Resource Center and Department of Plant Pathology, Throckmorton Hall, Kansas Wheat Innovation Center, 1990 Kimball Ave, Manhattan, Kansas, USA
| | - Mary Guttieri
- USDA Agricultural Research Service, Center for Grain and Animal Health Research, Hard Winter Wheat Genetics Research Unit, 4008 Throckmorton Hall, 1712 Claflin Road, Manhattan, Kansas
| | - Allan K Fritz
- Department of Agronomy, Kansas State University, 4012 Throckmorton Hall, 1712 Claflin Road, Manhattan, Kansas, USA
| | - Jesse Poland
- King Abdullah University of Science and Technology, Center for Desert Agriculture, Building 2, Level 3, Office 3236, 4700 KAUST Thuwal, Kingdom of Saudi Arabia
| | - Eduard Akhunov
- Wheat Genetics Resource Center and Department of Plant Pathology, Throckmorton Hall, Kansas Wheat Innovation Center, 1990 Kimball Ave, Manhattan, Kansas, USA
| | - Scott Haley
- Department of Soil and Crop Sciences, Colorado State University, 307 University Ave, Fort Collins, Colorado, USA
| | - Esten Mason
- Department of Soil and Crop Sciences, Colorado State University, 307 University Ave, Fort Collins, Colorado, USA
| | - Punya Nachappa
- Department of Agricultural Biology, Colorado State University, 307 University Ave, Fort Collins, Colorado, USA
| |
Collapse
|
4
|
Niu J, Ma S, Zheng S, Zhang C, Lu Y, Si Y, Tian S, Shi X, Liu X, Naeem MK, Sun H, Hu Y, Wu H, Cui Y, Chen C, Long W, Zhang Y, Gu M, Cui M, Lu Q, Zhou W, Peng J, Akhunov E, He F, Zhao S, Ling HQ. Whole-genome sequencing of diverse wheat accessions uncovers genetic changes during modern breeding in China and the United States. Plant Cell 2023; 35:4199-4216. [PMID: 37647532 PMCID: PMC10689146 DOI: 10.1093/plcell/koad229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 07/25/2023] [Accepted: 08/08/2023] [Indexed: 09/01/2023]
Abstract
Breeding has dramatically changed the plant architecture of wheat (Triticum aestivum), resulting in the development of high-yielding varieties adapted to modern farming systems. However, how wheat breeding shaped the genomic architecture of this crop remains poorly understood. Here, we performed a comprehensive comparative analysis of a whole-genome resequencing panel of 355 common wheat accessions (representing diverse landraces and modern cultivars from China and the United States) at the phenotypic and genomic levels. The genetic diversity of modern wheat cultivars was clearly reduced compared to landraces. Consistent with these genetic changes, most phenotypes of cultivars from China and the United States were significantly altered. Of the 21 agronomic traits investigated, 8 showed convergent changes between the 2 countries. Moreover, of the 207 loci associated with these 21 traits, more than half overlapped with genomic regions that showed evidence of selection. The distribution of selected loci between the Chinese and American cultivars suggests that breeding for increased productivity in these 2 regions was accomplished by pyramiding both shared and region-specific variants. This work provides a framework to understand the genetic architecture of the adaptation of wheat to diverse agricultural production environments, as well as guidelines for optimizing breeding strategies to design better wheat varieties.
Collapse
Affiliation(s)
- Jianqing Niu
- Hainan Yazhou Bay Seed Laboratory, Hainan, Sanya 572024, China
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Shengwei Ma
- Hainan Yazhou Bay Seed Laboratory, Hainan, Sanya 572024, China
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Shusong Zheng
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Chi Zhang
- BGI Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Yaru Lu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yaoqi Si
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Shuiquan Tian
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaoli Shi
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiaolin Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Muhammad Kashif Naeem
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Hua Sun
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yafei Hu
- BGI Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Huilan Wu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yan Cui
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Chunlin Chen
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Wenbo Long
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yue Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Mengjun Gu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Man Cui
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Qiao Lu
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wenjuan Zhou
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Junhua Peng
- Huazhi Bio-tech Company Ltd., Changsha, Hunan 410125, China
| | - Eduard Akhunov
- Wheat Genetic Resources Center, Kansas State University, Manhattan, KS 66506, USA
| | - Fei He
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Shancen Zhao
- BGI Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Hong-Qing Ling
- Hainan Yazhou Bay Seed Laboratory, Hainan, Sanya 572024, China
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| |
Collapse
|
5
|
Zhang J, Xiong H, Burguener GF, Vasquez-Gross H, Liu Q, Debernardi JM, Akhunova A, Garland-Campbell K, Kianian SF, Brown-Guedira G, Pozniak C, Faris JD, Akhunov E, Dubcovsky J. Sequencing 4.3 million mutations in wheat promoters to understand and modify gene expression. Proc Natl Acad Sci U S A 2023; 120:e2306494120. [PMID: 37703281 PMCID: PMC10515147 DOI: 10.1073/pnas.2306494120] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 08/03/2023] [Indexed: 09/15/2023] Open
Abstract
Wheat is an important contributor to global food security, and further improvements are required to feed a growing human population. Functional genetics and genomics tools can help us to understand the function of different genes and to engineer beneficial changes. In this study, we used a promoter capture assay to sequence 2-kb regions upstream of all high-confidence annotated genes from 1,513 mutagenized plants from the tetraploid wheat variety Kronos. We identified 4.3 million induced mutations with an accuracy of 99.8%, resulting in a mutation density of 41.9 mutations per kb. We also remapped Kronos exome capture reads to Chinese Spring RefSeq v1.1, identified 4.7 million mutations, and predicted their effects on annotated genes. Using these predictions, we identified 59% more nonsynonymous substitutions and 49% more truncation mutations than in the original study. To show the biological value of the promoter dataset, we selected two mutations within the promoter of the VRN-A1 vernalization gene. Both mutations, located within transcription factor binding sites, significantly altered VRN-A1 expression, and one reduced the number of spikelets per spike. These publicly available sequenced mutant datasets provide rapid and inexpensive access to induced variation in the promoters and coding regions of most wheat genes. These mutations can be used to understand and modulate gene expression and phenotypes for both basic and commercial applications, where limited governmental regulations can facilitate deployment. These mutant collections, together with gene editing, provide valuable tools to accelerate functional genetic studies in this economically important crop.
Collapse
Affiliation(s)
- Junli Zhang
- Department of Plant Sciences, University of California, Davis, CA95616
| | - Hongchun Xiong
- Department of Plant Sciences, University of California, Davis, CA95616
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing100081, China
| | - Germán F. Burguener
- Department of Plant Sciences, University of California, Davis, CA95616
- HHMI, Chevy Chase, MD20815
| | - Hans Vasquez-Gross
- Department of Plant Sciences, University of California, Davis, CA95616
- Nevada Bioinformatics Center, University of Nevada, Reno, NV89557
| | - Qiujie Liu
- Department of Plant Sciences, University of California, Davis, CA95616
- HHMI, Chevy Chase, MD20815
| | - Juan M. Debernardi
- Department of Plant Sciences, University of California, Davis, CA95616
- HHMI, Chevy Chase, MD20815
| | - Alina Akhunova
- Department of Plant Pathology, Kansas State University, Manhattan, KS66506
| | - Kimberly Garland-Campbell
- United States Department of Agriculture - Agricultural Research Service, Wheat Health, Genetics and Quality Research Unit, Pullman, WA99164
| | - Shahryar F. Kianian
- United States Department of Agriculture - Agricultural Research Service, Cereal Disease Laboratory, Saint Paul, MN55108-6086
| | - Gina Brown-Guedira
- United States Department of Agriculture - Agricultural Research Service, Plant Science Research Unit, Raleigh, NC27695
| | - Curtis Pozniak
- Crop Development Centre, University of Saskatchewan, SaskatoonS7N 5A8, Canada
| | - Justin D. Faris
- United States Department of Agriculture - Agricultural Research Service, Cereal Crops Research Unit, Northern Crop Science Laboratory, Fargo, ND58102
| | - Eduard Akhunov
- Department of Plant Pathology, Kansas State University, Manhattan, KS66506
| | - Jorge Dubcovsky
- Department of Plant Sciences, University of California, Davis, CA95616
- HHMI, Chevy Chase, MD20815
| |
Collapse
|
6
|
Bian R, Liu N, Xu Y, Su Z, Chai L, Bernardo A, St Amand P, Fritz A, Zhang G, Rupp J, Akhunov E, Jordan KW, Bai G. Quantitative trait loci for rolled leaf in a wheat EMS mutant from Jagger. Theor Appl Genet 2023; 136:52. [PMID: 36912970 DOI: 10.1007/s00122-023-04284-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 11/26/2022] [Indexed: 06/18/2023]
Abstract
Two QTLs with major effects on rolled leaf trait were consistently detected on chromosomes 1A (QRl.hwwg-1AS) and 5A (QRl.hwwg-5AL) in the field experiments. Rolled leaf (RL) is a morphological strategy to protect plants from dehydration under stressed field conditions. Identification of quantitative trait loci (QTLs) underlining RL is essential to breed drought-tolerant wheat cultivars. A mapping population of 154 recombinant inbred lines was developed from the cross between JagMut1095, a mutant of Jagger, and Jagger to identify quantitative trait loci (QTLs) for the RL trait. A linkage map of 3106 cM was constructed with 1003 unique SNPs from 21 wheat chromosomes. Two consistent QTLs were identified for RL on chromosomes 1A (QRl.hwwg-1AS) and 5A (QRl.hwwg-5AL) in all field experiments. QRl.hwwg-1AS explained 24-56% of the phenotypic variation and QRl.hwwg-5AL explained up to 20% of the phenotypic variation. The combined percent phenotypic variation associated with the two QTLs was up to 61%. Analyses of phenotypic and genotypic data of recombinants generated from heterogeneous inbred families of JagMut1095 × Jagger delimited QRl.hwwg-1AS to a 6.04 Mb physical interval. This work lays solid foundation for further fine mapping and map-based cloning of QRl.hwwg-1AS.
Collapse
Affiliation(s)
- Ruolin Bian
- Department of Agronomy, Kansas State University, Manhattan, KS, 66506, USA
| | - Na Liu
- Department of Agronomy, Kansas State University, Manhattan, KS, 66506, USA
- Henan Agricultural University, Zhengzhou, 450002, Henan Province, China
| | - Yuzhou Xu
- Department of Agronomy, Kansas State University, Manhattan, KS, 66506, USA
| | - Zhenqi Su
- Department of Agronomy, Kansas State University, Manhattan, KS, 66506, USA
- China Agricultural University, Beijing, 100083, China
| | - Lingling Chai
- Department of Agronomy, Kansas State University, Manhattan, KS, 66506, USA
- China Agricultural University, Beijing, 100083, China
| | - Amy Bernardo
- USDA-ARS, Hard Winter Wheat Genetics Research Unit, Manhattan, KS, 66506, USA
| | - Paul St Amand
- USDA-ARS, Hard Winter Wheat Genetics Research Unit, Manhattan, KS, 66506, USA
| | - Allan Fritz
- Department of Agronomy, Kansas State University, Manhattan, KS, 66506, USA
| | - Guorong Zhang
- Department of Agronomy, Kansas State University, Manhattan, KS, 66506, USA
| | - Jessica Rupp
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA
| | - Eduard Akhunov
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA
| | - Katherine W Jordan
- USDA-ARS, Hard Winter Wheat Genetics Research Unit, Manhattan, KS, 66506, USA
| | - Guihua Bai
- Department of Agronomy, Kansas State University, Manhattan, KS, 66506, USA.
- USDA-ARS, Hard Winter Wheat Genetics Research Unit, Manhattan, KS, 66506, USA.
| |
Collapse
|
7
|
Wang W, Yu Z, He F, Bai G, Trick HN, Akhunova A, Akhunov E. Multiplexed promoter and gene editing in wheat using a virus-based guide RNA delivery system. Plant Biotechnol J 2022; 20:2332-2341. [PMID: 36070109 PMCID: PMC9674318 DOI: 10.1111/pbi.13910] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [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: 03/14/2022] [Revised: 07/20/2022] [Accepted: 08/07/2022] [Indexed: 06/15/2023]
Abstract
The low efficiency of genetic transformation and gene editing across diverse cultivars hinder the broad application of CRISPR technology for crop improvement. The development of virus-based methods of CRISPR-Cas system delivery into the plant cells holds great promise to overcome these limitations. Here, we perform direct inoculation of wheat leaves with the barley stripe mosaic virus (BSMV) transcripts to deliver guide RNAs (sgRNA) into the Cas9-expressing wheat. We demonstrate that wheat inoculation with the pool of BSMV-sgRNAs could be used to generate heritable precise deletions in the promoter region of a transcription factor and to perform multiplexed editing of agronomic genes. We transfer the high-expressing locus of Cas9 into adapted spring and winter cultivars by marker-assisted introgression and use of the BSMV-sgRNAs to edit two agronomic genes. A strategy presented in our study could be applied to any adapted cultivar for creating new cis-regulatory diversity or large-scale editing of multiple genes in biological pathways or QTL regions, opening possibilities for the effective engineering of crop genomes, and accelerating gene discovery and trait improvement efforts.
Collapse
Affiliation(s)
- Wei Wang
- Department of Plant PathologyKansas State UniversityManhattanKSUSA
- Wheat Genetic Resources CenterKansas State UniversityManhattanKSUSA
| | - Zitong Yu
- Department of Plant PathologyKansas State UniversityManhattanKSUSA
- Wheat Genetic Resources CenterKansas State UniversityManhattanKSUSA
| | - Fei He
- Department of Plant PathologyKansas State UniversityManhattanKSUSA
- Present address:
State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental Biology, Chinese Academy of SciencesBeijingChina
| | - Guihua Bai
- Hard Winter Wheat Genetics Research UnitUSDA‐ARSManhattanKSUSA
| | - Harold N. Trick
- Department of Plant PathologyKansas State UniversityManhattanKSUSA
| | - Alina Akhunova
- Department of Plant PathologyKansas State UniversityManhattanKSUSA
- Integrated Genomic FacilityKansas State UniversityManhattanKSUSA
| | - Eduard Akhunov
- Department of Plant PathologyKansas State UniversityManhattanKSUSA
- Wheat Genetic Resources CenterKansas State UniversityManhattanKSUSA
| |
Collapse
|
8
|
Taagen E, Jordan K, Akhunov E, Sorrells ME, Jannink JL. If It Ain't Broke, Don't Fix It: Evaluating the Effect of Increased Recombination on Response to Selection for Wheat Breeding. G3 Genes|Genomes|Genetics 2022; 12:6798772. [PMID: 36331396 PMCID: PMC9713416 DOI: 10.1093/g3journal/jkac291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Accepted: 10/14/2022] [Indexed: 11/06/2022]
Abstract
Abstract
Meiotic recombination is a source of allelic diversity, but the low frequency and biased distribution of crossovers that occur during meiosis limits the genetic variation available to plant breeders. Simulation studies previously identified that increased recombination frequency can retain more genetic variation and drive greater genetic gains than wildtype recombination. Our study was motivated by the need to define desirable recombination intervals in regions of the genome with fewer crossovers. We hypothesized that deleterious variants, which can negatively impact phenotypes and occur at higher frequencies in low recombining regions where they are linked in repulsion with favorable loci, may offer a signal for positioning shifts of recombination distributions. Genomic selection breeding simulation models based on empirical wheat data were developed to evaluate increased recombination frequency and changing recombination distribution on response to selection. Comparing high and low values for a range of simulation parameters identified that few combinations retained greater genetic variation and fewer still achieved higher genetic gain than wildtype. More recombination was associated with loss of genomic prediction accuracy, which outweighed the benefits of disrupting repulsion linkages. Irrespective of recombination frequency or distribution and deleterious variant annotation, enhanced response to selection under increased recombination required polygenic trait architecture, high heritability, an initial scenario of more repulsion than coupling linkages, and greater than six cycles of genomic selection. Altogether, the outcomes of this research discourage a controlled recombination approach to genomic selection in wheat as a more efficient path to retaining genetic variation and increasing genetic gains compared to existing breeding methods.
Collapse
Affiliation(s)
- Ella Taagen
- Corresponding author: Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA.
| | - Katherine Jordan
- USDA-ARS, Hard Winter Wheat Genetics Research Unit, Manhattan, KS 66502, USA
- Department of Plant Pathology, Kansas State University, Manhattan, KS 66502, USA
| | - Eduard Akhunov
- Department of Plant Pathology, Kansas State University, Manhattan, KS 66502, USA
| | - Mark E Sorrells
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca NY 14853, USA
| | - Jean-Luc Jannink
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca NY 14853, USA
- USDA-ARS, R.W. Holley Center, Cornell University, Ithaca, NY 14853, USA
| |
Collapse
|
9
|
Guo Y, Betzen B, Salcedo A, He F, Bowden RL, Fellers JP, Jordan KW, Akhunova A, Rouse MN, Szabo LJ, Akhunov E. Population genomics of Puccinia graminis f.sp. tritici highlights the role of admixture in the origin of virulent wheat rust races. Nat Commun 2022; 13:6287. [PMID: 36271077 PMCID: PMC9587050 DOI: 10.1038/s41467-022-34050-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: 03/31/2022] [Accepted: 10/12/2022] [Indexed: 12/25/2022] Open
Abstract
Puccinia graminis f.sp. tritici (Pgt) causes stem rust disease in wheat that can result in severe yield losses. The factors driving the evolution of its virulence and adaptation remain poorly characterized. We utilize long-read sequencing to develop a haplotype-resolved genome assembly of a U.S. isolate of Pgt. Using Pgt haplotypes as a reference, we characterize the structural variants (SVs) and single nucleotide polymorphisms in a diverse panel of isolates. SVs impact the repertoire of predicted effectors, secreted proteins involved in host-pathogen interaction, and show evidence of purifying selection. By analyzing global and local genomic ancestry we demonstrate that the origin of 8 out of 12 Pgt clades is linked with either somatic hybridization or sexual recombination between the diverged donor populations. Our study shows that SVs and admixture events appear to play an important role in broadening Pgt virulence and the origin of highly virulent races, creating a resource for studying the evolution of Pgt virulence and preventing future epidemic outbreaks.
Collapse
Affiliation(s)
- Yuanwen Guo
- grid.36567.310000 0001 0737 1259Department of Plant Pathology, Kansas State University, Manhattan, KS USA
| | - Bliss Betzen
- grid.36567.310000 0001 0737 1259Department of Plant Pathology, Kansas State University, Manhattan, KS USA ,grid.36567.310000 0001 0737 1259Present Address: USDA-APHIS-PPQ Field Operations, Kansas State University, Manhattan, KS USA
| | - Andres Salcedo
- grid.36567.310000 0001 0737 1259Department of Plant Pathology, Kansas State University, Manhattan, KS USA ,grid.40803.3f0000 0001 2173 6074Present Address: Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC USA
| | - Fei He
- grid.36567.310000 0001 0737 1259Department of Plant Pathology, Kansas State University, Manhattan, KS USA ,grid.9227.e0000000119573309Present Address: State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Robert L. Bowden
- grid.512831.cUSDA-ARS, Hard Winter Wheat Genetics Research Unit, Manhattan, KS USA
| | - John P. Fellers
- grid.512831.cUSDA-ARS, Hard Winter Wheat Genetics Research Unit, Manhattan, KS USA
| | - Katherine W. Jordan
- grid.36567.310000 0001 0737 1259Department of Plant Pathology, Kansas State University, Manhattan, KS USA ,grid.512831.cUSDA-ARS, Hard Winter Wheat Genetics Research Unit, Manhattan, KS USA
| | - Alina Akhunova
- grid.36567.310000 0001 0737 1259Department of Plant Pathology, Kansas State University, Manhattan, KS USA ,grid.36567.310000 0001 0737 1259Integrated Genomics Facility, Kansas State University, Manhattan, KS USA
| | - Mathew N. Rouse
- grid.512864.c0000 0000 8881 3436Department of Plant Pathology, University of Minnesota & USDA-ARS, Cereal Disease Lab, St. Paul, MN USA
| | - Les J. Szabo
- grid.512864.c0000 0000 8881 3436Department of Plant Pathology, University of Minnesota & USDA-ARS, Cereal Disease Lab, St. Paul, MN USA
| | - Eduard Akhunov
- grid.36567.310000 0001 0737 1259Department of Plant Pathology, Kansas State University, Manhattan, KS USA ,grid.36567.310000 0001 0737 1259Wheat Genetics Resource Center, Kansas State University, Manhattan, KS USA
| |
Collapse
|
10
|
He F, Wang W, Rutter WB, Jordan KW, Ren J, Taagen E, DeWitt N, Sehgal D, Sukumaran S, Dreisigacker S, Reynolds M, Halder J, Sehgal SK, Liu S, Chen J, Fritz A, Cook J, Brown-Guedira G, Pumphrey M, Carter A, Sorrells M, Dubcovsky J, Hayden MJ, Akhunova A, Morrell PL, Szabo L, Rouse M, Akhunov E. Genomic variants affecting homoeologous gene expression dosage contribute to agronomic trait variation in allopolyploid wheat. Nat Commun 2022; 13:826. [PMID: 35149708 PMCID: PMC8837796 DOI: 10.1038/s41467-022-28453-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [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: 04/02/2021] [Accepted: 01/26/2022] [Indexed: 12/23/2022] Open
Abstract
Allopolyploidy greatly expands the range of possible regulatory interactions among functionally redundant homoeologous genes. However, connection between the emerging regulatory complexity and expression and phenotypic diversity in polyploid crops remains elusive. Here, we use diverse wheat accessions to map expression quantitative trait loci (eQTL) and evaluate their effects on the population-scale variation in homoeolog expression dosage. The relative contribution of cis- and trans-eQTL to homoeolog expression variation is strongly affected by both selection and demographic events. Though trans-acting effects play major role in expression regulation, the expression dosage of homoeologs is largely influenced by cis-acting variants, which appear to be subjected to selection. The frequency and expression of homoeologous gene alleles showing strong expression dosage bias are predictive of variation in yield-related traits, and have likely been impacted by breeding for increased productivity. Our study highlights the importance of genomic variants affecting homoeolog expression dosage in shaping agronomic phenotypes and points at their potential utility for improving yield in polyploid crops.
Collapse
Affiliation(s)
- Fei He
- Department of Plant Pathology, Kansas State University, Manhattan, KS, USA.,State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Wei Wang
- Department of Plant Pathology, Kansas State University, Manhattan, KS, USA.,Wheat Genetic Resources Center, Kansas State University, Manhattan, KS, USA
| | - William B Rutter
- Department of Plant Pathology, Kansas State University, Manhattan, KS, USA.,USDA-ARS, U.S. Vegetable Laboratory, Charleston, SC, USA
| | - Katherine W Jordan
- Department of Plant Pathology, Kansas State University, Manhattan, KS, USA.,USDA-ARS, Hard Winter Wheat Genetics Research Unit, Manhattan, KS, USA
| | - Jie Ren
- Department of Plant Pathology, Kansas State University, Manhattan, KS, USA.,Integrated Genomics Facility, Kansas State University, Manhattan, KS, USA
| | - Ellie Taagen
- School of Integrative Plant Science, Cornell University, Ithaca, NY, USA
| | - Noah DeWitt
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC, USA.,USDA-ARS SAA, Plant Science Research, Raleigh, NC, USA
| | - Deepmala Sehgal
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
| | | | | | - Matthew Reynolds
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
| | - Jyotirmoy Halder
- Department of Agronomy, Horticulture and Plant Science, South Dakota State University, Brookings, SD, USA
| | - Sunish Kumar Sehgal
- Department of Agronomy, Horticulture and Plant Science, South Dakota State University, Brookings, SD, USA
| | - Shuyu Liu
- Texas A&M AgriLife Research, Amarillo, TX, USA
| | - Jianli Chen
- Department of Plant Sciences, University of Idaho, Aberdeen, ID, USA
| | - Allan Fritz
- Department of Agronomy, Kansas State University, Manhattan, KS, USA
| | - Jason Cook
- Department of Plant Sciences & Plant Pathology, Montana State University, Bozeman, MT, USA
| | - Gina Brown-Guedira
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC, USA.,USDA-ARS SAA, Plant Science Research, Raleigh, NC, USA
| | - Mike Pumphrey
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, USA
| | - Arron Carter
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, USA
| | - Mark Sorrells
- School of Integrative Plant Science, Cornell University, Ithaca, NY, USA
| | - Jorge Dubcovsky
- Department of Plant Sciences, University of California, Davis, CA, USA
| | - Matthew J Hayden
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, Australia.,Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, Australia
| | - Alina Akhunova
- Department of Plant Pathology, Kansas State University, Manhattan, KS, USA.,Integrated Genomics Facility, Kansas State University, Manhattan, KS, USA
| | - Peter L Morrell
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, USA
| | - Les Szabo
- USDA-ARS Cereal Disease Lab, St. Paul, MN, USA
| | | | - Eduard Akhunov
- Department of Plant Pathology, Kansas State University, Manhattan, KS, USA. .,Wheat Genetic Resources Center, Kansas State University, Manhattan, KS, USA.
| |
Collapse
|
11
|
Glenn P, Zhang J, Brown-Guedira G, DeWitt N, Cook JP, Li K, Akhunov E, Dubcovsky J. Identification and characterization of a natural polymorphism in FT-A2 associated with increased number of grains per spike in wheat. Theor Appl Genet 2022; 135:679-692. [PMID: 34825926 PMCID: PMC8866389 DOI: 10.1007/s00122-021-03992-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 11/02/2021] [Indexed: 05/16/2023]
Abstract
We discovered a natural FT-A2 allele that increases grain number per spike in both pasta and bread wheat with limited effect on heading time. Increases in wheat grain yield are necessary to meet future global food demands. A previous study showed that loss-of-function mutations in FLOWERING LOCUS T2 (FT2) increase spikelet number per spike (SNS), an important grain yield component. However, these mutations were also associated with reduced fertility, offsetting the beneficial effect of the increases in SNS on grain number. Here, we report a natural mutation resulting in an aspartic acid to alanine change at position 10 (D10A) associated with significant increases in SNS and no negative effects on fertility. Using a high-density genetic map, we delimited the SNS candidate region to a 5.2-Mb region on chromosome 3AS including 28 genes. Among them, only FT-A2 showed a non-synonymous polymorphism (D10A) present in two different populations segregating for the SNS QTL on chromosome arm 3AS. These results, together with the known effect of the ft-A2 mutations on SNS, suggest that variation in FT-A2 is the most likely cause of the observed differences in SNS. We validated the positive effects of the A10 allele on SNS, grain number, and grain yield per spike in near-isogenic tetraploid wheat lines and in an hexaploid winter wheat population. The A10 allele is present at very low frequency in durum wheat and at much higher frequency in hexaploid wheat, particularly in winter and fall-planted spring varieties. These results suggest that the FT-A2 A10 allele may be particularly useful for improving grain yield in durum wheat and fall-planted common wheat varieties.
Collapse
Affiliation(s)
- Priscilla Glenn
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Junli Zhang
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | | | - Noah DeWitt
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC, 27695, USA
| | - Jason P Cook
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT, USA
| | - Kun Li
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, 20815, USA
| | - Eduard Akhunov
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA
| | - Jorge Dubcovsky
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, 20815, USA.
| |
Collapse
|
12
|
Wang W, Tian B, Pan Q, Chen Y, He F, Bai G, Akhunova A, Trick HN, Akhunov E. Expanding the range of editable targets in the wheat genome using the variants of the Cas12a and Cas9 nucleases. Plant Biotechnol J 2021; 19:2428-2441. [PMID: 34270168 PMCID: PMC8633491 DOI: 10.1111/pbi.13669] [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] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 06/25/2021] [Accepted: 07/12/2021] [Indexed: 06/13/2023]
Abstract
The development of CRISPR-based editors recognizing distinct protospacer-adjacent motifs (PAMs), or having different spacer length/structure requirements broadens the range of possible genomic applications. We evaluated the natural and engineered variants of Cas12a (FnCas12a and LbCas12a) and Cas9 for their ability to induce mutations in endogenous genes controlling important agronomic traits in wheat. Unlike FnCas12a, LbCas12a-induced mutations in the wheat genome, even though with a lower rate than that reported for SpCas9. The eight-fold improvement in the gene editing efficiency was achieved for LbCas12a by using the guides flanked by ribozymes and driven by the RNA polymerase II promoter from switchgrass. The efficiency of multiplexed genome editing (MGE) using LbCas12a was mostly similar to that obtained using the simplex RNA guides and showed substantial increase after subjecting transgenic plants to high-temperature treatment. We successfully applied LbCas12a-MGE for generating heritable mutations in a gene controlling grain size and weight in wheat. We showed that the range of editable loci in the wheat genome could be further expanded by using the engineered variants of Cas12a (LbCas12a-RVR) and Cas9 (Cas9-NG and xCas9) that recognize the TATV and NG PAMs, respectively, with the Cas9-NG showing higher editing efficiency on the targets with atypical PAMs compared to xCas9. In conclusion, our study reports a set of validated natural and engineered variants of Cas12a and Cas9 editors for targeting loci in the wheat genome not amenable to modification using the original SpCas9 nuclease.
Collapse
Affiliation(s)
- Wei Wang
- Department of Plant PathologyKansas State UniversityManhattanKSUSA
| | - Bin Tian
- Department of Plant PathologyKansas State UniversityManhattanKSUSA
| | - Qianli Pan
- Department of Plant PathologyKansas State UniversityManhattanKSUSA
| | - Yueying Chen
- Department of Plant PathologyKansas State UniversityManhattanKSUSA
| | - Fei He
- Department of Plant PathologyKansas State UniversityManhattanKSUSA
| | - Guihua Bai
- Hard Winter Wheat Genetics Research UnitUSDA‐ARSManhattanKSUSA
| | - Alina Akhunova
- Department of Plant PathologyKansas State UniversityManhattanKSUSA
- Integrated Genomics FacilityKansas State UniversityManhattanKSUSA
| | - Harold N. Trick
- Department of Plant PathologyKansas State UniversityManhattanKSUSA
| | - Eduard Akhunov
- Department of Plant PathologyKansas State UniversityManhattanKSUSA
| |
Collapse
|
13
|
Isham K, Wang R, Zhao W, Wheeler J, Klassen N, Akhunov E, Chen J. QTL mapping for grain yield and three yield components in a population derived from two high-yielding spring wheat cultivars. Theor Appl Genet 2021; 134:2079-2095. [PMID: 33687497 PMCID: PMC8263538 DOI: 10.1007/s00122-021-03806-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 02/24/2021] [Indexed: 05/07/2023]
Abstract
Four genomic regions on chromosomes 4A, 6A, 7B, and 7D were discovered, each with multiple tightly linked QTL (QTL clusters) associated with two to three yield components. The 7D QTL cluster was associated with grain yield, fertile spikelet number per spike, thousand kernel weight, and heading date. It was located in the flanking region of FT-D1, a homolog gene of Arabidopsis FLOWERING LOCUS T, a major gene that regulates wheat flowering. Genetic manipulation of yield components is an important approach to increase grain yield in wheat (Triticum aestivum). The present study used a mapping population comprised of 181 doubled haploid lines derived from two high-yielding spring wheat cultivars, UI Platinum and LCS Star. The two cultivars and the derived population were assessed for six traits in eight field trials primarily in Idaho in the USA. The six traits were grain yield, fertile spikelet number per spike, productive tiller number per unit area, thousand kernel weight, heading date, and plant height. Quantitative Trait Locus (QTL) analysis of the six traits was conducted using 14,236 single-nucleotide polymorphism (SNP) markers generated from the wheat 90 K SNP and the exome and promoter capture arrays. Of the 19 QTL detected, 14 were clustered in four chromosomal regions on 4A, 6A, 7B and 7D. Each of the four QTL clusters was associated with multiple yield component traits, and these traits were often negatively correlated with one another. As a result, additional QTL dissection studies are needed to optimize trade-offs among yield component traits for specific production environments. Kompetitive allele-specific PCR markers for the four QTL clusters were developed and assessed in an elite spring wheat panel of 170 lines, and eight of the 14 QTL were validated. The two parents contain complementary alleles for the four QTL clusters, suggesting the possibility of improving grain yield via genetic recombination of yield component loci.
Collapse
Affiliation(s)
- Kyle Isham
- Department of Plant Sciences, University of Idaho, Aberdeen, ID, USA
| | - Rui Wang
- Department of Plant Sciences, University of Idaho, Aberdeen, ID, USA
| | - Weidong Zhao
- Department of Plant Sciences, University of Idaho, Aberdeen, ID, USA
| | - Justin Wheeler
- Department of Plant Sciences, University of Idaho, Aberdeen, ID, USA
| | - Natalie Klassen
- Department of Plant Sciences, University of Idaho, Aberdeen, ID, USA
| | - Eduard Akhunov
- Department of Plant Sciences, Kansas State University, Manhattan, KS, USA
| | - Jianli Chen
- Department of Plant Sciences, University of Idaho, Aberdeen, ID, USA.
| |
Collapse
|
14
|
Nyine M, Adhikari E, Clinesmith M, Aiken R, Betzen B, Wang W, Davidson D, Yu Z, Guo Y, He F, Akhunova A, Jordan KW, Fritz AK, Akhunov E. The Haplotype-Based Analysis of Aegilops tauschii Introgression Into Hard Red Winter Wheat and Its Impact on Productivity Traits. Front Plant Sci 2021; 12:716955. [PMID: 34484280 PMCID: PMC8416154 DOI: 10.3389/fpls.2021.716955] [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] [Received: 05/29/2021] [Accepted: 07/20/2021] [Indexed: 05/13/2023]
Abstract
The introgression from wild relatives have a great potential to broaden the availability of beneficial allelic diversity for crop improvement in breeding programs. Here, we assessed the impact of the introgression from 21 diverse accessions of Aegilops tauschii, the diploid ancestor of the wheat D genome, into 6 hard red winter wheat cultivars on yield and yield component traits. We used 5.2 million imputed D genome SNPs identified by the whole-genome sequencing of parental lines and the sequence-based genotyping of introgression population, including 351 BC1F3:5 lines. Phenotyping data collected from the irrigated and non-irrigated field trials revealed that up to 23% of the introgression lines (ILs) produce more grain than the parents and check cultivars. Based on 16 yield stability statistics, the yield of 12 ILs (3.4%) was stable across treatments, years, and locations; 5 of these lines were also high yielding lines, producing 9.8% more grain than the average yield of check cultivars. The most significant SNP- and haplotype-trait associations were identified on chromosome arms 2DS and 6DL for the spikelet number per spike (SNS), on chromosome arms 2DS, 3DS, 5DS, and 7DS for grain length (GL) and on chromosome arms 1DL, 2DS, 6DL, and 7DS for grain width (GW). The introgression of haplotypes from A. tauschii parents was associated with an increase in SNS, which was positively correlated with a heading date (HD), whereas the haplotypes from hexaploid wheat parents were associated with an increase in GW. We show that the haplotypes on 2DS associated with an increase in the spikelet number and HD are linked with multiple introgressed alleles of Ppd-D1 identified by the whole-genome sequencing of A. tauschii parents. Meanwhile, some introgressed haplotypes exhibited significant pleiotropic effects with the direction of effects on the yield component traits being largely consistent with the previously reported trade-offs, there were haplotype combinations associated with the positive trends in yield. The characterized repertoire of the introgressed haplotypes derived from A. tauschii accessions with the combined positive effects on yield and yield component traits in elite germplasm provides a valuable source of alleles for improving the productivity of winter wheat by optimizing the contribution of component traits to yield.
Collapse
Affiliation(s)
- Moses Nyine
- Department of Plant Pathology, Kansas State University, Manhattan, KS, United States
| | - Elina Adhikari
- Department of Plant Pathology, Kansas State University, Manhattan, KS, United States
| | - Marshall Clinesmith
- Department of Agronomy, Kansas State University, Manhattan, KS, United States
| | - Robert Aiken
- Department of Agronomy, Kansas State University, Manhattan, KS, United States
| | - Bliss Betzen
- Department of Plant Pathology, Kansas State University, Manhattan, KS, United States
| | - Wei Wang
- Department of Plant Pathology, Kansas State University, Manhattan, KS, United States
| | - Dwight Davidson
- Department of Plant Pathology, Kansas State University, Manhattan, KS, United States
| | - Zitong Yu
- Department of Plant Pathology, Kansas State University, Manhattan, KS, United States
| | - Yuanwen Guo
- Department of Plant Pathology, Kansas State University, Manhattan, KS, United States
| | - Fei He
- Department of Plant Pathology, Kansas State University, Manhattan, KS, United States
| | - Alina Akhunova
- Integrated Genomics Facility, Kansas State University, Manhattan, KS, United States
| | - Katherine W. Jordan
- Department of Plant Pathology, Kansas State University, Manhattan, KS, United States
- United States Department of Agriculture, Agricultural Research Service Hard Winter Wheat Genetics Research Unit, Manhattan, KS, United States
| | - Allan K. Fritz
- Department of Agronomy, Kansas State University, Manhattan, KS, United States
| | - Eduard Akhunov
- Department of Plant Pathology, Kansas State University, Manhattan, KS, United States
- *Correspondence: Eduard Akhunov
| |
Collapse
|
15
|
Jordan KW, He F, de Soto MF, Akhunova A, Akhunov E. Differential chromatin accessibility landscape reveals structural and functional features of the allopolyploid wheat chromosomes. Genome Biol 2020; 21:176. [PMID: 32684157 PMCID: PMC7368981 DOI: 10.1186/s13059-020-02093-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [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: 10/09/2019] [Accepted: 07/06/2020] [Indexed: 12/19/2022] Open
Abstract
Background Our understanding of how the complexity of the wheat genome influences the distribution of chromatin states along the homoeologous chromosomes is limited. Using a differential nuclease sensitivity assay, we investigate the chromatin states of the coding and repetitive regions of the allopolyploid wheat genome. Results Although open chromatin is found to be significantly enriched around genes, the majority of MNase-sensitive regions are located within transposable elements (TEs). Chromatin of the smaller D genome is more accessible than that of the larger A and B genomes. Chromatin states of different TEs vary among families and are influenced by the TEs’ chromosomal position and proximity to genes. While the chromatin accessibility of genes is influenced by proximity to TEs, and not by their position on the chromosomes, we observe a negative chromatin accessibility gradient along the telomere-centromere axis in the intergenic regions, positively correlated with the distance between genes. Both gene expression levels and homoeologous gene expression bias are correlated with chromatin accessibility in promoter regions. The differential nuclease sensitivity assay accurately predicts previously detected centromere locations. SNPs located within more accessible chromatin explain a higher proportion of genetic variance for a number of agronomic traits than SNPs located within more closed chromatin. Conclusions Chromatin states in the wheat genome are shaped by the interplay of repetitive and gene-encoding regions that are predictive of the functional and structural organization of chromosomes, providing a powerful framework for detecting genomic features involved in gene regulation and prioritizing genomic variation to explain phenotypes.
Collapse
Affiliation(s)
- Katherine W Jordan
- Department of Plant Pathology, Kansas State University, Manhattan, KS, USA.,USDA-ARS, Hard Winter Wheat Genetics Research Unit, Manhattan, KS, USA
| | - Fei He
- Department of Plant Pathology, Kansas State University, Manhattan, KS, USA
| | - Monica Fernandez de Soto
- Department of Plant Pathology, Kansas State University, Manhattan, KS, USA.,Integrated Genomics Facility, Kansas State University, Manhattan, KS, USA.,Genomic Sciences Laboratory, North Carolina State University, Raleigh, NC, USA
| | - Alina Akhunova
- Department of Plant Pathology, Kansas State University, Manhattan, KS, USA.,Integrated Genomics Facility, Kansas State University, Manhattan, KS, USA
| | - Eduard Akhunov
- Department of Plant Pathology, Kansas State University, Manhattan, KS, USA.
| |
Collapse
|
16
|
Bolus S, Akhunov E, Coaker G, Dubcovsky J. Dissection of Cell Death Induction by Wheat Stem Rust Resistance Protein Sr35 and Its Matching Effector AvrSr35. Mol Plant Microbe Interact 2020; 33:308-319. [PMID: 31556346 PMCID: PMC7309591 DOI: 10.1094/mpmi-08-19-0216-r] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [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] [Indexed: 05/27/2023]
Abstract
Nucleotide-binding leucine-rich repeat receptors (NLRs) are the most abundant type of immune receptors in plants and can trigger a rapid cell-death (hypersensitive) response upon sensing pathogens. We previously cloned the wheat NLR Sr35, which encodes a coiled-coil (CC) NLR that confers resistance to the virulent wheat stem rust race Ug99. Here, we investigated Sr35 signaling after Agrobacterium-mediated transient expression in Nicotiana benthamiana. Expression of Sr35 in N. benthamiana leaves triggered a mild cell-death response, which is enhanced in the autoactive mutant Sr35 D503V. The N-terminal tagging of Sr35 with green fluorescent protein (GFP) blocked the induction of cell death, whereas a C-terminal GFP tag did not. No domain truncations of Sr35 generated cell-death responses as strong as the wild type, but a truncation including the NB-ARC (nucleotide binding adaptor) shared by APAF-1, R proteins, and CED-4 domains in combination with the D503V autoactive mutation triggered cell death. In addition, coexpression of Sr35 with the matching pathogen effector protein AvrSr35 resulted in robust cell death and electrolyte leakage levels that were similar to autoactive Sr35 and significantly higher than Sr35 alone. Coexpression of Sr35-CC-NB-ARC and AvrSr35 did not induce cell death, confirming the importance of the leucine-rich repeat (LRR) domain for AvrSr35 recognition. These findings were confirmed through Agrobacterium-mediated transient expression in barley. Taken together, these results implicate the CC-NB-ARC domains of Sr35 in inducing cell death and the LRR domain in AvrSr35 recognition.[Formula: see text] Copyright © 2020 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.
Collapse
Affiliation(s)
- Stephen Bolus
- Department of Plant Sciences, University of California, Davis, CA 95616, U.S.A
- Department of Plant Pathology, University of California, Davis
| | - Eduard Akhunov
- Department of Plant Pathology, Kansas State University, Manhattan, KS 66506, U.S.A
| | - Gitta Coaker
- Department of Plant Pathology, University of California, Davis
| | - Jorge Dubcovsky
- Department of Plant Sciences, University of California, Davis, CA 95616, U.S.A
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, U.S.A
| |
Collapse
|
17
|
DeWitt N, Guedira M, Lauer E, Sarinelli M, Tyagi P, Fu D, Hao Q, Murphy JP, Marshall D, Akhunova A, Jordan K, Akhunov E, Brown‐Guedira G. Sequence-based mapping identifies a candidate transcription repressor underlying awn suppression at the B1 locus in wheat. New Phytol 2020; 225:326-339. [PMID: 31465541 PMCID: PMC6916393 DOI: 10.1111/nph.16152] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [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: 05/15/2019] [Accepted: 08/16/2019] [Indexed: 05/27/2023]
Abstract
Awns are stiff, hair-like structures which grow from the lemmas of wheat (Triticum aestivum) and other grasses that contribute to photosynthesis and play a role in seed dispersal. Variation in awn length in domesticated wheat is controlled primarily by three major genes, most commonly the dominant awn suppressor Tipped1 (B1). This study identifies a transcription repressor responsible for awn inhibition at the B1 locus. Association mapping was combined with analysis in biparental populations to delimit B1 to a distal region of 5AL colocalized with QTL for number of spikelets per spike, kernel weight, kernel length, and test weight. Fine-mapping located B1 to a region containing only two predicted genes, including C2H2 zinc finger transcriptional repressor TraesCS5A02G542800 upregulated in developing spikes of awnless individuals. Deletions encompassing this candidate gene were present in awned mutants of an awnless wheat. Sequence polymorphisms in the B1 coding region were not observed in diverse wheat germplasm whereas a nearby polymorphism was highly predictive of awn suppression. Transcriptional repression by B1 is the major determinant of awn suppression in global wheat germplasm. It is associated with increased number of spikelets per spike and decreased kernel size.
Collapse
Affiliation(s)
- Noah DeWitt
- Department of Crop and Soil SciencesNorth Carolina State UniversityRaleighNC27695USA
| | - Mohammed Guedira
- Department of Crop and Soil SciencesNorth Carolina State UniversityRaleighNC27695USA
| | - Edwin Lauer
- Department of Crop and Soil SciencesNorth Carolina State UniversityRaleighNC27695USA
| | - Martin Sarinelli
- Department of Crop and Soil SciencesNorth Carolina State UniversityRaleighNC27695USA
| | - Priyanka Tyagi
- Department of Crop and Soil SciencesNorth Carolina State UniversityRaleighNC27695USA
| | - Daolin Fu
- Department of Plant SciencesUniversity of IdahoMoscowID83844USA
| | - QunQun Hao
- Department of Plant SciencesUniversity of IdahoMoscowID83844USA
| | - J. Paul Murphy
- Department of Crop and Soil SciencesNorth Carolina State UniversityRaleighNC27695USA
| | - David Marshall
- Department of Crop and Soil SciencesNorth Carolina State UniversityRaleighNC27695USA
- USDA‐ARS SAAPlant Science ResearchRaleighNC27695USA
| | - Alina Akhunova
- Department of Plant PathologyKansas State UniversityManhattanKS66506USA
| | - Katherine Jordan
- Department of Plant PathologyKansas State UniversityManhattanKS66506USA
| | - Eduard Akhunov
- Department of Plant PathologyKansas State UniversityManhattanKS66506USA
| | - Gina Brown‐Guedira
- Department of Crop and Soil SciencesNorth Carolina State UniversityRaleighNC27695USA
- USDA‐ARS SAAPlant Science ResearchRaleighNC27695USA
| |
Collapse
|
18
|
Gardiner LJ, Brabbs T, Akhunov A, Jordan K, Budak H, Richmond T, Singh S, Catchpole L, Akhunov E, Hall A. Integrating genomic resources to present full gene and putative promoter capture probe sets for bread wheat. Gigascience 2019; 8:5304888. [PMID: 30715311 PMCID: PMC6461119 DOI: 10.1093/gigascience/giz018] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [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: 07/05/2018] [Revised: 11/21/2018] [Accepted: 01/27/2019] [Indexed: 11/17/2022] Open
Abstract
Background Whole-genome shotgun resequencing of wheat is expensive because of its large, repetitive genome. Moreover, sequence data can fail to map uniquely to the reference genome, making it difficult to unambiguously assign variation. Resequencing using target capture enables sequencing of large numbers of individuals at high coverage to reliably identify variants associated with important agronomic traits. Previous studies have implemented complementary DNA/exon or gene-based probe sets in which the promoter and intron sequence is largely missing alongside newly characterized genes from the recent improved reference sequences. Results We present and validate 2 gold standard capture probe sets for hexaploid bread wheat, a gene and a putative promoter capture, which are designed using recently developed genome sequence and annotation resources. The captures can be combined or used independently. We demonstrate that the capture probe sets effectively enrich the high-confidence genes and putative promoter regions that were identified in the genome alongside a large proportion of the low-confidence genes and associated promoters. Finally, we demonstrate successful sample multiplexing that allows generation of adequate sequence coverage for single-nucleotide polymorphism calling while significantly reducing cost per sample for gene and putative promoter capture. Conclusions We show that a capture design employing an “island strategy” can enable analysis of the large gene/putative promoter space of wheat with only 2 × 160 Mbp probe sets. Furthermore, these assays extend the regions of the wheat genome that are amenable to analyses beyond its exome, providing tools for detailed characterization of these regulatory regions in large populations.
Collapse
Affiliation(s)
- Laura-Jayne Gardiner
- Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, UK.,IBM Research, The Hartree Centre STFC Laboratory, Sci-Tech Daresbury, Warrington, WA4 4AD, UK
| | - Thomas Brabbs
- Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, UK
| | - Alina Akhunov
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA
| | - Katherine Jordan
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA
| | - Hikmet Budak
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT, 59717, USA
| | - Todd Richmond
- Roche Sequencing Solutions, 500 S Rosa Road, Madison, WI, 53719, USA
| | - Sukhwinder Singh
- CIMMYT, Calle Dr Norman E Borlaug, Ciudad Obregon, 85208, Mexico
| | - Leah Catchpole
- Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, UK
| | - Eduard Akhunov
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA
| | - Anthony Hall
- Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, UK.,School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TU, UK
| |
Collapse
|
19
|
Wang W, Pan Q, Tian B, He F, Chen Y, Bai G, Akhunova A, Trick HN, Akhunov E. Gene editing of the wheat homologs of TONNEAU1-recruiting motif encoding gene affects grain shape and weight in wheat. Plant J 2019; 100:251-264. [PMID: 31219637 PMCID: PMC6851855 DOI: 10.1111/tpj.14440] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [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: 04/01/2019] [Revised: 06/02/2019] [Accepted: 06/10/2019] [Indexed: 05/08/2023]
Abstract
Grain size and weight are important components of a suite of yield-related traits in crops. Here, we showed that the CRISPR-Cas9 gene editing of TaGW7, a homolog of rice OsGW7 encoding a TONNEAU1-recruiting motif (TRM) protein, affects grain shape and weight in allohexaploid wheat. By editing the TaGW7 homoeologs in the B and D genomes, we showed that mutations in either of the two or both genomes increased the grain width and weight but reduced the grain length. The effect sizes of mutations in the TaGW7 gene homoeologs coincided with the relative levels of their expression in the B and D genomes. The effects of gene editing on grain morphology and weight traits were dosage dependent with the double-copy mutant showing larger effect than the respective single copy mutants. The TaGW7-centered gene co-expression network indicated that this gene is involved in the pathways regulating cell division and organ growth, also confirmed by the cellular co-localization of TaGW7 with α- and β-tubulin proteins, the building blocks of microtubule arrays. The analyses of exome capture data in tetraploid domesticated and wild emmer, and hexaploid wheat revealed the loss of diversity around TaGW7-associated with domestication selection, suggesting that TaGW7 is likely to play an important role in the evolution of yield component traits in wheat. Our study showed how integrating CRISPR-Cas9 system with cross-species comparison can help to uncover the function of a gene fixed in wheat for allelic variants targeted by domestication selection and select targets for engineering new gene variants for crop improvement.
Collapse
Affiliation(s)
- Wei Wang
- Department of Plant PathologyKansas State UniversityManhattanKSUSA
| | - Qianli Pan
- Department of Plant PathologyKansas State UniversityManhattanKSUSA
| | - Bin Tian
- Department of Plant PathologyKansas State UniversityManhattanKSUSA
| | - Fei He
- Department of Plant PathologyKansas State UniversityManhattanKSUSA
| | - Yueying Chen
- Department of Plant PathologyKansas State UniversityManhattanKSUSA
| | - Guihua Bai
- USDA‐ARS Hard Winter Wheat Genetics Research UnitManhattanKSUSA
| | - Alina Akhunova
- Department of Plant PathologyKansas State UniversityManhattanKSUSA
- Integrated Genomics FacilityKansas State UniversityManhattanKSUSA
| | - Harold N. Trick
- Department of Plant PathologyKansas State UniversityManhattanKSUSA
| | - Eduard Akhunov
- Department of Plant PathologyKansas State UniversityManhattanKSUSA
| |
Collapse
|
20
|
Kuzay S, Xu Y, Zhang J, Katz A, Pearce S, Su Z, Fraser M, Anderson JA, Brown-Guedira G, DeWitt N, Peters Haugrud A, Faris JD, Akhunov E, Bai G, Dubcovsky J. Identification of a candidate gene for a QTL for spikelet number per spike on wheat chromosome arm 7AL by high-resolution genetic mapping. Theor Appl Genet 2019; 132:2689-2705. [PMID: 31254024 PMCID: PMC6708044 DOI: 10.1007/s00122-019-03382-5] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 06/12/2019] [Accepted: 06/16/2019] [Indexed: 05/21/2023]
Abstract
A high-resolution genetic map combined with haplotype analyses identified a wheat ortholog of rice gene APO1 as the best candidate gene for a 7AL locus affecting spikelet number per spike. A better understanding of the genes controlling differences in wheat grain yield components can accelerate the improvements required to satisfy future food demands. In this study, we identified a promising candidate gene underlying a quantitative trait locus (QTL) on wheat chromosome arm 7AL regulating spikelet number per spike (SNS). We used large heterogeneous inbred families ( > 10,000 plants) from two crosses to map the 7AL QTL to an 87-kb region (674,019,191-674,106,327 bp, RefSeq v1.0) containing two complete and two partial genes. In this region, we found three major haplotypes that were designated as H1, H2 and H3. The H2 haplotype contributed the high-SNS allele in both H1 × H2 and H2 × H3 segregating populations. The ancestral H3 haplotype is frequent in wild emmer (48%) but rare (~ 1%) in cultivated wheats. By contrast, the H1 and H2 haplotypes became predominant in modern cultivated durum and common wheat, respectively. Among the four candidate genes, only TraesCS7A02G481600 showed a non-synonymous polymorphism that differentiated H2 from the other two haplotypes. This gene, designated here as WHEAT ORTHOLOG OF APO1 (WAPO1), is an ortholog of the rice gene ABERRANT PANICLE ORGANIZATION 1 (APO1), which affects spikelet number. Taken together, the high-resolution genetic map, the association between polymorphisms in the different mapping populations with differences in SNS, and the known role of orthologous genes in other grass species suggest that WAPO-A1 is the most likely candidate gene for the 7AL SNS QTL among the four genes identified in the candidate gene region.
Collapse
Affiliation(s)
- Saarah Kuzay
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Yunfeng Xu
- Department of Agronomy, Kansas State University, Manhattan, KS, 66506, USA
| | - Junli Zhang
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Andrew Katz
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, 80523, USA
| | - Stephen Pearce
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, 80523, USA
| | - Zhenqi Su
- Department of Agronomy, Kansas State University, Manhattan, KS, 66506, USA
| | - Max Fraser
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, 55108, USA
| | - James A Anderson
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, 55108, USA
| | | | - Noah DeWitt
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC, 27695, USA
| | | | - Justin D Faris
- USDA-Agricultural Research Service, Cereal Crops Research Unit, Edward T. Schafer Agricultural Research Center, Fargo, ND, 58102, USA
| | - Eduard Akhunov
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA
| | - Guihua Bai
- Department of Agronomy, Kansas State University, Manhattan, KS, 66506, USA.
- USDA-ARS, Hard Winter Wheat Genetics Research Unit, Manhattan, KS, 66506, USA.
| | - Jorge Dubcovsky
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, 20815, USA.
| |
Collapse
|
21
|
Varella AC, Weaver DK, Blake NK, Hofland ML, Heo HY, Cook JP, Lamb PF, Jordan KW, Akhunov E, Chao S, Talbert LE. Analysis of recombinant inbred line populations derived from wheat landraces to identify new genes for wheat stem sawfly resistance. Theor Appl Genet 2019; 132:2195-2207. [PMID: 31049630 DOI: 10.1007/s00122-019-03347-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Accepted: 04/20/2019] [Indexed: 06/09/2023]
Abstract
Wheat landrace accessions were chosen from areas of the world with historical European wheat stem sawfly (Cephus pygmaeus L.) selection pressure to develop six recombinant inbred line (RIL) populations. Molecular maps were constructed, and resistance due to antibiosis and antixenosis was assessed at sites in Montana naturally infested by Cephus cinctus Norton, the wheat stem sawfly (WSS). Novel QTLs were identified along with QTL previously identified in elite germplasm. A newly identified QTL on chromosome 1B provided a new source for pith-filled solid stems. An allele for resistance on chromosome 4A unrelated to solid stems was identified in four of the six RIL populations. A landrace from Turkey, PI 166471, contained alleles at three QTLs causing high levels of larval mortality. None of the QTLs were related to stem solidness, but their combined effect provided resistance similar to that observed in a solid-stemmed check cultivar. These results show the utility of genetic populations derived from geographically targeted landrace accessions to identify new alleles for insect resistance. New PCR-based molecular markers were developed for introgression of novel alleles for WSS resistance into elite lines. Comparison of results with previous analysis of elite cultivars addresses changes in allele frequencies during the wheat breeding process.
Collapse
Affiliation(s)
- Andrea C Varella
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT, 59717, USA
| | - David K Weaver
- Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, MT, 59717, USA
| | - Nancy K Blake
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT, 59717, USA
| | - Megan L Hofland
- Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, MT, 59717, USA
| | - Hwa-Young Heo
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT, 59717, USA
| | - Jason P Cook
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT, 59717, USA
| | - Peggy F Lamb
- Department of Research Centers, Montana State University, Bozeman, MT, 59717, USA
| | - Katherine W Jordan
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA
| | - Eduard Akhunov
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA
| | - Shiaoman Chao
- Cereal Crops Research Unit, USDA-ARS, Fargo, ND, 58102, USA
| | - Luther E Talbert
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT, 59717, USA.
| |
Collapse
|
22
|
He F, Pasam R, Shi F, Kant S, Keeble-Gagnere G, Kay P, Forrest K, Fritz A, Hucl P, Wiebe K, Knox R, Cuthbert R, Pozniak C, Akhunova A, Morrell PL, Davies JP, Webb SR, Spangenberg G, Hayes B, Daetwyler H, Tibbits J, Hayden M, Akhunov E. Exome sequencing highlights the role of wild-relative introgression in shaping the adaptive landscape of the wheat genome. Nat Genet 2019; 51:896-904. [PMID: 31043759 DOI: 10.1038/s41588-019-0382-2] [Citation(s) in RCA: 153] [Impact Index Per Article: 30.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 02/26/2019] [Indexed: 11/09/2022]
Abstract
Introgression is a potential source of beneficial genetic diversity. The contribution of introgression to adaptive evolution and improvement of wheat as it was disseminated worldwide remains unknown. We used targeted re-sequencing of 890 diverse accessions of hexaploid and tetraploid wheat to identify wild-relative introgression. Introgression, and selection for improvement and environmental adaptation, each reduced deleterious allele burden. Introgression increased diversity genome wide and in regions harboring major agronomic genes, and contributed alleles explaining a substantial proportion of phenotypic variation. These results suggest that historic gene flow from wild relatives made a substantial contribution to the adaptive diversity of modern bread wheat.
Collapse
Affiliation(s)
- Fei He
- Department of Plant Pathology, Kansas State University, Manhattan, KS, USA
| | - Raj Pasam
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, Victoria, Australia
| | - Fan Shi
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, Victoria, Australia
| | - Surya Kant
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, Victoria, Australia
| | | | - Pippa Kay
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, Victoria, Australia
| | - Kerrie Forrest
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, Victoria, Australia
| | - Allan Fritz
- Department of Agronomy, Kansas State University, Manhattan, KS, USA
| | - Pierre Hucl
- Crop Development Centre, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Krystalee Wiebe
- Crop Development Centre, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Ron Knox
- Swift Current Research and Development Centre, Swift Current, Saskatchewan, Canada
| | - Richard Cuthbert
- Swift Current Research and Development Centre, Swift Current, Saskatchewan, Canada
| | - Curtis Pozniak
- Crop Development Centre, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Alina Akhunova
- Department of Plant Pathology, Kansas State University, Manhattan, KS, USA.,Integrated Genomics Facility, Kansas State University, Manhattan, KS, USA
| | - Peter L Morrell
- Department of Agronomy and Plant Genetics, University of Minnesota, St Paul, MN, USA
| | - John P Davies
- Corteva Agriscience, Agriculture Division of DowDuPont, Indianapolis, IN, USA
| | - Steve R Webb
- Corteva Agriscience, Agriculture Division of DowDuPont, Indianapolis, IN, USA
| | - German Spangenberg
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, Victoria, Australia.,School of Applied Systems Biology, La Trobe University, Bundoora, Victoria, Australia
| | - Ben Hayes
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, Victoria, Australia.,Queensland Alliance for Agriculture and Food Innovation, Centre for Animal Science, University of Queensland, St Lucia, Queensland, Australia
| | - Hans Daetwyler
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, Victoria, Australia.,School of Applied Systems Biology, La Trobe University, Bundoora, Victoria, Australia
| | - Josquin Tibbits
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, Victoria, Australia.,School of Applied Systems Biology, La Trobe University, Bundoora, Victoria, Australia
| | - Matthew Hayden
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, Victoria, Australia. .,School of Applied Systems Biology, La Trobe University, Bundoora, Victoria, Australia.
| | - Eduard Akhunov
- Department of Plant Pathology, Kansas State University, Manhattan, KS, USA.
| |
Collapse
|
23
|
Gardiner LJ, Brabbs T, Akhunov A, Jordan K, Budak H, Richmond T, Singh S, Catchpole L, Akhunov E, Hall A. Integrating genomic resources to present full gene and putative promoter capture probe sets for bread wheat. Gigascience 2019. [PMID: 30715311 DOI: 10.1101/363663] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2023] Open
Abstract
BACKGROUND Whole-genome shotgun resequencing of wheat is expensive because of its large, repetitive genome. Moreover, sequence data can fail to map uniquely to the reference genome, making it difficult to unambiguously assign variation. Resequencing using target capture enables sequencing of large numbers of individuals at high coverage to reliably identify variants associated with important agronomic traits. Previous studies have implemented complementary DNA/exon or gene-based probe sets in which the promoter and intron sequence is largely missing alongside newly characterized genes from the recent improved reference sequences. RESULTS We present and validate 2 gold standard capture probe sets for hexaploid bread wheat, a gene and a putative promoter capture, which are designed using recently developed genome sequence and annotation resources. The captures can be combined or used independently. We demonstrate that the capture probe sets effectively enrich the high-confidence genes and putative promoter regions that were identified in the genome alongside a large proportion of the low-confidence genes and associated promoters. Finally, we demonstrate successful sample multiplexing that allows generation of adequate sequence coverage for single-nucleotide polymorphism calling while significantly reducing cost per sample for gene and putative promoter capture. CONCLUSIONS We show that a capture design employing an "island strategy" can enable analysis of the large gene/putative promoter space of wheat with only 2 × 160 Mbp probe sets. Furthermore, these assays extend the regions of the wheat genome that are amenable to analyses beyond its exome, providing tools for detailed characterization of these regulatory regions in large populations.
Collapse
Affiliation(s)
- Laura-Jayne Gardiner
- Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, UK
- IBM Research, The Hartree Centre STFC Laboratory, Sci-Tech Daresbury, Warrington, WA4 4AD, UK
| | - Thomas Brabbs
- Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, UK
| | - Alina Akhunov
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA
| | - Katherine Jordan
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA
| | - Hikmet Budak
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT, 59717, USA
| | - Todd Richmond
- Roche Sequencing Solutions, 500 S Rosa Road, Madison, WI, 53719, USA
| | - Sukhwinder Singh
- CIMMYT, Calle Dr Norman E Borlaug, Ciudad Obregon, 85208, Mexico
| | - Leah Catchpole
- Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, UK
| | - Eduard Akhunov
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA
| | - Anthony Hall
- Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, UK
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TU, UK
| |
Collapse
|
24
|
Gardiner LJ, Brabbs T, Akhunov A, Jordan K, Budak H, Richmond T, Singh S, Catchpole L, Akhunov E, Hall A. Integrating genomic resources to present full gene and putative promoter capture probe sets for bread wheat. Gigascience 2019. [PMID: 30715311 DOI: 10.5524/100554] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/11/2023] Open
Abstract
BACKGROUND Whole-genome shotgun resequencing of wheat is expensive because of its large, repetitive genome. Moreover, sequence data can fail to map uniquely to the reference genome, making it difficult to unambiguously assign variation. Resequencing using target capture enables sequencing of large numbers of individuals at high coverage to reliably identify variants associated with important agronomic traits. Previous studies have implemented complementary DNA/exon or gene-based probe sets in which the promoter and intron sequence is largely missing alongside newly characterized genes from the recent improved reference sequences. RESULTS We present and validate 2 gold standard capture probe sets for hexaploid bread wheat, a gene and a putative promoter capture, which are designed using recently developed genome sequence and annotation resources. The captures can be combined or used independently. We demonstrate that the capture probe sets effectively enrich the high-confidence genes and putative promoter regions that were identified in the genome alongside a large proportion of the low-confidence genes and associated promoters. Finally, we demonstrate successful sample multiplexing that allows generation of adequate sequence coverage for single-nucleotide polymorphism calling while significantly reducing cost per sample for gene and putative promoter capture. CONCLUSIONS We show that a capture design employing an "island strategy" can enable analysis of the large gene/putative promoter space of wheat with only 2 × 160 Mbp probe sets. Furthermore, these assays extend the regions of the wheat genome that are amenable to analyses beyond its exome, providing tools for detailed characterization of these regulatory regions in large populations.
Collapse
Affiliation(s)
- Laura-Jayne Gardiner
- Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, UK
- IBM Research, The Hartree Centre STFC Laboratory, Sci-Tech Daresbury, Warrington, WA4 4AD, UK
| | - Thomas Brabbs
- Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, UK
| | - Alina Akhunov
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA
| | - Katherine Jordan
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA
| | - Hikmet Budak
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT, 59717, USA
| | - Todd Richmond
- Roche Sequencing Solutions, 500 S Rosa Road, Madison, WI, 53719, USA
| | - Sukhwinder Singh
- CIMMYT, Calle Dr Norman E Borlaug, Ciudad Obregon, 85208, Mexico
| | - Leah Catchpole
- Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, UK
| | - Eduard Akhunov
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA
| | - Anthony Hall
- Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, UK
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TU, UK
| |
Collapse
|
25
|
Wang W, Simmonds J, Pan Q, Davidson D, He F, Battal A, Akhunova A, Trick HN, Uauy C, Akhunov E. Gene editing and mutagenesis reveal inter-cultivar differences and additivity in the contribution of TaGW2 homoeologues to grain size and weight in wheat. Theor Appl Genet 2018; 131:2463-2475. [PMID: 30136108 PMCID: PMC6208945 DOI: 10.1007/s00122-018-3166-7] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Accepted: 08/14/2018] [Indexed: 05/18/2023]
Abstract
KEY MESSAGE CRISPR-Cas9-based genome editing and EMS mutagenesis revealed inter-cultivar differences and additivity in the contribution of TaGW2 homoeologues to grain size and weight in wheat. The TaGW2 gene homoeologues have been reported to be negative regulators of grain size (GS) and thousand grain weight (TGW) in wheat. However, the contribution of each homoeologue to trait variation among different wheat cultivars is not well documented. We used the CRISPR-Cas9 system and TILLING to mutagenize each homoeologous gene copy in cultivars Bobwhite and Paragon, respectively. Plants carrying single-copy nonsense mutations in different genomes showed different levels of GS/TGW increase, with TGW increasing by an average of 5.5% (edited lines) and 5.3% (TILLING mutants). In any combination, the double homoeologue mutants showed higher phenotypic effects than the respective single-genome mutants. The double mutants had on average 12.1% (edited) and 10.5% (TILLING) higher TGW with respect to wild-type lines. The highest increase in GS and TGW was shown for triple mutants of both cultivars, with increases in 16.3% (edited) and 20.7% (TILLING) in TGW. The additive effects of the TaGW2 homoeologues were also demonstrated by the negative correlation between the functional gene copy number and GS/TGW in Bobwhite mutants and an F2 population. The highest single-genome increases in GS and TGW in Paragon and Bobwhite were obtained by mutations in the B and D genomes, respectively. These inter-cultivar differences in the phenotypic effects between the TaGW2 gene homoeologues coincide with inter-cultivar differences in the homoeologue expression levels. These results indicate that GS/TGW variation in wheat can be modulated by the dosage of homoeologous genes with inter-cultivar differences in the magnitude of the individual homoeologue effects.
Collapse
Affiliation(s)
- Wei Wang
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA
| | - James Simmonds
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Qianli Pan
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA
| | - Dwight Davidson
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA
| | - Fei He
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA
| | - Abdulhamit Battal
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
- Yuzuncu Yil University, Van, Turkey
| | - Alina Akhunova
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA
- Integrated Genomics Facility, Kansas State University, Manhattan, KS, USA
| | - Harold N Trick
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA
| | - Cristobal Uauy
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK.
| | - Eduard Akhunov
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA.
| |
Collapse
|
26
|
Zhang J, Gizaw SA, Bossolini E, Hegarty J, Howell T, Carter AH, Akhunov E, Dubcovsky J. Identification and validation of QTL for grain yield and plant water status under contrasting water treatments in fall-sown spring wheats. Theor Appl Genet 2018; 131:1741-1759. [PMID: 29767279 PMCID: PMC6061171 DOI: 10.1007/s00122-018-3111-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Accepted: 05/07/2018] [Indexed: 05/04/2023]
Abstract
KEY MESSAGE Chromosome regions affecting grain yield, grain yield components and plant water status were identified and validated in fall-sown spring wheats grown under full and limited irrigation. Increases in wheat production are required to feed a growing human population. To understand the genetic basis of grain yield in fall-sown spring wheats, we performed a genome-wide association study (GWAS) including 262 photoperiod-insensitive spring wheat accessions grown under full and limited irrigation treatments. Analysis of molecular variance showed that 4.1% of the total variation in the panel was partitioned among accessions originally developed under fall-sowing or spring-sowing conditions, 11.7% among breeding programs within sowing times and 84.2% among accessions within breeding programs. We first identified QTL for grain yield, yield components and plant water status that were significant in at least three environments in the GWAS, and then selected those that were also significant in at least two environments in a panel of eight biparental mapping populations. We identified and validated 14 QTL for grain yield, 15 for number of spikelets per spike, one for kernel number per spike, 11 for kernel weight and 9 for water status, which were not associated with differences in plant height or heading date. We detected significant correlations among traits and colocated QTL that were consistent with those correlations. Among those, grain yield and plant water status were negatively correlated in all environments, and six QTL for these traits were colocated or tightly linked (< 1 cM). QTL identified and validated in this study provide useful information for the improvement of fall-sown spring wheats under full and limited irrigation.
Collapse
Affiliation(s)
- Junli Zhang
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Shiferaw Abate Gizaw
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, 99164, USA
| | - Eligio Bossolini
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Joshua Hegarty
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Tyson Howell
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Arron H Carter
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, 99164, USA
| | - Eduard Akhunov
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66502, USA
| | - Jorge Dubcovsky
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, 20815, USA.
| |
Collapse
|
27
|
Elbasyoni IS, Lorenz AJ, Guttieri M, Frels K, Baenziger PS, Poland J, Akhunov E. A comparison between genotyping-by-sequencing and array-based scoring of SNPs for genomic prediction accuracy in winter wheat. Plant Sci 2018; 270:123-130. [PMID: 29576064 DOI: 10.1016/j.plantsci.2018.02.019] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [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: 10/10/2017] [Revised: 01/29/2018] [Accepted: 02/17/2018] [Indexed: 05/26/2023]
Abstract
The utilization of DNA molecular markers in plant breeding to maximize selection response via marker-assisted selection (MAS) and genomic selection (GS) has revolutionized plant breeding. A key factor affecting GS applicability is the choice of molecular marker platform. Genotyping-by-sequencing scored SNPs (GBS-scored SNPs) provides a large number of markers, albeit with high rates of missing data. Array scored SNPs are of high quality, but the cost per sample is substantially higher. The objectives of this study were 1) compare GBS-scored SNPs, and array scored SNPs for genomic selection applications, and 2) compare estimates of genomic kinship and population structure calculated using the two marker platforms. SNPs were compared in a diversity panel consisting of 299 hard winter wheat (Triticum aestivum L.) accessions that were part of a multi-year, multi-environments association mapping study. The panel was phenotyped in Ithaca, Nebraska for heading date, plant height, days to physiological maturity and grain yield in 2012 and 2013. The panel was genotyped using GBS-scored SNPs, and array scored SNPs. Results indicate that GBS-scored SNPs is comparable to or better than Array-scored SNPs for genomic prediction application. Both platforms identified the same genetic patterns in the panel where 90% of the lines were classified to common genetic groups. Overall, we concluded that GBS-scored SNPs have the potential to be the marker platform of choice for genetic diversity and genomic selection in winter wheat.
Collapse
Affiliation(s)
| | - A J Lorenz
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, 55108-6026, United States
| | - M Guttieri
- USDA Agricultural Research Service, Hard Winter Wheat Genetics Research Unit, Manhattan, KS, 66506-5502, United States
| | - K Frels
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, 55108-6026, United States
| | - P S Baenziger
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE, 68583-0915, United States
| | - J Poland
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506-5502, United States
| | - E Akhunov
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506-5502, United States
| |
Collapse
|
28
|
Wang W, Pan Q, He F, Akhunova A, Chao S, Trick H, Akhunov E. Transgenerational CRISPR-Cas9 Activity Facilitates Multiplex Gene Editing in Allopolyploid Wheat. CRISPR J 2018; 1:65-74. [PMID: 30627700 PMCID: PMC6319321 DOI: 10.1089/crispr.2017.0010] [Citation(s) in RCA: 106] [Impact Index Per Article: 17.7] [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] [Indexed: 02/02/2023] Open
Abstract
The CRISPR-Cas9-based multiplexed gene editing (MGE) provides a powerful method to modify multiple genomic regions simultaneously controlling different agronomic traits in crops. We applied the MGE construct built by combining the tandemly arrayed tRNA–gRNA units to generate heritable mutations in the TaGW2, TaLpx-1, and TaMLO genes of hexaploid wheat. The knockout mutations generated by this construct in all three homoeologous copies of one of the target genes, TaGW2, resulted in a substantial increase in seed size and thousand grain weight. We showed that the non-modified gRNA targets in the early generation plants can be edited by CRISPR-Cas9 in the following generations. Our results demonstrate that transgenerational gene editing activity can serve as the source of novel variation in the progeny of CRISPR-Cas9-expressing plants and suggest that the Cas9-inducible trait transfer for crop improvement can be achieved by crossing the plants expressing the gene editing constructs with the lines of interest.
Collapse
Affiliation(s)
- Wei Wang
- Department of Plant Pathology, Kansas State University, Manhattan, Kansas
| | - Qianli Pan
- Department of Plant Pathology, Kansas State University, Manhattan, Kansas
| | - Fei He
- Department of Plant Pathology, Kansas State University, Manhattan, Kansas
| | - Alina Akhunova
- Department of Plant Pathology, Kansas State University, Manhattan, Kansas.,Integrated Genomics Facility, Kansas State University, Manhattan, Kansas
| | - Shiaoman Chao
- USDA-ARS Cereal Crops Research Unit, Fargo, North Dakota
| | - Harold Trick
- Department of Plant Pathology, Kansas State University, Manhattan, Kansas
| | - Eduard Akhunov
- Department of Plant Pathology, Kansas State University, Manhattan, Kansas
| |
Collapse
|
29
|
Salcedo A, Rutter W, Wang S, Akhunova A, Bolus S, Chao S, Anderson N, De Soto MF, Rouse M, Szabo L, Bowden RL, Dubcovsky J, Akhunov E. Variation in the AvrSr35 gene determines Sr35 resistance against wheat stem rust race Ug99. Science 2017; 358:1604-1606. [PMID: 29269474 PMCID: PMC6518949 DOI: 10.1126/science.aao7294] [Citation(s) in RCA: 113] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Accepted: 11/09/2017] [Indexed: 01/04/2023]
Abstract
Puccinia graminis f. sp. tritici (Pgt) causes wheat stem rust, a devastating fungal disease. The Sr35 resistance gene confers immunity against this pathogen's most virulent races, including Ug99. We used comparative whole-genome sequencing of chemically mutagenized and natural Pgt isolates to identify a fungal gene named AvrSr35 that is required for Sr35 avirulence. The AvrSr35 gene encodes a secreted protein capable of interacting with Sr35 and triggering the immune response. We show that the origin of Pgt isolates virulent on Sr35 is associated with the nonfunctionalization of the AvrSr35 gene by the insertion of a mobile element. The discovery of AvrSr35 provides a new tool for Pgt surveillance, identification of host susceptibility targets, and characterization of the molecular determinants of immunity in wheat.
Collapse
Affiliation(s)
- Andres Salcedo
- Department of Plant Pathology, Kansas State University, Manhattan, KS 66506, USA
| | - William Rutter
- Department of Plant Pathology, Kansas State University, Manhattan, KS 66506, USA
| | - Shichen Wang
- Department of Plant Pathology, Kansas State University, Manhattan, KS 66506, USA
| | - Alina Akhunova
- Integrated Genomics Facility, Kansas State University, Manhattan, KS 66506, USA
| | - Stephen Bolus
- Department of Plant Sciences, University of California, Davis, CA 95616, USA
| | - Shiaoman Chao
- U.S. Department of Agriculture, Agricultural Research Service (USDA-ARS) Cereal Crops Research Unit, Fargo, ND 58102, USA
| | - Nickolas Anderson
- Department of Plant Pathology, Kansas State University, Manhattan, KS 66506, USA
| | | | - Matthew Rouse
- USDA-ARS, Cereal Disease Laboratory, St. Paul, MN 55108, USA
- Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108, USA
| | - Les Szabo
- USDA-ARS, Cereal Disease Laboratory, St. Paul, MN 55108, USA
- Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108, USA
| | - Robert L. Bowden
- USDA-ARS, Hard Winter Wheat Genetics Research Unit, Manhattan, KS 66506, USA
| | - Jorge Dubcovsky
- Department of Plant Sciences, University of California, Davis, CA 95616, USA
- Howard Hughes Medical Institute (HHMI), Chevy Chase, MD 20815, USA
| | - Eduard Akhunov
- Department of Plant Pathology, Kansas State University, Manhattan, KS 66506, USA
- Corresponding author.
| |
Collapse
|
30
|
Hu Y, Wu Q, Peng Z, Sprague SA, Wang W, Park J, Akhunov E, Jagadish KSV, Nakata PA, Cheng N, Hirschi KD, White FF, Park S. Silencing of OsGRXS17 in rice improves drought stress tolerance by modulating ROS accumulation and stomatal closure. Sci Rep 2017; 7:15950. [PMID: 29162892 PMCID: PMC5698295 DOI: 10.1038/s41598-017-16230-7] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [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: 07/14/2017] [Accepted: 11/09/2017] [Indexed: 12/02/2022] Open
Abstract
Glutaredoxins (GRXs) modulate redox-dependent signaling pathways and have emerged as key mediators in plant responses to environmental stimuli. Here we report that RNAi-mediated suppression of Oryza sativa GRXS17 (OsGRXS17) improved drought tolerance in rice. Gene expression studies showed that OsGRXS17 was present throughout the plant and that transcript abundance increased in response to drought stress and abscisic acid (ABA) treatment. Localization studies, utilizing GFP-OsGRXS17 fusion proteins, indicated that OsGRXS17 resides in both the cytoplasm and the nuclear envelope. Under drought stress conditions, rice plants with reduced OsGRXS17 expression showed lower rates of water loss and stomatal conductance, higher relative water content, and enhanced survival compared to wild-type controls. Further characterization of the OsGRXS17 down-regulated plants revealed an elevation in H2O2 production within the guard cells, increased sensitivity to ABA, and a reduction in stomatal apertures. The findings demonstrate a critical link between OsGRXS17, the modulation of guard cell H2O2 concentrations, and stomatal closure, expanding our understanding of the mechanisms governing plant responses to drought.
Collapse
Affiliation(s)
- Ying Hu
- Department of Horticulture and Natural Resources, Kansas State University, Manhattan, KS, 66506, USA.,Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA
| | - Qingyu Wu
- Department of Horticulture and Natural Resources, Kansas State University, Manhattan, KS, 66506, USA.,Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA
| | - Zhao Peng
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA.,Department of Plant Pathology, University of Florida, Gainesville, FL, 32611, USA
| | - Stuart A Sprague
- Department of Horticulture and Natural Resources, Kansas State University, Manhattan, KS, 66506, USA
| | - Wei Wang
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA
| | - Jungeun Park
- Department of Horticulture and Natural Resources, Kansas State University, Manhattan, KS, 66506, USA
| | - Eduard Akhunov
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA
| | | | - Paul A Nakata
- United States Department of Agriculture/Agricultural Research Service, Children's Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Ninghui Cheng
- United States Department of Agriculture/Agricultural Research Service, Children's Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Kendal D Hirschi
- United States Department of Agriculture/Agricultural Research Service, Children's Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Frank F White
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA. .,Department of Plant Pathology, University of Florida, Gainesville, FL, 32611, USA.
| | - Sunghun Park
- Department of Horticulture and Natural Resources, Kansas State University, Manhattan, KS, 66506, USA.
| |
Collapse
|
31
|
Shi F, Tibbits J, Pasam RK, Kay P, Wong D, Petkowski J, Forrest KL, Hayes BJ, Akhunova A, Davies J, Webb S, Spangenberg GC, Akhunov E, Hayden MJ, Daetwyler HD. Exome sequence genotype imputation in globally diverse hexaploid wheat accessions. Theor Appl Genet 2017; 130:1393-1404. [PMID: 28378053 DOI: 10.1007/s00122-017-2895-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Accepted: 03/18/2017] [Indexed: 06/07/2023]
Abstract
Imputing genotypes from the 90K SNP chip to exome sequence in wheat was moderately accurate. We investigated the factors that affect imputation and propose several strategies to improve accuracy. Imputing genetic marker genotypes from low to high density has been proposed as a cost-effective strategy to increase the power of downstream analyses (e.g. genome-wide association studies and genomic prediction) for a given budget. However, imputation is often imperfect and its accuracy depends on several factors. Here, we investigate the effects of reference population selection algorithms, marker density and imputation algorithms (Beagle4 and FImpute) on the accuracy of imputation from low SNP density (9K array) to the Infinium 90K single-nucleotide polymorphism (SNP) array for a collection of 837 hexaploid wheat Watkins landrace accessions. Based on these results, we then used the best performing reference selection and imputation algorithms to investigate imputation from 90K to exome sequence for a collection of 246 globally diverse wheat accessions. Accession-to-nearest-entry and genomic relationship-based methods were the best performing selection algorithms, and FImpute resulted in higher accuracy and was more efficient than Beagle4. The accuracy of imputing exome capture SNPs was comparable to imputing from 9 to 90K at approximately 0.71. This relatively low imputation accuracy is in part due to inconsistency between 90K and exome sequence formats. We also found the accuracy of imputation could be substantially improved to 0.82 when choosing an equivalent number of exome SNP, instead of 90K SNPs on the existing array, as the lower density set. We present a number of recommendations to increase the accuracy of exome imputation.
Collapse
Affiliation(s)
- Fan Shi
- Agriculture Victoria, Agriculture Research Division, AgriBio, Centre for AgriBioscience, Bundoora, VIC, Australia.
| | - Josquin Tibbits
- Agriculture Victoria, Agriculture Research Division, AgriBio, Centre for AgriBioscience, Bundoora, VIC, Australia
| | - Raj K Pasam
- Agriculture Victoria, Agriculture Research Division, AgriBio, Centre for AgriBioscience, Bundoora, VIC, Australia
| | - Pippa Kay
- Agriculture Victoria, Agriculture Research Division, AgriBio, Centre for AgriBioscience, Bundoora, VIC, Australia
| | - Debbie Wong
- Agriculture Victoria, Agriculture Research Division, AgriBio, Centre for AgriBioscience, Bundoora, VIC, Australia
| | - Joanna Petkowski
- Agriculture Victoria, Agriculture Research Division, AgriBio, Centre for AgriBioscience, Bundoora, VIC, Australia
| | - Kerrie L Forrest
- Agriculture Victoria, Agriculture Research Division, AgriBio, Centre for AgriBioscience, Bundoora, VIC, Australia
| | - Ben J Hayes
- Agriculture Victoria, Agriculture Research Division, AgriBio, Centre for AgriBioscience, Bundoora, VIC, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, Australia
| | - Alina Akhunova
- Department of Plant Pathology, Kansas State University, Manhattan, KS, USA
- Integrated Genomics Facility, Kansas State University, Manhattan, KS, USA
| | | | | | - German C Spangenberg
- Agriculture Victoria, Agriculture Research Division, AgriBio, Centre for AgriBioscience, Bundoora, VIC, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, Australia
| | - Eduard Akhunov
- Department of Plant Pathology, Kansas State University, Manhattan, KS, USA
| | - Matthew J Hayden
- Agriculture Victoria, Agriculture Research Division, AgriBio, Centre for AgriBioscience, Bundoora, VIC, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, Australia
| | - Hans D Daetwyler
- Agriculture Victoria, Agriculture Research Division, AgriBio, Centre for AgriBioscience, Bundoora, VIC, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, Australia
| |
Collapse
|
32
|
Rutter WB, Salcedo A, Akhunova A, He F, Wang S, Liang H, Bowden RL, Akhunov E. Divergent and convergent modes of interaction between wheat and Puccinia graminis f. sp. tritici isolates revealed by the comparative gene co-expression network and genome analyses. BMC Genomics 2017; 18:291. [PMID: 28403814 PMCID: PMC5389088 DOI: 10.1186/s12864-017-3678-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Accepted: 04/03/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Two opposing evolutionary constraints exert pressure on plant pathogens: one to diversify virulence factors in order to evade plant defenses, and the other to retain virulence factors critical for maintaining a compatible interaction with the plant host. To better understand how the diversified arsenals of fungal genes promote interaction with the same compatible wheat line, we performed a comparative genomic analysis of two North American isolates of Puccinia graminis f. sp. tritici (Pgt). RESULTS The patterns of inter-isolate divergence in the secreted candidate effector genes were compared with the levels of conservation and divergence of plant-pathogen gene co-expression networks (GCN) developed for each isolate. Comprative genomic analyses revealed substantial level of interisolate divergence in effector gene complement and sequence divergence. Gene Ontology (GO) analyses of the conserved and unique parts of the isolate-specific GCNs identified a number of conserved host pathways targeted by both isolates. Interestingly, the degree of inter-isolate sub-network conservation varied widely for the different host pathways and was positively associated with the proportion of conserved effector candidates associated with each sub-network. While different Pgt isolates tended to exploit similar wheat pathways for infection, the mode of plant-pathogen interaction varied for different pathways with some pathways being associated with the conserved set of effectors and others being linked with the diverged or isolate-specific effectors. CONCLUSIONS Our data suggest that at the intra-species level pathogen populations likely maintain divergent sets of effectors capable of targeting the same plant host pathways. This functional redundancy may play an important role in the dynamic of the "arms-race" between host and pathogen serving as the basis for diverse virulence strategies and creating conditions where mutations in certain effector groups will not have a major effect on the pathogen's ability to infect the host.
Collapse
Affiliation(s)
- William B. Rutter
- Department of Plant Pathology, Kansas State University, Manhattan, KS 66506 USA
- USDA-ARS, U.S. Vegetable Laboratory, 2700 Savannah Highway, Charleston, SC 29414 USA
| | - Andres Salcedo
- Department of Plant Pathology, Kansas State University, Manhattan, KS 66506 USA
| | - Alina Akhunova
- Integrated Genomics Facility, Kansas State University, Manhattan, KS 66506 USA
| | - Fei He
- Department of Plant Pathology, Kansas State University, Manhattan, KS 66506 USA
| | - Shichen Wang
- Department of Plant Pathology, Kansas State University, Manhattan, KS 66506 USA
- TEES-AgriLife Center for Bioinformatics and Genomic Systems Engineering, Texas A&M University, 101 Gateway, Suite A, College Station, TX 77845 USA
| | - Hanquan Liang
- Integrated Genomics Facility, Kansas State University, Manhattan, KS 66506 USA
- School of Data and Computer Science, Sun Yat-sen University, Guangzhou, 510006 China
| | - Robert L. Bowden
- USDA ARS, Hard Winter Wheat Genetics Research Unit, Throckmorton Plant Sciences Center, Manhattan, KS 66506 USA
| | - Eduard Akhunov
- Department of Plant Pathology, Kansas State University, Manhattan, KS 66506 USA
| |
Collapse
|
33
|
Balcárková B, Frenkel Z, Škopová M, Abrouk M, Kumar A, Chao S, Kianian SF, Akhunov E, Korol AB, Doležel J, Valárik M. A High Resolution Radiation Hybrid Map of Wheat Chromosome 4A. Front Plant Sci 2017; 7:2063. [PMID: 28119729 PMCID: PMC5222868 DOI: 10.3389/fpls.2016.02063] [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] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Accepted: 12/26/2016] [Indexed: 05/18/2023]
Abstract
Bread wheat has a large and complex allohexaploid genome with low recombination level at chromosome centromeric and peri-centromeric regions. This significantly hampers ordering of markers, contigs of physical maps and sequence scaffolds and impedes obtaining of high-quality reference genome sequence. Here we report on the construction of high-density and high-resolution radiation hybrid (RH) map of chromosome 4A supported by high-density chromosome deletion map. A total of 119 endosperm-based RH lines of two RH panels and 15 chromosome deletion bin lines were genotyped with 90K iSelect single nucleotide polymorphism (SNP) array. A total of 2316 and 2695 markers were successfully mapped to the 4A RH and deletion maps, respectively. The chromosome deletion map was ordered in 19 bins and allowed precise identification of centromeric region and verification of the RH panel reliability. The 4A-specific RH map comprises 1080 mapping bins and spans 6550.9 cR with a resolution of 0.13 Mb/cR. Significantly higher mapping resolution in the centromeric region was observed as compared to recombination maps. Relatively even distribution of deletion frequency along the chromosome in the RH panel was observed and putative functional centromere was delimited within a region characterized by two SNP markers.
Collapse
Affiliation(s)
- Barbora Balcárková
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural ResearchOlomouc, Czechia
| | - Zeev Frenkel
- Institute of Evolution, University of HaifaHaifa, Israel
| | - Monika Škopová
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural ResearchOlomouc, Czechia
| | - Michael Abrouk
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural ResearchOlomouc, Czechia
| | - Ajay Kumar
- Department of Plant Sciences, North Dakota State University, FargoND, USA
| | - Shiaoman Chao
- Biosciences Research Laboratory, United States Department of Agriculture-Agricultural Research Service, FargoND, USA
| | - Shahryar F. Kianian
- Cereal Disease Laboratory, United States Department of Agriculture-Agricultural Research Service, University of Minnesota, St. PaulMN, USA
| | - Eduard Akhunov
- Department of Plant Pathology, Kansas State University, ManhattanKS, USA
| | | | - Jaroslav Doležel
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural ResearchOlomouc, Czechia
| | - Miroslav Valárik
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural ResearchOlomouc, Czechia
| |
Collapse
|
34
|
Nirmala J, Chao S, Olivera P, Babiker EM, Abeyo B, Tadesse Z, Imtiaz M, Talbert L, Blake NK, Akhunov E, Pumphrey MO, Jin Y, Rouse MN. Markers Linked to Wheat Stem Rust Resistance Gene Sr11 Effective to Puccinia graminis f. sp. tritici Race TKTTF. Phytopathology 2016; 106:1352-1358. [PMID: 27359266 DOI: 10.1094/phyto-04-16-0165-r] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [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
Wheat stem rust, caused by Puccinia graminis f. sp. tritici, can cause severe yield losses on susceptible wheat varieties and cultivars. Although stem rust can be controlled by the use of genetic resistance, population dynamics of P. graminis f. sp. tritici can frequently lead to defeat of wheat stem rust resistance genes. P. graminis f. sp. tritici race TKTTF caused a severe epidemic in Ethiopia on Ug99-resistant 'Digalu' in 2013 and 2014. The gene Sr11 confers resistance to race TKTTF and is present in 'Gabo 56'. We identified seven single-nucleotide polymorphism (SNP) markers linked to Sr11 from a cross between Gabo 56 and 'Chinese Spring' exploiting a 90K Infinium iSelect Custom beadchip. Five SNP markers were validated on a 'Berkut'/'Scalavatis' population that segregated for Sr11, using KBioscience competitive allele-specific polymerase chain reaction (KASP) assays. Two of the SNP markers, KASP_6BL_IWB10724 and KASP_6BL_IWB72471, were predictive of Sr11 among wheat genetic stocks, cultivars, and breeding lines from North America, Ethiopia, and Pakistan. These markers can be utilized to select for Sr11 in wheat breeding and to detect the presence of Sr11 in uncharacterized germplasm.
Collapse
Affiliation(s)
- Jayaveeramuthu Nirmala
- First, twelfth, and thirteenth authors: Cereal Disease Laboratory, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), St. Paul, MN 55108; second author: Cereal Crops Research, USDA-ARS, Fargo, ND, 58102; third, twelfth, and thirteenth authors: Department of Plant Pathology, University of Minnesota, St. Paul 55108; fourth author: Small Grains and Potato Germplasm Research Unit, USDA-ARS, Aberdeen, ID 83210; fifth author: International Maize and Wheat Improvement Center (CIMMYT)-Ethiopia, Addis Ababa, Ethiopia; sixth author: Ethiopian Institute of Agricultural Research, Kulumsa Agricultural Research Center, Kulumsa, Ethiopia; seventh author: CIMMYT-Pakistan, Islamabad, Pakistan; eighth and ninth authors: Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman 59717; tenth author: Department of Plant Pathology, Kansas State University, Manhattan 66506; and eleventh author: Department of Crop and Soil Sciences, Washington State University, Pullman, 99164
| | - Shiaoman Chao
- First, twelfth, and thirteenth authors: Cereal Disease Laboratory, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), St. Paul, MN 55108; second author: Cereal Crops Research, USDA-ARS, Fargo, ND, 58102; third, twelfth, and thirteenth authors: Department of Plant Pathology, University of Minnesota, St. Paul 55108; fourth author: Small Grains and Potato Germplasm Research Unit, USDA-ARS, Aberdeen, ID 83210; fifth author: International Maize and Wheat Improvement Center (CIMMYT)-Ethiopia, Addis Ababa, Ethiopia; sixth author: Ethiopian Institute of Agricultural Research, Kulumsa Agricultural Research Center, Kulumsa, Ethiopia; seventh author: CIMMYT-Pakistan, Islamabad, Pakistan; eighth and ninth authors: Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman 59717; tenth author: Department of Plant Pathology, Kansas State University, Manhattan 66506; and eleventh author: Department of Crop and Soil Sciences, Washington State University, Pullman, 99164
| | - Pablo Olivera
- First, twelfth, and thirteenth authors: Cereal Disease Laboratory, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), St. Paul, MN 55108; second author: Cereal Crops Research, USDA-ARS, Fargo, ND, 58102; third, twelfth, and thirteenth authors: Department of Plant Pathology, University of Minnesota, St. Paul 55108; fourth author: Small Grains and Potato Germplasm Research Unit, USDA-ARS, Aberdeen, ID 83210; fifth author: International Maize and Wheat Improvement Center (CIMMYT)-Ethiopia, Addis Ababa, Ethiopia; sixth author: Ethiopian Institute of Agricultural Research, Kulumsa Agricultural Research Center, Kulumsa, Ethiopia; seventh author: CIMMYT-Pakistan, Islamabad, Pakistan; eighth and ninth authors: Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman 59717; tenth author: Department of Plant Pathology, Kansas State University, Manhattan 66506; and eleventh author: Department of Crop and Soil Sciences, Washington State University, Pullman, 99164
| | - Ebrahiem M Babiker
- First, twelfth, and thirteenth authors: Cereal Disease Laboratory, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), St. Paul, MN 55108; second author: Cereal Crops Research, USDA-ARS, Fargo, ND, 58102; third, twelfth, and thirteenth authors: Department of Plant Pathology, University of Minnesota, St. Paul 55108; fourth author: Small Grains and Potato Germplasm Research Unit, USDA-ARS, Aberdeen, ID 83210; fifth author: International Maize and Wheat Improvement Center (CIMMYT)-Ethiopia, Addis Ababa, Ethiopia; sixth author: Ethiopian Institute of Agricultural Research, Kulumsa Agricultural Research Center, Kulumsa, Ethiopia; seventh author: CIMMYT-Pakistan, Islamabad, Pakistan; eighth and ninth authors: Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman 59717; tenth author: Department of Plant Pathology, Kansas State University, Manhattan 66506; and eleventh author: Department of Crop and Soil Sciences, Washington State University, Pullman, 99164
| | - Bekele Abeyo
- First, twelfth, and thirteenth authors: Cereal Disease Laboratory, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), St. Paul, MN 55108; second author: Cereal Crops Research, USDA-ARS, Fargo, ND, 58102; third, twelfth, and thirteenth authors: Department of Plant Pathology, University of Minnesota, St. Paul 55108; fourth author: Small Grains and Potato Germplasm Research Unit, USDA-ARS, Aberdeen, ID 83210; fifth author: International Maize and Wheat Improvement Center (CIMMYT)-Ethiopia, Addis Ababa, Ethiopia; sixth author: Ethiopian Institute of Agricultural Research, Kulumsa Agricultural Research Center, Kulumsa, Ethiopia; seventh author: CIMMYT-Pakistan, Islamabad, Pakistan; eighth and ninth authors: Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman 59717; tenth author: Department of Plant Pathology, Kansas State University, Manhattan 66506; and eleventh author: Department of Crop and Soil Sciences, Washington State University, Pullman, 99164
| | - Zerihun Tadesse
- First, twelfth, and thirteenth authors: Cereal Disease Laboratory, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), St. Paul, MN 55108; second author: Cereal Crops Research, USDA-ARS, Fargo, ND, 58102; third, twelfth, and thirteenth authors: Department of Plant Pathology, University of Minnesota, St. Paul 55108; fourth author: Small Grains and Potato Germplasm Research Unit, USDA-ARS, Aberdeen, ID 83210; fifth author: International Maize and Wheat Improvement Center (CIMMYT)-Ethiopia, Addis Ababa, Ethiopia; sixth author: Ethiopian Institute of Agricultural Research, Kulumsa Agricultural Research Center, Kulumsa, Ethiopia; seventh author: CIMMYT-Pakistan, Islamabad, Pakistan; eighth and ninth authors: Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman 59717; tenth author: Department of Plant Pathology, Kansas State University, Manhattan 66506; and eleventh author: Department of Crop and Soil Sciences, Washington State University, Pullman, 99164
| | - Muhammad Imtiaz
- First, twelfth, and thirteenth authors: Cereal Disease Laboratory, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), St. Paul, MN 55108; second author: Cereal Crops Research, USDA-ARS, Fargo, ND, 58102; third, twelfth, and thirteenth authors: Department of Plant Pathology, University of Minnesota, St. Paul 55108; fourth author: Small Grains and Potato Germplasm Research Unit, USDA-ARS, Aberdeen, ID 83210; fifth author: International Maize and Wheat Improvement Center (CIMMYT)-Ethiopia, Addis Ababa, Ethiopia; sixth author: Ethiopian Institute of Agricultural Research, Kulumsa Agricultural Research Center, Kulumsa, Ethiopia; seventh author: CIMMYT-Pakistan, Islamabad, Pakistan; eighth and ninth authors: Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman 59717; tenth author: Department of Plant Pathology, Kansas State University, Manhattan 66506; and eleventh author: Department of Crop and Soil Sciences, Washington State University, Pullman, 99164
| | - Luther Talbert
- First, twelfth, and thirteenth authors: Cereal Disease Laboratory, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), St. Paul, MN 55108; second author: Cereal Crops Research, USDA-ARS, Fargo, ND, 58102; third, twelfth, and thirteenth authors: Department of Plant Pathology, University of Minnesota, St. Paul 55108; fourth author: Small Grains and Potato Germplasm Research Unit, USDA-ARS, Aberdeen, ID 83210; fifth author: International Maize and Wheat Improvement Center (CIMMYT)-Ethiopia, Addis Ababa, Ethiopia; sixth author: Ethiopian Institute of Agricultural Research, Kulumsa Agricultural Research Center, Kulumsa, Ethiopia; seventh author: CIMMYT-Pakistan, Islamabad, Pakistan; eighth and ninth authors: Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman 59717; tenth author: Department of Plant Pathology, Kansas State University, Manhattan 66506; and eleventh author: Department of Crop and Soil Sciences, Washington State University, Pullman, 99164
| | - Nancy K Blake
- First, twelfth, and thirteenth authors: Cereal Disease Laboratory, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), St. Paul, MN 55108; second author: Cereal Crops Research, USDA-ARS, Fargo, ND, 58102; third, twelfth, and thirteenth authors: Department of Plant Pathology, University of Minnesota, St. Paul 55108; fourth author: Small Grains and Potato Germplasm Research Unit, USDA-ARS, Aberdeen, ID 83210; fifth author: International Maize and Wheat Improvement Center (CIMMYT)-Ethiopia, Addis Ababa, Ethiopia; sixth author: Ethiopian Institute of Agricultural Research, Kulumsa Agricultural Research Center, Kulumsa, Ethiopia; seventh author: CIMMYT-Pakistan, Islamabad, Pakistan; eighth and ninth authors: Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman 59717; tenth author: Department of Plant Pathology, Kansas State University, Manhattan 66506; and eleventh author: Department of Crop and Soil Sciences, Washington State University, Pullman, 99164
| | - Eduard Akhunov
- First, twelfth, and thirteenth authors: Cereal Disease Laboratory, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), St. Paul, MN 55108; second author: Cereal Crops Research, USDA-ARS, Fargo, ND, 58102; third, twelfth, and thirteenth authors: Department of Plant Pathology, University of Minnesota, St. Paul 55108; fourth author: Small Grains and Potato Germplasm Research Unit, USDA-ARS, Aberdeen, ID 83210; fifth author: International Maize and Wheat Improvement Center (CIMMYT)-Ethiopia, Addis Ababa, Ethiopia; sixth author: Ethiopian Institute of Agricultural Research, Kulumsa Agricultural Research Center, Kulumsa, Ethiopia; seventh author: CIMMYT-Pakistan, Islamabad, Pakistan; eighth and ninth authors: Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman 59717; tenth author: Department of Plant Pathology, Kansas State University, Manhattan 66506; and eleventh author: Department of Crop and Soil Sciences, Washington State University, Pullman, 99164
| | - Michael O Pumphrey
- First, twelfth, and thirteenth authors: Cereal Disease Laboratory, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), St. Paul, MN 55108; second author: Cereal Crops Research, USDA-ARS, Fargo, ND, 58102; third, twelfth, and thirteenth authors: Department of Plant Pathology, University of Minnesota, St. Paul 55108; fourth author: Small Grains and Potato Germplasm Research Unit, USDA-ARS, Aberdeen, ID 83210; fifth author: International Maize and Wheat Improvement Center (CIMMYT)-Ethiopia, Addis Ababa, Ethiopia; sixth author: Ethiopian Institute of Agricultural Research, Kulumsa Agricultural Research Center, Kulumsa, Ethiopia; seventh author: CIMMYT-Pakistan, Islamabad, Pakistan; eighth and ninth authors: Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman 59717; tenth author: Department of Plant Pathology, Kansas State University, Manhattan 66506; and eleventh author: Department of Crop and Soil Sciences, Washington State University, Pullman, 99164
| | - Yue Jin
- First, twelfth, and thirteenth authors: Cereal Disease Laboratory, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), St. Paul, MN 55108; second author: Cereal Crops Research, USDA-ARS, Fargo, ND, 58102; third, twelfth, and thirteenth authors: Department of Plant Pathology, University of Minnesota, St. Paul 55108; fourth author: Small Grains and Potato Germplasm Research Unit, USDA-ARS, Aberdeen, ID 83210; fifth author: International Maize and Wheat Improvement Center (CIMMYT)-Ethiopia, Addis Ababa, Ethiopia; sixth author: Ethiopian Institute of Agricultural Research, Kulumsa Agricultural Research Center, Kulumsa, Ethiopia; seventh author: CIMMYT-Pakistan, Islamabad, Pakistan; eighth and ninth authors: Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman 59717; tenth author: Department of Plant Pathology, Kansas State University, Manhattan 66506; and eleventh author: Department of Crop and Soil Sciences, Washington State University, Pullman, 99164
| | - Matthew N Rouse
- First, twelfth, and thirteenth authors: Cereal Disease Laboratory, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), St. Paul, MN 55108; second author: Cereal Crops Research, USDA-ARS, Fargo, ND, 58102; third, twelfth, and thirteenth authors: Department of Plant Pathology, University of Minnesota, St. Paul 55108; fourth author: Small Grains and Potato Germplasm Research Unit, USDA-ARS, Aberdeen, ID 83210; fifth author: International Maize and Wheat Improvement Center (CIMMYT)-Ethiopia, Addis Ababa, Ethiopia; sixth author: Ethiopian Institute of Agricultural Research, Kulumsa Agricultural Research Center, Kulumsa, Ethiopia; seventh author: CIMMYT-Pakistan, Islamabad, Pakistan; eighth and ninth authors: Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman 59717; tenth author: Department of Plant Pathology, Kansas State University, Manhattan 66506; and eleventh author: Department of Crop and Soil Sciences, Washington State University, Pullman, 99164
| |
Collapse
|
35
|
Rawat N, Pumphrey MO, Liu S, Zhang X, Tiwari VK, Ando K, Trick HN, Bockus WW, Akhunov E, Anderson JA, Gill BS. Wheat Fhb1 encodes a chimeric lectin with agglutinin domains and a pore-forming toxin-like domain conferring resistance to Fusarium head blight. Nat Genet 2016; 48:1576-1580. [DOI: 10.1038/ng.3706] [Citation(s) in RCA: 208] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Accepted: 09/29/2016] [Indexed: 11/09/2022]
|
36
|
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.
Collapse
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
| |
Collapse
|
37
|
Cruz C, Peterson G, Bockus W, Kankanala P, Dubcovsky J, Jordan K, Akhunov E, Chumley F, Baldelomar F, Valent B. The 2NS Translocation from Aegilops ventricosa Confers Resistance to the Triticum Pathotype of Magnaporthe oryzae. Crop Sci 2016; 56:990-1000. [PMID: 27814405 PMCID: PMC5087972 DOI: 10.2135/cropsci2015.07.0410] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Accepted: 01/21/2016] [Indexed: 05/20/2023]
Abstract
Wheat blast is a serious disease caused by the fungus Magnaporthe oryzae (Triticum pathotype) (MoT). The objective of this study was to determine the effect of the 2NS translocation from Aegilops ventricosa (Zhuk.) Chennav on wheat head and leaf blast resistance. Disease phenotyping experiments were conducted in growth chamber, greenhouse, and field environments. Among 418 cultivars of wheat (Triticum aestivum L.), those with 2NS had 50.4 to 72.3% less head blast than those without 2NS when inoculated with an older MoT isolate under growth chamber conditions. When inoculated with recently collected isolates, cultivars with 2NS had 64.0 to 80.5% less head blast. Under greenhouse conditions when lines were inoculated with an older MoT isolate, those with 2NS had a significant head blast reduction. With newer isolates, not all lines with 2NS showed a significant reduction in head blast, suggesting that the genetic background and/or environment may influence the expression of any resistance conferred by 2NS. However, when near-isogenic lines (NILs) with and without 2NS were planted in the field, there was strong evidence that 2NS conferred resistance to head blast. Results from foliar inoculations suggest that the resistance to head infection that is imparted by the 2NS translocation does not confer resistance to foliar disease. In conclusion, the 2NS translocation was associated with significant reductions in head blast in both spring and winter wheat.
Collapse
Affiliation(s)
- C.D. Cruz
- Dep. of Plant Pathology, Kansas State Univ., 1712 Claflin Rd., Manhattan, KS 66506
| | | | - W.W. Bockus
- Dep. of Plant Pathology, Kansas State Univ., 1712 Claflin Rd., Manhattan, KS 66506
| | - P. Kankanala
- Dep. of Plant Pathology, Kansas State Univ., 1712 Claflin Rd., Manhattan, KS 66506
| | - J. Dubcovsky
- Howard Hughes Medical Institute, Chevy Chase, MD 20815
| | - K.W. Jordan
- Dep. of Plant Pathology, Kansas State Univ., 1712 Claflin Rd., Manhattan, KS 66506
| | - E. Akhunov
- Dep. of Plant Pathology, Kansas State Univ., 1712 Claflin Rd., Manhattan, KS 66506
| | - F. Chumley
- Dep. of Plant Pathology, Kansas State Univ., 1712 Claflin Rd., Manhattan, KS 66506
| | - F.D. Baldelomar
- Asociación Nacional de Productores de Oleaginosas y Trigo, Av. Ovidio Barbery esq. Jaime Mendoza, Santa Cruz de la Sierra, Bolivia
| | - B. Valent
- Dep. of Plant Pathology, Kansas State Univ., 1712 Claflin Rd., Manhattan, KS 66506
| |
Collapse
|
38
|
Hofstad AN, Nussbaumer T, Akhunov E, Shin S, Kugler KG, Kistler HC, Mayer KFX, Muehlbauer GJ. Examining the Transcriptional Response in Wheat Near-Isogenic Lines to Infection and Deoxynivalenol Treatment. Plant Genome 2016; 9. [PMID: 27898755 DOI: 10.3835/plantgenome2015.05.0032] [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: 05/20/2023]
Abstract
head blight (FHB) is a disease caused predominantly by the fungal pathogen that affects wheat and other small-grain cereals and can lead to severe yield loss and reduction in grain quality. Trichothecene mycotoxins, such as deoxynivalenol (DON), accumulate during infection and increase pathogen virulence and decrease grain quality. The locus on wheat chromosome 3BS confers Type II resistance to FHB and resistance to the spread of infection on the spike and has been associated with resistance to DON accumulation. To gain a better genetic understanding of the functional role of and resistance or susceptibility to FHB, we examined DON and ergosterol accumulation, FHB resistance, and the whole-genome transcriptomic response using RNA-seq in a near-isogenic line (NIL) pair carrying the resistant and susceptible alleles for during infection and DON treatment. Our results provide a gene expression atlas for the resistant and susceptible wheat- interaction. The DON concentration and transcriptomic results show that the rachis is a key location for conferring Type II resistance. In addition, the wheat transcriptome analysis revealed a set of -responsive genes that may play a role in resistance and a set of DON-responsive genes that may play a role in trichothecene resistance. Transcriptomic results from the pathogen show that the genome responds differently to the host level of resistance. The results of this study extend our understanding of host and pathogen responses in the wheat- interaction.
Collapse
|
39
|
Tiwari VK, Wang S, Danilova T, Koo DH, Vrána J, Kubaláková M, Hribova E, Rawat N, Kalia B, Singh N, Friebe B, Doležel J, Akhunov E, Poland J, Sabir JSM, Gill BS. Exploring the tertiary gene pool of bread wheat: sequence assembly and analysis of chromosome 5M(g) of Aegilops geniculata. Plant J 2015; 84:733-46. [PMID: 26408103 DOI: 10.1111/tpj.13036] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [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: 07/24/2015] [Revised: 09/03/2015] [Accepted: 09/14/2015] [Indexed: 05/07/2023]
Abstract
Next-generation sequencing (NGS) provides a powerful tool for the discovery of important genes and alleles in crop plants and their wild relatives. Despite great advances in NGS technologies, whole-genome shotgun sequencing is cost-prohibitive for species with complex genomes. An attractive option is to reduce genome complexity to a single chromosome prior to sequencing. This work describes a strategy for studying the genomes of distant wild relatives of wheat by isolating single chromosomes from addition or substitution lines, followed by chromosome sorting using flow cytometry and sequencing of chromosomal DNA by NGS technology. We flow-sorted chromosome 5M(g) from a wheat/Aegilops geniculata disomic substitution line [DS5M(g) (5D)] and sequenced it using an Illumina HiSeq 2000 system at approximately 50 × coverage. Paired-end sequences were assembled and used for structural and functional annotation. A total of 4236 genes were annotated on 5M(g) , in close agreement with the predicted number of genes on wheat chromosome 5D (4286). Single-gene FISH indicated no major chromosomal rearrangements between chromosomes 5M(g) and 5D. Comparing chromosome 5M(g) with model grass genomes identified synteny blocks in Brachypodium distachyon, rice (Oryza sativa), sorghum (Sorghum bicolor) and barley (Hordeum vulgare). Chromosome 5M(g) -specific SNPs and cytogenetic probe-based resources were developed and validated. Deletion bin-mapped and ordered 5M(g) SNP markers will be useful to track 5M-specific introgressions and translocations. This study provides a detailed sequence-based analysis of the composition of a chromosome from a distant wild relative of bread wheat, and opens up opportunities to develop genomic resources for wild germplasm to facilitate crop improvement.
Collapse
Affiliation(s)
- Vijay K Tiwari
- Department of Plant Pathology, Wheat Genetics Resource Center, Kansas State University Manhattan, Manhattan, KS, 66506, USA
| | - Shichen Wang
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66502, USA
| | - Tatiana Danilova
- Department of Plant Pathology, Wheat Genetics Resource Center, Kansas State University Manhattan, Manhattan, KS, 66506, USA
| | - Dal Hoe Koo
- Department of Plant Pathology, Wheat Genetics Resource Center, Kansas State University Manhattan, Manhattan, KS, 66506, USA
| | - Jan Vrána
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, CZ 78371, Olomouc, Czech Republic
| | - Marie Kubaláková
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, CZ 78371, Olomouc, Czech Republic
| | - Eva Hribova
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, CZ 78371, Olomouc, Czech Republic
| | - Nidhi Rawat
- Department of Plant Pathology, Wheat Genetics Resource Center, Kansas State University Manhattan, Manhattan, KS, 66506, USA
| | - Bhanu Kalia
- Department of Plant Pathology, Wheat Genetics Resource Center, Kansas State University Manhattan, Manhattan, KS, 66506, USA
| | - Narinder Singh
- Department of Plant Pathology, Wheat Genetics Resource Center, Kansas State University Manhattan, Manhattan, KS, 66506, USA
| | - Bernd Friebe
- Department of Plant Pathology, Wheat Genetics Resource Center, Kansas State University Manhattan, Manhattan, KS, 66506, USA
| | - Jaroslav Doležel
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, CZ 78371, Olomouc, Czech Republic
| | - Eduard Akhunov
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66502, USA
| | - Jesse Poland
- Department of Plant Pathology, Wheat Genetics Resource Center, Kansas State University Manhattan, Manhattan, KS, 66506, USA
| | - Jamal S M Sabir
- Biotechnology Research Group, Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
| | - Bikram S Gill
- Department of Plant Pathology, Wheat Genetics Resource Center, Kansas State University Manhattan, Manhattan, KS, 66506, USA
| |
Collapse
|
40
|
Liu Z, El-Basyoni I, Kariyawasam G, Zhang G, Fritz A, Hansen J, Marais F, Friskop A, Chao S, Akhunov E, Baenziger PS. Evaluation and Association Mapping of Resistance to Tan Spot and Stagonospora Nodorum Blotch in Adapted Winter Wheat Germplasm. Plant Dis 2015; 99:1333-1341. [PMID: 30690997 DOI: 10.1094/pdis-11-14-1131-re] [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: 05/05/2023]
Abstract
Tan spot and Stagonospora nodorum blotch (SNB), often occurring together, are two economically significant diseases of wheat in the Northern Great Plains of the United States. They are caused by the fungi Pyrenophora tritici-repentis and Parastagonospora nodorum, respectively, both of which produce multiple necrotrophic effectors (NE) to cause disease. In this work, 120 hard red winter wheat (HRWW) cultivars or elite lines, mostly from the United States, were evaluated in the greenhouse for their reactions to the two diseases as well as NE produced by the two pathogens. One P. nodorum isolate (Sn4) and four Pyrenophora tritici-repentis isolates (Pti2, 331-9, DW5, and AR CrossB10) were used separately in the disease evaluations. NE sensitivity evaluation included ToxA, Ptr ToxB, SnTox1, and SnTox3. The numbers of lines that were rated highly resistant to individual isolates ranged from 11 (9%) to 30 (25%) but only six lines (5%) were highly resistant to all isolates, indicating limited sources of resistance to both diseases in the U.S. adapted HRWW germplasm. Sensitivity to ToxA was identified in 83 (69%) of the lines and significantly correlated with disease caused by Sn4 and Pti2, whereas sensitivity to other NE was present at much lower frequency and had no significant association with disease. As expected, association mapping located ToxA and SnTox3 sensitivity to chromosome arm 5BL and 5BS, respectively. A total of 24 potential quantitative trait loci was identified with -log (P value) > 3.0 on 12 chromosomes, some of which are novel. This work provides valuable information and tools for HRWW production and breeding in the Northern Great Plains.
Collapse
Affiliation(s)
- Zhaohui Liu
- Department of Plant Pathology, North Dakota State University, Fargo 58102
| | - Ibrahim El-Basyoni
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln 68583
| | | | - Guorong Zhang
- Agricultural Research Center-Hays, Kansas State University, Hays 67601
| | - Allan Fritz
- Department of Agronomy, Kansas State University, Manhattan 66506
| | - Jana Hansen
- Department of Plant Pathology, North Dakota State University, Fargo
| | - Francois Marais
- Department of Plant Science, North Dakota State University, Fargo
| | - Andrew Friskop
- Department of Plant Pathology, North Dakota State University, Fargo
| | - Shiaoman Chao
- United States Department of Agriculture-Agricultural Research Service, Biosciences Research Laboratory, Fargo, ND, 58105
| | - Eduard Akhunov
- Department of Plant Pathology, Kansas State University Manhattan
| | | |
Collapse
|
41
|
Kalous JR, Martin JM, Sherman JD, Heo HY, Blake NK, Lanning SP, Eckhoff JLA, Chao S, Akhunov E, Talbert LE. Impact of the D genome and quantitative trait loci on quantitative traits in a spring durum by spring bread wheat cross. Theor Appl Genet 2015; 128:1799-811. [PMID: 26037088 DOI: 10.1007/s00122-015-2548-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2014] [Accepted: 05/22/2015] [Indexed: 05/24/2023]
Abstract
The impact of the D genome and QTL in the A and B genomes on agronomic performance of hexaploid wheat and tetraploid durum was determined using novel recombinant inbred line populations derived from interploid crosses. Genetic differences between common hexaploid (6X) bread wheat (Triticum aestivum, 2n = 6x = 42, genome, AABBDD) and tetraploid (4X) durum wheat (T. turgidum subsp. durum, 2n = 4x = 28, genome, AABB) may exist due to effects of the D genome and allelic differences at loci in the A and B genomes. Previous work allowed identification of a 6X by 4X cross combination that resulted in a large number of fertile recombinant progeny at both ploidy levels. In this study, interspecific recombinant inbred line populations at both 4X and 6X ploidy with 88 and 117 individuals, respectively, were developed from a cross between Choteau spring wheat (6X) and Mountrail durum wheat (4X). The presence of the D genome in the 6X population resulted in increased yield, tiller number, kernel weight, and kernel size, as well as a decrease in stem solidness, test weight and seed per spike. Similar results were found with a second RIL population containing 152 lines from 18 additional 6X by 4X crosses. Several QTL for agronomic and quality traits were identified in both the 4X and 6X populations. Although negatively impacted by the lack of the D genome, kernel weight in Mountrail (4X) was higher than Choteau (6X) due to positive alleles from Mountrail on chromosomes 3B and 7A. These and other favorable alleles may be useful for introgression between ploidy levels.
Collapse
Affiliation(s)
- J R Kalous
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT, 59717, USA
| | | | | | | | | | | | | | | | | | | |
Collapse
|
42
|
Maccaferri M, Ricci A, Salvi S, Milner SG, Noli E, Martelli PL, Casadio R, Akhunov E, Scalabrin S, Vendramin V, Ammar K, Blanco A, Desiderio F, Distelfeld A, Dubcovsky J, Fahima T, Faris J, Korol A, Massi A, Mastrangelo AM, Morgante M, Pozniak C, N'Diaye A, Xu S, Tuberosa R. A high-density, SNP-based consensus map of tetraploid wheat as a bridge to integrate durum and bread wheat genomics and breeding. Plant Biotechnol J 2015; 13:648-63. [PMID: 25424506 DOI: 10.1111/pbi.12288] [Citation(s) in RCA: 179] [Impact Index Per Article: 19.9] [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: 08/05/2014] [Revised: 09/26/2014] [Accepted: 10/03/2014] [Indexed: 05/20/2023]
Abstract
Consensus linkage maps are important tools in crop genomics. We have assembled a high-density tetraploid wheat consensus map by integrating 13 data sets from independent biparental populations involving durum wheat cultivars (Triticum turgidum ssp. durum), cultivated emmer (T. turgidum ssp. dicoccum) and their ancestor (wild emmer, T. turgidum ssp. dicoccoides). The consensus map harboured 30 144 markers (including 26 626 SNPs and 791 SSRs) half of which were present in at least two component maps. The final map spanned 2631 cM of all 14 durum wheat chromosomes and, differently from the individual component maps, all markers fell within the 14 linkage groups. Marker density per genetic distance unit peaked at centromeric regions, likely due to a combination of low recombination rate in the centromeric regions and even gene distribution along the chromosomes. Comparisons with bread wheat indicated fewer regions with recombination suppression, making this consensus map valuable for mapping in the A and B genomes of both durum and bread wheat. Sequence similarity analysis allowed us to relate mapped gene-derived SNPs to chromosome-specific transcripts. Dense patterns of homeologous relationships have been established between the A- and B-genome maps and between nonsyntenic homeologous chromosome regions as well, the latter tracing to ancient translocation events. The gene-based homeologous relationships are valuable to infer the map location of homeologs of target loci/QTLs. Because most SNP and SSR markers were previously mapped in bread wheat, this consensus map will facilitate a more effective integration and exploitation of genes and QTL for wheat breeding purposes.
Collapse
Affiliation(s)
- Marco Maccaferri
- Department of Agricultural Sciences (DipSA), University of Bologna, Bologna, Italy
| | - Andrea Ricci
- Department of Agricultural Sciences (DipSA), University of Bologna, Bologna, Italy
| | - Silvio Salvi
- Department of Agricultural Sciences (DipSA), University of Bologna, Bologna, Italy
| | - Sara Giulia Milner
- Department of Agricultural Sciences (DipSA), University of Bologna, Bologna, Italy
| | - Enrico Noli
- Department of Agricultural Sciences (DipSA), University of Bologna, Bologna, Italy
| | | | - Rita Casadio
- Biocomputing Group, University of Bologna, Bologna, Italy
| | - Eduard Akhunov
- Department of Plant Pathology, Kansas State University, Manhattan, KS, USA
| | - Simone Scalabrin
- Istituto di Genomica Applicata, Udine, Italy
- Dipartimento di Scienze Agrarie e Ambientali, University of Udine, Udine, Italy
| | - Vera Vendramin
- Istituto di Genomica Applicata, Udine, Italy
- Dipartimento di Scienze Agrarie e Ambientali, University of Udine, Udine, Italy
| | | | - Antonio Blanco
- Dipartimento di Biologia e Chimica Agro-forestale ed ambientale, Università di Bari, Aldo Moro, Bari, Italy
| | - Francesca Desiderio
- Consiglio per la ricerca e la sperimentazione in agricoltura, Genomics Research Centre, Fiorenzuola d'Arda, Italy
| | - Assaf Distelfeld
- Faculty of Life Sciences, Department of Molecular Biology and Ecology of Plants, Tel Aviv University, Tel Aviv, Israel
| | - Jorge Dubcovsky
- Department of Plant Sciences, University of California, Davis, CA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Tzion Fahima
- Department of Evolutionary and Environmental Biology, Institute of Evolution, Faculty of Science and Science Education, University of Haifa, Haifa, Israel
| | - Justin Faris
- USDA-ARS Cereal Crops Research Unit, Fargo, ND, USA
| | - Abraham Korol
- Department of Evolutionary and Environmental Biology, Institute of Evolution, Faculty of Science and Science Education, University of Haifa, Haifa, Israel
| | - Andrea Massi
- Società Produttori Sementi Bologna (PSB), Argelato, Italy
| | - Anna Maria Mastrangelo
- Consiglio per la ricerca e la sperimentazione in agricoltura, Cereal Research Centre, Foggia, Italy
| | - Michele Morgante
- Istituto di Genomica Applicata, Udine, Italy
- Dipartimento di Scienze Agrarie e Ambientali, University of Udine, Udine, Italy
| | - Curtis Pozniak
- Crop Development Centre and Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK, Canada
| | - Amidou N'Diaye
- Crop Development Centre and Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK, Canada
| | - Steven Xu
- USDA-ARS Cereal Crops Research Unit, Fargo, ND, USA
| | - Roberto Tuberosa
- Department of Agricultural Sciences (DipSA), University of Bologna, Bologna, Italy
| |
Collapse
|
43
|
Chen S, Rouse MN, Zhang W, Jin Y, Akhunov E, Wei Y, Dubcovsky J. Fine mapping and characterization of Sr21, a temperature-sensitive diploid wheat resistance gene effective against the Puccinia graminis f. sp. tritici Ug99 race group. Theor Appl Genet 2015; 128:645-56. [PMID: 25634104 PMCID: PMC5086425 DOI: 10.1007/s00122-015-2460-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [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: 08/30/2014] [Accepted: 01/10/2015] [Indexed: 05/22/2023]
Abstract
KEY MESSAGE The diploid wheat stem rust resistance gene Sr21 confers temperature-sensitive resistance to isolates of the Ug99 group and maps to the middle of the long arm of chromosome 2A (m). A race of Puccinia graminis f. sp. tritici, the causal pathogen of stem rust of wheat, known as Ug99, and its variants, are virulent to plants carrying stem rust resistance genes currently deployed in most wheat cultivars worldwide. Therefore, identification, mapping and deployment of effective resistance genes are critical to reduce this threat. Resistance gene Sr21 identified in diploid wheat T. monococcum can be effective against races from the Ug99 race group, but both susceptible and partial resistant reactions have been reported in previous studies. To clarify this conflicting information we screened four monogenic lines with Sr21 and four susceptible controls with 16 Pgt isolates including five isolates of the Ug99 race group under three different temperatures and three different photoperiods. We observed that, temperature influences the interaction between monogenic lines with Sr21 and Ug99 race group isolates, and may be one source of previous inconsistencies. This result indicates that, although Sr21 confers partial resistance against Ug99, its effectiveness can be modulated by environmental conditions and should not be deployed alone. Using two large diploid wheat-mapping populations (total 3,788 F2 plants) we mapped Sr21 approximately 50 cM from the centromere on the long arm of chromosome 2A(m) within a 0.20 cM interval flanked by sequence-based markers FD527726 and EX594406. The closely linked markers identified in this study will be useful to reduce the T. monococcum segments introgressed into common wheat, accelerate Sr21 deployment in wheat breeding programs, and facilitate the map-based cloning of this gene.
Collapse
Affiliation(s)
- Shisheng Chen
- Department of Plant Sciences, University of California, Davis, CA95616
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, P. R. China
| | - Matthew N. Rouse
- USDA-ARS Cereal Disease Laboratory and Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108
| | - Wenjun Zhang
- Department of Plant Sciences, University of California, Davis, CA95616
| | - Yue Jin
- USDA-ARS Cereal Disease Laboratory and Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108
| | - Eduard Akhunov
- Kansas State University, Dept. Plant Pathology, Manhattan, KS 66506
| | - Yuming Wei
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, P. R. China
| | - Jorge Dubcovsky
- Department of Plant Sciences, University of California, Davis, CA95616
- Howard Hughes Medical Institute, Chevy Chase, MD 20815
| |
Collapse
|
44
|
Jordan KW, Wang S, Lun Y, Gardiner LJ, MacLachlan R, Hucl P, Wiebe K, Wong D, Forrest KL, Sharpe AG, Sidebottom CH, Hall N, Toomajian C, Close T, Dubcovsky J, Akhunova A, Talbert L, Bansal UK, Bariana HS, Hayden MJ, Pozniak C, Jeddeloh JA, Hall A, Akhunov E. A haplotype map of allohexaploid wheat reveals distinct patterns of selection on homoeologous genomes. Genome Biol 2015; 16:48. [PMID: 25886949 PMCID: PMC4389885 DOI: 10.1186/s13059-015-0606-4] [Citation(s) in RCA: 184] [Impact Index Per Article: 20.4] [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: 09/26/2014] [Accepted: 02/04/2015] [Indexed: 12/21/2022] Open
Abstract
Background Bread wheat is an allopolyploid species with a large, highly repetitive genome. To investigate the impact of selection on variants distributed among homoeologous wheat genomes and to build a foundation for understanding genotype-phenotype relationships, we performed population-scale re-sequencing of a diverse panel of wheat lines. Results A sample of 62 diverse lines was re-sequenced using the whole exome capture and genotyping-by-sequencing approaches. We describe the allele frequency, functional significance, and chromosomal distribution of 1.57 million single nucleotide polymorphisms and 161,719 small indels. Our results suggest that duplicated homoeologous genes are under purifying selection. We find contrasting patterns of variation and inter-variant associations among wheat genomes; this, in addition to demographic factors, could be explained by differences in the effect of directional selection on duplicated homoeologs. Only a small fraction of the homoeologous regions harboring selected variants overlapped among the wheat genomes in any given wheat line. These selected regions are enriched for loci associated with agronomic traits detected in genome-wide association studies. Conclusions Evidence suggests that directional selection in allopolyploids rarely acted on multiple parallel advantageous mutations across homoeologous regions, likely indicating that a fitness benefit could be obtained by a mutation at any one of the homoeologs. Additional advantageous variants in other homoelogs probably either contributed little benefit, or were unavailable in populations subjected to directional selection. We hypothesize that allopolyploidy may have increased the likelihood of beneficial allele recovery by broadening the set of possible selection targets. Electronic supplementary material The online version of this article (doi:10.1186/s13059-015-0606-4) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Katherine W Jordan
- Department Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA.
| | - Shichen Wang
- Department Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA.
| | - Yanni Lun
- Department Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA. .,Integrated Genomics Facility, Kansas State University, Manhattan, KS, 66506, USA.
| | - Laura-Jayne Gardiner
- Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK.
| | - Ron MacLachlan
- Department Plant Sciences, University of Saskatchewan, Saskatoon, SK, S7N 5A8, Canada.
| | - Pierre Hucl
- Department Plant Sciences, University of Saskatchewan, Saskatoon, SK, S7N 5A8, Canada.
| | - Krysta Wiebe
- Department Plant Sciences, University of Saskatchewan, Saskatoon, SK, S7N 5A8, Canada.
| | - Debbie Wong
- Department Environment and Primary Industries, Bundoora, VIC, 3083, Australia.
| | - Kerrie L Forrest
- Department Environment and Primary Industries, Bundoora, VIC, 3083, Australia.
| | | | - Andrew G Sharpe
- National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK, S7N 0 W9, Canada.
| | | | - Neil Hall
- Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK.
| | | | - Timothy Close
- Department Botany & Plant Sciences, University of California, Riverside, CA, 92521, USA.
| | - Jorge Dubcovsky
- Department Plant Sciences, University of California, Davis, CA, 95616, USA. .,Howard Hughes Medical Institute, Chevy Chase, MD, 20815, USA.
| | - Alina Akhunova
- Department Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA. .,Integrated Genomics Facility, Kansas State University, Manhattan, KS, 66506, USA.
| | - Luther Talbert
- Department Plant Sciences & Plant Pathology, Montana State University, Bozeman, MT, 59717, USA.
| | - Urmil K Bansal
- Plant Breeding Institute-Cobbitty, The University of Sydney, PMB4011, Narellan, NSW, 2567, Australia.
| | - Harbans S Bariana
- Plant Breeding Institute-Cobbitty, The University of Sydney, PMB4011, Narellan, NSW, 2567, Australia.
| | - Matthew J Hayden
- Department Environment and Primary Industries, Bundoora, VIC, 3083, Australia.
| | - Curtis Pozniak
- Department Plant Sciences, University of Saskatchewan, Saskatoon, SK, S7N 5A8, Canada.
| | | | - Anthony Hall
- Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK.
| | - Eduard Akhunov
- Department Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA.
| |
Collapse
|
45
|
Sela H, Ezrati S, Ben-Yehuda P, Manisterski J, Akhunov E, Dvorak J, Breiman A, Korol A. Linkage disequilibrium and association analysis of stripe rust resistance in wild emmer wheat (Triticum turgidum ssp. dicoccoides) population in Israel. Theor Appl Genet 2014; 127:2453-63. [PMID: 25223542 DOI: 10.1007/s00122-014-2389-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2013] [Accepted: 08/28/2014] [Indexed: 05/22/2023]
Abstract
Rapid LD decay in wild emmer population from Israel allows high-resolution association mapping. Known and putative new stripe rust resistance genes were found. Genome-wide association mapping (GWAM) is becoming an important tool for the discovery and mapping of loci underlying trait variation in crops, but in the wild relatives of crops the use of GWAM has been limited. Critical factors for the use of GWAM are the levels of linkage disequilibrium (LD) and genetic diversity in mapped populations, particularly in those of self-pollinating species. Here, we report LD estimation in a population of 128 accessions of self-pollinating wild emmer, Triticum turgidum ssp. dicoccoides, the progenitor of cultivated wheat, collected in Israel. LD decayed fast along wild emmer chromosomes and reached the background level within 1 cM. We employed GWAM for the discovery and mapping of genes for resistance to three isolates of Puccinia striiformis, the causative agent of wheat stripe rust. The wild emmer population was genotyped with the wheat iSelect assay including 8643 gene-associated SNP markers (wheat 9K Infinium) of which 2,278 were polymorphic. The significance of association between stripe rust resistance and each of the polymorphic SNP was tested using mixed linear model implemented in EMMA software. The model produced satisfactory results and uncovered four significant associations on chromosome arms 1BS, 1BL and 3AL. The locus on 1BS was located in a region known to contain stripe rust resistance genes. These results show that GWAM is an effective strategy for gene discovery and mapping in wild emmer that will accelerate the utilization of this genetic resource in wheat breeding.
Collapse
Affiliation(s)
- Hanan Sela
- The Institute for Cereal Crops Improvement, Tel-Aviv University, P.O. Box 39040, 69978, Tel Aviv, Israel,
| | | | | | | | | | | | | | | |
Collapse
|
46
|
Crespo-Herrera LA, Akhunov E, Garkava-Gustavsson L, Jordan KW, Smith CM, Singh RP, Ahman I. Mapping resistance to the bird cherry-oat aphid and the greenbug in wheat using sequence-based genotyping. Theor Appl Genet 2014; 127:1963-73. [PMID: 25112202 DOI: 10.1007/s00122-014-2352-5] [Citation(s) in RCA: 7] [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] [Received: 02/26/2014] [Accepted: 07/04/2014] [Indexed: 05/24/2023]
Abstract
Identification of novel resistance QTL against wheat aphids. First QTL-resistance report for R. padi in wheat and chromosome 2DL for S. graminum . These sources have potential use in wheat breeding. The aphids Rhopalosiphum padi and Schizaphis graminum are important pests of common wheat (Triticum aestivum L.). Characterization of the genetic bases of resistance sources is crucial to facilitate the development of resistant wheat cultivars to these insects. We examined 140 recombinant inbred lines (RILs) from the cross of Seri M82 wheat (susceptible) with the synthetic hexaploid wheat CWI76364 (resistant). RILs were phenotyped for R. padi antibiosis and tolerance traits. Phenotyping of S. graminum resistance was based on leaf chlorosis in a greenhouse screening and the number of S. graminum/tiller in the field. RILs were also scored for pubescence. Using a sequence-based genotyping method, we located genomic regions associated with these resistance traits. A quantitative trait locus (QTL) for R. padi antibiosis (QRp.slu.4BL) that explained 10.2 % of phenotypic variation was found in chromosome 4BL and located 14.6 cM apart from the pubescence locus. We found no association between plant pubescence and the resistance traits. We found two QTLs for R. padi tolerance (QRp.slu.5AL and QRp.slu.5BL) in chromosomes 5AL and 5BL, with an epistatic interaction between a locus in chromosome 3AL (EnQRp.slu.5AL) and QRp.slu.5AL. These genomic regions explained about 35 % of the phenotypic variation. We re-mapped a previously reported gene for S. graminum resistance (putatively Gba) in 7DL and found a novel QTL associated with the number of aphids/tiller (QGb.slu-2DL) in chromosome 2DL. This is the first report on the genetic mapping of R. padi resistance in wheat and the first report where chromosome 2DL is shown to be associated with S. graminum resistance.
Collapse
Affiliation(s)
- L A Crespo-Herrera
- Department of Plant Breeding, Swedish University of Agricultural Sciences, P.O. Box 101, 23053, Alnarp, Sweden,
| | | | | | | | | | | | | |
Collapse
|
47
|
Wang S, Wong D, Forrest K, Allen A, Chao S, Huang BE, Maccaferri M, Salvi S, Milner SG, Cattivelli L, Mastrangelo AM, Whan A, Stephen S, Barker G, Wieseke R, Plieske J, Lillemo M, Mather D, Appels R, Dolferus R, Brown-Guedira G, Korol A, Akhunova AR, Feuillet C, Salse J, Morgante M, Pozniak C, Luo MC, Dvorak J, Morell M, Dubcovsky J, Ganal M, Tuberosa R, Lawley C, Mikoulitch I, Cavanagh C, Edwards KJ, Hayden M, Akhunov E. Characterization of polyploid wheat genomic diversity using a high-density 90,000 single nucleotide polymorphism array. Plant Biotechnol J 2014; 12:787-796. [PMID: 24646323 DOI: 10.1111/pbi.12183/pdf] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Received: 10/29/2013] [Revised: 01/29/2014] [Accepted: 02/05/2014] [Indexed: 05/29/2023]
Abstract
High-density single nucleotide polymorphism (SNP) genotyping arrays are a powerful tool for studying genomic patterns of diversity, inferring ancestral relationships between individuals in populations and studying marker-trait associations in mapping experiments. We developed a genotyping array including about 90,000 gene-associated SNPs and used it to characterize genetic variation in allohexaploid and allotetraploid wheat populations. The array includes a significant fraction of common genome-wide distributed SNPs that are represented in populations of diverse geographical origin. We used density-based spatial clustering algorithms to enable high-throughput genotype calling in complex data sets obtained for polyploid wheat. We show that these model-free clustering algorithms provide accurate genotype calling in the presence of multiple clusters including clusters with low signal intensity resulting from significant sequence divergence at the target SNP site or gene deletions. Assays that detect low-intensity clusters can provide insight into the distribution of presence-absence variation (PAV) in wheat populations. A total of 46 977 SNPs from the wheat 90K array were genetically mapped using a combination of eight mapping populations. The developed array and cluster identification algorithms provide an opportunity to infer detailed haplotype structure in polyploid wheat and will serve as an invaluable resource for diversity studies and investigating the genetic basis of trait variation in wheat.
Collapse
Affiliation(s)
- Shichen Wang
- Department of Plant Pathology, Kansas State University, Manhattan, KS, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
48
|
Wang S, Wong D, Forrest K, Allen A, Chao S, Huang BE, Maccaferri M, Salvi S, Milner SG, Cattivelli L, Mastrangelo AM, Whan A, Stephen S, Barker G, Wieseke R, Plieske J, Lillemo M, Mather D, Appels R, Dolferus R, Brown‐Guedira G, Korol A, Akhunova AR, Feuillet C, Salse J, Morgante M, Pozniak C, Luo M, Dvorak J, Morell M, Dubcovsky J, Ganal M, Tuberosa R, Lawley C, Mikoulitch I, Cavanagh C, Edwards KJ, Hayden M, Akhunov E. Characterization of polyploid wheat genomic diversity using a high‐density 90 000 single nucleotide polymorphism array. Plant Biotechnol J 2014; 12:787-96. [PMID: 24646323 PMCID: PMC4265271 DOI: 10.1111/pbi.12183] [Citation(s) in RCA: 1065] [Impact Index Per Article: 106.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2013] [Revised: 01/29/2014] [Accepted: 02/05/2014] [Indexed: 05/18/2023]
Affiliation(s)
- Shichen Wang
- Department of Plant Pathology Kansas State University Manhattan KS USA
| | - Debbie Wong
- Department of Environment and Primary Industry AgriBioSciences La Trobe R&D Park Bundoora Vic. Australia
| | - Kerrie Forrest
- Department of Environment and Primary Industry AgriBioSciences La Trobe R&D Park Bundoora Vic. Australia
| | - Alexandra Allen
- School of Biological Sciences University of Bristol Bristol UK
| | - Shiaoman Chao
- US Department of Agriculture–Agricultural Research Service Biosciences Research Laboratory Fargo ND USA
| | - Bevan E. Huang
- Commonwealth Scientific and Industrial Research Organization Computational Informatics and Food Futures National Research Flagship Dutton Park Qld Australia
| | - Marco Maccaferri
- Department of Agricultural Sciences University of Bologna Bologna Italy
| | - Silvio Salvi
- Department of Agricultural Sciences University of Bologna Bologna Italy
| | - Sara G. Milner
- Department of Agricultural Sciences University of Bologna Bologna Italy
| | - Luigi Cattivelli
- Consiglio per la Ricerca e la sperimentazione in Agricoltura Genomics Research Centre Fiorenzuola d'arda Italy
| | - Anna M. Mastrangelo
- Consiglio per la Ricerca e la sperimentazione in Agricoltura Cereal Research Centre Foggia Italy
| | - Alex Whan
- Commonwealth Scientific and Industrial Research Organization Plant Industry and Food Futures National Research Flagship Canberra ACT Australia
| | - Stuart Stephen
- Commonwealth Scientific and Industrial Research Organization Plant Industry and Food Futures National Research Flagship Canberra ACT Australia
| | - Gary Barker
- School of Biological Sciences University of Bristol Bristol UK
| | | | | | - Morten Lillemo
- Department of Plant Sciences Norwegian University of Life Sciences Ås Norway
| | - Diane Mather
- Waite Research Institute School of Agriculture, Food and Wine University of Adelaide Urrbrae SA Australia
| | | | - Rudy Dolferus
- Commonwealth Scientific and Industrial Research Organization Plant Industry and Food Futures National Research Flagship Canberra ACT Australia
| | - Gina Brown‐Guedira
- US Department of Agriculture–Agricultural Research Service Eastern Regional Small Grains Genotyping Laboratory Raleigh NC USA
| | - Abraham Korol
- Department of Evolutionary and Environmental Biology and Institute of Evolution University of Haifa Mount Carmel Haifa Israel
| | - Alina R. Akhunova
- K‐State Integrated Genomics Facility Kansas State University Manhattan KS USA
| | - Catherine Feuillet
- INRA – Université Blaise Pascal, UMR 1095 Genetics Diversity and Ecophysiology of Cereals Clermont‐Ferrand France
| | - Jerome Salse
- INRA – Université Blaise Pascal, UMR 1095 Genetics Diversity and Ecophysiology of Cereals Clermont‐Ferrand France
| | - Michele Morgante
- Department of Crop and Environmental Sciences University of Udine Via delle Scienze Udine Italy
| | - Curtis Pozniak
- Crop Development Centre and Department of Plant Sciences University of Saskatchewan Saskatoon SK Canada
| | - Ming‐Cheng Luo
- Department of Plant Sciences University of California Davis CA USA
| | - Jan Dvorak
- Department of Plant Sciences University of California Davis CA USA
| | - Matthew Morell
- Commonwealth Scientific and Industrial Research Organization Plant Industry and Food Futures National Research Flagship Canberra ACT Australia
| | - Jorge Dubcovsky
- Department of Plant Sciences University of California Davis CA USA
- Howard Hughes Medical Institute Chevy Chase MD USA
| | | | - Roberto Tuberosa
- Department of Agricultural Sciences University of Bologna Bologna Italy
| | | | | | - Colin Cavanagh
- Commonwealth Scientific and Industrial Research Organization Plant Industry and Food Futures National Research Flagship Canberra ACT Australia
| | | | - Matthew Hayden
- Department of Environment and Primary Industry AgriBioSciences La Trobe R&D Park Bundoora Vic. Australia
| | - Eduard Akhunov
- Department of Plant Pathology Kansas State University Manhattan KS USA
| | | |
Collapse
|
49
|
Abstract
MOTIVATION Recent technological advances are allowing many laboratories to sequence their research organisms. Available de novo assemblers leave repetitive portions of the genome poorly assembled. Some genomes contain high proportions of transposable elements, and transposable elements appear to be a major force behind diversity and adaptation. Few de novo assemblers for transposable elements exist, and most have either been designed for small genomes or 454 reads. RESULTS In this article, we present a new transposable element de novo assembler, Tedna, which assembles a set of transposable elements directly from the reads. Tedna uses Illumina paired-end reads, the most widely used sequencing technology for de novo assembly, and forms full-length transposable elements. AVAILABILITY AND IMPLEMENTATION Tedna is available at http://urgi.versailles.inra.fr/Tools/Tedna, under the GPLv3 license. It is written in C++11 and only requires the Sparsehash Package, freely available under the New BSD License. Tedna can be used on standard computers with limited RAM resources, although it may also use large memory for better results. Most of the code is parallelized and thus ready for large infrastructures.
Collapse
Affiliation(s)
- Matthias Zytnicki
- INRA, URGI, Plant Breeding and Biology, Versailles 78026, France and Department of Plant Pathology, Kansas State University, Manhattan, KS 66506, USA
| | - Eduard Akhunov
- INRA, URGI, Plant Breeding and Biology, Versailles 78026, France and Department of Plant Pathology, Kansas State University, Manhattan, KS 66506, USA
| | - Hadi Quesneville
- INRA, URGI, Plant Breeding and Biology, Versailles 78026, France and Department of Plant Pathology, Kansas State University, Manhattan, KS 66506, USA
| |
Collapse
|
50
|
Tiwari VK, Wang S, Sehgal S, Vrána J, Friebe B, Kubaláková M, Chhuneja P, Doležel J, Akhunov E, Kalia B, Sabir J, Gill BS. SNP Discovery for mapping alien introgressions in wheat. BMC Genomics 2014; 15:273. [PMID: 24716476 PMCID: PMC4051138 DOI: 10.1186/1471-2164-15-273] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [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: 12/23/2013] [Accepted: 03/31/2014] [Indexed: 11/30/2022] Open
Abstract
Background Monitoring alien introgressions in crop plants is difficult due to the lack of genetic and molecular mapping information on the wild crop relatives. The tertiary gene pool of wheat is a very important source of genetic variability for wheat improvement against biotic and abiotic stresses. By exploring the 5Mg short arm (5MgS) of Aegilops geniculata, we can apply chromosome genomics for the discovery of SNP markers and their use for monitoring alien introgressions in wheat (Triticum aestivum L). Results The short arm of chromosome 5Mg of Ae. geniculata Roth (syn. Ae. ovata L.; 2n = 4x = 28, UgUgMgMg) was flow-sorted from a wheat line in which it is maintained as a telocentric chromosome. DNA of the sorted arm was amplified and sequenced using an Illumina Hiseq 2000 with ~45x coverage. The sequence data was used for SNP discovery against wheat homoeologous group-5 assemblies. A total of 2,178 unique, 5MgS-specific SNPs were discovered. Randomly selected samples of 59 5MgS-specific SNPs were tested (44 by KASPar assay and 15 by Sanger sequencing) and 84% were validated. Of the selected SNPs, 97% mapped to a chromosome 5Mg addition to wheat (the source of t5MgS), and 94% to 5Mg introgressed from a different accession of Ae. geniculata substituting for chromosome 5D of wheat. The validated SNPs also identified chromosome segments of 5MgS origin in a set of T5D-5Mg translocation lines; eight SNPs (25%) mapped to TA5601 [T5DL · 5DS-5MgS(0.75)] and three (8%) to TA5602 [T5DL · 5DS-5MgS (0.95)]. SNPs (gsnp_5ms83 and gsnp_5ms94), tagging chromosome T5DL · 5DS-5MgS(0.95) with the smallest introgression carrying resistance to leaf rust (Lr57) and stripe rust (Yr40), were validated in two released germplasm lines with Lr57 and Yr40 genes. Conclusion This approach should be widely applicable for the identification of species/genome-specific SNPs. The development of a large number of SNP markers will facilitate the precise introgression and monitoring of alien segments in crop breeding programs and further enable mapping and cloning novel genes from the wild relatives of crop plants.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Bikram S Gill
- Wheat Genetics Resource Center, Department of Plant Pathology, Kansas State University, Manhattan, KS 66506, USA.
| |
Collapse
|