1
|
Zhang Q, Wei W, Zuansun X, Zhang S, Wang C, Liu N, Qiu L, Wang W, Guo W, Ma J, Peng H, Hu Z, Sun Q, Xie C. Fine Mapping of the Leaf Rust Resistance Gene Lr65 in Spelt Wheat 'Altgold'. FRONTIERS IN PLANT SCIENCE 2021; 12:666921. [PMID: 34262578 PMCID: PMC8274547 DOI: 10.3389/fpls.2021.666921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 05/04/2021] [Indexed: 06/13/2023]
Abstract
Wheat leaf rust (also known as brown rust), caused by the fungal pathogen Puccinia triticina Erikss. (Pt), is one by far the most troublesome wheat disease worldwide. The exploitation of resistance genes has long been considered as the most effective and sustainable method to control leaf rust in wheat production. Previously the leaf rust resistance gene Lr65 has been mapped to the distal end of chromosome arm 2AS linked to molecular marker Xbarc212. In this study, Lr65 was delimited to a 0.8 cM interval between flanking markers Alt-64 and AltID-11, by employing two larger segregating populations obtained from crosses of the resistant parent Altgold Rotkorn (ARK) with the susceptible parents Xuezao and Chinese Spring (CS), respectively. 24 individuals from 622 F2 plants of crosses between ARK and CS were obtained that showed the recombination between Lr65 gene and the flanking markers Alt-64 and AltID-11. With the aid of the CS reference genome sequence (IWGSC RefSeq v1.0), one SSR marker was developed between the interval matched to the Lr65-flanking marker and a high-resolution genetic linkage map was constructed. The Lr65 was finally located to a region corresponding to 60.11 Kb of the CS reference genome. The high-resolution genetic linkage map founded a solid foundation for the map-based cloning of Lr65 and the co-segregating marker will facilitate the marker-assisted selection (MAS) of the target gene.
Collapse
|
2
|
Jain N, Rani S, Sharma C, Sinha N, Singh A, Sharma JB, Prasad P, Saripalli G, Sharma PK, Balyan HS, Gupta PK, Prabhu KV. Large-scale stage-specific regulation of gene expression during host-pathogen interactions in CSP44 bread wheat carrying APR gene Lr48. FUNCTIONAL PLANT BIOLOGY : FPB 2020; 47:203-225. [PMID: 32007128 DOI: 10.1071/fp18336] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2018] [Accepted: 10/18/2019] [Indexed: 06/10/2023]
Abstract
Genome-wide transcriptome analysis was undertaken in a leaf-rust resistant bread wheat line CSP44 (selected from Australian cv. Condor) carrying the adult plant resistance (APR) gene Lr48. Two pre-adult plant (P-AP) susceptible stages (S48 and S96) and two adult plant (AP) resistant stages (R48 and R96) were used for RNA-seq. At the susceptible P-AP stage (during S48 to S96), expression increased in 2062 genes, and declined in 130 genes; 1775 of 2062 differentially expressed genes (DEGs) also exhibited high expression during early incompatible stage R48. Comparison of S96 with R96 showed that the expression of 80 genes was enhanced and that of 208 genes declined at the AP stage. At the resistant AP stage (during R48 to R96), expression of mere 25 genes increased and that of 126 genes declined. Apparently, the resistance during late adult stage (R96) is caused by regulation of the expression of relatively fewer genes, although at pre-adult stage (S48 to S96), expression of large number of genes increased; expression of majority of these genes kept on increasing during adult stage at R48 also. These and other results of the present study suggest that APR may mimic some kind of systemic acquired resistance (SAR). The host-specific DEGs belonged to 10 different classes including genes involved in defence, transport, epigenetics, photosynthesis, genes encoding some transcription factors etc. The pathogen (Puccinia triticina) specific DEGs (including three genes encoding known biotrophic effectors) seem to help the pathogen in infection/growth through large-scale stage-specific enhanced expression of host's genes. A putative candidate gene for Lr48 containing protein kinase domain (its ortholog in rice encoding OsWAK8) was also identified.
Collapse
Affiliation(s)
- Neelu Jain
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
| | - Sushma Rani
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
| | - Chanchal Sharma
- Chaudhary Charan Singh University, Meerut 250004, UP, India; and Department of Biotechnology, College of Engineering, Daegu University, Gyeongsan City, Gyeongbook 38453, South Korea
| | - Nivedita Sinha
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
| | - Anupam Singh
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
| | - Jai Bhagwan Sharma
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
| | - Pramod Prasad
- Indian Institute of Wheat and Barley Research, Regional Station, Flowerdale, Shimla 171002, India
| | | | | | | | | | - Kumble Vinod Prabhu
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India; and Protection of Plant Varieties and Farmers' Rights Authority, Govt. of India, Ministry of Agriculture & Farmers Welfare, New Delhi 110012 (India)
| |
Collapse
|
3
|
Liu W, Kolmer J, Rynearson S, Chen X, Gao L, Anderson JA, Turner MK, Pumphrey M. Identifying Loci Conferring Resistance to Leaf and Stripe Rusts in a Spring Wheat Population ( Triticum aestivum) via Genome-Wide Association Mapping. PHYTOPATHOLOGY 2019; 109:1932-1940. [PMID: 31282284 DOI: 10.1094/phyto-04-19-0143-r] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
A previous genome-wide association study (GWAS) for leaf rust (caused by Puccinia triticina) resistance identified 46 resistance quantitative trait loci (QTL) in an elite spring wheat leaf rust resistance diversity panel. With the aim of characterizing the pleiotropic resistance sources to both leaf rust and stripe rust (caused by P. striiformis f. sp. tritici), stripe rust responses were tested in five U.S. environments at the adult-plant stage and to five U.S. races at the seedling stage. The data revealed balanced phenotypic distributions in this population except for the seedling response to P. striiformis f. sp. tritici race PSTv-37. GWAS for stripe rust resistance discovered a total of 21 QTL significantly associated with all-stage or field resistance on chromosomes 1B, 1D, 2B, 3B, 4A, 5A, 5B, 5D, 6A, 6B, 7A, and 7B. Previously documented pleiotropic resistance genes Yr18/Lr34 and Yr46/Lr67 and tightly linked genes Yr17-Lr37 and Yr30-Sr2-Lr27 were also detected in this population. In addition, stripe rust resistance QTL Yrswp-2B.1, Yrswp-3B, and Yrswp-7B colocated with leaf rust resistance loci 2B_3, 3B_t2, and 7B_4, respectively. Haplotype analysis uncovered that Yrswp-3B and 3B_t2 were either tightly linked genes or the same gene for resistance to both stripe and leaf rusts. Single nucleotide polymorphism markers IWB35950, IWB74350, and IWB72134 for the 3B QTL conferring resistance to both rusts should be useful in incorporating the resistance allele(s) in new cultivars.
Collapse
Affiliation(s)
- Weizhen Liu
- School of Computer Science and Technology, Wuhan University of Technology, Wuhan, Hubei 430070, China
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA 99164-6430, U.S.A
| | - James Kolmer
- Cereal Disease Laboratory, U.S. Department of Agriculture Agricultural Research Service, St. Paul, MN 55108, U.S.A
- Department of Plant Pathology, University of Minnesota, St. Paul, MN 55018, U.S.A
| | - Sheri Rynearson
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA 99164-6430, U.S.A
| | - Xianming Chen
- Wheat Health, Genetics, and Quality Research Unit, U.S. Department of Agriculture Agricultural Research Service, Pullman, WA 99164-6430, U.S.A
- Department of Plant Pathology, Washington State University, Pullman, WA 99164-6430, U.S.A
| | - Liangliang Gao
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108, U.S.A
- Department of Plant Pathology, Kansas State University, Manhattan, KS 66502, U.S.A
| | - James A Anderson
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108, U.S.A
| | - M Kathryn Turner
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108, U.S.A
- The Land Institute, Salina, KS 67401, U.S.A
| | - Michael Pumphrey
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA 99164-6430, U.S.A
| |
Collapse
|
4
|
Godoy JG, Rynearson S, Chen X, Pumphrey M. Genome-Wide Association Mapping of Loci for Resistance to Stripe Rust in North American Elite Spring Wheat Germplasm. PHYTOPATHOLOGY 2018; 108:234-245. [PMID: 28952421 DOI: 10.1094/phyto-06-17-0195-r] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Stripe rust, caused by Puccinia striiformis f. sp. tritici, is a major yield-limiting foliar disease of wheat (Triticum aestivum) worldwide. In this study, the genetic variability of elite spring wheat germplasm from North America was investigated to characterize the genetic basis of effective all-stage and adult plant resistance (APR) to stripe rust. A genome-wide association study was conducted using 237 elite spring wheat lines genotyped with an Illumina Infinium 90K single-nucleotide polymorphism array. All-stage resistance was evaluated at seedling stage in controlled conditions and field evaluations were conducted under natural disease pressure in eight environments across Washington State. High heritability estimates and correlations between infection type and severity were observed. Ten loci for race-specific all-stage resistance were confirmed from previous mapping studies. Three potentially new loci associated with race-specific all-stage resistance were identified on chromosomes 1D, 2A, and 5A. For APR, 11 highly significant quantitative trait loci (QTL) (false discovery rate < 0.01) were identified, of which 3 QTL on chromosomes 3A, 5D, and 7A are reported for the first time. The QTL identified in this study can be used to enrich the current gene pool and improve the diversity of resistance to stripe rust disease.
Collapse
Affiliation(s)
- Jayfred Gaham Godoy
- First, second, and fourth authors: Department of Crop and Soil Sciences, Washington State University, Pullman 99164-6420; and third author: United States Department of Agriculture-Agricultural Research Service and Department of Plant Pathology, Washington State University, Pullman 99164-6430
| | - Sheri Rynearson
- First, second, and fourth authors: Department of Crop and Soil Sciences, Washington State University, Pullman 99164-6420; and third author: United States Department of Agriculture-Agricultural Research Service and Department of Plant Pathology, Washington State University, Pullman 99164-6430
| | - Xianming Chen
- First, second, and fourth authors: Department of Crop and Soil Sciences, Washington State University, Pullman 99164-6420; and third author: United States Department of Agriculture-Agricultural Research Service and Department of Plant Pathology, Washington State University, Pullman 99164-6430
| | - Michael Pumphrey
- First, second, and fourth authors: Department of Crop and Soil Sciences, Washington State University, Pullman 99164-6420; and third author: United States Department of Agriculture-Agricultural Research Service and Department of Plant Pathology, Washington State University, Pullman 99164-6430
| |
Collapse
|
5
|
Liu W, Maccaferri M, Bulli P, Rynearson S, Tuberosa R, Chen X, Pumphrey M. Genome-wide association mapping for seedling and field resistance to Puccinia striiformis f. sp. tritici in elite durum wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2017; 130:649-667. [PMID: 28039515 DOI: 10.1007/s00122-016-2841-9] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2016] [Accepted: 12/13/2016] [Indexed: 05/06/2023]
Abstract
Genome-wide association analysis in tetraploid wheat revealed novel and diverse loci for seedling and field resistance to stripe rust in elite spring durum wheat accessions from worldwide. Improving resistance to stripe rust, caused by Puccinia striiformis f. sp. tritici, is a major objective for wheat breeding. To identify effective stripe rust resistance loci, a genome-wide association study (GWAS) was conducted using 232 elite durum wheat (Triticum turgidum ssp. durum) lines from worldwide breeding programs. Genotyping with the 90 K iSelect wheat single nucleotide polymorphism (SNP) array resulted in 11,635 markers distributed across the genome. Response to stripe rust infection at the seedling stage revealed resistant and susceptible accessions present in rather balanced frequencies for the six tested races, with a higher frequency of susceptible responses to United States races as compared to Italian races (61.1 vs. 43.1% of susceptible accessions). Resistance at the seedling stage only partially explained adult plant resistance, which was found to be more frequent with 67.7% of accessions resistant across six nurseries in the United States. GWAS identified 82 loci associated with seedling stripe rust resistance, five of which were significant at the false discovery rate adjusted P value <0.1 and 11 loci were detected for the field response at the adult plant stages in at least two environments. Notably, Yrdurum-1BS.1 showed the largest effect for both seedling and field resistance, and is therefore considered as a major locus for resistance in tetraploid wheat. Our GWAS study is the first of its kind for stripe rust resistance in tetraploid wheat and provides an overview of resistance in elite germplasm and reports new loci that can be used in breeding resistant cultivars.
Collapse
Affiliation(s)
- Weizhen Liu
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, 99164-6420, USA.
| | - Marco Maccaferri
- Department of Agricultural Sciences, University of Bologna, 40127, Bologna, Italy
| | - Peter Bulli
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, 99164-6420, USA
| | - Sheri Rynearson
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, 99164-6420, USA
| | - Roberto Tuberosa
- Department of Agricultural Sciences, University of Bologna, 40127, Bologna, Italy
| | - Xianming Chen
- Wheat Health, Genetics, and Quality Research Unit, USDA-ARS, Pullman, WA, 99164-6430, USA
- Department of Plant Pathology, Washington State University, Pullman, WA, 99164-6430, USA
| | - Michael Pumphrey
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, 99164-6420, USA.
| |
Collapse
|