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Golzar H, Shankar M, Sznajder B, Fox R, Reeves K, Mather DE. Genetic mapping of loci affecting seedling and adult-plant resistance to powdery mildew derived from two CIMMYT wheat lines. PLANTA 2024; 260:13. [PMID: 38809276 DOI: 10.1007/s00425-024-04444-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 05/16/2024] [Indexed: 05/30/2024]
Abstract
MAIN CONCLUSION PM3 and PM8 alleles carried by two CIMMYT wheat lines confer powdery mildew resistance in seedlings and/or adult plants. A stage-specific epistatic interaction was observed between PM3 and PM8. Powdery mildew is an important foliar disease of wheat. Major genes for resistance, which have been widely used in wheat breeding programs, are typically effective against only limited numbers of virulence genes of the pathogen. The main aim of this study was to map resistance loci in wheat lines 7HRWSN58 and ZWW09-149 from the International Maize and Wheat Improvement Center (CIMMYT). Doubled haploid populations (Magenta/7HRWSN58 and Emu Rock/ZWW09-149) were developed and grown in controlled environment experiments and inoculated with a composite of Blumeria graminis f.sp. tritici isolates that had been collected at various locations in Western Australia. Plants were assessed for powdery mildew symptoms (percentage leaf area diseased) on seedlings and adult plants. Populations were subjected to genotyping-by-sequencing and assayed for known SNPs in the resistance gene PM3. Linkage maps were constructed, and markers were anchored to the wheat reference genome sequence. In both populations, there were asymptomatic lines that exhibited no symptoms. Among symptomatic lines, disease severity varied widely. In the Magenta/7HRWSN58 population, most of the observed variation was attributed to the PM3 region of chromosome 1A, with the allele from 7HRWSN58 conferring resistance in seedlings and adult plants. In the Emu Rock/ZWW09-149 population, two interacting quantitative trait loci were mapped: one at PM3 and the other on chromosome 1B. The Emu Rock/ZWW09-149 population was confirmed to segregate for a 1BL·1RS translocation that carries the PM8 powdery mildew resistance gene from rye. Consistent with previous reports that PM8-derived resistance can be suppressed by PM3 alleles, the observed interaction between the quantitative trait loci on chromosomes 1A and 1B indicated that the PM3 allele carried by ZWW09-149 suppresses PM8-derived resistance from ZWW09-149, but only at the seedling stage. In adult plants, the PM8 region conferred resistance regardless of the PM3 genotype. The resistance sources and molecular markers that were investigated here could be useful in wheat breeding.
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Affiliation(s)
- Hossein Golzar
- Department of Primary Industries and Regional Development, 3 Baron Hay Ct, South Perth, WA, 6151, Australia
| | - Manisha Shankar
- Department of Primary Industries and Regional Development, 3 Baron Hay Ct, South Perth, WA, 6151, Australia.
- School of Agriculture and Environment, University of Western Australia, 35 Stirling Hwy, Crawley, WA, 6009, Australia.
| | - Beata Sznajder
- School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, PMB 1, Glen Osmond, SA, 5064, Australia
| | - Rebecca Fox
- School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, PMB 1, Glen Osmond, SA, 5064, Australia
| | - Karyn Reeves
- Department of Primary Industries and Regional Development, 3 Baron Hay Ct, South Perth, WA, 6151, Australia
| | - Diane E Mather
- School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, PMB 1, Glen Osmond, SA, 5064, Australia
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2
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Jin Y, Yu Z, Su F, Fang T, Liu S, Xu H, Wang J, Xiao B, Han G, Li H, Ma P. Evaluation and Identification of Powdery Mildew Resistance Genes in Aegilops tauschii and Emmer Wheat Accessions. PLANT DISEASE 2024:PDIS08231667RE. [PMID: 38173259 DOI: 10.1094/pdis-08-23-1667-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Powdery mildew, caused by Blumeria graminis f. sp. tritici (Bgt), is a serious threat to wheat (Triticum aestivum L.) production. Narrow genetic basis of common wheat boosted the demand for diversified donors against powdery mildew. Aegilops tauschii Coss (2n = 2x = DD) and emmer wheat (2n = 4x = AABB), as the ancestor species of common wheat, are important gene donors for genetic improvement of common wheat. In this study, a total of 71 Ae. tauschii and 161 emmer wheat accessions were first evaluated for their powdery mildew resistance using the Bgt isolate E09. Thirty-three Ae. tauschii (46.5%) and 108 emmer wheat accessions (67.1%) were resistant. Then, all these accessions were tested by the diagnostic markers for 21 known Pm genes. The results showed that Pm2 alleles were detected in all the 71 Ae. tauschii and only Pm4 alleles were detected in 20 of 161 emmer wheat accessions. After haplotype analysis, we identified four Pm4 alleles (Pm4a, Pm4b, Pm4d, and Pm4f) in the emmer wheat accessions and three Pm2 alleles (Pm2d, Pm2e, and Pm2g) in the Ae. tauschii. Further resistance spectrum analysis indicated that these resistance accessions displayed different resistance reactions to different Bgt isolates, implying they may have other Pm genes apart from Pm2 and/or Pm4 alleles. Notably, a new Pm2 allele, Pm2S, was identified in Ae. tauschii, which contained a 64-bp deletion in the first exon and formed a new termination site at the 513th triplet of the shifted reading frame compared with reported Pm2 alleles. The phylogenetic tree of Pm2S showed that the kinship of Pm2S was close to Pm2h. To efficiently and accurately detect Pm2S and distinguish with other Pm2 alleles in Ae. tauschii background, a diagnostic marker, YTU-QS-3, was developed, and its effectiveness was verified. This study provided valuable Pm alleles and enriched the genetic diversity of the powdery mildew resistance in wheat improvement.
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Affiliation(s)
- Yuli Jin
- Yantai Key Laboratory of Characteristic Agricultural Bioresource Conservation and Germplasm Innovative Utilization, College of Life Sciences, Yantai University, Yantai 264005, China
| | - Ziyang Yu
- Yantai Key Laboratory of Characteristic Agricultural Bioresource Conservation and Germplasm Innovative Utilization, College of Life Sciences, Yantai University, Yantai 264005, China
| | - Fuyu Su
- Yantai Key Laboratory of Characteristic Agricultural Bioresource Conservation and Germplasm Innovative Utilization, College of Life Sciences, Yantai University, Yantai 264005, China
| | - Tianying Fang
- Yantai Key Laboratory of Characteristic Agricultural Bioresource Conservation and Germplasm Innovative Utilization, College of Life Sciences, Yantai University, Yantai 264005, China
| | - Shuang Liu
- Yantai Key Laboratory of Characteristic Agricultural Bioresource Conservation and Germplasm Innovative Utilization, College of Life Sciences, Yantai University, Yantai 264005, China
| | - Hongxing Xu
- School of Life Sciences, Henan University, Kaifeng, Henan 475004, China
| | - Jiaojiao Wang
- Yantai Key Laboratory of Characteristic Agricultural Bioresource Conservation and Germplasm Innovative Utilization, College of Life Sciences, Yantai University, Yantai 264005, China
| | - Bei Xiao
- Yantai Key Laboratory of Characteristic Agricultural Bioresource Conservation and Germplasm Innovative Utilization, College of Life Sciences, Yantai University, Yantai 264005, China
| | - Guohao Han
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050021, China
| | - Hongjie Li
- The National Engineering Laboratory of Crop Molecular Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Pengtao Ma
- Yantai Key Laboratory of Characteristic Agricultural Bioresource Conservation and Germplasm Innovative Utilization, College of Life Sciences, Yantai University, Yantai 264005, China
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3
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Wang J, Xu H, Qie Y, Han R, Sun X, Zhao Y, Xiao B, Qian Z, Huang X, Liu R, Zhang J, Liu C, Jin Y, Ma P. Evaluation and identification of powdery mildew-resistant genes in 137 wheat relatives. Front Genet 2024; 15:1342239. [PMID: 38327832 PMCID: PMC10847533 DOI: 10.3389/fgene.2024.1342239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 01/02/2024] [Indexed: 02/09/2024] Open
Abstract
Powdery mildew is one of the most severe diseases affecting wheat yield and quality and is caused by Blumeria graminis f. sp. tritici (Bgt). Host resistance is the preferred strategy to prevent this disease. However, the narrow genetic basis of common wheat has increased the demand for diversified germplasm resources against powdery mildew. Wheat relatives, especially the secondary gene pool of common wheat, are important gene donors in the genetic improvement of common wheat because of its abundant genetic variation and close kinship with wheat. In this study, a series of 137 wheat relatives, including 53 Triticum monococcum L. (2n = 2x = 14, AA), 6 T. urartu Thumanjan ex Gandilyan (2n = 2x = 14, AA), 9 T. timopheevii Zhuk. (2n = 4x = 28, AAGG), 66 T. aestivum subsp. spelta (2n = 6x = 42, AABBDD), and 3 Aegilops speltoides (2n = 2x = 14, SS) were systematically evaluated for their powdery mildew resistance and composition of Pm genes. Out of 137 (60.58%) accessions, 83 were resistant to Bgt isolate E09 at the seedling stage, and 116 of 137 (84.67%) wheat relatives were resistant to the mixture of Bgt isolates at the adult stage. This indicates that these accessions show a high level of resistance to powdery mildew. Some 31 markers for 23 known Pm genes were used to test these 137 accessions, and, in the results, only Pm2, Pm4, Pm6, Pm58, and Pm68 were detected. Among them, three Pm4 alleles (Pm4a, Pm4b, and Pm4f) were identified in 4 T. subsp. spelta accessions. q-RT PCR further confirmed that Pm4 alleles played a role in disease resistance in these four accessions. The phylogenetic tree showed that the kinship of Pm4 was close to Pm24 and Sr62. This study not only provides reference information and valuable germplasm resources for breeding new wheat varieties with disease resistance but also lays a foundation for enriching the genetic basis of wheat resistance to powdery mildew.
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Affiliation(s)
- Jiaojiao Wang
- Yantai Key Laboratory of Characteristic Agricultural Bioresource Conservation & Germplasm Innovative Utilization, College of Life Sciences, Yantai University, Yantai, China
| | - Hongxing Xu
- School of Life Sciences, Henan University, Kaifeng, Henan, China
| | - Yanmin Qie
- Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences, Hebei Key Laboratory of Crop Genetics and Breeding, Shijiazhuang, China
| | - Ran Han
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Xiaohui Sun
- Institute of Grain and Oil Crops, Yantai Academy of Agricultural Science, Yantai, China
| | - Ya Zhao
- Yantai Key Laboratory of Characteristic Agricultural Bioresource Conservation & Germplasm Innovative Utilization, College of Life Sciences, Yantai University, Yantai, China
| | - Bei Xiao
- Yantai Key Laboratory of Characteristic Agricultural Bioresource Conservation & Germplasm Innovative Utilization, College of Life Sciences, Yantai University, Yantai, China
| | - Zejun Qian
- Yantai Key Laboratory of Characteristic Agricultural Bioresource Conservation & Germplasm Innovative Utilization, College of Life Sciences, Yantai University, Yantai, China
| | - Xiaomei Huang
- Yantai Key Laboratory of Characteristic Agricultural Bioresource Conservation & Germplasm Innovative Utilization, College of Life Sciences, Yantai University, Yantai, China
| | - Ruishan Liu
- Yantai Key Laboratory of Characteristic Agricultural Bioresource Conservation & Germplasm Innovative Utilization, College of Life Sciences, Yantai University, Yantai, China
| | - Jiadong Zhang
- Yantai Key Laboratory of Characteristic Agricultural Bioresource Conservation & Germplasm Innovative Utilization, College of Life Sciences, Yantai University, Yantai, China
| | - Cheng Liu
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Yuli Jin
- Yantai Key Laboratory of Characteristic Agricultural Bioresource Conservation & Germplasm Innovative Utilization, College of Life Sciences, Yantai University, Yantai, China
| | - Pengtao Ma
- Yantai Key Laboratory of Characteristic Agricultural Bioresource Conservation & Germplasm Innovative Utilization, College of Life Sciences, Yantai University, Yantai, China
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Chaudhary N, Salgotra RK, Chauhan BS. Genetic Enhancement of Cereals Using Genomic Resources for Nutritional Food Security. Genes (Basel) 2023; 14:1770. [PMID: 37761910 PMCID: PMC10530810 DOI: 10.3390/genes14091770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 09/04/2023] [Accepted: 09/06/2023] [Indexed: 09/29/2023] Open
Abstract
Advances in genomics resources have facilitated the evolution of cereal crops with enhanced yield, improved nutritional values, and heightened resistance to various biotic and abiotic stresses. Genomic approaches present a promising avenue for the development of high-yielding varieties, thereby ensuring food and nutritional security. Significant improvements have been made within the omics domain, specifically in genomics, transcriptomics, and proteomics. The advent of Next-Generation Sequencing (NGS) techniques has yielded an immense volume of data, accompanied by substantial progress in bioinformatic tools for proficient analysis. The synergy between genomics and computational tools has been acknowledged as pivotal for unravelling the intricate mechanisms governing genome-wide gene regulation. Within this review, the essential genomic resources are delineated, and their harmonization in the enhancement of cereal crop varieties is expounded upon, with a paramount focus on fulfilling the nutritional requisites of humankind. Furthermore, an encompassing compendium of the available genomic resources for cereal crops is presented, accompanied by an elucidation of their judicious utilization in the advancement of crop attributes.
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Affiliation(s)
- Neeraj Chaudhary
- School of Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Jammu, Chatha, Jammu 180009, Jammu and Kashmir, India; (N.C.); (R.K.S.)
| | - Romesh Kumar Salgotra
- School of Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Jammu, Chatha, Jammu 180009, Jammu and Kashmir, India; (N.C.); (R.K.S.)
| | - Bhagirath Singh Chauhan
- Queensland Alliance for Agriculture and Food Innovation (QAAFI), The University of Queensland, Gatton, QLD 4343, Australia
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Hasan N, Choudhary S, Naaz N, Sharma N, Laskar RA. Recent advancements in molecular marker-assisted selection and applications in plant breeding programmes. J Genet Eng Biotechnol 2021; 19:128. [PMID: 34448979 PMCID: PMC8397809 DOI: 10.1186/s43141-021-00231-1] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Accepted: 08/17/2021] [Indexed: 11/28/2022]
Abstract
Background DNA markers improved the productivity and accuracy of classical plant breeding by means of marker-assisted selection (MAS). The enormous number of quantitative trait loci (QTLs) mapping read for different plant species have given a plenitude of molecular marker-gene associations. Main body of the abstract In this review, we have discussed the positive aspects of molecular marker-assisted selection and its precise applications in plant breeding programmes. Molecular marker-assisted selection has considerably shortened the time for new crop varieties to be brought to the market. To explore the information about DNA markers, many reviews have been published in the last few decades; all these reviews were intended by plant breeders to obtain information on molecular genetics. In this review, we intended to be a synopsis of recent developments of DNA markers and their application in plant breeding programmes and devoted to early breeders with little or no knowledge about the DNA markers. The progress made in molecular plant breeding, plant genetics, genomics selection, and editing of genome contributed to the comprehensive understanding of DNA markers and provides several proofs on the genetic diversity available in crop plants and greatly complemented plant breeding devices. Short conclusion MAS has revolutionized the process of plant breeding with acceleration and accuracy, which is continuously empowering plant breeders around the world.
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Affiliation(s)
- Nazarul Hasan
- Cytogenetic and Plant Breeding Lab, Department of Botany, Aligarh Muslim University, Aligarh, U.P, 202002, India.
| | - Sana Choudhary
- Cytogenetic and Plant Breeding Lab, Department of Botany, Aligarh Muslim University, Aligarh, U.P, 202002, India
| | - Neha Naaz
- Cytogenetic and Plant Breeding Lab, Department of Botany, Aligarh Muslim University, Aligarh, U.P, 202002, India
| | - Nidhi Sharma
- Cytogenetic and Plant Breeding Lab, Department of Botany, Aligarh Muslim University, Aligarh, U.P, 202002, India
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6
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Wu X, Bian Q, Gao Y, Ni X, Sun Y, Xuan Y, Cao Y, Li T. Evaluation of resistance to powdery mildew and identification of resistance genes in wheat cultivars. PeerJ 2021; 9:e10425. [PMID: 33510966 PMCID: PMC7808266 DOI: 10.7717/peerj.10425] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 11/03/2020] [Indexed: 11/20/2022] Open
Abstract
Wheat powdery mildew, caused by the biotrophic fungus Blumeria graminis f. sp. tritici (Bgt), is a serious disease of wheat worldwide that can cause significant yield losses. Growing resistant cultivars is the most cost-effective and eco-soundly strategy to manage the disease. Therefore, a high breeding priority is to identify genes that can be readily used either singly or in combination for effective resistance to powdery mildew and also in combination with genes for resistance to other diseases. Yunnan Province, with complex and diverse ecological environments and climates, is one of the main wheat growing regions in China. This region provides initial inoculum for starting epidemics of wheat powdery mildew in the region and other regions and thus, plays a key role in the regional and large-scale epidemics of the disease throughout China. The objectives of this study were to evaluate seedling resistance of 69 main wheat cultivars to powdery mildew and to determine the presence of resistance genes Pm3, Pm8, Pm13, Pm16, and Pm21in these cultivars using gene specific DNA markers. Evaluation of 69 wheat cultivars with six Bgt isolates showed that only four cultivars were resistant to all tested isolates, indicating that the overall level of powdery mildew resistance of Yunnan wheat cultivars is inadequate. The molecular marker results showed that 27 cultivars likely have at least one of these genes. Six cultivars were found likely to have Pm3,18 likely to have Pm8,5 likely to have Pm16,and 3 likely to have Pm21. No cultivar was found to carry Pm13. The information on the presence of the Pmresistance genes in Yunnan wheat cultivars can be used in future wheat disease breeding programs. In particular, cultivars carrying Pm21, which is effective against all Bgtraces in China, should be pyramided with other effective genes to developing new cultivars with durable resistance to powdery mildew.
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Affiliation(s)
- Xianxin Wu
- College of Plant Protection, Shenyang Agricultural University Shenyang China
| | - Qiang Bian
- National Pesticide Engineering Research Center, Nankai University Nanjing China
| | - Yue Gao
- College of Plant Protection, Shenyang Agricultural University Shenyang China
| | - Xinyu Ni
- College of Plant Protection, Shenyang Agricultural University Shenyang China
| | - Yanqiu Sun
- College of Plant Protection, Shenyang Agricultural University Shenyang China
| | - Yuanhu Xuan
- College of Plant Protection, Shenyang Agricultural University Shenyang China
| | - Yuanyin Cao
- College of Plant Protection, Shenyang Agricultural University Shenyang China
| | - Tianya Li
- College of Plant Protection, Shenyang Agricultural University Shenyang China
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7
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Salgotra RK, Stewart CN. Functional Markers for Precision Plant Breeding. Int J Mol Sci 2020; 21:E4792. [PMID: 32640763 PMCID: PMC7370099 DOI: 10.3390/ijms21134792] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 06/19/2020] [Accepted: 07/02/2020] [Indexed: 01/24/2023] Open
Abstract
Advances in molecular biology including genomics, high-throughput sequencing, and genome editing enable increasingly faster and more precise cultivar development. Identifying genes and functional markers (FMs) that are highly associated with plant phenotypic variation is a grand challenge. Functional genomics approaches such as transcriptomics, targeting induced local lesions in genomes (TILLING), homologous recombinant (HR), association mapping, and allele mining are all strategies to identify FMs for breeding goals, such as agronomic traits and biotic and abiotic stress resistance. The advantage of FMs over other markers used in plant breeding is the close genomic association of an FM with a phenotype. Thereby, FMs may facilitate the direct selection of genes associated with phenotypic traits, which serves to increase selection efficiencies to develop varieties. Herein, we review the latest methods in FM development and how FMs are being used in precision breeding for agronomic and quality traits as well as in breeding for biotic and abiotic stress resistance using marker assisted selection (MAS) methods. In summary, this article describes the use of FMs in breeding for development of elite crop cultivars to enhance global food security goals.
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Affiliation(s)
- Romesh K. Salgotra
- School of Biotechnology, Sher-e-Kashmir University of Agricultural Sciences & Technology of Jammu, Chatha, Jammu 190008, India
| | - C. Neal Stewart
- Department of Plant Sciences, University of Tennessee, Knoxville, TN 37996, USA
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8
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Positional cloning of PmCH1357 reveals the origin and allelic variation of the Pm2 gene for powdery mildew resistance in wheat. ACTA ACUST UNITED AC 2019. [DOI: 10.1016/j.cj.2019.08.004] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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9
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A search for 4 specific markers linked to Pm3 alleles for resistance to powdery mildew (Blumeria graminis) in rye (Secale cereale). BIOLOGICAL LETTERS 2019. [DOI: 10.2478/biolet-2019-0004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Abstract
To investigate powdery mildew resistance in rye (Secale cereale), 397 inbred lines of winter rye were tested for susceptibility to infection with Blumeria graminis f. sp. secalis. The 50 most tolerant lines and 50 most infected lines were chosen for comparison. They were next tested for the presence of 4 markers linked to 4 alleles for resistance to powdery mildew, identified earlier in common wheat (Triticum aestivum). We found Pm3a only in 3 susceptible genotypes of winter rye, although this marker is linked to the powdery mildew resistance gene in wheat. The other 3 markers linked to Blumeria graminis f. sp. secalis resistance genes (Pm3b, Pm3c, Pm3d) were found in neither resistant nor susceptible rye genotypes.
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Tomkowiak A, Skowrońska R, Weigt D, Kwiatek M, Nawracała J, Kowalczewski PŁ, Pluta M. Identification of Powdery Mildew Blumeria graminis f. sp. tritici Resistance Genes in Selected Wheat Varieties and Development of Multiplex PCR. OPEN CHEM 2019. [DOI: 10.1515/chem-2019-0024] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
AbstractThe aim of the study was to identify thePm2, Pm3a, Pm4bandPm6genes and to develop multiplex PCR reaction conditions to reduce time and limit analysis costs. The following molecular markers were used for gene identification:Xcfd81, Whs350andXgwm205(forPm2),Pm3a(forPm3a),STS_241andXgwm382(forPm4b),NAU/BCDSTS 135-2(forPm6). Plant material consisted of 7 popular European wheat varieties from the wheat collection at the Department of Genetics and Plant Breeding of the Poznań University of Life Sciences. The field experiment was established in 2017 and 2018 on 10 m2plots in a randomized complete block design in three replicates in the Dłoń Agricultural Experimental Farm of the Poznań University of Life Sciences (51°41’23.835”N 017°4’1.414”E). The analyses demonstrated that the accumulation of all identifiedPmgenes was found in the Assosan variety. The accumulation of thePm2, Pm4bandPm6genes was found in Atomic, Bussard, Lear, Sparta, Tonacja and Ulka varieties. The work also involved developing multiplex PCR conditions forXcfd81andSTS_241andXcfd81andXgwm382primer pairs, allowing the simultaneous identification of thePm2andPm4bgenes.
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Affiliation(s)
- Agnieszka Tomkowiak
- Department of Genetics and Plant Breeding, Faculty of Agronomy and Bioengineering, Poznań, University of Life Sciences, 11 Dojazd Str, 60-632 Poznań, Poznań, Poland
| | - Roksana Skowrońska
- Department of Genetics and Plant Breeding, Faculty of Agronomy and Bioengineering, Poznań, University of Life Sciences, 11 Dojazd Str, 60-632 Poznań, Poznań, Poland
| | - Dorota Weigt
- Department of Genetics and Plant Breeding, Faculty of Agronomy and Bioengineering, Poznań, University of Life Sciences, 11 Dojazd Str, 60-632 Poznań, Poznań, Poland
| | - Michał Kwiatek
- Department of Genetics and Plant Breeding, Faculty of Agronomy and Bioengineering, Poznań, University of Life Sciences, 11 Dojazd Str, 60-632 Poznań, Poznań, Poland
| | - Jerzy Nawracała
- Department of Genetics and Plant Breeding, Faculty of Agronomy and Bioengineering, Poznań, University of Life Sciences, 11 Dojazd Str, 60-632 Poznań, Poznań, Poland
| | - Przemysław Łukasz Kowalczewski
- Institute of Food Technology of Plant Origin, Faculty of Food Science and Nutrition, Poznań, University of Life Sciences, 31 Wojska Polskiego Str, 60-624 Poznań, Poznań, Poland
| | - Mateusz Pluta
- Department of Genetics and Plant Breeding, Faculty of Agronomy and Bioengineering, Poznań, University of Life Sciences, 11 Dojazd Str, 60-632 Poznań, Poznań, Poland
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11
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Stadlmeier M, Hartl L, Mohler V. Usefulness of a Multiparent Advanced Generation Intercross Population With a Greatly Reduced Mating Design for Genetic Studies in Winter Wheat. FRONTIERS IN PLANT SCIENCE 2018; 9:1825. [PMID: 30574161 PMCID: PMC6291512 DOI: 10.3389/fpls.2018.01825] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 11/23/2018] [Indexed: 05/05/2023]
Abstract
Multiparent advanced generation intercross (MAGIC) populations were recently developed to allow the high-resolution mapping of quantitative traits. We present a genetic linkage map of an elite but highly diverse eight-founder MAGIC population in common wheat (Triticum aestivum L.). Our MAGIC population is composed of 394 F6:8 recombinant inbred lines lacking significant signatures of population structure. The linkage map included 5435 SNP markers distributed over 2804 loci and spanning 5230 cM. The analysis of population parameters, including genetic structure, kinship, founder probabilities, and linkage disequilibrium and congruency to other maps indicated appropriate construction of both the population and the genetic map. It was shown that eight-founder MAGIC populations exhibit a greater number of loci and higher recombination rates, especially in the pericentromeric regions, compared to four-founder MAGIC, and biparental populations. In addition, our greatly simplified eight-parental MAGIC mating design with an additional eight-way intercross step was found to be equivalent to a MAGIC design with all 210 possible four-way crosses regarding the levels of missing founder assignments and the number of recombination events. Furthermore, the MAGIC population captured 71.7% of the allelic diversity available in the German wheat breeding gene pool. As a proof of principle, we demonstrated the application of the resource for quantitative trait loci mapping analyzing seedling resistance to powdery mildew. As wheat is a crop with many breeding objectives, this resource will allow scientists and breeders to carry out genetic studies for a wide range of breeder-relevant parameters in a single genetic background and reveal possible interactions between traits of economic importance.
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Affiliation(s)
- Melanie Stadlmeier
- Bavarian State Research Center for Agriculture, Institute for Crop Science and Plant Breeding, Freising, Germany
- TUM School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany
| | - Lorenz Hartl
- Bavarian State Research Center for Agriculture, Institute for Crop Science and Plant Breeding, Freising, Germany
| | - Volker Mohler
- Bavarian State Research Center for Agriculture, Institute for Crop Science and Plant Breeding, Freising, Germany
- TUM School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany
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12
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Genome-wide identification and resistance expression analysis of the NBS gene family in Triticum urartu. Genes Genomics 2017. [DOI: 10.1007/s13258-017-0526-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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13
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Dong Y, Zhang Y, Xiao Y, Yan J, Liu J, Wen W, Zhang Y, Jing R, Xia X, He Z. Cloning of TaSST genes associated with water soluble carbohydrate content in bread wheat stems and development of a functional marker. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2016; 129:1061-70. [PMID: 26883047 DOI: 10.1007/s00122-016-2683-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Accepted: 01/23/2016] [Indexed: 05/21/2023]
Abstract
We cloned TaSST genes, developed a gene-specific marker for TaSST-D1, and identified three QTL in the Doumai/Shi 4185 RIL population. TaSST-D1 is within one of the three QTL. Sucrose:sucrose-1-fructosyltransferase (1-SST), a critical enzyme in the fructan biosynthetic pathway, is significantly and positively associated with water soluble carbohydrate (WSC) content in bread wheat stems. In the present study, wheat 1-SST genes (TaSST) were isolated and located on chromosomes 4A, 7A and 7D. Sequence analysis of TaSST-D1 revealed 15 single nucleotide polymorphisms (SNP) in the third exon between cultivars with higher and lower WSC content. A cleaved amplified polymorphism sequence (CAPS) marker, WSC7D, based on the polymorphism at position 1216 (C-G) was developed to discriminate the two alleles. WSC7D was located on chromosome 7DS using a recombinant inbred line (RIL) population from a Doumai/Shi 4185 cross, and a set of Chinese Spring nullisomic-tetrasomic lines. TaSST-D1 co-segregated with the CAPS marker WSC7D and was linked to SNP marker BS00108793_51 on chromosome 7DS at a genetic distance of 6.1 cM. It explained 8.8, 10.9, and 11.3% of the phenotypic variances in trials at Beijing and Shijiazhuang as well as the averaged data from those environments, respectively. Two additional QTL (QWSC.caas-4BS and QWSC.caas-7AS) besides TaSST-D1 were mapped in the RIL population. One hundred and forty-nine Chinese wheat cultivars and advanced lines tested in four environments were used to validate a highly significant (P < 0.01) association between WSC7D and WSC content in wheat stems. WSC7D can be used as a gene-specific marker for improvement of stem WSC content in wheat breeding programs.
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Affiliation(s)
- Yan Dong
- National Wheat Improvement Center, Institute of Crop Science, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, 100081, Beijing, China
| | - Yan Zhang
- National Wheat Improvement Center, Institute of Crop Science, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, 100081, Beijing, China
| | - Yonggui Xiao
- National Wheat Improvement Center, Institute of Crop Science, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, 100081, Beijing, China
| | - Jun Yan
- Cotton Research Institute, CAAS, Huanghedadao, Anyang, Henan, China
| | - Jindong Liu
- National Wheat Improvement Center, Institute of Crop Science, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, 100081, Beijing, China
| | - Weie Wen
- College of Agronomy, Xinjiang Agricultural University, 311 Nongda East Road, 830052, Urumqi, Xinjiang, China
| | - Yong Zhang
- National Wheat Improvement Center, Institute of Crop Science, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, 100081, Beijing, China
| | - Ruilian Jing
- National Wheat Improvement Center, Institute of Crop Science, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, 100081, Beijing, China
| | - Xianchun Xia
- National Wheat Improvement Center, Institute of Crop Science, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, 100081, Beijing, China.
| | - Zhonghu He
- National Wheat Improvement Center, Institute of Crop Science, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, 100081, Beijing, China
- International Maize and Wheat Improvement Center (CIMMYT) China Office, c/o CAAS, 12 Zhongguancun South Street, 100081, Beijing, China
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14
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Xu H, Yi Y, Ma P, Qie Y, Fu X, Xu Y, Zhang X, An D. Molecular tagging of a new broad-spectrum powdery mildew resistance allele Pm2c in Chinese wheat landrace Niaomai. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2015; 128:2077-84. [PMID: 26133735 DOI: 10.1007/s00122-015-2568-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Accepted: 06/16/2015] [Indexed: 05/07/2023]
Abstract
A new broad-spectrum powdery mildew resistance allele Pm2c was identified and mapped in Chinese wheat landrace Niaomai. Chinese wheat landrace Niaomai showed resistance to 27 of 28 Chinese Blumeria graminis f. sp tritici (Bgt) races. Genetic analysis of an F2 population and its derived F2:3 families from the cross Niaomai × Mingxian 169 and backcross population, Niaomai/2*Mingxian 169, indicated that the resistance of Niaomai to Bgt races was conferred by a single dominant resistance gene, temporarily designated PmNM. Molecular tagging showed that PmNM was located on chromosome 5DS and flanked by SSR markers Xcfd81 and Xcfd78 with the genetic distances of 0.1/0.4 cM and 4.9/7.5 cM, respectively. Niaomai showed a different array of responses compared to lines with Pm2a, Pm2b, PmD57-5D, PmLX66, PmX3986-2 and Pm48 genes, sharing the same Xcfd81 allele but differing from Xcfd78 allele for Pm2a and Pm2b lines. Allelism tests based on crosses of Niaomai with Ulka/8*Cc and KM2939 showed that PmNM is allelic to Pm2a and Pm2b. We concluded that PmNM is a new allele of Pm2, re-designated Pm2c. Pm2c could be transferred into wheat cultivars by marker-assisted selection to improve the powdery mildew resistance of breeding cultivars/lines.
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Affiliation(s)
- Hongxing Xu
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, 050021, Hebei, China
| | - Yanjie Yi
- School of Bioengineering, Henan University of Technology, Zhengzhou, 450001, Henan, China
| | - Pengtao Ma
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, 050021, Hebei, China
| | - Yanmin Qie
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, 050021, Hebei, China
| | - Xiaoyi Fu
- Shijiazhuang Academy of Agricultural and Forestry Sciences, Shijiazhuang, 050041, Hebei, China
| | - Yunfeng Xu
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, 050021, Hebei, China
| | - Xiaotian Zhang
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, 050021, Hebei, China
| | - Diaoguo An
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, 050021, Hebei, China.
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15
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Yang H, Jian J, Li X, Renshaw D, Clements J, Sweetingham MW, Tan C, Li C. Application of whole genome re-sequencing data in the development of diagnostic DNA markers tightly linked to a disease-resistance locus for marker-assisted selection in lupin (Lupinus angustifolius). BMC Genomics 2015; 16:660. [PMID: 26329386 PMCID: PMC4557927 DOI: 10.1186/s12864-015-1878-5] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Accepted: 08/24/2015] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND Molecular marker-assisted breeding provides an efficient tool to develop improved crop varieties. A major challenge for the broad application of markers in marker-assisted selection is that the marker phenotypes must match plant phenotypes in a wide range of breeding germplasm. In this study, we used the legume crop species Lupinus angustifolius (lupin) to demonstrate the utility of whole genome sequencing and re-sequencing on the development of diagnostic markers for molecular plant breeding. RESULTS Nine lupin cultivars released in Australia from 1973 to 2007 were subjected to whole genome re-sequencing. The re-sequencing data together with the reference genome sequence data were used in marker development, which revealed 180,596 to 795,735 SNP markers from pairwise comparisons among the cultivars. A total of 207,887 markers were anchored on the lupin genetic linkage map. Marker mining obtained an average of 387 SNP markers and 87 InDel markers for each of the 24 genome sequence assembly scaffolds bearing markers linked to 11 genes of agronomic interest. Using the R gene PhtjR conferring resistance to phomopsis stem blight disease as a test case, we discovered 17 candidate diagnostic markers by genotyping and selecting markers on a genetic linkage map. A further 243 candidate diagnostic markers were discovered by marker mining on a scaffold bearing non-diagnostic markers linked to the PhtjR gene. Nine out from the ten tested candidate diagnostic markers were confirmed as truly diagnostic on a broad range of commercial cultivars. Markers developed using these strategies meet the requirements for broad application in molecular plant breeding. CONCLUSIONS We demonstrated that low-cost genome sequencing and re-sequencing data were sufficient and very effective in the development of diagnostic markers for marker-assisted selection. The strategies used in this study may be applied to any trait or plant species. Whole genome sequencing and re-sequencing provides a powerful tool to overcome current limitations in molecular plant breeding, which will enable plant breeders to precisely pyramid favourable genes to develop super crop varieties to meet future food demands.
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Affiliation(s)
- Huaan Yang
- Department of Agriculture and Food Western Australia, 3 Baron-Hay Court, South Perth, 6151, Australia.
| | - Jianbo Jian
- Beijing Genome Institute - Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen, 518083, China.
| | - Xuan Li
- Beijing Genome Institute - Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen, 518083, China.
| | - Daniel Renshaw
- Department of Agriculture and Food Western Australia, 3 Baron-Hay Court, South Perth, 6151, Australia.
| | - Jonathan Clements
- Department of Agriculture and Food Western Australia, 3 Baron-Hay Court, South Perth, 6151, Australia.
| | - Mark W Sweetingham
- Department of Agriculture and Food Western Australia, 3 Baron-Hay Court, South Perth, 6151, Australia.
| | - Cong Tan
- State Agricultural Biotechnology Centre, Murdoch University, Murdoch, 6150, Australia.
| | - Chengdao Li
- Department of Agriculture and Food Western Australia, 3 Baron-Hay Court, South Perth, 6151, Australia.
- State Agricultural Biotechnology Centre, Murdoch University, Murdoch, 6150, Australia.
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16
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Kage U, Kumar A, Dhokane D, Karre S, Kushalappa AC. Functional molecular markers for crop improvement. Crit Rev Biotechnol 2015; 36:917-30. [DOI: 10.3109/07388551.2015.1062743] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Udaykumar Kage
- Plant Science Department, McGill University, Sainte-Anne-de-Bellevue, Quebec, Canada, H9X3V9
| | - Arun Kumar
- Plant Science Department, McGill University, Sainte-Anne-de-Bellevue, Quebec, Canada, H9X3V9
| | - Dhananjay Dhokane
- Plant Science Department, McGill University, Sainte-Anne-de-Bellevue, Quebec, Canada, H9X3V9
| | - Shailesh Karre
- Plant Science Department, McGill University, Sainte-Anne-de-Bellevue, Quebec, Canada, H9X3V9
| | - Ajjamada C. Kushalappa
- Plant Science Department, McGill University, Sainte-Anne-de-Bellevue, Quebec, Canada, H9X3V9
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17
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Hao Y, Parks R, Cowger C, Chen Z, Wang Y, Bland D, Murphy JP, Guedira M, Brown-Guedira G, Johnson J. Molecular characterization of a new powdery mildew resistance gene Pm54 in soft red winter wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2015; 128:465-76. [PMID: 25533209 DOI: 10.1007/s00122-014-2445-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Accepted: 12/11/2014] [Indexed: 05/12/2023]
Abstract
A new powdery mildew resistance gene Pm54 was identified on chromosome 6BL in soft red winter wheat. Powdery mildew is causing increasing damage to wheat production in the southeastern USA. To combat the disease, a continuing need exists to discover new genes for powdery mildew resistance and to incorporate those genes into breeding programs. Pioneer(®) variety 26R61 (shortened as 26R61) and AGS 2000 have been used as checks in the Uniform Southern Soft Red Winter Wheat Nursery for a decade, and both have provided good resistance across regions during that time. In the present study, a genetic analysis of mildew resistance was conducted on a RIL population developed from a cross of 26R61 and AGS 2000. Phenotypic evaluation was conducted in the field at Plains, GA, and Raleigh, NC, in 2012 and 2013, a total of four environments. Three quantitative trait loci (QTL) with major effect were consistently detected on wheat chromosomes 2BL, 4A and 6BL. The 2BL QTL contributed by 26R61 was different from Pm6, a widely used gene in the southeastern USA. The other two QTL were identified from AGS 2000. The 6BL QTL was subsequently characterized as a simple Mendelian factor when the population was inoculated with a single Blumeria graminis f. sp. tritici (Bgt) isolate in controlled environments. Since there is no known powdery mildew resistance gene (Pm) on this particular location of common wheat, the gene was designated Pm54. The closely linked marker Xbarc134 was highly polymorphic in a set of mildew differentials, indicating that the marker should be useful for pyramiding Pm54 with other Pm genes by marker-assisted selection.
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Affiliation(s)
- Yuanfeng Hao
- Department of Crop and Soil Sciences, University of Georgia, Griffin Campus, Griffin, GA, 30223, USA,
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18
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Harris MO, Friesen TL, Xu SS, Chen MS, Giron D, Stuart JJ. Pivoting from Arabidopsis to wheat to understand how agricultural plants integrate responses to biotic stress. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:513-531. [PMID: 25504642 DOI: 10.1093/jxb/eru465] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
In this review, we argue for a research initiative on wheat's responses to biotic stress. One goal is to begin a conversation between the disparate communities of plant pathology and entomology. Another is to understand how responses to a variety of agents of biotic stress are integrated in an important crop. We propose gene-for-gene interactions as the focus of the research initiative. On the parasite's side is an Avirulence (Avr) gene that encodes one of the many effector proteins the parasite applies to the plant to assist with colonization. On the plant's side is a Resistance (R) gene that mediates a surveillance system that detects the Avr protein directly or indirectly and triggers effector-triggered plant immunity. Even though arthropods are responsible for a significant proportion of plant biotic stress, they have not been integrated into important models of plant immunity that come from plant pathology. A roadblock has been the absence of molecular evidence for arthropod Avr effectors. Thirty years after this evidence was discovered in a plant pathogen, there is now evidence for arthropods with the cloning of the Hessian fly's vH13 Avr gene. After reviewing the two models of plant immunity, we discuss how arthropods could be incorporated. We end by showing features that make wheat an interesting system for plant immunity, including 479 resistance genes known from agriculture that target viruses, bacteria, fungi, nematodes, insects, and mites. It is not likely that humans will be subsisting on Arabidopsis in the year 2050. It is time to start understanding how agricultural plants integrate responses to biotic stress.
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Affiliation(s)
- M O Harris
- Department of Entomology, North Dakota State University, Fargo, ND 58105, USA
| | - T L Friesen
- USDA-ARS, Cereal Crops Research Unit, Fargo, ND USA
| | - S S Xu
- USDA-ARS, Cereal Crops Research Unit, Fargo, ND USA
| | - M S Chen
- USDA-ARS, Hard Winter Wheat Genetics Research Unit, Kansas State University, Manhattan, KS, USA
| | - D Giron
- Institut de Recherche sur la Biologie de l'Insecte UMR 7261 CNRS/Université François-Rabelais de Tours, Tours, France
| | - J J Stuart
- Department of Entomology, Purdue University, West Lafayette, IN, USA
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19
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Stirnweis D, Milani SD, Brunner S, Herren G, Buchmann G, Peditto D, Jordan T, Keller B. Suppression among alleles encoding nucleotide-binding-leucine-rich repeat resistance proteins interferes with resistance in F1 hybrid and allele-pyramided wheat plants. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2014; 79:893-903. [PMID: 24942051 DOI: 10.1111/tpj.12592] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2014] [Revised: 06/06/2014] [Accepted: 06/12/2014] [Indexed: 05/24/2023]
Abstract
The development of high-yielding varieties with broad-spectrum durable disease resistance is the ultimate goal of crop breeding. In plants, immune receptors of the nucleotide-binding-leucine-rich repeat (NB-LRR) class mediate race-specific resistance against pathogen attack. When employed in agriculture this type of resistance is often rapidly overcome by newly adapted pathogen races. The stacking of different resistance genes or alleles in F1 hybrids or in pyramided lines is a promising strategy for achieving more durable resistance. Here, we identify a molecular mechanism which can negatively interfere with the allele-pyramiding approach. We show that pairwise combinations of different alleles of the powdery mildew resistance gene Pm3 in F1 hybrids and stacked transgenic wheat lines can result in suppression of Pm3-based resistance. This effect is independent of the genetic background and solely dependent on the Pm3 alleles. Suppression occurs at the post-translational level, as levels of RNA and protein in the suppressed alleles are unaffected. Using a transient expression system in Nicotiana benthamiana, the LRR domain was identified as the domain conferring suppression. The results of this study suggest that the expression of closely related NB-LRR resistance genes or alleles in the same genotype can lead to dominant-negative interactions. These findings provide a molecular explanation for the frequently observed ineffectiveness of resistance genes introduced from the secondary gene pool into polyploid crop species and mark an important step in overcoming this limitation.
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Affiliation(s)
- Daniel Stirnweis
- Institute of Plant Biology, University of Zürich, Zollikerstrasse 107, CH-8008, Zürich, Switzerland
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20
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Hurni S, Brunner S, Stirnweis D, Herren G, Peditto D, McIntosh RA, Keller B. The powdery mildew resistance gene Pm8 derived from rye is suppressed by its wheat ortholog Pm3. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2014; 79:904-13. [PMID: 24942074 DOI: 10.1111/tpj.12593] [Citation(s) in RCA: 82] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2014] [Revised: 06/06/2014] [Accepted: 06/12/2014] [Indexed: 05/20/2023]
Abstract
The powdery mildew resistance gene Pm8 derived from rye is located on a 1BL.1RS chromosome translocation in wheat. However, some wheat lines with this translocation do not show resistance to isolates of the wheat powdery mildew pathogen avirulent to Pm8 due to an unknown genetically dominant suppression mechanism. Here we show that lines with suppressed Pm8 activity contain an intact and expressed Pm8 gene. Therefore, the absence of Pm8 function in certain 1BL.1RS-containing wheat lines is not the result of gene loss or mutation but is based on suppression. The wheat gene Pm3, an ortholog of rye Pm8, suppressed Pm8-mediated powdery mildew resistance in lines containing Pm8 in a transient single-cell expression assay. This result was further confirmed in transgenic lines with combined Pm8 and Pm3 transgenes. Expression analysis revealed that suppression is not the result of gene silencing, either in wheat 1BL.1RS translocation lines carrying Pm8 or in transgenic genotypes with both Pm8 and Pm3 alleles. In addition, a similar abundance of the PM8 and PM3 proteins in single or double homozygous transgenic lines suggested that a post-translational mechanism is involved in suppression of Pm8. Co-expression of Pm8 and Pm3 genes in Nicotiana benthamiana leaves followed by co-immunoprecipitation analysis showed that the two proteins interact. Therefore, the formation of a heteromeric protein complex might result in inefficient or absent signal transmission for the defense reaction. These data provide a molecular explanation for the suppression of resistance genes in certain genetic backgrounds and suggest ways to circumvent it in future plant breeding.
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Affiliation(s)
- Severine Hurni
- Institute of Plant Biology, University of Zürich, Zollikerstrasse 107, CH-8008, Zürich, Switzerland
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21
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From genomics to functional markers in the era of next-generation sequencing. Biotechnol Lett 2013; 36:417-26. [PMID: 24129954 DOI: 10.1007/s10529-013-1377-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 07/14/2013] [Accepted: 09/25/2013] [Indexed: 12/11/2022]
Abstract
The availability of complete genome sequences, along with other genomic resources for Arabidopsis, rice, pigeon pea, soybean and other crops, has revolutionized our understanding of the genetic make-up of plants. Next-generation DNA sequencing (NGS) has facilitated single nucleotide polymorphism discovery in plants. Functionally-characterized sequences can be identified and functional markers (FMs) for important traits can be developed at an ever-increasing ease. FMs are derived from sequence polymorphisms found in allelic variants of a functional gene. Linkage disequilibrium-based association mapping and homologous recombinants have been developed for identification of "perfect" markers for their use in crop improvement practices. Compared with many other molecular markers, FMs derived from the functionally characterized sequence genes using NGS techniques and their use provide opportunities to develop high-yielding plant genotypes resistant to various stresses at a fast pace.
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22
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Troch V, Audenaert K, Vanheule A, Bekaert B, Höfte M, Haesaert G. Evaluation of Resistance to Powdery Mildew in Triticale Seedlings and Adult Plants. PLANT DISEASE 2013; 97:410-417. [PMID: 30722401 DOI: 10.1094/pdis-02-12-0161-re] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Triticale (×Triticosecale) is the intergeneric hybrid between the female parent wheat and the male parent rye. With the expansion of the triticale growing area, powdery mildew emerged on this new host and has become a significant disease on triticale. Recent research demonstrated that this "new" powdery mildew on triticale has emerged through a host range expansion of powdery mildew of wheat. Moreover, this expansion occurred recently and multiple times at different locations in Europe. An effective and environmentally sensitive approach to controlling powdery mildew involves breeding crop plants for resistance. The main goal of this study was to identify the presence of powdery mildew resistance in commercial triticale cultivars. First, the avirulence (AVR) genes and gene complexity carried by this new powdery mildew population on triticale were characterized. Virulence was identified for all the resistance genes evaluated in the present study, and virulence frequencies higher than 50% were recorded on the genes Pm3f, Pm5b, Pm6, Pm7, Pm8, and Pm17. Using molecular markers, the presence of resistance genes Pm3f and Pm17 was identified in certain triticale cultivars. The triticale cultivars were also evaluated for the presence of quantitative resistance at adult plant growth stages in a 2-year field experiment. Despite the high disease pressure, cultivars highly resistant at the adult-plant growth stages were identified. Because 'Grenado' also showed effective race-specific resistance, this cultivar could be of high value for breeding for durable resistance to powdery mildew. Altogether, this study reveals valuable information on the presence of powdery mildew resistance in commercial triticale cultivars, which can be used in breeding programs in triticale. Additionally, this study underscores the need to broaden the base of powdery mildew resistance in triticale through introgression and deployment of new sources of mildew resistance, including quantitative resistance.
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Affiliation(s)
- V Troch
- Faculty of Applied Bioscience Engineering, University College Ghent (Ghent University Association), and Department of Crop Protection, Laboratory of Phytopathology, Ghent University
| | - K Audenaert
- Faculty of Applied Bioscience Engineering, University College Ghent (Ghent University Association), and Department of Crop Protection, Laboratory of Phytopathology, Ghent University
| | - A Vanheule
- Faculty of Applied Bioscience Engineering, University College Ghent (Ghent University Association), and Department of Crop Protection, Laboratory of Phytopathology, Ghent University
| | - B Bekaert
- Faculty of Applied Bioscience Engineering, University College Ghent (Ghent University Association)
| | - M Höfte
- Department of Crop Protection, Laboratory of Phytopathology
| | - G Haesaert
- Faculty of Applied Bioscience Engineering, University College Ghent (Ghent University Association), and Department of Crop Protection, Laboratory of Phytopathology, Ghent University, BE-9000 Ghent, Belgium
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23
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Hua L, Wu J, Chen C, Wu W, He X, Lin F, Wang L, Ashikawa I, Matsumoto T, Wang L, Pan Q. The isolation of Pi1, an allele at the Pik locus which confers broad spectrum resistance to rice blast. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2012; 125:1047-55. [PMID: 22643901 DOI: 10.1007/s00122-012-1894-7] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2012] [Accepted: 05/11/2012] [Indexed: 05/04/2023]
Abstract
We report the isolation of Pi1, a gene conferring broad-spectrum resistance to rice blast (Magnaporthe oryzae). Using loss- and gain-of-function approaches, we demonstrate that Pi1 is an allele at the Pik locus. Like other alleles at this locus, Pi1 consists of two genes. A functional nucleotide polymorphism (FNP) was identified that allows differentiation of Pi1 from other Pik alleles and other non-Pik genes. A extensive germplasm survey using this FNP reveals that Pi1 is a rare allele in germplasm collections and one that has conferred durable resistance to a broad spectrum of pathogen isolates.
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Affiliation(s)
- Lixia Hua
- State Key Laboratory for Conservation and Utilization of Subtropic Agrobioresources, Laboratory of Plant Resistance and Genetics, College of Natural Resources and Environmental Sciences, South China Agricultural University, Guangzhou 510642, China
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24
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Jakobson I, Reis D, Tiidema A, Peusha H, Timofejeva L, Valárik M, Kladivová M, Simková H, Doležel J, Järve K. Fine mapping, phenotypic characterization and validation of non-race-specific resistance to powdery mildew in a wheat-Triticum militinae introgression line. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2012; 125:609-623. [PMID: 22534789 DOI: 10.1007/s00122-012-1856-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2011] [Accepted: 03/21/2012] [Indexed: 05/31/2023]
Abstract
Introgression of several genomic loci from tetraploid Triticum militinae into bread wheat cv. Tähti has increased resistance of introgression line 8.1 to powdery mildew in seedlings and adult plants. In our previous work, only a major quantitative trait locus (QTL) on chromosome 4AL of the line 8.1 contributed significantly to resistance, whereas QTL on chromosomes 1A, 1B, 2A, 5A and 5B were detected merely on a suggestive level. To verify and characterize all QTLs in the line 8.1, a mapping population of double haploid lines was established. Testing for seedling resistance to 16 different races/mixtures of Blumeria graminis f. sp. tritici revealed four highly significant non-race-specific resistance QTL including the main QTL on chromosome 4AL, and a race-specific QTL on chromosome 5B. The major QTL on chromosome 4AL (QPm.tut-4A) as well as QTL on chromosome 5AL and a newly detected QTL on 7AL were highly effective at the adult stage. The QPm.tut-4A QTL accounts on average for 33-49 % of the variation in resistance in the double haploid population. Interactions between the main QTL QPm.tut-4A and the minor QTL were evaluated and discussed. A population of 98 F(2) plants from a cross of susceptible cv. Chinese Spring and the line 8.1 was created that allowed mapping the QPm.tut-4A locus to the proximal 2.5-cM region of the introgressed segment on chromosome 4AL. The results obtained in this work make it feasible to use QPm.tut-4A in resistance breeding and provide a solid basis for positional cloning of the major QTL.
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Affiliation(s)
- Irena Jakobson
- Department of Gene Technology, Tallinn University of Technology, Akadeemia tee 15, 12618, Tallinn, Estonia.
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Lu Q, Bjørnstad Å, Ren Y, Asad MA, Xia X, Chen X, Ji F, Shi J, Lillemo M. Partial resistance to powdery mildew in German spring wheat 'Naxos' is based on multiple genes with stable effects in diverse environments. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2012; 125:297-309. [PMID: 22434502 DOI: 10.1007/s00122-012-1834-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2011] [Accepted: 02/17/2012] [Indexed: 05/10/2023]
Abstract
Powdery mildew is one of the most important wheat diseases in temperate regions of the world. Resistance breeding is considered to be an economical and environmentally benign way to control this disease. The German spring wheat cv. 'Naxos' exhibits high levels of partial and race non-specific resistance to powdery mildew in the field and is a valuable source in resistance breeding. The main objective of the present study was to map the genetic factors behind the resistance in Naxos, based on a population of recombinant inbred lines (RIL) from a cross with the susceptible CIMMYT breeding line SHA3/CBRD. Powdery mildew severity was evaluated in six field trials in Norway and four field trials in China. The major quantitative trait locus (QTL) with resistance from Naxos was detected close to the Pm3 locus on 1AS in all environments, and explained up to 35% of the phenotypic variation. Naxos was shown to carry another major QTL on 2DL and minor ones on 2BL and 7DS. QTL with resistance from SHA3/CBRD were detected on 1RS, 2DLc, 6BL and 7AL. The QTL on the 1B/1R translocation showed highly variable effects across environments corresponding to known virulence differences against Pm8. SHA3/CBRD was shown to possess the Pm3 haplotype on 1AS, but none of the known Pm3a-g alleles. The RIL population did not provide any evidence to suggest that the Pm3 allele of SHA3/CBRD acted as a suppressor of Pm8.
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Affiliation(s)
- Qiongxian Lu
- Department of Plant and Environmental Sciences, Norwegian University of Life Sciences, PO Box 5003, 1432 Aas, Norway
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Liu Y, He Z, Appels R, Xia X. Functional markers in wheat: current status and future prospects. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2012; 125:1-10. [PMID: 22366867 DOI: 10.1007/s00122-012-1829-3] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2011] [Accepted: 02/11/2012] [Indexed: 05/18/2023]
Abstract
Functional markers (FM) are developed from sequence polymorphisms present in allelic variants of a functional gene at a locus. FMs accurately discriminate alleles of a targeted gene, and are ideal molecular markers for marker-assisted selection in wheat breeding. In this paper, we summarize FMs developed and used in common wheat. To date, more than 30 wheat loci associated with processing quality, agronomic traits, and disease resistance, have been cloned, and 97 FMs were developed to identify 93 alleles based on the sequences of those genes. A general approach is described for isolation of wheat genes and development of FMs based on in silico cloning and comparative genomics. The divergence of DNA sequences of different alleles that affect gene function is summarized. In addition, 14 molecular markers specific for alien genes introduced from common wheat relatives were also described. This paper provides updated information on all FMs and gene-specific STS markers developed so far in wheat and should facilitate their application in wheat breeding programs.
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Affiliation(s)
- Yanan Liu
- National Wheat Improvement Centre, The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
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Hao Y, Chen Z, Wang Y, Bland D, Buck J, Brown-Guedira G, Johnson J. Characterization of a major QTL for adult plant resistance to stripe rust in US soft red winter wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2011; 123:1401-11. [PMID: 21830107 DOI: 10.1007/s00122-011-1675-8] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2011] [Accepted: 07/26/2011] [Indexed: 05/21/2023]
Abstract
Stripe rust, caused by Puccinia striiformis f. sp. tritici, is an important disease of soft red winter wheat in the eastern region of the USA. Pioneer 26R61 has provided effective resistance to stripe rust for 10 years. To elucidate the genetic basis of the resistance, a mapping population of 178 recombinant inbred lines (RILs) was developed using single-seed descent from a cross between Pioneer 26R61 and the susceptible cultivar AGS 2000. A genetic map with 895 markers covering all 21 chromosomes was used for QTL analysis. One major QTL was detected, explaining up to 56.0% of the mean phenotypic variation, flanked by markers Xbarc124 and Xgwm359, and assigned to the distal 22% of the short arm of wheat chromosome 2A. Evidence showed that it was different from Yr17 derived from Ae. ventricosa, the only formally named Yr gene in 2AS, and the QTL was temporarily designated as YrR61. In addition, a minor QTL, QYr.uga-6AS, probably conditioned high-temperature adult plant resistance. The QTL explained 6-7% of the trait variation. Preliminary test of the flanking markers for YrR61, in two cultivars and two promising breeding lines with Pioneer 26R61 in their pedigree, indicated that YrR61 was present in these cultivars and lines, and these markers could therefore be used in marker-assisted selection.
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Affiliation(s)
- Yuanfeng Hao
- Department of Crop and Soil Sciences, University of Georgia, Griffin Campus, Griffin, GA 30223, USA
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McIntosh RA, Zhang P, Cowger C, Parks R, Lagudah ES, Hoxha S. Rye-derived powdery mildew resistance gene Pm8 in wheat is suppressed by the Pm3 locus. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2011; 123:359-367. [PMID: 21509697 DOI: 10.1007/s00122-011-1589-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2011] [Accepted: 03/29/2011] [Indexed: 05/30/2023]
Abstract
Genetic suppression of disease resistance is occasionally observed in hexaploid wheat or in its interspecific crosses. The phenotypic effects of genes moved to wheat from relatives with lower ploidy are often smaller than in the original sources, suggesting the presence of modifiers or partial inhibitors in wheat, especially dilution effects caused by possible variation at orthologous loci. However, there is little current understanding of the underlying genetics of suppression. The discovery of suppression in some wheat genotypes of the cereal rye chromosome 1RS-derived gene Pm8 for powdery mildew resistance offered an opportunity for analysis. A single gene for suppression was identified at or near the closely linked storage protein genes Gli-A1 and Glu-A3, which are also closely associated with the Pm3 locus on chromosome 1AS. The Pm3 locus is a complex of expressed alleles and pseudogenes embedded among Glu-A3 repeats. In the current report, we explain why earlier work indicated that the mildew suppressor was closely associated with specific Gli-A1 and Glu-A3 alleles, and predict that suppression of Pm8 involves translated gene products from the Pm3 locus.
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Affiliation(s)
- Robert A McIntosh
- Plant Breeding Institute Cobbitty, University of Sydney, Narellan, NSW 2567, Australia.
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Hayashi K, Yasuda N, Fujita Y, Koizumi S, Yoshida H. Identification of the blast resistance gene Pit in rice cultivars using functional markers. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2010; 121:1357-67. [PMID: 20589366 DOI: 10.1007/s00122-010-1393-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2010] [Accepted: 06/14/2010] [Indexed: 05/04/2023]
Abstract
DNA markers that allow for identification of resistance genes in rice germplasm have a great advantage in resistance breeding because they can assess the existence of the genes without laborious inoculation tests. Functional markers (FMs), which are designed from functional polymorphisms within the sequence of genes, are unaffected by nonfunctional allelic variation and make it possible to identify an individual gene. We previously showed that the resistance function of the rice blast resistance gene Pit in a resistant cultivar, K59, was mainly acquired by up-regulated promoter activity through the insertion of a long terminal repeat (LTR) retrotransposon upstream of Pit. Here, we developed PCR-based DNA markers derived from the LTR-retrotransposon sequence and used these markers to screen worldwide accessions of rice germplasm. We identified 5 cultivars with the LTR-retrotransposon insertion out of 68 rice accessions. The sequence and expression pattern of Pit in the five cultivars were the same as those in K59 and all showed Pit-mediated blast resistance. The results suggest that the functional Pit identified using the markers was derived from a common progenitor. Additionally, comparison of the Pit coding sequences between K59 and susceptible cultivars revealed that one nucleotide polymorphism, which caused an amino acid substitution, offered another target for a FM. These results indicate that our DNA markers should enhance prediction of Pit function and be applicable to a range of rice varieties/landraces cultivated in various regions worldwide and belonging to the temperate japonica, tropical japonica, and indica groups.
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Affiliation(s)
- K Hayashi
- National Agricultural Research Center, National Agriculture and Food Research Organization (NARO), Tsukuba, Japan.
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Maxwell JJ, Lyerly JH, Srnic G, Parks R, Cowger C, Marshall D, Brown-Guedira G, Murphy JP. MlAB10
: A Triticum turgidum
Subsp. dicoccoides
Derived Powdery Mildew Resistance Gene Identified in Common Wheat. CROP SCIENCE 2010; 50:2261-2267. [PMID: 0 DOI: 10.2135/cropsci2010.04.0195] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Affiliation(s)
- J. J. Maxwell
- LDB-Independence; 2332 Henley Ave. Independence IA 50644
| | - J. H. Lyerly
- Dep. of Crop Science; North Carolina State Univ.; Raleigh NC 27695
| | - G. Srnic
- Pioneer- Hybrid International, Inc.; Via Madre Teresa Di Calcuta; 2/4, 26030 Pessina Cremonese CR Italy
| | - R. Parks
- USDA-ARS Plant Sciences Research; Dep. of Plant Pathology; North Carolina State Univ.; Raleigh NC 27695
| | - C. Cowger
- USDA-ARS Plant Sciences Research; Dep. of Plant Pathology; North Carolina State Univ.; Raleigh NC 27695
| | - D. Marshall
- USDA-ARS Plant Sciences Research; Dep. of Plant Pathology; North Carolina State Univ.; Raleigh NC 27695
| | - G. Brown-Guedira
- USDA-ARS Plant Sciences Research; Dep. of Crop Science; North Carolina State Univ.; Raleigh NC 27695
| | - J. P. Murphy
- Dep. of Crop Science; North Carolina State Univ.; Raleigh NC 27695
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Kumar GR, Sakthivel K, Sundaram R, Neeraja C, Balachandran S, Rani NS, Viraktamath B, Madhav M. Allele mining in crops: Prospects and potentials. Biotechnol Adv 2010; 28:451-61. [DOI: 10.1016/j.biotechadv.2010.02.007] [Citation(s) in RCA: 88] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2009] [Revised: 09/21/2009] [Accepted: 09/25/2009] [Indexed: 12/26/2022]
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Genetic Diversity of the Pm3 Powdery Mildew Resistance Alleles in Wheat Gene Bank Accessions as Assessed by Molecular Markers. DIVERSITY-BASEL 2010. [DOI: 10.3390/d2050768] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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Bhullar NK, Zhang Z, Wicker T, Keller B. Wheat gene bank accessions as a source of new alleles of the powdery mildew resistance gene Pm3: a large scale allele mining project. BMC PLANT BIOLOGY 2010; 10:88. [PMID: 20470444 PMCID: PMC3095356 DOI: 10.1186/1471-2229-10-88] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2010] [Accepted: 05/17/2010] [Indexed: 05/18/2023]
Abstract
BACKGROUND In the last hundred years, the development of improved wheat cultivars has led to the replacement of landraces and traditional varieties by modern cultivars. This has resulted in a decline in the genetic diversity of agriculturally used wheat. However, the diversity lost in the elite material is somewhat preserved in crop gene banks. Therefore, the gene bank accessions provide the basis for genetic improvement of crops for specific traits and and represent rich sources of novel allelic variation. RESULTS We have undertaken large scale molecular allele mining to isolate new alleles of the powdery mildew resistance gene Pm3 from wheat gene bank accessions. The search for new Pm3 alleles was carried out on a geographically diverse set of 733 wheat accessions originating from 20 countries. Pm3 specific molecular tools as well as classical pathogenicity tests were used to characterize the accessions. Two new functional Pm3 alleles were identified out of the eight newly cloned Pm3 sequences. These new resistance alleles were isolated from accessions from China and Nepal. Thus, the repertoire of functional Pm3 alleles now includes 17 genes, making it one of the largest allelic series of plant resistance genes. The combined information on resistant and susceptible Pm3 sequences will allow to study molecular function and specificity of functional Pm3 alleles. CONCLUSIONS This study demonstrates that molecular allele mining on geographically defined accessions is a useful strategy to rapidly characterize the diversity of gene bank accessions at a specific genetic locus of agronomical importance. The identified wheat accessions with new resistance specificities can be used for marker-assisted transfer of the Pm3 alleles to modern wheat lines.
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Affiliation(s)
- Navreet K Bhullar
- Institute of Plant Biology, University of Zurich, Zollikerstrasse 107, 8008 Zurich, Switzerland
- Institute of Plant, Animal and Agroecosystem Sciences, Swiss Federal Institute of Technology, Universitätsstrasse 2, 8092 Zurich, Switzerland
| | - Zhiqing Zhang
- Institute of Plant Biology, University of Zurich, Zollikerstrasse 107, 8008 Zurich, Switzerland
- College of Food Science, Sichuan Agricultural University, 625014, Sichuan Yaan, China
| | - Thomas Wicker
- Institute of Plant Biology, University of Zurich, Zollikerstrasse 107, 8008 Zurich, Switzerland
| | - Beat Keller
- Institute of Plant Biology, University of Zurich, Zollikerstrasse 107, 8008 Zurich, Switzerland
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Wang ZN, Huang XQ, Cloutier S. Recruitment of closely linked genes for divergent functions: the seed storage protein (Glu-3) and powdery mildew (Pm3) genes in wheat (Triticum aestivum L.). Funct Integr Genomics 2009; 10:241-51. [PMID: 20012664 DOI: 10.1007/s10142-009-0150-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2009] [Revised: 11/03/2009] [Accepted: 11/09/2009] [Indexed: 11/25/2022]
Abstract
Wheat seed storage protein gene loci (Glu-3) and powdery mildew resistance gene loci (Pm3 and Pm3-like) are closely linked on the short arms of homoeologous group 1 chromosomes. To study the structural organization of the Glu-3/Pm3 loci, three bacterial artificial chromosome clones were sequenced from the A, B, and D genomes of hexaploid wheat. The A and B genome clones contained a Glu-3 adjacent to a Pm3-like gene organized in a conserved Glu-3/SFR159/Pm3-like structure. The D genome clone contained clusters of resistance gene analogs but no Pm3. Its similarity to the A and B genome was limited to the Glu-3/SFR159 region. Comparison of the B genome PM3-like deduced amino acid sequence with known PM3 functional isotypes reinforced the hypothesis of allelic evolution via block exchange by gene conversion/recombination. The advent of glutenin genes and the formation of the Glu-3/SFR159/Pm3 locus occurred after divergence of wheat from rice and Brachypodium. Comparison of the A genome homologous sequences permitted an estimate of time of divergence of approximately 0.3 million years ago. The B genome sequences were not colinear indicating that they could either be paralogs or represent different B genome progenitors. Analysis of the 11 complete retrotransposons indicated a time of divergence ranging from 0.29 to 5.62 million years ago, consistent with their complex nested structure.
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Affiliation(s)
- Zi-Ning Wang
- Cereal Research Centre, Agriculture and Agri-Food Canada, 195 Dafoe Road, Winnipeg, MB, Canada, R3T 2M9
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LI GQ, FANG TL, ZHU J, GAO LL, LI S, XIE CJ, YANG ZM, SUN QX, LIU ZY. Molecular Identification of a Powdery Mildew Resistance Gene from Common Wheat Cultivar Brock. ZUOWU XUEBAO 2009. [DOI: 10.3724/sp.j.1006.2009.01613] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Loarce Y, Sanz MJ, Irigoyen ML, Fominaya A, Ferrer E. Mapping of STS markers obtained from oat resistance gene analog sequences. Genome 2009; 52:608-19. [DOI: 10.1139/g09-038] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Two previously isolated resistance gene analogs (RGAs) of oat have been located as RFLPs in the reference map of Avena byzantina ‘Kanota’ × Avena sativa ‘Ogle’ in regions either homologous or homoeologous to loci for resistance to Puccinia coronata , the causal agent of crown rust. In this study, the RGAs were mapped in two recombinant inbred line (RIL) populations that segregate for crown rust resistance: the diploid Avena strigosa × Avena wiestii RIL population (Asw), which has been used for mapping the complex locus PcA, and the hexaploid MN841801-1 × Noble-2 RIL population (MN), in which QTLs have been located. To obtain single-locus markers, RGAs were converted to sequence tagged site (STS) markers using a procedure involving extension of the original RGA sequence lengths by PCR genome walking, amplification and cloning of the parental fragments, and identification of single nucleotide polymorphisms. The procedure successfully obtained STSs from different members of the L7M2 family of sequences, the initial NBS of which have nucleotide similarities of >83%. However, for RGA III2.18, the parental lines were not polymorphic for the STSs assayed. A sequence characterized amplified region (SCAR) marker with features of an RGA had been previously identified for gene Pc94. This marker was also mapped in the above RIL populations. Markers based on RGA L7M2 co-localized with markers defining the QTL Prq1a in linkage group MN3, and were located 15.2 cM from PcA in linkage group AswAC. The SCAR marker for Pc94 was also located in the QTL Prq1a but at 39.5 cM from PcA in AswAC, indicating that the NBS-LRR sequence represented by this marker is not related to PcA. L7M2 was also excluded as a member of the PcA cluster, although it could be an appropriate marker for the Prq1a cluster if chromosome rearrangements are postulated.
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Affiliation(s)
- Yolanda Loarce
- Department of Cell Biology and Genetics, University of Alcalá, Campus Universitario, 28871 Alcalá de Henares, Madrid, Spain
| | - María Jesús Sanz
- Department of Cell Biology and Genetics, University of Alcalá, Campus Universitario, 28871 Alcalá de Henares, Madrid, Spain
| | - María Luisa Irigoyen
- Department of Cell Biology and Genetics, University of Alcalá, Campus Universitario, 28871 Alcalá de Henares, Madrid, Spain
| | - Araceli Fominaya
- Department of Cell Biology and Genetics, University of Alcalá, Campus Universitario, 28871 Alcalá de Henares, Madrid, Spain
| | - Esther Ferrer
- Department of Cell Biology and Genetics, University of Alcalá, Campus Universitario, 28871 Alcalá de Henares, Madrid, Spain
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Bhullar NK, Street K, Mackay M, Yahiaoui N, Keller B. Unlocking wheat genetic resources for the molecular identification of previously undescribed functional alleles at the Pm3 resistance locus. Proc Natl Acad Sci U S A 2009; 106:9519-24. [PMID: 19470492 PMCID: PMC2686639 DOI: 10.1073/pnas.0904152106] [Citation(s) in RCA: 104] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2008] [Indexed: 11/18/2022] Open
Abstract
The continuous improvement of crop plants is essential for agriculture in the coming decades and relies on the use of genetic variability through breeding. However, domestication and modern breeding have reduced diversity in the crop germplasm. Global gene banks conserve diversity, but these resources remain underexplored owing to a lack of efficient strategies to isolate important alleles. Here we describe a large-scale allele-mining project at the molecular level. We first selected a set of 1,320 bread wheat landraces from a database of 16,089 accessions, using the focused identification of germplasm strategy. On the basis of a hierarchical selection procedure on this set, we then isolated 7 resistance alleles of the powdery mildew resistance gene Pm3, doubling the known functional allelic diversity at this locus. This targeted approach for molecular utilization of gene bank accessions reveals landraces as a rich resource of new functional alleles. This strategy can be implemented for other studies on the molecular diversity of agriculturally important genes, as well as for molecular breeding.
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Affiliation(s)
- Navreet K. Bhullar
- Institute of Plant Biology, University of Zurich, 8008 Zurich, Switzerland
| | - Kenneth Street
- International Center for Agricultural Research in the Dry Areas, Aleppo, Syria; and
| | | | - Nabila Yahiaoui
- Institute of Plant Biology, University of Zurich, 8008 Zurich, Switzerland
| | - Beat Keller
- Institute of Plant Biology, University of Zurich, 8008 Zurich, Switzerland
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Yahiaoui N, Kaur N, Keller B. Independent evolution of functional Pm3 resistance genes in wild tetraploid wheat and domesticated bread wheat. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2009; 57:846-856. [PMID: 18980638 DOI: 10.1111/j.1365-313x.2008.03731.x] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
The Pm3 alleles of cultivated bread wheat confer gene for gene resistance to the powdery mildew fungus. They represent a particular case of plant disease resistance gene evolution, because of their recent origin and possible evolution after the formation of hexaploid wheat. The Pm3 locus is conserved in tetraploid wheat, thereby allowing the comparative evolutionary study of the same resistance locus in a domesticated species and in one of its wild ancestors. We have identified 61 Pm3 allelic sequences from wild and domesticated tetraploid wheat subspecies. The Pm3 sequences corresponded to 24 different haplotypes. They showed low sequence diversity, differing by only a few polymorphic sequence blocks that were further reshuffled between alleles by gene conversion and recombination. Polymorphic sequence blocks are different from the blocks found in functional Pm3 alleles of hexaploid wheat, indicating an independent evolution of the Pm3 loci in the two species. A new functional gene was identified in a wild wheat accession from Syria. This gene, Pm3k, conferred intermediate race-specific resistance to powdery mildew, and consists of a mosaic of gene segments derived from non-functional alleles. This demonstrates that Pm3-based resistance is not very frequent in wild tetraploid wheat, and that the evolution of functional resistance genes occurred independently in wild tetraploid and bread wheat. The Pm3 sequence variability and geographic distribution indicated that diversity was higher in wild emmer wheat from the Levant area, compared with the accessions from Turkey. Further screens for Pm3 functional genes in wild wheat should therefore focus on accessions from the Levant region.
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Affiliation(s)
- Nabila Yahiaoui
- Institute of Plant Biology, University of Zürich, Zürich, Switzerland.
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40
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He XY, Zhang YL, He ZH, Wu YP, Xiao YG, Ma CX, Xia XC. Characterization of phytoene synthase 1 gene (Psy1) located on common wheat chromosome 7A and development of a functional marker. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2008; 116:213-21. [PMID: 17943267 DOI: 10.1007/s00122-007-0660-8] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2007] [Accepted: 09/27/2007] [Indexed: 05/08/2023]
Abstract
Phytoene synthase (Psy), a critical enzyme in the carotenoid biosynthetic pathway, demonstrated high association with the yellow pigment (YP) content in wheat grain. Characterization of Psy genes and the development of functional markers for them are of importance for marker-assisted selection in wheat breeding. In this study, the full-length genomic DNA sequence of a Psy gene (Psy-A1) located on chromosome 7A, was characterized by in silico cloning and experimental validation. The cloned Psy-A1 comprises six exons and five introns, 4,175 bp in total, and an ORF of 1,284 bp. A co-dominant marker, YP7A, was developed based on polymorphisms of two haplotypes of Psy-A1, yielding 194 and 231-bp fragments in cultivars with high and low YP content, respectively. The marker YP7A was mapped on chromosome 7AL using an RIL population from cross PH82-2/Neixing 188, and a set of Chinese Spring nullisomic-tetrasomic lines and ditelosomic line 7AS. Psy-A1, co-segregating with the STS marker YP7A, was linked to SSR marker Xwmc809 on chromosome 7AL with a genetic distance of 5.8 cM, and explained 20-28% of the phenotypic variance for YP content across three environments. A total of 217 Chinese wheat cultivars and advanced lines were used to validate the association between the polymorphic band pattern and grain YP content. The results showed that the functional marker YP7A was closely related to grain YP content and, therefore, could be used in wheat breeding programs targeting of YP content for various wheat-based products.
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Affiliation(s)
- X Y He
- Institute of Crop Science, National Wheat Improvement Center/The National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences (CAAS), Zhongguancun South Street 12, Beijing 100081, China
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Glynn NC, Comstock JC, Sood SG, Dang PM, Chaparro JX. Isolation of nucleotide binding site-leucine rich repeat and kinase resistance gene analogues from sugarcane (Saccharum spp.). PEST MANAGEMENT SCIENCE 2008; 64:48-56. [PMID: 17935262 DOI: 10.1002/ps.1469] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
BACKGROUND Resistance gene analogues (RGAs) have been isolated from many crops and offer potential in breeding for disease resistance through marker-assisted selection, either as closely linked or as perfect markers. Many R-gene sequences contain kinase domains, and indeed kinase genes have been reported as being proximal to R-genes, making kinase analogues an additionally promising target. The first step towards utilizing RGAs as markers for disease resistance is isolation and characterization of the sequences. RESULTS Sugarcane clone US01-1158 was identified as resistant to yellow leaf caused by the sugarcane yellow leaf virus (SCYLV) and moderately resistant to rust caused by Puccinia melanocephala Sydow & Sydow. Degenerate primers that had previously proved useful for isolating RGAs and kinase analogues in wheat and soybean were used to amplify DNA from sugarcane (Saccharum spp.) clone US-01-1158. Sequences generated from 1512 positive clones were assembled into 134 contigs of between two and 105 sequences. Comparison of the contig consensuses with the NCBI sequence database using BLASTx showed that 20 had sequence homology to nuclear binding site and leucine rich repeat (NBS-LRR) RGAs, and eight to kinase genes. Alignment of the deduced amino acid sequences with similar sequences from the NCBI database allowed the identification of several conserved domains. The alignment and resulting phenetic tree showed that many of the sequences had greater similarity to sequences from other species than to one another. CONCLUSION The use of degenerate primers is a useful method for isolating novel sugarcane RGA and kinase gene analogues. Further studies are needed to evaluate the role of these genes in disease resistance.
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Affiliation(s)
- Neil C Glynn
- USDA-ARS, Sugarcane Field Station, 12990 US Hwy 441N, Canal Point, 33438 FL, USA.
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