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Wang B, Meng T, Xiao B, Yu T, Yue T, Jin Y, Ma P. Fighting wheat powdery mildew: from genes to fields. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:196. [PMID: 37606731 DOI: 10.1007/s00122-023-04445-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 08/07/2023] [Indexed: 08/23/2023]
Abstract
KEY MESSAGE Host resistance conferred by Pm genes provides an effective strategy to control powdery mildew. The study of Pm genes helps modern breeding develop toward more intelligent and customized. Powdery mildew of wheat is one of the most destructive diseases seriously threatening the crop yield and quality worldwide. The genetic research on powdery mildew (Pm) resistance has entered a new era. Many Pm genes from wheat and its wild and domesticated relatives have been mined and cloned. Meanwhile, modern breeding strategies based on high-throughput sequencing and genome editing are emerging and developing toward more intelligent and customized. This review highlights mining and cloning of Pm genes, molecular mechanism studies on the resistance and avirulence genes, and prospects for genomic-assisted breeding for powdery mildew resistance in wheat.
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Affiliation(s)
- Bo Wang
- Yantai Key Laboratory of Characteristic Agricultural Biological Resource Conservation and Germplasm Innovative Utilization, College of Life Sciences, Yantai University, Yantai, 264005, China
| | - Ting Meng
- Yantai Key Laboratory of Characteristic Agricultural Biological Resource Conservation and Germplasm Innovative Utilization, College of Life Sciences, Yantai University, Yantai, 264005, China
| | - Bei Xiao
- Yantai Key Laboratory of Characteristic Agricultural Biological Resource Conservation and Germplasm Innovative Utilization, College of Life Sciences, Yantai University, Yantai, 264005, China
| | - Tianying Yu
- Yantai Key Laboratory of Characteristic Agricultural Biological Resource Conservation and Germplasm Innovative Utilization, College of Life Sciences, Yantai University, Yantai, 264005, China
| | - Tingyan Yue
- Yantai Key Laboratory of Characteristic Agricultural Biological Resource Conservation and Germplasm Innovative Utilization, College of Life Sciences, Yantai University, Yantai, 264005, China
| | - Yuli Jin
- Yantai Key Laboratory of Characteristic Agricultural Biological Resource Conservation and Germplasm Innovative Utilization, College of Life Sciences, Yantai University, Yantai, 264005, China
| | - Pengtao Ma
- Yantai Key Laboratory of Characteristic Agricultural Biological Resource Conservation and Germplasm Innovative Utilization, College of Life Sciences, Yantai University, Yantai, 264005, China.
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2
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Jin Y, Gu T, Li X, Liu H, Han G, Shi Z, Zhou Y, Fan J, Wang J, Liu W, Zhao H, An D. Characterization of a new splicing variant of powdery mildew resistance gene Pm4 in synthetic hexaploid wheat YAV249. FRONTIERS IN PLANT SCIENCE 2022; 13:1048252. [PMID: 36388539 PMCID: PMC9644285 DOI: 10.3389/fpls.2022.1048252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 10/10/2022] [Indexed: 06/16/2023]
Abstract
Powdery mildew, caused by Blumeria graminis f. sp. tritici (Bgt), is a destructive fungal disease of wheat throughout the world. Utilization of effective powdery mildew resistance genes and cultivars is considered as the most economic, efficient, and environmental-friendly method to control this disease. Synthetic hexaploid wheat (SHW), which was developed through hybridization of diploid Aegilops and tetraploid wheat, is a valuable genetic resource for resistance to powdery mildew. SHW line YAV249 showed high levels of resistance to powdery mildew at both the seedling and adult stages. Genetic analysis indicated that the resistance was controlled by a single dominant gene, temporarily designated PmYAV. Bulked segregant analysis with wheat 660K single nucleotide polymorphism (SNP) array scanning and marker analysis showed that PmYAV was located on chromosome 2AL and flanked by markers Xgdm93 and Xwgrc763, respectively, with genetic distances of 0.8 cM and 1.2 cM corresponding to a physic interval of 1.89 Mb on the Chinese Spring reference genome sequence v1.0. Sequence alignment analysis demonstrated that the sequence of PmYAV was consistent with that of Pm4a but generated an extra splicing event. When inoculated with different Bgt isolates, PmYAV showed a significantly different spectrum from Pm4a, hence it might be a new resistant resource for improvement of powdery mildew resistance. The flanked markers GDM93 and WGRC763, and the co-segregated markers BCD1231 and JS717/JS718 were confirmed to be easily performed in marker-assisted selection (MAS) of PmYAV. Using MAS strategy, PmYAV was transferred into the commercial cultivar Kenong 199 (KN199) and a wheat line YK13 was derived at generation BC3F3 from the population of YAV249/4*KN199 due to its excellent agronomic traits and resistance to powdery mildew. In conclusion, an alternative splicing variant of Pm4 was identified in this study, which informed the regulation of Pm4 gene function.
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Affiliation(s)
- Yuli Jin
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, Hebei, China
| | - Tiantian Gu
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, Hebei, China
| | - Xiuquan Li
- The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Hong Liu
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, Hebei, China
| | - Guohao Han
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, Hebei, China
| | - Zhipeng Shi
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, Hebei, China
| | - Yilin Zhou
- The State Key Laboratory for Biology of Plant Disease and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jieru Fan
- The State Key Laboratory for Biology of Plant Disease and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jing Wang
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, Hebei, China
| | - Wei Liu
- The State Key Laboratory for Biology of Plant Disease and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - He Zhao
- Institute of Biotechnology and Food Science, Hebei Academy of Agriculture and Forestry Science/the Key Laboratory of Plant Genetic Engineering of Hebei Province, Shijiazhuang, Hebei, China
| | - Diaoguo An
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, Hebei, China
- The Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
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Wheat genomic study for genetic improvement of traits in China. SCIENCE CHINA. LIFE SCIENCES 2022; 65:1718-1775. [PMID: 36018491 DOI: 10.1007/s11427-022-2178-7] [Citation(s) in RCA: 53] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 08/10/2022] [Indexed: 01/17/2023]
Abstract
Bread wheat (Triticum aestivum L.) is a major crop that feeds 40% of the world's population. Over the past several decades, advances in genomics have led to tremendous achievements in understanding the origin and domestication of wheat, and the genetic basis of agronomically important traits, which promote the breeding of elite varieties. In this review, we focus on progress that has been made in genomic research and genetic improvement of traits such as grain yield, end-use traits, flowering regulation, nutrient use efficiency, and biotic and abiotic stress responses, and various breeding strategies that contributed mainly by Chinese scientists. Functional genomic research in wheat is entering a new era with the availability of multiple reference wheat genome assemblies and the development of cutting-edge technologies such as precise genome editing tools, high-throughput phenotyping platforms, sequencing-based cloning strategies, high-efficiency genetic transformation systems, and speed-breeding facilities. These insights will further extend our understanding of the molecular mechanisms and regulatory networks underlying agronomic traits and facilitate the breeding process, ultimately contributing to more sustainable agriculture in China and throughout the world.
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Identification of a Pm4 Allele as a Powdery Mildew Resistance Gene in Wheat Line Xiaomaomai. Int J Mol Sci 2022; 23:ijms23031194. [PMID: 35163113 PMCID: PMC8835823 DOI: 10.3390/ijms23031194] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 01/05/2022] [Accepted: 01/18/2022] [Indexed: 02/01/2023] Open
Abstract
Powdery mildew, caused by Blumeria graminis f. sp. tritici (Bgt), is one of the most destructive foliar diseases of wheat. In this study, we combined the bulked segregant RNA sequencing (BSR-seq) and comparative genomics analysis to localize the powdery mildew resistance gene in Chinese landrace Xiaomaomai. Genetic analysis of F1 plants from a crossing of Xiaomaomai × Lumai23 and the derived F2 population suggests that a single recessive gene, designated as pmXMM, confers the resistance in this germplasm. A genetic linkage map was constructed using the newly developed SNP markers and pmXMM was mapped to the distal end of chromosome 2AL. The two flanking markers 2AL15 and 2AL34 were closely linked to pmXMM at the genetic distance of 3.9 cM and 1.4 cM, respectively. Using the diagnostic primers of Pm4, we confirmed that Xiaomaomai carries a Pm4 allele and the gene function was further validated by the virus-induced gene silencing (VIGS). In addition, we systematically analyzed pmXMM in comparison with the other Pm4 alleles. The results suggest that pmXMM is identical to Pm4d and Pm4e at sequence level. Pm4b is also not different from Pm4c according to their genome/amino acid sequences. Only a few nucleotide variances were detected between pmXMM and Pm4a/b, which indicate the haplotype variation of the Pm4 gene.
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Hinterberger V, Douchkov D, Lück S, Kale S, Mascher M, Stein N, Reif JC, Schulthess AW. Mining for New Sources of Resistance to Powdery Mildew in Genetic Resources of Winter Wheat. FRONTIERS IN PLANT SCIENCE 2022; 13:836723. [PMID: 35300015 PMCID: PMC8922026 DOI: 10.3389/fpls.2022.836723] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 01/31/2022] [Indexed: 05/02/2023]
Abstract
Genetic pathogen control is an economical and sustainable alternative to the use of chemicals. In order to breed resistant varieties, information about potentially unused genetic resistance mechanisms is of high value. We phenotyped 8,316 genotypes of the winter wheat collection of the German Federal ex situ gene bank for Agricultural and Horticultural Crops, Germany, for resistance to powdery mildew (PM), Blumeria graminis f. sp. tritici, one of the most important biotrophic pathogens in wheat. To achieve this, we used a semi-automatic phenotyping facility to perform high-throughput detached leaf assays. This data set, combined with genotyping-by-sequencing (GBS) marker data, was used to perform a genome-wide association study (GWAS). Alleles of significantly associated markers were compared with SNP profiles of 171 widely grown wheat varieties in Germany to identify currently unexploited resistance conferring genes. We also used the Chinese Spring reference genome annotation and various domain prediction algorithms to perform a domain enrichment analysis and produced a list of candidate genes for further investigation. We identified 51 significantly associated regions. In most of these, the susceptible allele was fixed in the tested commonly grown wheat varieties. Eleven of these were located on chromosomes for which no resistance conferring genes have been previously reported. In addition to enrichment of leucine-rich repeats (LRR), we saw enrichment of several domain types so far not reported as relevant to PM resistance, thus, indicating potentially novel candidate genes for the disease resistance research and prebreeding in wheat.
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Affiliation(s)
| | - Dimitar Douchkov
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany
| | - Stefanie Lück
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany
| | - Sandip Kale
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany
| | - Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany
- Center for Integrated Breeding Research (CiBreed), Georg-August-University, Göttingen, Germany
| | - Jochen C. Reif
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany
| | - Albert W. Schulthess
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany
- *Correspondence: Albert W. Schulthess
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Bajpai S, Shukla PS, Asiedu S, Pruski K, Prithiviraj B. A Biostimulant Preparation of Brown Seaweed Ascophyllum nodosum Suppresses Powdery Mildew of Strawberry. THE PLANT PATHOLOGY JOURNAL 2019; 35:406-416. [PMID: 31632216 PMCID: PMC6788409 DOI: 10.5423/ppj.oa.03.2019.0066] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 05/17/2019] [Accepted: 05/21/2019] [Indexed: 05/24/2023]
Abstract
Strawberry, an important fruit crop, is susceptible to a large number of pathogens that reduce fruit quality and productivity. In this study, the effect of a biostimulant prepared from Ascophyllum nodosum extract (ANE) (0.1%, 0.2%, and 0.3%) was evaluated on powdery mildew progression under greenhouse and field conditions. In the greenhouse, application of 0.2% ANE showed maximum reduction in powdery mildew progression as compared to the control. Forty-eight hour post-inoculation, foliar spray of 0.2% ANE reduced spore germination by 75%. Strawberry leaves sprayed with ANE showed higher total phenolic and flavonoid content in response to powdery mildew infection. Furthermore, application of ANE elicited defense response in strawberry plants by induction of defense-related enzymes, such as phenylalanine ammonia lyase, polyphenol oxidase, and peroxidase activity. In field conditions, foliar spray of 0.2% ANE showed a reduction of 37.2% of natural incidence of powdery mildew infection as compared to the control. ANE sprayed plant also reduces the severity of powdery mildew infection under natural conditions. These results indicate that application of ANE induces the strawberry plant's active defense against powdery mildew infection by induction of secondary metabolism and regulating the activities of defense-related enzymes.
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Affiliation(s)
- Sruti Bajpai
- Marine Bio-products Research Laboratory, Department of Plant, Food and Environmental Sciences, Dalhousie University, Truro, NS B2N 5E3,
Canada
| | - Pushp Sheel Shukla
- Marine Bio-products Research Laboratory, Department of Plant, Food and Environmental Sciences, Dalhousie University, Truro, NS B2N 5E3,
Canada
| | - Samuel Asiedu
- Department of Plant, Food and Environmental Sciences, Dalhousie University, Truro, NS B2N 5E3,
Canada
| | - Kris Pruski
- Department of Plant, Food and Environmental Sciences, Dalhousie University, Truro, NS B2N 5E3,
Canada
| | - Balakrishnan Prithiviraj
- Marine Bio-products Research Laboratory, Department of Plant, Food and Environmental Sciences, Dalhousie University, Truro, NS B2N 5E3,
Canada
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Li G, Cowger C, Wang X, Carver BF, Xu X. Characterization of Pm65, a new powdery mildew resistance gene on chromosome 2AL of a facultative wheat cultivar. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:2625-2632. [PMID: 31214740 DOI: 10.1007/s00122-019-03377-2] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2019] [Accepted: 06/09/2019] [Indexed: 05/18/2023]
Abstract
A new powdery mildew resistance gene that can be readily used in wheat breeding, Pm65, was identified in the facultative wheat cultivar Xinmai 208 and mapped to the terminal region of chromosome 2AL. Wheat powdery mildew, a widely occurring disease caused by the biotrophic fungus Blumeriagraminis f. sp. tritici (Bgt), poses a serious threat to wheat production. A high breeding priority is to identify powdery mildew resistance genes that can be readily used either alone or in gene complexes involving other disease resistance genes. An F2 population and 227 F2:3 families derived from the cross Xinmai 208 × Stardust were generated to map a powdery mildew resistance gene in Xinmai 208, a high-yielding Chinese wheat cultivar. Genetic analysis indicated that Xinmai 208 carries a single dominant powdery mildew resistance gene, designated herein Pm65, and linkage analysis delimited Pm65 to a 0.5 cM interval covering 531.8 Kb (763,289,667-763,821,463 bp) on chromosome 2AL in the Chinese Spring reference sequence. An allelism test indicated that Pm65 is a new gene about 10.3 cM distal to the Pm4 locus. Pm65 was 0.3 cM proximal to Xstars355 and 0.2 cM distal to Xstars356. It conferred near-immunity to 19 of 20 Bgt isolates collected from different wheat-growing regions of the USA. Coming from a high-yield potential cultivar, Pm65 can be directly used to enhance powdery mildew resistance in wheat. The newly developed SSR markers Xstars355 and Xstars356 have the potential to tag Pm65 for wheat improvement.
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Affiliation(s)
- Genqiao Li
- Wheat, Peanut, and Other Field Crops Research Unit, USDA-ARS, Stillwater, OK, 74075, USA
- Plant and Soil Science Department, Oklahoma State University, Stillwater, OK, 74078, USA
| | | | - Xuewen Wang
- Genetics Department, The University of Georgia, Athens, GA, 30602, USA
| | - Brett F Carver
- Plant and Soil Science Department, Oklahoma State University, Stillwater, OK, 74078, USA
| | - Xiangyang Xu
- Wheat, Peanut, and Other Field Crops Research Unit, USDA-ARS, Stillwater, OK, 74075, USA.
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Ullah KN, Li N, Shen T, Wang P, Tang W, Ma S, Zhang Z, Jia H, Kong Z, Ma Z. Fine mapping of powdery mildew resistance gene Pm4e in bread wheat (Triticum aestivum L.). PLANTA 2018; 248:1319-1328. [PMID: 30128601 DOI: 10.1007/s00425-018-2990-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2018] [Accepted: 08/13/2018] [Indexed: 05/18/2023]
Abstract
Fine mapping of wheat powdery mildew-resistance gene Pm4e to a 0.19 cM interval with sequence-based markers provides the foundation for map-based cloning and marker-assisted selection with breeder-friendly markers. Powdery mildew caused by Blumeria graminis f. sp. tritici is a wheat foliar disease that poses a serious threat to global wheat production. Pm4 is a resistance gene locus that has played a key role in controlling this disease in wheat production and a few resistance alleles of this locus have been identified. We have previously mapped the Pm4e allele to a 6.7 cM interval on chromosome 2AL. In this study, Pm4e was delimited to a 0.19 cM interval flanked by Xwgrc763 and Xwgrc865, through employment of a larger segregating population, derived from the cross of resistant parent D29 with susceptible parent Yangmai 158 (Y158), and enrichment of the genetic interval with markers developed on Chinese Spring (C.S.) survey sequence. In this interval, Pm4e co-segregated with a few markers, some of which were either D29-dominant or Y158-dominant, implying great sequence variation in the interval between D29 and Y158. Most of these co-segregation markers could not differentiate the Pm4 alleles from each other. Survey of 55 wheat cultivars with four co-dominant markers showed that the Pm4e-co-segregating loci always co-exist. Annotation of the Pm4e interval-corresponding C.S. sequence revealed more than a dozen resistance gene analogs clustered in a 2.4 Mb region, although C.S. is susceptible to the Pm4e-avirulent isolate Bgt2. This study has established the foundation for map-based cloning of Pm4e. Moreover, some of the co-dominant markers developed in this study could help in marker-assisted transfer of Pm4e into elite cultivars.
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Affiliation(s)
- Khan Nasr Ullah
- The Applied Plant Genomics Laboratory of Crop Genomics and Bioinformatics Centre, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Na Li
- The Applied Plant Genomics Laboratory of Crop Genomics and Bioinformatics Centre, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Tao Shen
- The Applied Plant Genomics Laboratory of Crop Genomics and Bioinformatics Centre, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Peisi Wang
- The Applied Plant Genomics Laboratory of Crop Genomics and Bioinformatics Centre, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Wenbin Tang
- The Applied Plant Genomics Laboratory of Crop Genomics and Bioinformatics Centre, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Shengwei Ma
- The Applied Plant Genomics Laboratory of Crop Genomics and Bioinformatics Centre, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Zhimeng Zhang
- The Applied Plant Genomics Laboratory of Crop Genomics and Bioinformatics Centre, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Haiyan Jia
- The Applied Plant Genomics Laboratory of Crop Genomics and Bioinformatics Centre, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Zhongxin Kong
- The Applied Plant Genomics Laboratory of Crop Genomics and Bioinformatics Centre, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Zhengqiang Ma
- The Applied Plant Genomics Laboratory of Crop Genomics and Bioinformatics Centre, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China.
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Wu P, Xie J, Hu J, Qiu D, Liu Z, Li J, Li M, Zhang H, Yang L, Liu H, Zhou Y, Zhang Z, Li H. Development of Molecular Markers Linked to Powdery Mildew Resistance Gene Pm4b by Combining SNP Discovery from Transcriptome Sequencing Data with Bulked Segregant Analysis (BSR-Seq) in Wheat. FRONTIERS IN PLANT SCIENCE 2018; 9:95. [PMID: 29491869 PMCID: PMC5817070 DOI: 10.3389/fpls.2018.00095] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Accepted: 01/17/2018] [Indexed: 05/21/2023]
Abstract
Powdery mildew resistance gene Pm4b, originating from Triticum persicum, is effective against the prevalent Blumeria graminis f. sp. tritici (Bgt) isolates from certain regions of wheat production in China. The lack of tightly linked molecular markers with the target gene prevents the precise identification of Pm4b during the application of molecular marker-assisted selection (MAS). The strategy that combines the RNA-Seq technique and the bulked segregant analysis (BSR-Seq) was applied in an F2:3 mapping population (237 families) derived from a pair of isogenic lines VPM1/7∗Bainong 3217 F4 (carrying Pm4b) and Bainong 3217 to develop more closely linked molecular markers. RNA-Seq analysis of the two phenotypically contrasting RNA bulks prepared from the representative F2:3 families generated 20,745,939 and 25,867,480 high-quality read pairs, and 82.8 and 80.2% of them were uniquely mapped to the wheat whole genome draft assembly for the resistant and susceptible RNA bulks, respectively. Variant calling identified 283,866 raw single nucleotide polymorphisms (SNPs) and InDels between the two bulks. The SNPs that were closely associated with the powdery mildew resistance were concentrated on chromosome 2AL. Among the 84 variants that were potentially associated with the disease resistance trait, 46 variants were enriched in an about 25 Mb region at the distal end of chromosome arm 2AL. Four Pm4b-linked SNP markers were developed from these variants. Based on the sequences of Chinese Spring where these polymorphic SNPs were located, 98 SSR primer pairs were designed to develop distal markers flanking the Pm4b gene. Three SSR markers, Xics13, Xics43, and Xics76, were incorporated in the new genetic linkage map, which located Pm4b in a 3.0 cM genetic interval spanning a 6.7 Mb physical genomic region. This region had a collinear relationship with Brachypodium distachyon chromosome 5, rice chromosome 4, and sorghum chromosome 6. Seven genes associated with disease resistance were predicted in this collinear genomic region, which included C2 domain protein, peroxidase activity protein, protein kinases of PKc_like super family, Mlo family protein, and catalytic domain of the serine/threonine kinases (STKc_IRAK like super family). The markers developed in the present study facilitate identification of Pm4b during its MAS practice.
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Affiliation(s)
- Peipei Wu
- The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- Department of Plant Pathology, China Agricultural University, Beijing, China
| | - Jingzhong Xie
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Jinghuang Hu
- The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Dan Qiu
- The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhiyong Liu
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Jingting Li
- College of Chemistry and Environment Engineering, Pingdingshan University, Pingdingshan, China
| | - Miaomiao Li
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Hongjun Zhang
- The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Li Yang
- The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Hongwei Liu
- The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yang Zhou
- The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhongjun Zhang
- Department of Plant Pathology, China Agricultural University, Beijing, China
| | - Hongjie Li
- The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
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