51
|
Harrington SA, Cobo N, Karafiátová M, Doležel J, Borrill P, Uauy C. Identification of a Dominant Chlorosis Phenotype Through a Forward Screen of the Triticum turgidum cv. Kronos TILLING Population. FRONTIERS IN PLANT SCIENCE 2019; 10:963. [PMID: 31396255 PMCID: PMC6667664 DOI: 10.3389/fpls.2019.00963] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Accepted: 07/10/2019] [Indexed: 05/19/2023]
Abstract
Durum wheat (Triticum turgidum) derives from a hybridization event approximately 400,000 years ago which led to the creation of an allotetraploid genome. The evolutionary recent origin of durum wheat means that its genome has not yet been fully diploidised. As a result, many of the genes present in the durum genome act in a redundant fashion, where loss-of-function mutations must be present in both gene copies to observe a phenotypic effect. Here, we use a novel set of induced variation within the cv. Kronos TILLING population to identify a locus controlling a dominant, environmentally dependent chlorosis phenotype. We carried out a forward screen of the sequenced cv. Kronos TILLING lines for senescence phenotypes and identified a line with a dominant early senescence and chlorosis phenotype. Mutant plants contained less chlorophyll throughout their development and displayed premature flag leaf senescence. A segregating population was classified into discrete phenotypic groups and subjected to bulked-segregant analysis using exome capture followed by next-generation sequencing. This allowed the identification of a single region on chromosome 3A, Yellow Early Senescence 1 (YES-1), which was associated with the mutant phenotype. While this phenotype was consistent across 4 years of field trials in the United Kingdom, the mutant phenotype was not observed when grown in Davis, CA (United States). To obtain further SNPs for fine-mapping, we isolated chromosome 3A using flow sorting and sequenced the entire chromosome. By mapping these reads against both the cv. Chinese Spring reference sequence and the cv. Kronos assembly, we could identify high-quality, novel EMS-induced SNPs in non-coding regions within YES-1 that were previously missed in the exome capture data. This allowed us to fine-map YES-1 to 4.3 Mb, containing 59 genes. Our study shows that populations containing induced variation can be sources of novel dominant variation in polyploid crop species, highlighting their importance in future genetic screens. We also demonstrate the value of using cultivar-specific genome assemblies alongside the gold-standard reference genomes particularly when working with non-coding regions of the genome. Further fine-mapping of the YES-1 locus will be pursued to identify the causal SNP underpinning this dominant, environmentally dependent phenotype.
Collapse
Affiliation(s)
| | - Nicolas Cobo
- Department of Plant Sciences, University of California, Davis, Davis, CA, United States
| | - Miroslava Karafiátová
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czechia
| | - Jaroslav Doležel
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czechia
| | - Philippa Borrill
- John Innes Centre, Norwich, United Kingdom
- School of Biosciences, University of Birmingham, Birmingham, United Kingdom
| | | |
Collapse
|
52
|
Narang D, Kaur S, Steuernagel B, Ghosh S, Dhillon R, Bansal M, Uauy C, Wulff BBH, Chhuneja P. Fine mapping of Aegilops peregrina co-segregating leaf and stripe rust resistance genes to distal-most end of 5DS. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:1473-1485. [PMID: 30706082 DOI: 10.1007/s00122-019-03293-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Accepted: 01/21/2019] [Indexed: 06/09/2023]
Abstract
Novel rust resistance genes LrP and YrP from Ae. peregrina identified on chromosome 5D and the linked markers will aid deployment of these genes in combination with other major/minor genes. Aegilops peregrina, a wild tetraploid relative of wheat with genome constitution UUSS, displays genetic variation for resistance to leaf and stripe (yellow) rust. The wheat Ae. peregrina introgression line, IL pau16058, harbouring leaf and stripe rust resistance, was crossed with wheat cv. WL711 to generate an F2:3 mapping population. Inheritance studies on this population indicated the transfer of dominant co-segregating resistance to leaf and stripe rust. Ethyl methane sulphonate mutagenesis of IL pau16058 identified independent loss-of-function mutants for leaf and stripe rust resistance, indicating that the leaf and stripe rust resistance is controlled by independent genes, herein designated LrP and YrP, respectively. A high-resolution genetic map of LrP and YrP was constructed using the Illumina Infinium iSelect 90K wheat array and resistance gene enrichment sequencing (RenSeq) markers. The map spans 4.19 cM on the distal-most region of the short arm of chromosome 5D, consisting of eight SNP markers and one microsatellite marker. LrP and YrP co-segregated with markers BS00163889 and 5DS44573_snp and was flanked distally by the SNP marker BS00129707 and proximally by 5DS149010, defining a 15.71 Mb region in the RefSeq v1.0 genome assembly.
Collapse
Affiliation(s)
- Deepika Narang
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, Punjab, 141004, India
| | - Satinder Kaur
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, Punjab, 141004, India
| | | | - Sreya Ghosh
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Roopan Dhillon
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, Punjab, 141004, India
| | - Mitaly Bansal
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, Punjab, 141004, India
| | - Cristobal Uauy
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | | | - Parveen Chhuneja
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, Punjab, 141004, India.
| |
Collapse
|
53
|
de Haro LA, Arellano SM, Novák O, Feil R, Dumón AD, Mattio MF, Tarkowská D, Llauger G, Strnad M, Lunn JE, Pearce S, Figueroa CM, del Vas M. Mal de Río Cuarto virus infection causes hormone imbalance and sugar accumulation in wheat leaves. BMC PLANT BIOLOGY 2019; 19:112. [PMID: 30902042 PMCID: PMC6431059 DOI: 10.1186/s12870-019-1709-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 03/11/2019] [Indexed: 05/05/2023]
Abstract
BACKGROUND Mal de Río Cuarto virus (MRCV) infects several monocotyledonous species including maize and wheat. Infected plants show shortened internodes, partial sterility, increased tillering and reduced root length. To better understand the molecular basis of the plant-virus interactions leading to these symptoms, we combined RNA sequencing with metabolite and hormone measurements. RESULTS More than 3000 differentially accumulated transcripts (DATs) were detected in MRCV-infected wheat plants at 21 days post inoculation compared to mock-inoculated plants. Infected plants exhibited decreased levels of TaSWEET13 transcripts, which are involved in sucrose phloem loading. Soluble sugars, starch, trehalose 6-phosphate (Tre6P), and organic and amino acids were all higher in MRCV-infected plants. In addition, several transcripts related to plant hormone metabolism, transport and signalling were increased upon MRCV infection. Transcripts coding for GA20ox, D14, MAX2 and SMAX1-like proteins involved in gibberellin biosynthesis and strigolactone signalling, were reduced. Transcripts involved in jasmonic acid, ethylene and brassinosteroid biosynthesis, perception and signalling and in auxin transport were also altered. Hormone measurements showed that jasmonic acid, brassinosteroids, abscisic acid and indole-3-acetic acid were significantly higher in infected leaves. CONCLUSIONS Our results indicate that MRCV causes a profound hormonal imbalance that, together with alterations in sugar partitioning, could account for the symptoms observed in MRCV-infected plants.
Collapse
Affiliation(s)
| | - Sofía Maité Arellano
- Instituto de Biotecnología, CICVyA, INTA, CONICET, Hurlingham, Buenos Aires Argentina
| | - Ondrej Novák
- Laboratory of Growth Regulators, Palacký University and Institute of Experimental Botany Czech Academy of Sciences, Šlechtitelů 27, CZ-78371 Olomouc, Czech Republic
| | - Regina Feil
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | | | | | - Danuše Tarkowská
- Laboratory of Growth Regulators, Palacký University and Institute of Experimental Botany Czech Academy of Sciences, Šlechtitelů 27, CZ-78371 Olomouc, Czech Republic
| | - Gabriela Llauger
- Instituto de Biotecnología, CICVyA, INTA, CONICET, Hurlingham, Buenos Aires Argentina
| | - Miroslav Strnad
- Laboratory of Growth Regulators, Palacký University and Institute of Experimental Botany Czech Academy of Sciences, Šlechtitelů 27, CZ-78371 Olomouc, Czech Republic
| | - John Edward Lunn
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Stephen Pearce
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO USA
| | | | - Mariana del Vas
- Instituto de Biotecnología, CICVyA, INTA, CONICET, Hurlingham, Buenos Aires Argentina
| |
Collapse
|
54
|
Zhang H, Fu Y, Guo H, Zhang L, Wang C, Song W, Yan Z, Wang Y, Ji W. Transcriptome and Proteome-Based Network Analysis Reveals a Model of Gene Activation in Wheat Resistance to Stripe Rust. Int J Mol Sci 2019; 20:ijms20051106. [PMID: 30836695 PMCID: PMC6429138 DOI: 10.3390/ijms20051106] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 02/24/2019] [Accepted: 02/27/2019] [Indexed: 12/20/2022] Open
Abstract
Stripe rust, caused by the pathogen Puccinia striiformis f. sp. tritici (Pst), is an important fungal foliar disease of wheat (Triticum aestivum). To study the mechanism underlying the defense of wheat to Pst, we used the next-generation sequencing and isobaric tags for relative and absolute quantification (iTRAQ) technologies to generate transcriptomic and proteomic profiles of seedling leaves at different stages under conditions of pathogen stress. By conducting comparative proteomic analysis using iTRAQ, we identified 2050, 2190, and 2258 differentially accumulated protein species at 24, 48, and 72 h post-inoculation (hpi). Using pairwise comparisons and weighted gene co-expression network analysis (WGCNA) of the transcriptome, we identified a stress stage-specific module enriching in transcription regulator genes. The homologs of several regulators, including splicing and transcription factors, were similarly identified as hub genes operating in the Pst-induced response network. Moreover, the Hsp70 protein were predicted as a key point in protein–protein interaction (PPI) networks from STRING database. Taking the genetics resistance gene locus into consideration, we identified 32 induced proteins in chromosome 1BS as potential candidates involved in Pst resistance. This study indicated that the transcriptional regulation model plays an important role in activating resistance-related genes in wheat responding to Pst stress.
Collapse
Affiliation(s)
- Hong Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Shaanxi 712100, China.
| | - Ying Fu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Shaanxi 712100, China.
| | - Huan Guo
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Shaanxi 712100, China.
| | - Lu Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Shaanxi 712100, China.
| | - Changyou Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Shaanxi 712100, China.
| | - Weining Song
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Shaanxi 712100, China.
| | - Zhaogui Yan
- College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China.
| | - Yajuan Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Shaanxi 712100, China.
- Shaanxi Research Station of Crop Gene Resource & Germplasm Enhancement, Ministry of Agriculture, Shaanxi 712100, China.
| | - Wanquan Ji
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Shaanxi 712100, China.
- Shaanxi Research Station of Crop Gene Resource & Germplasm Enhancement, Ministry of Agriculture, Shaanxi 712100, China.
| |
Collapse
|
55
|
Bettgenhaeuser J, Krattinger SG. Rapid gene cloning in cereals. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:699-711. [PMID: 30341495 DOI: 10.1007/s00122-018-3210-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 10/12/2018] [Indexed: 05/03/2023]
Abstract
The large and complex genomes of many cereals hindered cloning efforts in the past. Advances in genomics now allow the rapid cloning of genes from humanity's most valuable crops. The past two decades were characterized by a genomics revolution that entailed profound changes to crop research, plant breeding, and agriculture. Today, high-quality reference sequences are available for all major cereal crop species. Large resequencing and pan-genome projects start to reveal a more comprehensive picture of the genetic makeup and the diversity among domesticated cereals and their wild relatives. These technological advancements will have a dramatic effect on dissecting genotype-phenotype associations and on gene cloning. In this review, we will highlight the status of the genomic resources available for various cereal crops and we will discuss their implications for gene cloning. A particular focus will be given to the cereal species barley and wheat, which are characterized by very large and complex genomes that have been inaccessible to rapid gene cloning until recently. With the advancements in genomics and the development of several rapid gene-cloning methods, it has now become feasible to tackle the cloning of most agriculturally important genes, even in wheat and barley.
Collapse
Affiliation(s)
- Jan Bettgenhaeuser
- Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Simon G Krattinger
- Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia.
| |
Collapse
|
56
|
Brinton J, Uauy C. A reductionist approach to dissecting grain weight and yield in wheat. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2019; 61:337-358. [PMID: 30421518 PMCID: PMC6492019 DOI: 10.1111/jipb.12741] [Citation(s) in RCA: 76] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Accepted: 11/07/2018] [Indexed: 05/20/2023]
Abstract
Grain yield is a highly polygenic trait that is influenced by the environment and integrates events throughout the life cycle of a plant. In wheat, the major grain yield components often present compensatory effects among them, which alongside the polyploid nature of wheat, makes their genetic and physiological study challenging. We propose a reductionist and systematic approach as an initial step to understand the gene networks regulating each individual yield component. Here, we focus on grain weight and discuss the importance of examining individual sub-components, not only to help in their genetic dissection, but also to inform our mechanistic understanding of how they interrelate. This knowledge should allow the development of novel combinations, across homoeologs and between complementary modes of action, thereby advancing towards a more integrated strategy for yield improvement. We argue that this will break barriers in terms of phenotypic variation, enhance our understanding of the physiology of yield, and potentially deliver improved on-farm yield.
Collapse
Affiliation(s)
- Jemima Brinton
- John Innes CentreNorwich Research ParkNorwich NR4 7UHUnited Kingdom
| | - Cristobal Uauy
- John Innes CentreNorwich Research ParkNorwich NR4 7UHUnited Kingdom
| |
Collapse
|
57
|
Keller B, Wicker T, Krattinger SG. Advances in Wheat and Pathogen Genomics: Implications for Disease Control. ANNUAL REVIEW OF PHYTOPATHOLOGY 2018; 56:67-87. [PMID: 30149791 DOI: 10.1146/annurev-phyto-080516-035419] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
The gene pool of wheat and its wild and domesticated relatives contains a plethora of resistance genes that can be exploited to make wheat more resilient to pathogens. Only a few of these genes have been isolated and studied at the molecular level. In recent years, we have seen a shift from classical breeding to genomics-assisted breeding, which makes use of the enormous advancements in DNA sequencing and high-throughput molecular marker technologies for wheat improvement. These genomic advancements have the potential to transform wheat breeding in the near future and to significantly increase the speed and precision at which new cultivars can be bred. This review highlights the genomic improvements that have been made in wheat and its pathogens over the past years and discusses their implications for disease-resistance breeding.
Collapse
Affiliation(s)
- Beat Keller
- Department of Plant and Microbial Biology, University of Zurich, 8008 Zurich, Switzerland;
| | - Thomas Wicker
- Department of Plant and Microbial Biology, University of Zurich, 8008 Zurich, Switzerland;
| | - Simon G Krattinger
- Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia;
| |
Collapse
|
58
|
Hussain M, Iqbal MA, Till BJ, Rahman MU. Identification of induced mutations in hexaploid wheat genome using exome capture assay. PLoS One 2018; 13:e0201918. [PMID: 30102729 PMCID: PMC6089429 DOI: 10.1371/journal.pone.0201918] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Accepted: 07/24/2018] [Indexed: 12/02/2022] Open
Abstract
Wheat is a staple food crop of many countries. Improving resilience to biotic and abiotic stresses remain key breeding targets. Among these, rust diseases are the most detrimental in terms of depressing wheat production. In the present study, chemical mutagenesis was used to induce mutations in the wheat variety NN-Gandum-1. This cultivar is moderately resistant to leaf and yellow rust. The aim of mutagenesis was to improve resistance to the disease as well as to study function of genes conferring resistance to the disease. In the present investigation, a 0.8% EMS dose was found optimum for supporting 45-55% germination of NN-Gandum-1. A total of 3,634 M2 fertile plants were produced from each of the M1 plant. Out of these, 33 (0.91%) and 20 plants (0.55%) showed absolute resistance to leaf and yellow rust, respectively. While 126 (3.46%) and 127 plants (3.49%) exhibited high susceptibility to the leaf and yellow rust, respectively. In the M4 generation, a total of 11 M4 lines (nine absolute resistant and two highly susceptible) and one wild type were selected for NGS-based exome capture assay. A total of 104,779 SNPs were identified that were randomly distributed throughout the wheat sub genomes (A, B and D). Induced mutations in intronic sequences predominated. The highest total number of SNPs detected in this assay were mapped to chr.2B (14,273 SNPs), which contains the highest number of targeted base pairs in the assay. The average mutation density across all regions interrogated was estimated to be one mutation per 20.91 Mb. The highest mutation frequency was found in chr.2D (1/11.7 kb) and the lowest in chr.7D (1/353.4 kb). Out of the detected mutations, 101 SNPs were filtered using analysis criteria aimed to enrich for mutations that may affect gene function. Out of these, one putative SNP detected in Lr21 were selected for further analysis. The SNP identified in chimeric allele (Lr21) of a resistant mutant (N1-252) was located in a NBS domain of chr.1BS at 3.4 Mb position. Through computational analysis, it was demonstrated that this identified SNP causes a substitution of glutamic acid with alanine, resulting in a predicted altered protein structure. This mutation, therefore, is a candidate for contributing to the resistance phenotype in the mutant line. Based on this work, we conclude that the wheat mutant resource developed is useful as a source of novel genetic variation for forward-genetic screens and also as a useful tool for gaining insights into the important biological circuits of different traits of complex genomes like wheat.
Collapse
Affiliation(s)
- Momina Hussain
- Plant Genomics & Mol. Breeding Lab, National Institute for Biotechnology & Genetic Engineering (NIBGE), Faisalabad, Pakistan
- Department of Biotechnology, Pakistan Institute of Engineering and Applied Sciences (PIEAS), Nilore, Islamabad, Pakistan
| | - Muhammad Atif Iqbal
- Plant Genomics & Mol. Breeding Lab, National Institute for Biotechnology & Genetic Engineering (NIBGE), Faisalabad, Pakistan
- Department of Biotechnology, Pakistan Institute of Engineering and Applied Sciences (PIEAS), Nilore, Islamabad, Pakistan
| | - Bradley J. Till
- University of Vienna, Department fürChromosomenbiologie, Vienna, Austria
| | - Mehboob-ur- Rahman
- Plant Genomics & Mol. Breeding Lab, National Institute for Biotechnology & Genetic Engineering (NIBGE), Faisalabad, Pakistan
- Department of Biotechnology, Pakistan Institute of Engineering and Applied Sciences (PIEAS), Nilore, Islamabad, Pakistan
| |
Collapse
|
59
|
Wu J, Zeng Q, Wang Q, Liu S, Yu S, Mu J, Huang S, Sela H, Distelfeld A, Huang L, Han D, Kang Z. SNP-based pool genotyping and haplotype analysis accelerate fine-mapping of the wheat genomic region containing stripe rust resistance gene Yr26. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2018; 131:1481-1496. [PMID: 29666883 DOI: 10.1007/s00122-018-3092-8] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 04/08/2018] [Indexed: 05/12/2023]
Abstract
NGS-assisted super pooling emerging as powerful tool to accelerate gene mapping and haplotype association analysis within target region uncovering specific linkage SNPs or alleles for marker-assisted gene pyramiding. Conventional gene mapping methods to identify genes associated with important agronomic traits require significant amounts of financial support and time. Here, a single nucleotide polymorphism (SNP)-based mapping approach, RNA-Seq and SNP array assisted super pooling analysis, was used for rapid mining of a candidate genomic region for stripe rust resistance gene Yr26 that has been widely used in wheat breeding programs in China. Large DNA and RNA super-pools were genotyped by Wheat SNP Array and sequenced by Illumina HiSeq, respectively. Hundreds of thousands of SNPs were identified and then filtered by multiple filtering criteria. Among selected SNPs, over 900 were found within an overlapping interval of less than 30 Mb as the Yr26 candidate genomic region in the centromeric region of chromosome arm 1BL. The 235 chromosome-specific SNPs were converted into KASP assays to validate the Yr26 interval in different genetic populations. Using a high-resolution mapping population (> 30,000 gametes), we confined Yr26 to a 0.003-cM interval. The Yr26 target region was anchored to the common wheat IWGSC RefSeq v1.0 and wild emmer WEWSeq v.1.0 sequences, from which 488 and 454 kb fragments were obtained. Several candidate genes were identified in the target genomic region, but there was no typical resistance gene in either genome region. Haplotype analysis identified specific SNPs linked to Yr26 and developed robust and breeder-friendly KASP markers. This integration strategy can be applied to accelerate generating many markers closely linked to target genes/QTL for a trait of interest in wheat and other polyploid species.
Collapse
Affiliation(s)
- Jianhui Wu
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Xianyang, 712100, Shaanxi, People's Republic of China
| | - Qingdong Zeng
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Xianyang, 712100, Shaanxi, People's Republic of China
| | - Qilin Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Xianyang, 712100, Shaanxi, People's Republic of China
| | - Shengjie Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Xianyang, 712100, Shaanxi, People's Republic of China
| | - Shizhou Yu
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Xianyang, 712100, Shaanxi, People's Republic of China
| | - Jingmei Mu
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Xianyang, 712100, Shaanxi, People's Republic of China
| | - Shuo Huang
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Xianyang, 712100, Shaanxi, People's Republic of China
| | - Hanan Sela
- The Institute for Cereal Crops Improvement, Tel-Aviv University, Tel Aviv, Israel
| | - Assaf Distelfeld
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel
- NRGene Ltd., Ness Ziona, Israel
- Helmholtz Zentrum München, Plant Genome and Systems Biology, Neuherberg, Germany
| | - Lili Huang
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Xianyang, 712100, Shaanxi, People's Republic of China
| | - Dejun Han
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Xianyang, 712100, Shaanxi, People's Republic of China.
| | - Zhensheng Kang
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Xianyang, 712100, Shaanxi, People's Republic of China.
| |
Collapse
|
60
|
Chen S, Zhang W, Bolus S, Rouse MN, Dubcovsky J. Identification and characterization of wheat stem rust resistance gene Sr21 effective against the Ug99 race group at high temperature. PLoS Genet 2018; 14:e1007287. [PMID: 29614079 PMCID: PMC5882135 DOI: 10.1371/journal.pgen.1007287] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Accepted: 03/05/2018] [Indexed: 11/24/2022] Open
Abstract
Wheat stem rust, caused by Puccinia graminis f. sp. tritici (Pgt), is a devastating foliar disease. The Ug99 race group has combined virulence to most stem rust (Sr) resistance genes deployed in wheat and is a threat to global wheat production. Here we identified a coiled-coil, nucleotide-binding leucine-rich repeat protein (NLR) completely linked to the Ug99 resistance gene Sr21 from Triticum monococcum. Loss-of-function mutations and transgenic complementation confirmed that this gene is Sr21. Sr21 transcripts were significantly higher at high temperatures, and this was associated with significant upregulation of pathogenesis related (PR) genes and increased levels of resistance at those temperatures. Introgression of Sr21 into hexaploid wheat resulted in lower levels of resistance than in diploid wheat, but transgenic hexaploid wheat lines with high levels of Sr21 expression showed high levels of resistance. Sr21 can be a valuable component of transgenic cassettes or gene pyramids combining multiple resistance genes against Ug99. Wheat stem rust is a devastating disease that is threatening global wheat production. The emergence of new virulent races of this pathogen in Africa, including the Ug99 race group, has prompted global efforts to find effective resistance genes. We report here the identification of stem rust resistance gene Sr21 that is effective against the Ug99 race group. We developed a diagnostic marker to accelerate its deployment in wheat breeding programs and demonstrated that the introduction of two Sr21 copies in transgenic wheat results in high levels of resistance. An unusual characteristic of Sr21 is its increased resistance to stem rust at high temperatures. We show here that this is associated with the ability of Sr21 to coordinate the upregulation of multiple pathogenesis related genes at high temperatures. These genes slow down the growth of the pathogen and result in the characteristic Sr21 intermediate resistance reaction at high temperatures. A better understanding of this temperature dependent resistance mechanism will be useful for controlling the rust pathogens in our changing environments.
Collapse
Affiliation(s)
- Shisheng Chen
- Department of Plant Sciences, University of California, Davis, Davis, CA, United States of America
| | - Wenjun Zhang
- Department of Plant Sciences, University of California, Davis, Davis, CA, United States of America
| | - Stephen Bolus
- Department of Plant Sciences, University of California, Davis, Davis, CA, United States of America
| | - Matthew N Rouse
- USDA-ARS Cereal Disease Laboratory and Department of Plant Pathology, University of Minnesota, St. Paul, MN, United States of America
| | - Jorge Dubcovsky
- Department of Plant Sciences, University of California, Davis, Davis, CA, United States of America
- Howard Hughes Medical Institute, Chevy Chase, MD, United States of America
| |
Collapse
|
61
|
Dracatos PM, Haghdoust R, Singh D, Park RF. Exploring and exploiting the boundaries of host specificity using the cereal rust and mildew models. THE NEW PHYTOLOGIST 2018; 218:453-462. [PMID: 29464724 DOI: 10.1111/nph.15044] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Accepted: 01/09/2018] [Indexed: 05/19/2023]
Abstract
Individual plants encounter a vast number of microbes including bacteria, viruses, fungi and oomycetes through their growth cycle, yet few of these pathogens are able to infect them. Plant species have diverged over millions of years, co-evolving with few specific pathogens. The host boundaries of most pathogen species can be clearly defined. In general, the greater the genetic divergence from the preferred host, the less likely that pathogen would be able to infect that plant species. Co-evolution and divergence also occur within pathogen species, leading to highly specialized subspecies with narrow host ranges. For example, cereal rust and mildew pathogens (Puccinia and Blumeria spp.) display high host specificity as a result of ongoing co-evolution with a narrow range of grass species. In rare cases, however, some plant species are in a transition from host to nonhost or are intermediate hosts (near nonhost). Barley was reported as a useful model for genetic and molecular studies of nonhost resistance due to rare susceptibility to numerous heterologous rust and mildew fungi. This review evaluates host specificity in numerous Puccinia/Blumeria-cereal pathosystems and discusses various approaches for transferring nonhost resistance (NHR) genes between crop species to reduce the impact of important diseases in food production.
Collapse
Affiliation(s)
- Peter Michael Dracatos
- Plant Breeding Institute, The University of Sydney, Cobbitty, Private Bag 4011, Narellan, NSW, 2567, Australia
| | - Rouja Haghdoust
- Plant Breeding Institute, The University of Sydney, Cobbitty, Private Bag 4011, Narellan, NSW, 2567, Australia
| | - Davinder Singh
- Plant Breeding Institute, The University of Sydney, Cobbitty, Private Bag 4011, Narellan, NSW, 2567, Australia
| | - Robert Fraser Park
- Plant Breeding Institute, The University of Sydney, Cobbitty, Private Bag 4011, Narellan, NSW, 2567, Australia
| |
Collapse
|
62
|
Lewis CM, Persoons A, Bebber DP, Kigathi RN, Maintz J, Findlay K, Bueno-Sancho V, Corredor-Moreno P, Harrington SA, Kangara N, Berlin A, García R, Germán SE, Hanzalová A, Hodson DP, Hovmøller MS, Huerta-Espino J, Imtiaz M, Mirza JI, Justesen AF, Niks RE, Omrani A, Patpour M, Pretorius ZA, Roohparvar R, Sela H, Singh RP, Steffenson B, Visser B, Fenwick PM, Thomas J, Wulff BBH, Saunders DGO. Potential for re-emergence of wheat stem rust in the United Kingdom. Commun Biol 2018; 1:13. [PMID: 30271900 PMCID: PMC6053080 DOI: 10.1038/s42003-018-0013-y] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Accepted: 01/11/2018] [Indexed: 12/05/2022] Open
Abstract
Wheat stem rust, a devastating disease of wheat and barley caused by the fungal pathogen Puccinia graminis f. sp. tritici, was largely eradicated in Western Europe during the mid-to-late twentieth century. However, isolated outbreaks have occurred in recent years. Here we investigate whether a lack of resistance in modern European varieties, increased presence of its alternate host barberry and changes in climatic conditions could be facilitating its resurgence. We report the first wheat stem rust occurrence in the United Kingdom in nearly 60 years, with only 20% of UK wheat varieties resistant to this strain. Climate changes over the past 25 years also suggest increasingly conducive conditions for infection. Furthermore, we document the first occurrence in decades of P. graminis on barberry in the UK . Our data illustrate that wheat stem rust does occur in the UK and, when climatic conditions are conducive, could severely harm wheat and barley production.
Collapse
Affiliation(s)
- Clare M Lewis
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | | | | | - Rose N Kigathi
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
- Pwani University, 195-80108, Kilifi, Kenya
| | - Jens Maintz
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Kim Findlay
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | | | | | | | | | - Anna Berlin
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, 750 07, Sweden
| | - Richard García
- Instituto Nacional de Investigación Agropecuaria (INIA) La Estanzuela, Mailbox 39173, Colonia, Uruguay
| | - Silvia E Germán
- Instituto Nacional de Investigación Agropecuaria (INIA) La Estanzuela, Mailbox 39173, Colonia, Uruguay
| | - Alena Hanzalová
- Crop Research Institute, Ruzyně, 161 06 Praha 6, Czech Republic
| | - David P Hodson
- International Maize and Wheat Improvement Center (CIMMYT), 5689, Addis Ababa, Ethiopia
| | | | | | | | - Javed Iqbal Mirza
- Crop Disease Research Program, National Agriculture Research Center, Islamabad, 44000, Pakistan
| | | | - Rients E Niks
- Wageningen University, Wageningen, 6700, The Netherlands
| | - Ali Omrani
- Faculty of Agriculture, Department of Plant Breeding and Biotechnology, University of Tabriz, Tabriz, 5166616471, Iran
| | | | | | - Ramin Roohparvar
- Seed and Plant Improvement Institute, Agricultural Research, Education and Extension Organization (AREEO), 4119, Karaj, Iran
| | - Hanan Sela
- Tel Aviv University, Tel Aviv, 69978, Israel
| | - Ravi P Singh
- CIMMYT, Apdo. Postal 6-641, D. F. México, 06600, Mexico
| | | | - Botma Visser
- University of the Free State, Bloemfontein, 9301, South Africa
| | | | - Jane Thomas
- National Institute of Agricultural Botany, Cambridge, CB3 0LE, UK
| | | | | |
Collapse
|
63
|
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: 110] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [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
|
64
|
Brinton J, Simmonds J, Uauy C. Ubiquitin-related genes are differentially expressed in isogenic lines contrasting for pericarp cell size and grain weight in hexaploid wheat. BMC PLANT BIOLOGY 2018; 18:22. [PMID: 29370763 PMCID: PMC5784548 DOI: 10.1186/s12870-018-1241-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Accepted: 01/17/2018] [Indexed: 05/25/2023]
Abstract
BACKGROUND There is an urgent need to increase global crop production. Identifying and combining specific genes controlling distinct biological processes holds the potential to enhance crop yields. Transcriptomics is a powerful tool to gain insights into the complex gene regulatory networks that underlie such traits, but relies on the availability of a high-quality reference sequence and accurate gene models. Previously, we identified a grain weight QTL on wheat chromosome 5A (5A QTL) which acts during early grain development to increase grain length through cell expansion in the pericarp. In this study, we performed RNA-sequencing on near isogenic lines (NILs) segregating for the 5A QTL and used the latest gene models to identify differentially regulated genes and pathways that potentially influence pericarp cell size and grain weight in wheat. RESULTS We sampled grains at 4 and 8 days post anthesis and found that genes associated with metabolism, biosynthesis, proteolysis and the defence response are upregulated during this stage of grain development in both NILs. We identified a specific set of 112 transcripts differentially expressed (DE) between 5A NILs at either time point, including eight potential candidates for the causal 5A gene and its downstream targets. The 112 DE transcripts had functional annotations including non-coding RNA, transposon-associated, cell-cycle control, ubiquitin-related, heat-shock, transcription and histone-related. Many of the genes identified belong to families that have been previously associated with seed/grain development in other species. Notably, we identified DE transcripts at almost all steps of the pathway associated with ubiquitin-mediated protein degradation. In the promoters of a subset of DE transcripts we identified enrichment of binding sites associated with C2H2, MYB/SANT, YABBY, AT-HOOK and Trihelix transcription factor families. CONCLUSIONS In this study, we identified DE transcripts with a diverse range of predicted biological functions, reflecting the complex nature of the pathways that control early grain development. Few of these are the direct orthologues of grain size genes in other species and none have been previously characterised in wheat. Further functional characterisation of these candidates and how they interact will provide novel insights into the control of grain size in cereals.
Collapse
|