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Li Y, Hu J, Lin H, Qiu D, Qu Y, Du J, Hou L, Ma L, Wu Q, Liu Z, Zhou Y, Li H. Mapping QTLs for adult-plant resistance to powdery mildew and stripe rust using a recombinant inbred line population derived from cross Qingxinmai × 041133. FRONTIERS IN PLANT SCIENCE 2024; 15:1397274. [PMID: 38779062 PMCID: PMC11109386 DOI: 10.3389/fpls.2024.1397274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Accepted: 04/16/2024] [Indexed: 05/25/2024]
Abstract
A recombinant inbred line (RIL) population derived from wheat landrace Qingxinmai and breeding line 041133 exhibited segregation in resistance to powdery mildew and stripe rust in five and three field tests, respectively. A 16K genotyping by target sequencing (GBTS) single-nucleotide polymorphism (SNP) array-based genetic linkage map was used to dissect the quantitative trait loci (QTLs) for disease resistance. Four and seven QTLs were identified for adult-plant resistance (APR) against powdery mildew and stripe rust. QPm.caas-1B and QPm.caas-5A on chromosomes 1B and 5A were responsible for the APR against powdery mildew in line 041133. QYr.caas-1B, QYr.caas-3B, QYr.caas-4B, QYr.caas-6B.1, QYr.caas-6B.2, and QYr.caas-7B detected on the five B-genome chromosomes of line 041133 conferred its APR to stripe rust. QPm.caas-1B and QYr.caas.1B were co-localized with the pleiotropic locus Lr46/Yr29/Sr58/Pm39/Ltn2. A Kompetitive Allele Specific Polymorphic (KASP) marker KASP_1B_668028290 was developed to trace QPm/Yr.caas.1B. Four lines pyramiding six major disease resistance loci, PmQ, Yr041133, QPm/Yr.caas-1B, QPm.caas-2B.1, QYr.caas-3B, and QPm.caas-6B, were developed. They displayed effective resistance against both powdery mildew and stripe rust at the seedling and adult-plant stages.
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Affiliation(s)
- Yahui Li
- College of Life and Environmental Science, Minzu University of China, Beijing, China
| | - Jinghuang Hu
- The National Engineering Laboratory of Crop Molecular Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Huailong Lin
- Jiushenghe Seed Industry Co. Ltd., Changji, China
| | - Dan Qiu
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Yunfeng Qu
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, China
| | - Jiuyuan Du
- Wheat Research Institute, Gansu Academy of Agricultural Sciences, Lanzhou, China
| | - Lu Hou
- Qinghai Academy of Agricultural and Forestry Sciences, Qinghai University/Key Laboratory of Agricultural Integrated Pest Management, Xining, China
| | - Lin Ma
- Datong Hui and Tu Autonomous County Agricultural Technology Extension Center, Xining, China
| | - Qiuhong Wu
- Institute of Biotechnology, Xianghu Laboratory, Hangzhou, China
| | - Zhiyong Liu
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Yijun Zhou
- College of Life and Environmental Science, Minzu University of China, Beijing, China
| | - Hongjie Li
- The National Engineering Laboratory of Crop Molecular Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- Institute of Biotechnology, Xianghu Laboratory, Hangzhou, China
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Wang W, Jin P, Zhang J, Tang Y, Zhao B, Yue W, Cheng P, Li Q, Wang B. Favorable Loci Identified for Stripe Rust Resistance in Chinese Winter Wheat Accessions via Genome-Wide Association Study. PLANT DISEASE 2024; 108:71-81. [PMID: 37467133 DOI: 10.1094/pdis-12-22-2842-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/21/2023]
Abstract
Stripe rust (or yellow rust), caused by Puccinia striiformis f. sp. tritici (Pst), is one of the most devastating diseases of wheat worldwide. Currently, the utilization of resistant cultivars is the most viable way to reduce yield losses. In this study, a panel of 188 wheat accessions from China was evaluated for stripe rust resistance, and genome-wide association studies were performed using high-quality Diversity Arrays Technology markers. According to the phenotype and genotype data, a total of 26 significant marker-trait associations were identified, representing 18 quantitative trait loci (QTLs) on chromosomes 1B, 2A, 2B, 3A, 3B, 5A, 5B, 6B, 7B, and 7D. Of the 18 QTLs, almost all were associated with adult plant resistance (APR) except QYr.nwsuaf-6B.2, which was associated with all-stage resistance (also known as seedling resistance). Three of the 18 QTLs were mapped far from previously identified Pst resistance genes and QTLs and were considered potentially new loci. The other 15 QTLs were mapped close to known resistance genes and QTLs. Subsequent haplotype analysis for QYr.nwsuaf-2A and QYr.nwsuaf-7B.3 revealed the degrees of resistance of the panel in the APR stage. In summary, the favorable alleles identified in this study may be useful in breeding for disease resistance to stripe rust.
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Affiliation(s)
- Wenli Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Pengfei Jin
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
- Shaanxi Key Laboratory of Chinese Jujube, School of Life Science, Yan'an University, Shaanxi 716000, China
| | - Jia Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yaqi Tang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Bingjie Zhao
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Weiyun Yue
- Tianshui Institute of Agricultural Science, Tianshui 741000, China
| | - Peng Cheng
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Qiang Li
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Baotong Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
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Yan Q, Jia G, Tan W, Tian R, Zheng X, Feng J, Luo X, Si B, Li X, Huang K, Wang M, Chen X, Ren Y, Yang S, Zhou X. Genome-wide QTL mapping for stripe rust resistance in spring wheat line PI 660122 using the Wheat 15K SNP array. FRONTIERS IN PLANT SCIENCE 2023; 14:1232897. [PMID: 37701804 PMCID: PMC10493333 DOI: 10.3389/fpls.2023.1232897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 07/31/2023] [Indexed: 09/14/2023]
Abstract
Introduction Stripe rust is a global disease of wheat. Identification of new resistance genes is key to developing and growing resistant varieties for control of the disease. Wheat line PI 660122 has exhibited a high level of stripe rust resistance for over a decade. However, the genetics of stripe rust resistance in this line has not been studied. A set of 239 recombinant inbred lines (RILs) was developed from a cross between PI 660122 and an elite Chinese cultivar Zhengmai 9023. Methods The RIL population was phenotyped for stripe rust response in three field environments and genotyped with the Wheat 15K single-nucleotide polymorphism (SNP) array. Results A total of nine quantitative trait loci (QTLs) for stripe rust resistance were mapped to chromosomes 1B (one QTL), 2B (one QTL), 4B (two QTLs), 4D (two QTLs), 6A (one QTL), 6D (one QTL), and 7D (one QTL), of which seven QTLs were stable and designated as QYrPI660122.swust-4BS, QYrPI660122.swust-4BL, QYrPI660122.swust-4DS, QYrPI660122.swust-4DL, QYrZM9023.swust-6AS, QYrZM9023.swust-6DS, and QYrPI660122.swust-7DS. QYrPI660122.swust-4DS was a major all-stage resistance QTL explaining the highest percentage (10.67%-20.97%) of the total phenotypic variation and was mapped to a 12.15-cM interval flanked by SNP markers AX-110046962 and AX-111093894 on chromosome 4DS. Discussion The QTL and their linked SNP markers in this study can be used in wheat breeding to improve resistance to stripe rust. In addition, 26 lines were selected based on stripe rust resistance and agronomic traits in the field for further selection and release of new cultivars.
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Affiliation(s)
- Qiong Yan
- Wheat Research Institute, School of Life Sciences and Engineering, Southwest University of Science and Technology, Mianyang, Sichuan, China
| | - Guoyun Jia
- Wheat Research Institute, School of Life Sciences and Engineering, Southwest University of Science and Technology, Mianyang, Sichuan, China
| | - Wenjing Tan
- Wheat Research Institute, School of Life Sciences and Engineering, Southwest University of Science and Technology, Mianyang, Sichuan, China
| | - Ran Tian
- Wheat Research Institute, School of Life Sciences and Engineering, Southwest University of Science and Technology, Mianyang, Sichuan, China
| | - Xiaochen Zheng
- Wheat Research Institute, School of Life Sciences and Engineering, Southwest University of Science and Technology, Mianyang, Sichuan, China
| | - Junming Feng
- Wheat Research Institute, School of Life Sciences and Engineering, Southwest University of Science and Technology, Mianyang, Sichuan, China
| | - Xiaoqin Luo
- Wheat Research Institute, School of Life Sciences and Engineering, Southwest University of Science and Technology, Mianyang, Sichuan, China
| | - Binfan Si
- Wheat Research Institute, School of Life Sciences and Engineering, Southwest University of Science and Technology, Mianyang, Sichuan, China
| | - Xin Li
- Wheat Research Institute, School of Life Sciences and Engineering, Southwest University of Science and Technology, Mianyang, Sichuan, China
| | - Kebing Huang
- Wheat Research Institute, School of Life Sciences and Engineering, Southwest University of Science and Technology, Mianyang, Sichuan, China
| | - Meinan Wang
- Department of Plant Pathology, Washington State University, Pullman, WA, United States
| | - Xianming Chen
- Department of Plant Pathology, Washington State University, Pullman, WA, United States
- Wheat Health, Genetics, and Quality Research Unit, US Department of Agriculture-Agricultural Research Service (USDA-ARS), Pullman, WA, United States
| | - Yong Ren
- Crop Characteristic Resources Creation and Utilization Key Laboratory of Sichuan Province, Mianyang Institute of Agricultural Science, Mianyang, Sichuan, China
| | - Suizhuang Yang
- Wheat Research Institute, School of Life Sciences and Engineering, Southwest University of Science and Technology, Mianyang, Sichuan, China
| | - Xinli Zhou
- Wheat Research Institute, School of Life Sciences and Engineering, Southwest University of Science and Technology, Mianyang, Sichuan, China
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Liu S, Liu D, Zhang C, Zhang W, Wang X, Mi Z, Gao X, Ren Y, Lan C, Liu X, Zhao Z, Liu J, Li H, Yuan F, Su B, Kang Z, Li C, Han D, Wang C, Cao X, Wu J. Slow stripe rusting in Chinese wheat Jimai 44 conferred by Yr29 in combination with a major QTL on chromosome arm 6AL. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:175. [PMID: 37498321 DOI: 10.1007/s00122-023-04420-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Accepted: 07/05/2023] [Indexed: 07/28/2023]
Abstract
YrJ44, a more effective slow rusting gene than Yr29, was localized to a 3.5-cM interval between AQP markers AX-109373479 and AX-109563479 on chromosome 6AL. "Slow rusting" (SR) is a type of adult plant resistance (APR) that can provide non-specific durable resistance to stripe rust in wheat. Chinese elite wheat cultivar Jimai 44 (JM44) has maintained SR to stripe rust in China since its release despite exposure to a changing and variable pathogen population. An F2:6 population comprising 295 recombinant inbred lines (RILs) derived from a cross between JM44 and susceptible cultivar Jimai 229 (JM229) was used in genetic analysis of the SR. The RILs and parental lines were evaluated for stripe rust response in five field environments and genotyped using the Affymetrix Wheat55K SNP array and 13 allele-specific quantitative PCR-based (AQP) markers. Two stable QTL on chromosome arms 1BL and 6AL were identified by inclusive composite interval mapping. The 1BL QTL was probably the pleiotropic gene Lr46/Yr29/Sr58. QYr.nwafu-6AL (hereafter named YrJ44), mapped in a 3.5-cM interval between AQP markers AX-109373479 and AX-109563479, was more effective than Yr29 in reducing disease severity and relative area under the disease progress curve (rAUDPC). RILs harboring both YrJ44 and Yr29 displayed levels of SR equal to the resistant parent JM44. The AQP markers linked with YrJ44 were polymorphic and significantly correlated with stripe rust resistance in a panel of 1,019 wheat cultivars and breeding lines. These results suggested that adequate SR resistance can be obtained by combining YrJ44 and Yr29 and the AQP markers can be used in breeding for durable stripe rust resistance.
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Affiliation(s)
- Shengjie Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
- State Key Laboratory of Crop Stress Biology for Arid Areas, Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Dan Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Chuanliang Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Wenjing Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Xiaoting Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Zhiwen Mi
- Key Laboratory of Agricultural Internet of Things, Ministry of Agriculture and Rural Affairs, Laboratory of Agricultural Information Perception and Intelligent Services, College of Mechanical and Electronic Engineering, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Xin Gao
- Crop Research Institute, Key Laboratory of Wheat Biology and Genetic Improvement in North Yellow and Huai River Valley, Ministry of Agriculture /Shandong Provincial Technology Innovation Center for Wheat, Shandong Academy of Agricultural Sciences / National Engineering Research Center for Wheat and Maize, Jinan, 250100, China
| | - Yong Ren
- Crop Characteristic Resources Creation and Utilization Key Laboratory of Sichuan Province, Mianyang Institute of Agricultural Science, Mianyang, 621023, Sichuan, China
| | - Caixia Lan
- College of Plant Science and Technology, Huazhong Agricultural University/Hubei Hongshan Laboratory, Wuhan, 430070, China
| | - Xiukun Liu
- Crop Research Institute, Key Laboratory of Wheat Biology and Genetic Improvement in North Yellow and Huai River Valley, Ministry of Agriculture /Shandong Provincial Technology Innovation Center for Wheat, Shandong Academy of Agricultural Sciences / National Engineering Research Center for Wheat and Maize, Jinan, 250100, China
| | - Zhendong Zhao
- Crop Research Institute, Key Laboratory of Wheat Biology and Genetic Improvement in North Yellow and Huai River Valley, Ministry of Agriculture /Shandong Provincial Technology Innovation Center for Wheat, Shandong Academy of Agricultural Sciences / National Engineering Research Center for Wheat and Maize, Jinan, 250100, China
| | - Jianjun Liu
- Crop Research Institute, Key Laboratory of Wheat Biology and Genetic Improvement in North Yellow and Huai River Valley, Ministry of Agriculture /Shandong Provincial Technology Innovation Center for Wheat, Shandong Academy of Agricultural Sciences / National Engineering Research Center for Wheat and Maize, Jinan, 250100, China
| | - Haosheng Li
- Crop Research Institute, Key Laboratory of Wheat Biology and Genetic Improvement in North Yellow and Huai River Valley, Ministry of Agriculture /Shandong Provincial Technology Innovation Center for Wheat, Shandong Academy of Agricultural Sciences / National Engineering Research Center for Wheat and Maize, Jinan, 250100, China
| | - Fengping Yuan
- State Key Laboratory of Crop Stress Biology for Arid Areas, Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Baofeng Su
- Key Laboratory of Agricultural Internet of Things, Ministry of Agriculture and Rural Affairs, Laboratory of Agricultural Information Perception and Intelligent Services, College of Mechanical and Electronic Engineering, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Zhensheng Kang
- State Key Laboratory of Crop Stress Biology for Arid Areas, Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Chunlian Li
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Dejun Han
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Changfa Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China.
| | - Xinyou Cao
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China.
- Crop Research Institute, Key Laboratory of Wheat Biology and Genetic Improvement in North Yellow and Huai River Valley, Ministry of Agriculture /Shandong Provincial Technology Innovation Center for Wheat, Shandong Academy of Agricultural Sciences / National Engineering Research Center for Wheat and Maize, Jinan, 250100, China.
| | - Jianhui Wu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China.
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Franco MF, Polacco AN, Campos PE, Pontaroli AC, Vanzetti LS. Genome-wide association study for resistance in bread wheat (Triticum aestivum L.) to stripe rust (Puccinia striiformis f. sp. tritici) races in Argentina. BMC PLANT BIOLOGY 2022; 22:543. [PMID: 36434507 PMCID: PMC9701071 DOI: 10.1186/s12870-022-03916-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 10/27/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Wheat stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is one of the most devastating diseases of the wheat crop. It causes significant reductions in both grain yield and grain quality. In recent years, new and more virulent races have overcome many of the known resistance genes in Argentinian germplasm. In order to identify loci conferring resistance to the local races of Pst for effective utilization in future breeding programs, a genome-wide association study (GWAS) was performed using a collection of 245 bread wheat lines genotyped with 90 K SNPs. RESULTS To search for adult plant resistance (APR) the panel was evaluated for disease severity (DS) and area under disease progress curve (AUDPC) in field trials during two years under natural infection conditions. To look for seedling or all-stage resistance (ASR) the panel was evaluated to determine infection type (IT) under greenhouse conditions against two prevalent races in Argentina. The phenotypic data showed that the panel possessed enough genetic variability for searching for sources of resistance to Pst. Significant correlations between years were observed for Pst response in the field and high heritability values were found for DS (H2 = 0.89) and AUDPC (H2 = 0.93). Based on GWAS, eight markers associated with Pst resistance (FDR < 0.01) were identified, of these, five were associated with ASR (on chromosomes 1B, 2A, 3A and 5B) and three with APR (on chromosomes 3B and 7A). These markers explained between 2% and 32.62% of the phenotypic variation. Five of the markers corresponded with previously reported Yr genes/QTL, while the other three (QYr.Bce.1B.sd.1, QYr.Bce.3A.sd and QYr.Bce.3B.APR.2) might be novel resistance loci. CONCLUSION Our results revealed high genetic variation for resistance to Argentinian stripe rust races in the germplasm used here. It constitutes a very promising step towards the improvement of Pst resistance of bread wheat in Argentina. Also, the identification of new resistance loci would represent a substantial advance for diversifying the current set of resistance genes and to advance in the improvement of the durable resistance to the disease.
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Affiliation(s)
- M F Franco
- Facultad de Ciencias Agrarias, Universidad Nacional de Mar del Plata, 7620, Balcarce, CP, Argentina.
- Consejo Nacional de Investigaciones Científicas Y Técnicas (CONICET), Buenos Aires, Argentina.
- Estación Experimental Agropecuaria INTA Balcarce, 7620, Balcarce, CP, Argentina.
| | - A N Polacco
- Facultad de Ciencias Agrarias, Universidad Nacional de Mar del Plata, 7620, Balcarce, CP, Argentina
| | - P E Campos
- Estación Experimental Agropecuaria INTA Bordenave, 8187, Bordenave, CP, Argentina
| | - A C Pontaroli
- Consejo Nacional de Investigaciones Científicas Y Técnicas (CONICET), Buenos Aires, Argentina
- Estación Experimental Agropecuaria INTA Balcarce, 7620, Balcarce, CP, Argentina
| | - L S Vanzetti
- Consejo Nacional de Investigaciones Científicas Y Técnicas (CONICET), Buenos Aires, Argentina
- Estación Experimental Agropecuaria INTA Marcos Juárez, 2580, Marcos Juárez, CP, Argentina
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Pang Y, Liu C, Lin M, Ni F, Li W, Cai J, Zhang Z, Zhu H, Liu J, Wu J, Bai G, Liu S. Mapping QTL for Adult-Plant Resistance to Stripe Rust in a Chinese Wheat Landrace. Int J Mol Sci 2022; 23:ijms23179662. [PMID: 36077059 PMCID: PMC9456275 DOI: 10.3390/ijms23179662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 08/17/2022] [Accepted: 08/19/2022] [Indexed: 11/24/2022] Open
Abstract
Wheat stripe (yellow) rust is a worldwide disease that seriously reduces wheat grain yield and quality. Adult-plant resistance (APR) to stripe rust is generally more durable but usually controlled by multiple genes with partial resistance. In this study, a recombinant inbred line population was developed from a cross between a Chinese wheat landrace, Tutoumai, with APR to stripe rust, and a highly susceptible wheat cultivar, Siyang 936. The population was genotyped by genotyping-by-sequencing and phenotyped for APR to stripe rust in four consecutive field experiments. Three QTLs, QYr.sdau-1BL, QYr.sdau-5BL, and QYr.sdau-6BL, were identified for APR to stripe rust, and explained 8.0–21.2%, 10.1–22.7%, and 11.6–18.0% of the phenotypic variation, respectively. QYr.sdau-1BL was further mapped to a 21.6 Mb region using KASP markers derived from SNPs identified by RNA-seq of the two parents. In the QYr.sdau-1BL region, 13 disease-resistance-related genes were differently expressed between the two parents, and therefore were considered as the putative candidates of QYr.sdau-1BL. This study provides favorable gene/QTL and high-throughput markers to breeding programs for marker-assisted selection of the wheat stripe rust APR genes.
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Affiliation(s)
- Yunlong Pang
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai’an 271018, China
| | - Chunxia Liu
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai’an 271018, China
| | - Meng Lin
- Department of Agronomy, Kansas State University, Manhattan, KS 66506, USA
| | - Fei Ni
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai’an 271018, China
| | - Wenhui Li
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai’an 271018, China
| | - Jin Cai
- Institute of Germplasm Resources and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Ziliang Zhang
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai’an 271018, China
| | - Huaqiang Zhu
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai’an 271018, China
| | - Jingxian Liu
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai’an 271018, China
| | - Jiajie Wu
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai’an 271018, China
| | - Guihua Bai
- Department of Agronomy, Kansas State University, Manhattan, KS 66506, USA
- Hard Winter Wheat Genetics Research Unit, Manhattan, KS 66506, USA
| | - Shubing Liu
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai’an 271018, China
- Correspondence:
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Zhou X, Li X, Han D, Yang S, Kang Z, Ren R. Genome-Wide QTL Mapping for Stripe Rust Resistance in Winter Wheat Pindong 34 Using a 90K SNP Array. FRONTIERS IN PLANT SCIENCE 2022; 13:932762. [PMID: 35873978 PMCID: PMC9296828 DOI: 10.3389/fpls.2022.932762] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Accepted: 06/08/2022] [Indexed: 05/27/2023]
Abstract
Winter wheat cultivar Pindong 34 has both adult-plant resistance (APR) and all-stage resistance (ASR) to stripe rust, which is caused by Puccinia striiformis f. sp. tritici (Pst). To map the quantitative trait loci (QTL) for stripe rust resistance, an F6-10 recombinant inbred line (RIL) population from a cross of Mingxian 169 × Pingdong 34 was phenotyped for stripe rust response over multiple years in fields under natural infection conditions and with selected Pst races under controlled greenhouse conditions, and genotyping was performed with a 90K single nucleotide polymorphism (SNP) array chip. Inclusive composite interval mapping (ICIM) identified 12 APR resistance QTLs and 3 ASR resistance QTLs. Among the 12 APR resistance QTLs, QYrpd.swust-1BL (explaining 9.24-13.33% of the phenotypic variation), QYrpd.swust-3AL.1 (11.41-14.80%), QYrpd.swust-3AL.2 (11.55-16.10%), QYrpd.swust-6BL (9.39-12.78%), QYrpd.swust-6DL (9.52-16.36%), QYrpd.swust-7AL (9.09-17.0%), and QYrpd.swust-7DL (8.87-11.38%) were more abundant than in the five tested environments and QYrpd.swust-1AS (11.05-12.72%), QYrpd.swust-1DL (9.81-13.05%), QYrpd.swust-2BL.1 (9.69-10.57%), QYrpd.swust-2BL.2 (10.36-12.97%), and QYrpd.swust-2BL.3 (9.54-13.15%) were significant in some of the tests. The three ASR resistance QTLs QYrpd.swust-2AS (9.69-13.58%), QYrpd.swust-2BL.4 (9.49-12.07%), and QYrpd.swust-7AS (16.16%) were detected based on the reactions in the seedlings tested with the CYR34 Pst race. Among the 15 QTLs detected in Pindong 34, the ASR resistance gene QYrpd.swust-7AS mapped on the short arm of chromosome 7A was likely similar to the previously reported QTL Yr61 in the region. The QTLs identified in the present study and their closely linked molecular markers could be useful for developing wheat cultivars with durable resistance to stripe rust.
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Affiliation(s)
- Xinli Zhou
- School of Life Sciences and Engineering, Wheat Research Institute, Southwest University of Science and Technology, Mianyang, China
| | - Xin Li
- School of Life Sciences and Engineering, Wheat Research Institute, Southwest University of Science and Technology, Mianyang, China
| | - Dejun Han
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Plant Protection, Northwest A&F University, Xianyang, China
| | - Suizhuang Yang
- School of Life Sciences and Engineering, Wheat Research Institute, Southwest University of Science and Technology, Mianyang, China
| | - Zhensheng Kang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Plant Protection, Northwest A&F University, Xianyang, China
| | - Runsheng Ren
- Excellence and Innovation Center, Jiangsu Academy of Agricultural Sciences, Nanjing, China
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8
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Tehseen MM, Tonk FA, Tosun M, Randhawa HS, Kurtulus E, Ozseven I, Akin B, Nur Zulfuagaoglu O, Nazari K. QTL Mapping of Adult Plant Resistance to Stripe Rust in a Doubled Haploid Wheat Population. Front Genet 2022; 13:900558. [PMID: 35646084 PMCID: PMC9131033 DOI: 10.3389/fgene.2022.900558] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Accepted: 04/13/2022] [Indexed: 12/20/2022] Open
Abstract
Stripe rust caused by Puccinia striiformis Westend. f. sp. tritici. is a major bread wheat disease worldwide with yield losses of up to 100% under severe disease pressure. The deployment of resistant cultivars with adult plant resistance to the disease provides a long-term solution to stripe rust of wheat. An advanced line from the International Winter Wheat Improvement Program (IWWIP) 130675 (Avd/Vee#1//1-27-6275/Cf 1770/3/MV171-C-17466) showed a high level of adult plant resistance to stripe rust in the field. To identify the adult plant resistance genes in this elite line, a mapping population of 190 doubled haploid (DH) lines was developed from a cross between line 130675 and the universal stripe rust-susceptible variety Avocet S. The DH population was evaluated at precision wheat stripe rust phenotyping platform, in Izmir during 2019, 2020, and 2021 cropping seasons under artificial inoculations. Composite interval mapping (CIM) identified two stable QTLs QYr.rcrrc-3B.1, and QYr.rcrrc-3B.2, which were detected in multiple years. In addition to these two QTLs, five more QTLs, QYr.rcrrc-1B, QYr.rcrrc-2A, QYr.rcrrc-3A, QYr.rcrrc-5A, and QYr.rcrrc-7D, were identified, which were specific to the cropping year (environment). All QTLs were derived from the resistant parent, except QYr.rcrrc-3A. The significant QTLs explained 3.4-20.6% of the phenotypic variance. SNP markers flanking the QTL regions can be amenable to marker-assisted selection. The best DH lines with high yield, end-use quality, and stripe rust resistance can be used for further selection for improved germplasm. SNP markers flanking the QTL regions can aid in identifying such lines.
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Affiliation(s)
| | | | - Muzaffer Tosun
- Department of Field Crops, Ege University, Izmir, Turkey
| | | | - Ezgi Kurtulus
- Turkey-ICARDA Regional Cereal Rust Research Center (RCRRC), Izmir, Turkey
| | - Izzet Ozseven
- Agean Agricultural Research Institute, Regional Cereal Rust Research Center (RCRRC), Izmir, Turkey
| | - Behyan Akin
- International Maize and Wheat Improvement Center (IWWIP-Turkey), Ankara, Turkey
| | | | - Kumarse Nazari
- Turkey-ICARDA Regional Cereal Rust Research Center (RCRRC), Izmir, Turkey
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9
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Ferjaoui S, Aouini L, Slimane RB, Ammar K, Dreisigacker S, Schouten HJ, Sapkota S, Bahri BA, Ben M'Barek S, Visser RGF, Kema GHJ, Hamza S. Deciphering resistance to Zymoseptoria tritici in the Tunisian durum wheat landrace accession 'Agili39'. BMC Genomics 2022; 23:372. [PMID: 35581550 PMCID: PMC9112612 DOI: 10.1186/s12864-022-08560-2] [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: 09/20/2021] [Accepted: 04/14/2022] [Indexed: 01/28/2023] Open
Abstract
Background Septoria tritici blotch (STB), caused by Zymoseptoria tritici (Z. tritici), is an important biotic threat to durum wheat in the entire Mediterranean Basin. Although most durum wheat cultivars are susceptible to Z. tritici, research in STB resistance in durum wheat has been limited. Results In our study, we have identified resistance to a wide array of Z. tritici isolates in the Tunisian durum wheat landrace accession ‘Agili39’. Subsequently, a recombinant inbred population was developed and tested under greenhouse conditions at the seedling stage with eight Z. tritici isolates and for five years under field conditions with three Z. tritici isolates. Mapping of quantitative trait loci (QTL) resulted in the identification of two major QTL on chromosome 2B designated as Qstb2B_1 and Qstb2B_2. The Qstb2B_1 QTL was mapped at the seedling and the adult plant stage (highest LOD 33.9, explained variance 61.6%), conferring an effective resistance against five Z. tritici isolates. The Qstb2B_2 conferred adult plant resistance (highest LOD 32.9, explained variance 42%) and has been effective at the field trials against two Z. tritici isolates. The physical positions of the flanking markers linked to Qstb2B_1 and Qstb2B_2 indicate that these two QTL are 5 Mb apart. In addition, we identified two minor QTL on chromosomes 1A (Qstb1A) and chromosome 7A (Qstb7A) (highest LODs 4.6 and 4.0, and explained variances of 16% and 9%, respectively) that were specific to three and one Z. tritici isolates, respectively. All identified QTL were derived from the landrace accession Agili39 that represents a valuable source for STB resistance in durum wheat. Conclusion This study demonstrates that Z. tritici resistance in the ‘Agili39’ landrace accession is controlled by two minor and two major QTL acting in an additive mode. We also provide evidence that the broad efficacy of the resistance to STB in ‘Agili 39’ is due to a natural pyramiding of these QTL. A sustainable use of this Z. tritici resistance source and a positive selection of the linked markers to the identified QTL will greatly support effective breeding for Z. tritici resistance in durum wheat. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08560-2.
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Affiliation(s)
- Sahbi Ferjaoui
- Laboratory of Bioaggressors and Integrated Protection in Agriculture (BPIA), National Institute of Agronomy of Tunisia (INAT), 43 Avenue Charles Nicolle, 1082 El Mahrajène, Tunis, Tunisia.,Present Address Field Crops Laboratory, Regional Field Crops Research Center of Beja (CRRGC), P.O. Box 9000, Beja, Tunisia
| | - Lamia Aouini
- Bio-Interaction and Plant Health, Wageningen University and Research, PO Box 16, 6700AA, Wageningen, The Netherlands.,The Graduate School 'Experimental Plant Sciences' (EPS), Wageningen Campus, 6708 PB, Wageningen, The Netherlands.,Present Address Center for Desert Agriculture, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Rim B Slimane
- Laboratory of Bioaggressors and Integrated Protection in Agriculture (BPIA), National Institute of Agronomy of Tunisia (INAT), 43 Avenue Charles Nicolle, 1082 El Mahrajène, Tunis, Tunisia.,Present address Higher Institute of Agronomy of Chott Meriam (ISA-CM), 4042, Sousse, Tunisia
| | - Karim Ammar
- International Maize and Wheat Improvement Center (CIMMYT), Apdo. Postal 6‑641, 06600, Mexico, D.F., Mexico
| | - Suzanne Dreisigacker
- International Maize and Wheat Improvement Center (CIMMYT), Apdo. Postal 6‑641, 06600, Mexico, D.F., Mexico
| | - Henk J Schouten
- Plant Breeding, Wageningen University and Research, P.O. Box 386, 6700 AJ, Wageningen, The Netherlands
| | - Suraj Sapkota
- Institute of Plant Breeding, Genetics and Genomics, Department of Plant Pathology and Institute of Plant Breeding, University of Georgia, Griffin, GA, 30223, USA.,Present Address United States Department of Agriculture USDA, Crop Genetics and Breeding Research Unit, Tifton, GA, USA
| | - Bochra A Bahri
- Laboratory of Bioaggressors and Integrated Protection in Agriculture (BPIA), National Institute of Agronomy of Tunisia (INAT), 43 Avenue Charles Nicolle, 1082 El Mahrajène, Tunis, Tunisia.,Institute of Plant Breeding, Genetics and Genomics, Department of Plant Pathology and Institute of Plant Breeding, University of Georgia, Griffin, GA, 30223, USA
| | - Sarrah Ben M'Barek
- CRP-Wheat Septoria Phenotyping Platform (CIMMYT-IRESA), Regional Field Crops Research Center of Beja (CRRGC), BP 350, 9000, Beja, Tunisia
| | - Richard G F Visser
- Plant Breeding, Wageningen University and Research, P.O. Box 386, 6700 AJ, Wageningen, The Netherlands
| | - Gert H J Kema
- Bio-Interaction and Plant Health, Wageningen University and Research, PO Box 16, 6700AA, Wageningen, The Netherlands.,Laboratory of Phytopathology, Wageningen University and Research, PO box 16, 6700AA, Wageningen, The Netherlands
| | - Sonia Hamza
- Laboratory of Bioaggressors and Integrated Protection in Agriculture (BPIA), National Institute of Agronomy of Tunisia (INAT), 43 Avenue Charles Nicolle, 1082 El Mahrajène, Tunis, Tunisia.
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10
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Jambuthenne DT, Riaz A, Athiyannan N, Alahmad S, Ng WL, Ziems L, Afanasenko O, Periyannan SK, Aitken E, Platz G, Godwin I, Voss-Fels KP, Dinglasan E, Hickey LT. Mining the Vavilov wheat diversity panel for new sources of adult plant resistance to stripe rust. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:1355-1373. [PMID: 35113190 PMCID: PMC9033734 DOI: 10.1007/s00122-022-04037-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 01/12/2022] [Indexed: 06/14/2023]
Abstract
Multi-year evaluation of the Vavilov wheat diversity panel identified new sources of adult plant resistance to stripe rust. Genome-wide association studies revealed the key genomic regions influencing resistance, including seven novel loci. Wheat stripe rust (YR) caused by Puccinia striiformis f. sp. tritici (Pst) poses a significant threat to global food security. Resistance genes commonly found in many wheat varieties have been rendered ineffective due to the rapid evolution of the pathogen. To identify novel sources of adult plant resistance (APR), 292 accessions from the N.I. Vavilov Institute of Plant Genetic Resources, Saint Petersburg, Russia, were screened for known APR genes (i.e. Yr18, Yr29, Yr46, Yr33, Yr39 and Yr59) using linked polymerase chain reaction (PCR) molecular markers. Accessions were evaluated against Pst (pathotype 134 E16 A + Yr17 + Yr27) at seedling and adult plant stages across multiple years (2014, 2015 and 2016) in Australia. Phenotypic analyses identified 132 lines that potentially carry novel sources of APR to YR. Genome-wide association studies (GWAS) identified 68 significant marker-trait associations (P < 0.001) for YR resistance, representing 47 independent quantitative trait loci (QTL) regions. Fourteen genomic regions overlapped with previously reported Yr genes, including Yr29, Yr56, Yr5, Yr43, Yr57, Yr30, Yr46, Yr47, Yr35, Yr36, Yrxy1, Yr59, Yr52 and YrYL. In total, seven QTL (positioned on chromosomes 1D, 2A, 3A, 3D, 5D, 7B and 7D) did not collocate with previously reported genes or QTL, indicating the presence of promising novel resistance factors. Overall, the Vavilov diversity panel provides a rich source of new alleles which could be used to broaden the genetic bases of YR resistance in modern wheat varieties.
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Affiliation(s)
- Dilani T Jambuthenne
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, Australia
| | - Adnan Riaz
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, Australia
| | - Naveenkumar Athiyannan
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, Australia
- Commonwealth Scientific and Industrial Research Organization (CSIRO), Agriculture and Food,, Canberra, ACT, Australia
| | - Samir Alahmad
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, Australia
| | - Wei Ling Ng
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, Australia
| | - Laura Ziems
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, Australia
| | - Olga Afanasenko
- Department of Plant Resistance To Diseases, All Russian Research Institute for Plant Protection, St Petersburg, Russia, 196608
| | - Sambasivam K Periyannan
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, Australia
- Commonwealth Scientific and Industrial Research Organization (CSIRO), Agriculture and Food,, Canberra, ACT, Australia
| | - Elizabeth Aitken
- School of Agriculture and Food Sciences, The University of Queensland, St Lucia, QLD, Australia
| | - Greg Platz
- Department of Agriculture and Fisheries, Hermitage Research Facility, Warwick, QLD, Australia
| | - Ian Godwin
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, Australia
| | - Kai P Voss-Fels
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, Australia
| | - Eric Dinglasan
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, Australia.
| | - Lee T Hickey
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, Australia.
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11
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Rollar S, Geyer M, Hartl L, Mohler V, Ordon F, Serfling A. Quantitative Trait Loci Mapping of Adult Plant and Seedling Resistance to Stripe Rust ( Puccinia striiformis Westend.) in a Multiparent Advanced Generation Intercross Wheat Population. FRONTIERS IN PLANT SCIENCE 2021; 12:684671. [PMID: 35003147 PMCID: PMC8733622 DOI: 10.3389/fpls.2021.684671] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 11/19/2021] [Indexed: 05/20/2023]
Abstract
Stripe rust caused by the biotrophic fungus Puccinia striiformis Westend. is one of the most important diseases of wheat worldwide, causing high yield and quality losses. Growing resistant cultivars is the most efficient way to control stripe rust, both economically and ecologically. Known resistance genes are already present in numerous cultivars worldwide. However, their effectiveness is limited to certain races within a rust population and the emergence of stripe rust races being virulent against common resistance genes forces the demand for new sources of resistance. Multiparent advanced generation intercross (MAGIC) populations have proven to be a powerful tool to carry out genetic studies on economically important traits. In this study, interval mapping was performed to map quantitative trait loci (QTL) for stripe rust resistance in the Bavarian MAGIC wheat population, comprising 394 F6 : 8 recombinant inbred lines (RILs). Phenotypic evaluation of the RILs was carried out for adult plant resistance in field trials at three locations across three years and for seedling resistance in a growth chamber. In total, 21 QTL for stripe rust resistance corresponding to 13 distinct chromosomal regions were detected, of which two may represent putatively new QTL located on wheat chromosomes 3D and 7D.
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Affiliation(s)
- Sandra Rollar
- Julius Kühn Institute (JKI) – Federal Research Centre for Cultivated Plants, Institute for Resistance Research and Stress Tolerance, Quedlinburg, Germany
| | - Manuel Geyer
- Bavarian State Research Center for Agriculture, Institute for Crop Science and Plant Breeding, 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
| | - Frank Ordon
- Julius Kühn Institute (JKI) – Federal Research Centre for Cultivated Plants, Institute for Resistance Research and Stress Tolerance, Quedlinburg, Germany
| | - Albrecht Serfling
- Julius Kühn Institute (JKI) – Federal Research Centre for Cultivated Plants, Institute for Resistance Research and Stress Tolerance, Quedlinburg, Germany
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12
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Zhou J, Singh RP, Ren Y, Bai B, Li Z, Yuan C, Li S, Huerta-Espino J, Liu D, Lan C. Identification of Two New Loci for Adult Plant Resistance to Leaf Rust and Stripe Rust in the Chinese Wheat Variety 'Neimai 836'. PLANT DISEASE 2021; 105:3705-3714. [PMID: 33779256 DOI: 10.1094/pdis-12-20-2654-re] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The characterization of leaf rust (caused by Puccinia triticina) and stripe rust (caused by Puccinia striiformis f. sp. tritici) resistance genes is the basis for breeding resistant wheat varieties and managing epidemics of these diseases in wheat. A cross between the susceptible wheat variety 'Apav#1' and resistant variety 'Neimai 836' was used to develop a mapping population containing 148 F5 recombinant inbred lines (RILs). Leaf rust phenotyping was done in field trials at Ciudad Obregón, Mexico, in 2017 and 2018, and stripe rust data were generated at Toluca, Mexico, in 2017 and in Mianyang, Ezhou, and Gansu, China, in 2019. Inclusive complete interval mapping (ICIM) was used to create a genetic map and identify significant resistance quantitative trait loci (QTL) with 2,350 polymorphic markers from a 15K wheat single-nucleotide polymorphism (SNP) array and simple-sequence repeats (SSRs). The pleiotropic multipathogen resistance gene Lr46/Yr29 and four QTL were identified, including two new loci, QLr.hzau-3BL and QYr.hzau-5AL, which explained 3 to 16% of the phenotypic variation in resistance to leaf rust and 7 to 14% of that to stripe rust. The flanking SNP markers for the two loci were converted to Kompetitive Allele-Specific PCR (KASP) markers and used to genotype a collection of 153 wheat lines, indicating the Chinese origin of the loci. Our results suggest that Neimai 836, which has been used as a parent for many wheat varieties in China, could be a useful source of high-level resistance to both leaf rust and stripe rust.
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Affiliation(s)
- Jingwei Zhou
- Huazhong Agricultural University, College of Plant Science & Technology, No. 1, Hongshan District, Wuhan 430070, Hubei Province, P.R. China
| | - Ravi P Singh
- International Maize and Wheat Improvement Center (CIMMYT), 06600 Mexico D.F., Mexico
| | - Yong Ren
- Mianyang Academy of Agricultural Science/Mianyang Branch of National Wheat Improvement Center, Mianyang 621023, Sichuan, P.R. China
| | - Bin Bai
- Wheat Research Institute, Gansu Academy of Agricultural Sciences, No. 1 Nongkeyuanxincun, Lanzhou 730070, Gansu Province, P.R. China
| | - Zhikang Li
- Huazhong Agricultural University, College of Plant Science & Technology, No. 1, Hongshan District, Wuhan 430070, Hubei Province, P.R. China
| | - Chan Yuan
- Huazhong Agricultural University, College of Plant Science & Technology, No. 1, Hongshan District, Wuhan 430070, Hubei Province, P.R. China
| | - Shunda Li
- Huazhong Agricultural University, College of Plant Science & Technology, No. 1, Hongshan District, Wuhan 430070, Hubei Province, P.R. China
| | - Julio Huerta-Espino
- Campo Experimental Valle de Mexico Instituto Nacional de Investigaciones Forestales Agricolas y Pecuarias (INIFAP), 56230 Chapingo, Edo. de Mexico, Mexico
| | - Demei Liu
- Northwest Institute of Plateau Biology, Chinese Academy of Sciences and Qinghai Provincial Key Laboratory of Crop Molecular Breeding and China and Qinghai Provincial Key Laboratory of Crop Molecular Breeding Northwest Institute of Plateau Biology, Innovation Academy for Seed Design, Xining 810008, P.R. China
| | - Caixia Lan
- Huazhong Agricultural University, College of Plant Science & Technology, No. 1, Hongshan District, Wuhan 430070, Hubei Province, P.R. China
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13
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Wu Y, Wang Y, Yao F, Long L, Li J, Li H, Pu Z, Li W, Jiang Q, Wang J, Wei Y, Ma J, Kang H, Qi P, Dai S, Deng M, Zheng Y, Jiang Y, Chen G. Molecular Mapping of a Novel Quantitative Trait Locus Conferring Adult Plant Resistance to Stripe Rust in Chinese Wheat Landrace Guangtoumai. PLANT DISEASE 2021; 105:1919-1925. [PMID: 32990521 DOI: 10.1094/pdis-07-20-1544-re] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Stripe rust (yellow rust), caused by Puccinia striiformis f. sp. tritici, is one of the most destructive diseases of wheat worldwide. Chinese wheat landrace Guangtoumai (GTM) exhibited a high level of resistance against predominant P. striiformis f. sp. tritici races in China at the adult plant stage. The objective of this research was to identify and map the major locus/loci for stripe rust resistance in GTM. A set of 212 recombinant inbred lines (RILs) was developed from a cross between GTM and Avocet S. The parents and RILs were evaluated in three field tests (2018, 2019, and 2020 at Chongzhou, Sichuan) with the currently predominant P. striiformis f. sp. tritici races for final disease severity and genotyped with the Wheat 55K single nucleotide polymorphism (SNP) array to construct a genetic map with 1,031 SNP markers. A major locus, named QYr.GTM-5DL, was detected on chromosome 5DL in GTM. The locus was mapped in a 2.75-cM interval flanked by SNP markers AX-109855976 and AX-109453419, explaining up to 44.4% of the total phenotypic variation. Since no known Yr genes have been reported on chromosome 5DL, QYr.GTM-5DL is very likely a novel adult plant resistance locus. Haplotype analysis revealed that the resistance allele displayed enhanced levels of stripe rust resistance and is likely present in 5.3% of the 247 surveyed Chinese wheat landraces. The derived cleaved amplified polymorphic sequence (dCAPS) marker dCAPS-5722, converted from a SNP marker tightly linked to QYr.GTM-5DL with 0.3 cM, was validated on a subset of RILs and 48 commercial wheat cultivars developed in Sichuan. The results indicated that QYr.GTM-5DL with its linked dCAPS marker could be used in marker-assisted selection to improve stripe rust resistance in breeding programs, and this quantitative trait locus will provide new and possibly durable resistance to stripe rust.
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Affiliation(s)
- Yu Wu
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130, P. R. China
| | - Yuqi Wang
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130, P. R. China
| | - Fangjie Yao
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130, P. R. China
| | - Li Long
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130, P. R. China
| | - Jing Li
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130, P. R. China
| | - Hao Li
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130, P. R. China
| | - Zhien Pu
- College of Agronomy, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130, P. R. China
| | - Wei Li
- College of Agronomy, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130, P. R. China
| | - Qiantao Jiang
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130, P. R. China
- State Key Laboratory of Crop Gene Exploitation and Utilization in Southwest China, Wenjiang, Chengdu, Sichuan 611130, P. R. China
| | - Jirui Wang
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130, P. R. China
- State Key Laboratory of Crop Gene Exploitation and Utilization in Southwest China, Wenjiang, Chengdu, Sichuan 611130, P. R. China
| | - Yuming Wei
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130, P. R. China
- State Key Laboratory of Crop Gene Exploitation and Utilization in Southwest China, Wenjiang, Chengdu, Sichuan 611130, P. R. China
| | - Jian Ma
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130, P. R. China
| | - Houyang Kang
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130, P. R. China
- State Key Laboratory of Crop Gene Exploitation and Utilization in Southwest China, Wenjiang, Chengdu, Sichuan 611130, P. R. China
| | - Pengfei Qi
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130, P. R. China
| | - Shoufen Dai
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130, P. R. China
| | - Mei Deng
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130, P. R. China
| | - Youliang Zheng
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130, P. R. China
- State Key Laboratory of Crop Gene Exploitation and Utilization in Southwest China, Wenjiang, Chengdu, Sichuan 611130, P. R. China
| | - Yunfeng Jiang
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130, P. R. China
| | - Guoyue Chen
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130, P. R. China
- State Key Laboratory of Crop Gene Exploitation and Utilization in Southwest China, Wenjiang, Chengdu, Sichuan 611130, P. R. China
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14
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Zhang P, Yan X, Gebrewahid TW, Zhou Y, Yang E, Xia X, He Z, Li Z, Liu D. Genome-wide association mapping of leaf rust and stripe rust resistance in wheat accessions using the 90K SNP array. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:1233-1251. [PMID: 33492413 DOI: 10.1007/s00122-021-03769-3] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 01/09/2021] [Indexed: 05/22/2023]
Abstract
A genome-wide association analysis identified diverse loci for seedling and adult plant resistance to leaf rust and stripe rust. KASP markers were developed and validated for marker-assisted selection. Wheat leaf rust and stripe rust cause significant losses in many wheat producing regions worldwide. The objective of this study was to identify chromosome regions conferring resistance to both leaf rust and stripe rust at the seedling and adult plant stages. A diversity panel of 268 wheat lines, including 207 accessions from different wheat growing regions in China, and 61 accessions from foreign countries, were evaluated for leaf rust response at seedling stage using eight Chinese Puccinia triticina pathotypes, and also tested for leaf rust and stripe rust at adult plant stage in multiple field environments. The panel was genotyped with the Wheat 90 K Illumina iSelect SNP array. Genome-wide association mapping (GWAS) was performed using the mixed linear model (MLM). Twenty-two resistance loci including the known Lr genes, Lr1, Lr26, Lr3ka, LrZH22, and 18 potentially new loci were identified associated with seedling resistance, explaining 4.6 to 25.2% of the phenotypic variance. Twenty-two and 23 adult plant resistance (APR) QTL associated with leaf and stripe rust, respectively, were identified at adult stage, explaining 4.2-11.5% and 4.4-9.7% of the phenotypic variance. Among them, QLr-2BS was the potentially most valuable all-stage resistance gene. Seven and six consistent APR QTL were identified in multiple environments including best linear unbiased prediction (BLUP) data, respectively. Comparison with previously mapped resistance loci indicated that three of the seven leaf rust resistance APR QTL, and two of the six stripe rust resistance APR QTL were new. Four potentially pleiotropic APR QTL, including Lr46/Yr29, QLr-2AL.1/QYr-2AL.1, QLr-2AL.2/QYr-2AL.2, and QLr-5BL/QYr-5BL.1, were identified. Twelve associated SNPs were converted into kompetitive allele-specific PCR (KASP) markers and verified in bi-parental populations. The study reports genetic loci conferring resistance to both diseases, and the closely linked markers should be applicable for marker-assisted wheat breeding.
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Affiliation(s)
- Peipei Zhang
- College of Plant Protection, State Key Laboratory of North China Crop Improvement and Regulation, Technological Innovation Center for Biological Control of Crop Diseases and Insect Pests of Hebei Province, Hebei Agricultural University, Baoding, 071000, Hebei, People's Republic of China
| | - Xiaocui Yan
- College of Plant Protection, State Key Laboratory of North China Crop Improvement and Regulation, Technological Innovation Center for Biological Control of Crop Diseases and Insect Pests of Hebei Province, Hebei Agricultural University, Baoding, 071000, Hebei, People's Republic of China
| | - Takele-Weldu Gebrewahid
- College of Plant Protection, State Key Laboratory of North China Crop Improvement and Regulation, Technological Innovation Center for Biological Control of Crop Diseases and Insect Pests of Hebei Province, Hebei Agricultural University, Baoding, 071000, Hebei, People's Republic of China
- College of Agriculture, Aksum University, Shire-Indaslassie 314, Tigray, Ethiopia
| | - Yue Zhou
- College of Biochemistry and Environmental Engineering, Baoding University, Baoding, 071001, Hebei, People's Republic of China
| | - Ennian Yang
- Key Laboratory of Biology and Genetic Breeding in Wheat (Southwest), Crop Research Institute, Sichuan Academy of Agricultural Science, #4 Shizishan Rd, Jinjiang, Chengdu, 610066, Sichuan, People's Republic of China
| | - Xianchun Xia
- Institute of Crop Science, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, People's Republic of China
| | - Zhonghu He
- Institute of Crop Science, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, People's Republic of China
| | - Zaifeng Li
- College of Plant Protection, State Key Laboratory of North China Crop Improvement and Regulation, Technological Innovation Center for Biological Control of Crop Diseases and Insect Pests of Hebei Province, Hebei Agricultural University, Baoding, 071000, Hebei, People's Republic of China.
| | - Daqun Liu
- College of Plant Protection, State Key Laboratory of North China Crop Improvement and Regulation, Technological Innovation Center for Biological Control of Crop Diseases and Insect Pests of Hebei Province, Hebei Agricultural University, Baoding, 071000, Hebei, People's Republic of China.
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15
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Huang S, Liu S, Zhang Y, Xie Y, Wang X, Jiao H, Wu S, Zeng Q, Wang Q, Singh RP, Bhavani S, Kang Z, Wang C, Han D, Wu J. Genome-Wide Wheat 55K SNP-Based Mapping of Stripe Rust Resistance Loci in Wheat Cultivar Shaannong 33 and Their Alleles Frequencies in Current Chinese Wheat Cultivars and Breeding Lines. PLANT DISEASE 2021; 105:1048-1056. [PMID: 32965178 DOI: 10.1094/pdis-07-20-1516-re] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Wheat cultivar Shaannong 33 (SN33) has remained highly resistant to stripe rust in the field since its release in 2009. To unravel the genetic architecture of stripe rust resistance, seedlings of 161 recombinant inbred lines (RILs) from the cross Avocet S × SN33 were evaluated with two isolates (PST-Lab.1 and PST-Lab.2) of the stripe rust pathogen (Puccinia striiformis f. sp. tritici) in the greenhouse, and the RILs were evaluated in naturally or artificially inoculated field sites during two cropping seasons. The RILs and parents were genotyped with the wheat 55K single-nucleotide polymorphism array. Three genomic regions conferring seedling resistance were mapped on chromosomes 1DS, 2AS, and 3DS, and four consistent quantitative trait loci (QTL) for adult-plant resistance (APR) were detected on 1BL, 2AS, 3DL, and 6BS. The 2AS locus conferring all-stage resistance was identified as the resistant gene Yr17 located on 2NS translocation. The QTL identified on 1BL and 6BS likely correspond to Yr29 and Yr78, respectively. An APR QTL on 3DL explaining 5.8 to 12.2% of the phenotypic variation is likely to be new. Molecular marker detection assays with the 2NS segment (Yr17), Yr29, Yr78, and QYrsn.nwafu-3DL on a panel of 420 current Chinese wheat cultivars and breeding lines indicated that these genes were present in 11.4, 7.6, 14.8, and 7.4% of entries, respectively. The interactions among these genes and QTL were additive, suggesting their potential value in enhancing stripe rust resistance breeding materials as observed in the resistant parent. In addition, we also identified two leaf necrosis genes, Ne1 and Ne2; however, the F1 plants from cross Avocet S × SN33 survived, indicating that SN33 probably has another allele of Ne1 which allows seed to be harvested.
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Affiliation(s)
- Shuo Huang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, P. R. China
| | - Shengjie Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, P. R. China
| | - Yibo Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, P. R. China
| | - Yanzhou Xie
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, P. R. China
| | - Xiaoting Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, P. R. China
| | - Hanxuan Jiao
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, P. R. China
| | - Shushu Wu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, P. R. China
| | - Qingdong Zeng
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, P. R. China
| | - Qilin Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, P. R. China
| | - Ravi P Singh
- International Maize and Wheat Improvement Center (CIMMYT), El Batan, Texcoco, Estado de Mexico 56237, Mexico
| | - Sridhar Bhavani
- International Maize and Wheat Improvement Center (CIMMYT), El Batan, Texcoco, Estado de Mexico 56237, Mexico
| | - Zhensheng Kang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, P. R. China
| | - Chengshe Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, P. R. China
| | - Dejun Han
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, P. R. China
| | - Jianhui Wu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, P. R. China
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16
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Tehseen MM, Tonk FA, Tosun M, Amri A, Sansaloni CP, Kurtulus E, Yazbek M, Al-Sham'aa K, Ozseven I, Safdar LB, Shehadeh A, Nazari K. Genome-wide association study of resistance to PstS2 and Warrior races of Puccinia striiformis f. sp. tritici (stripe rust) in bread wheat landraces. THE PLANT GENOME 2021; 14:e20066. [PMID: 33615748 DOI: 10.1002/tpg2.20066] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 09/03/2020] [Accepted: 09/05/2020] [Indexed: 05/20/2023]
Abstract
Stripe or yellow rust, caused by Puccinia striiformis Westend. f. sp. tritici is a major threat to bread wheat production worldwide. The breakdown in resistance of certain major genes and newly emerging aggressive races of stripe rusts pose serious concerns in all main wheat growing areas of the world. To identify new sources of resistance and associated QTL for effective utilization in future breeding programs an association mapping (AM) panel comprising of 600 bread wheat landraces collected from eight different countries conserved at ICARDA gene bank were evaluated for seedling and adult plant resistance against the PstS2 and Warrior races of stripe rust at the Regional Cereal Rust Research Center (RCRRC), Izmir, Turkey during 2016, 2018 and 2019. A set of 25,169 informative SNP markers covering the whole genome were used to examine the population structure, linkage disequilibrium and marker-trait associations in the AM panel. The genome-wide association study (GWAS) was carried out using a Mixed Linear Model (MLM). We identified 47 SNP markers across 19 chromosomes with significant SNP-trait associations for both seedling stage and adult plant resistance. The threshold of significance for all SNP-trait associations was determined by the false discovery rate (q) ≤ 0.05. Three genomic regions (QYr.1D_APR, QYr.3A_seedling and QYr.7D_seedling) identified in this study do not correspond to previously reported Yr genes or QTL, suggesting new genomic regions for stripe rust resistance.
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Affiliation(s)
| | | | - Muzaffer Tosun
- Department of Field Crops, Ege University, Izmir, Turkey
| | - Ahmed Amri
- ICARDA-PreBreeding & Genebank Operations, Biodiversity and Crop Improvement Program, Rabat, Morocco
| | | | - Ezgi Kurtulus
- Turkey-ICARDA Regional Cereal Rust Research Center (RCRRC), P.O. Box 35661, Menemen, Izmir, Turkey
| | - Mariana Yazbek
- ICARDA-Genetic Resources, PreBreeding & Genebank Operations, Biodiversity and Crop Improvement Program, Terbol, Lebanon
| | | | - Izzet Ozseven
- Agean Agricultural Research Institute, Regional Cereal Rust Research Center (RCRRC), P.O. Box 35661, Menemen, Izmir, Turkey
| | - Luqman Bin Safdar
- Department of Plant Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Ali Shehadeh
- ICARDA-Genetic Resources, PreBreeding & Genebank Operations, Biodiversity and Crop Improvement Program, Terbol, Lebanon
| | - Kumarse Nazari
- Turkey-ICARDA Regional Cereal Rust Research Center (RCRRC), P.O. Box 35661, Menemen, Izmir, Turkey
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Yao F, Long L, Wang Y, Duan L, Zhao X, Jiang Y, Li H, Pu Z, Li W, Jiang Q, Wang J, Wei Y, Ma J, Kang H, Dai S, Qi P, Zheng Y, Chen X, Chen G. Population structure and genetic basis of the stripe rust resistance of 140 Chinese wheat landraces revealed by a genome-wide association study. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2020; 301:110688. [PMID: 33218646 DOI: 10.1016/j.plantsci.2020.110688] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 09/16/2020] [Accepted: 09/18/2020] [Indexed: 06/11/2023]
Abstract
Stripe rust caused by Puccinia striiformis f. sp. tritici (Pst) is one of the most devastating foliar diseases in wheat. Host resistance is the most effective strategy for the management of the disease. To screen for accessions with stable resistance and identify effective stripe rust resistance loci, a genome-wide association study (GWAS) was conducted using a panel of 140 Chinese wheat landraces. The panel was evaluated for stripe rust response at the adult-plant stage at six field-year environments with mixed races and at the seedling stage with two separate predominant races of the pathogen, and genotyped with the genome-wide Diversity Arrays Technology markers. The panel displayed abundant phenotypic variation in stripe rust responses, with 9 landraces showing stable resistance to the mixture of Pst races at the adult-plant stage in the field and 10 landraces showing resistance to individual races at the seedling stage in the greenhouse. GWAS identified 12 quantitative trait loci (QTL) significantly (P ≤ 0.001) associated to stripe rust resistance using the field data of at least two environments and 18 QTL using the seedling data with two races. Among these QTL, 10 were presumably novel, including 4 for adult-plant resistance mapped to chromosomes 1B (QYrcl.sicau-1B.3), 4A (QYrcl.sicau-4A.3), 6A (QYrcl.sicau-6A.2) and 7B (QYrcl.sicau-7B.2) and 6 for all-stage resistance mapped to chromosomes 2D (QYrcl.sicau-2D.1), 3B (QYrcl.sicau-3B.3), 3D (QYrcl.sicau-3D), 4B (QYrcl.sicau-4B), 6A (QYrcl.sicau-6A.1) and 6D (QYrcl.sicau-6D). The landraces with stable resistance can be used for developing wheat cultivars with effective resistance to stripe rust.
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Affiliation(s)
- Fangjie Yao
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130, PR China; State Key Laboratory of Crop Gene Exploitation and Utilization in Southwest China, Wenjiang, Chengdu, Sichuan 611130, PR China
| | - Li Long
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130, PR China; State Key Laboratory of Crop Gene Exploitation and Utilization in Southwest China, Wenjiang, Chengdu, Sichuan 611130, PR China
| | - Yuqi Wang
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130, PR China; State Key Laboratory of Crop Gene Exploitation and Utilization in Southwest China, Wenjiang, Chengdu, Sichuan 611130, PR China
| | - Luyao Duan
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130, PR China; State Key Laboratory of Crop Gene Exploitation and Utilization in Southwest China, Wenjiang, Chengdu, Sichuan 611130, PR China
| | - Xuyang Zhao
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130, PR China; State Key Laboratory of Crop Gene Exploitation and Utilization in Southwest China, Wenjiang, Chengdu, Sichuan 611130, PR China
| | - Yunfeng Jiang
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130, PR China
| | - Hao Li
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130, PR China
| | - Zhien Pu
- College of Agronomy, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130, PR China
| | - Wei Li
- College of Agronomy, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130, PR China
| | - Qiantao Jiang
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130, PR China; State Key Laboratory of Crop Gene Exploitation and Utilization in Southwest China, Wenjiang, Chengdu, Sichuan 611130, PR China
| | - Jirui Wang
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130, PR China; State Key Laboratory of Crop Gene Exploitation and Utilization in Southwest China, Wenjiang, Chengdu, Sichuan 611130, PR China
| | - Yuming Wei
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130, PR China; State Key Laboratory of Crop Gene Exploitation and Utilization in Southwest China, Wenjiang, Chengdu, Sichuan 611130, PR China
| | - Jian Ma
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130, PR China
| | - Houyang Kang
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130, PR China; State Key Laboratory of Crop Gene Exploitation and Utilization in Southwest China, Wenjiang, Chengdu, Sichuan 611130, PR China
| | - Shoufen Dai
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130, PR China
| | - Pengfei Qi
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130, PR China
| | - Youliang Zheng
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130, PR China; State Key Laboratory of Crop Gene Exploitation and Utilization in Southwest China, Wenjiang, Chengdu, Sichuan 611130, PR China
| | - Xianming Chen
- US Department of Agriculture, Agricultural Research Service, Wheat Health, Genetics and Quality Research Unit, Department of Plant Pathology, Washington State University, Pullman, WA 99164, USA
| | - Guoyue Chen
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130, PR China; State Key Laboratory of Crop Gene Exploitation and Utilization in Southwest China, Wenjiang, Chengdu, Sichuan 611130, PR China.
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18
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Jia M, Yang L, Zhang W, Rosewarne G, Li J, Yang E, Chen L, Wang W, Liu Y, Tong H, He W, Zhang Y, Zhu Z, Gao C. Genome-wide association analysis of stripe rust resistance in modern Chinese wheat. BMC PLANT BIOLOGY 2020; 20:491. [PMID: 33109074 PMCID: PMC7590722 DOI: 10.1186/s12870-020-02693-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 10/12/2020] [Indexed: 05/05/2023]
Abstract
BACKGROUND Stripe rust (yellow rust) is a significant disease for bread wheat (Triticum aestivum L.) worldwide. A genome-wide association study was conducted on 240 Chinese wheat cultivars and elite lines genotyped with the wheat 90 K single nucleotide polymorphism (SNP) arrays to decipher the genetic architecture of stripe rust resistance in Chinese germplasm. RESULTS Stripe rust resistance was evaluated at the adult plant stage in Pixian and Xindu in Sichuan province in the 2015-2016 cropping season, and in Wuhan in Hubei province in the 2013-2014, 2016-2017 and 2018-2019 cropping seasons. Twelve stable loci for stripe rust resistance were identified by GWAS using TASSEL and GAPIT software. These loci were distributed on chromosomes 1B, 1D, 2A, 2B, 3A, 3B, 4B (3), 4D, 6D, and 7B and explained 3.6 to 10.3% of the phenotypic variation. Six of the loci corresponded with previously reported genes/QTLs, including Sr2/Yr30/Lr27, while the other six (QYr.hbaas-1BS, QYr.hbaas-2BL, QYr.hbaas-3AL, QYr.hbaas-4BL.3, QYr.hbaas-4DL, and QYr.hbaas-6DS) are probably novel. The results suggest high genetic diversity for stripe rust resistance in this population. The resistance alleles of QYr.hbaas-2AS, QYr.hbaas-3BS, QYr.hbaas-4DL, and QYr.hbaas-7BL were rare in the present panel, indicating their potential use in breeding for stripe rust resistance in China. Eleven penta-primer amplification refractory mutation system (PARMS) markers were developed from SNPs significantly associated with seven mapped QTLs. Twenty-seven genes were predicted for mapped QTLs. Six of them were considered as candidates for their high relative expression levels post-inoculation. CONCLUSION The resistant germplasm, mapped QTLs, and PARMS markers developed in this study are resources for enhancing stripe rust resistance in wheat breeding.
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Affiliation(s)
- Mengjie Jia
- Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Food Crops Institute, Hubei Academy of Agricultural Sciences/Hubei Engineering and Technology Research Center of Wheat/Wheat Disease Biology Research Station for Central China, Wuhan, 430064, China
- College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Lijun Yang
- Institute of Plant Protection and Soil Science, Hubei Academy of Agricultural Sciences, Wuhan, 430064, China
| | - Wei Zhang
- Department of Plant Sciences, North Dakota State University, Fargo, North Dakota, 58108-6050, USA
| | - Garry Rosewarne
- Department of Jobs, Precincts and Regions, Agriculture Victoria, 110 Natimuk Road, Horsham, Victoria, 3400, Australia
- International Maize and Wheat Improvement Center (CIMMYT), Apdo. Postal 6-641, 06600, Mexico D.F., Mexico
| | - Junhui Li
- Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Food Crops Institute, Hubei Academy of Agricultural Sciences/Hubei Engineering and Technology Research Center of Wheat/Wheat Disease Biology Research Station for Central China, Wuhan, 430064, China
| | - Enian Yang
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, China
| | - Ling Chen
- Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Food Crops Institute, Hubei Academy of Agricultural Sciences/Hubei Engineering and Technology Research Center of Wheat/Wheat Disease Biology Research Station for Central China, Wuhan, 430064, China
| | - Wenxue Wang
- Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Food Crops Institute, Hubei Academy of Agricultural Sciences/Hubei Engineering and Technology Research Center of Wheat/Wheat Disease Biology Research Station for Central China, Wuhan, 430064, China
| | - Yike Liu
- Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Food Crops Institute, Hubei Academy of Agricultural Sciences/Hubei Engineering and Technology Research Center of Wheat/Wheat Disease Biology Research Station for Central China, Wuhan, 430064, China
| | - Hanwen Tong
- Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Food Crops Institute, Hubei Academy of Agricultural Sciences/Hubei Engineering and Technology Research Center of Wheat/Wheat Disease Biology Research Station for Central China, Wuhan, 430064, China
| | - Weijie He
- Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Food Crops Institute, Hubei Academy of Agricultural Sciences/Hubei Engineering and Technology Research Center of Wheat/Wheat Disease Biology Research Station for Central China, Wuhan, 430064, China
| | - Yuqing Zhang
- Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Food Crops Institute, Hubei Academy of Agricultural Sciences/Hubei Engineering and Technology Research Center of Wheat/Wheat Disease Biology Research Station for Central China, Wuhan, 430064, China
| | - Zhanwang Zhu
- Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Food Crops Institute, Hubei Academy of Agricultural Sciences/Hubei Engineering and Technology Research Center of Wheat/Wheat Disease Biology Research Station for Central China, Wuhan, 430064, China.
| | - Chunbao Gao
- Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Food Crops Institute, Hubei Academy of Agricultural Sciences/Hubei Engineering and Technology Research Center of Wheat/Wheat Disease Biology Research Station for Central China, Wuhan, 430064, China.
- Hubei Collaborative Innovation Center for Grain Industry, Yangtze university, Jingzhou, 434025, China.
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Wu J, Wang X, Chen N, Yu R, Yu S, Wang Q, Huang S, Wang H, Singh RP, Bhavani S, Kang Z, Han D, Zeng Q. Association Analysis Identifies New Loci for Resistance to Chinese Yr26-Virulent Races of the Stripe Rust Pathogen in a Diverse Panel of Wheat Germplasm. PLANT DISEASE 2020; 104:1751-1762. [PMID: 32293995 DOI: 10.1094/pdis-12-19-2663-re] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Stripe rust caused by Puccinia striiformis f. sp. tritici (Pst) is one of the most destructive fungal diseases of wheat worldwide. The expanding Yr26-virulent Pst race (V26) group overcomes almost all currently deployed resistance genes in China and has continued to accumulate new virulence. Investigating the genetic architecture of stripe rust resistance in common wheat is an important basis for a successful utilization of resistance in breeding programs. A panel of 410 exotic wheat germplasms was used for characterizing new stripe rust resistance loci. This panel was genotyped using high-density wheat 660K single-nucleotide polymorphism (SNP) array, and phenotypic evaluation of seedlings for stripe rust resistance was performed using multiple Pst races. Thirty-five loci conferring resistance were identified through genome-wide association mapping, and explained phenotypic variances ranged from 53 to 75%. Of these, 14 were colocated in the proximity of the known loci, including cataloged Yr genes Yr9, Yr10, Yr26, Yr33, Yr47, Yr56, Yr57, Yr64, Yr67, Yr72, and Yr81 and three temporarily designated as YrCen, YrNP63, and YrRC detected in our quantitative trait locus (QTL) mapping studies. Seven of them (Yr9, Yr10, Yr24/26, Yr81, YrCEN, YrNP63, and YrRC) were confirmed by molecular detection or genetic analysis. New loci that were identified to be different from reported Yr genes need further confirmation. Nine QTL with significantly large phenotypic effect on resistance to all tested races were considered as major loci for effective resistance. The identified loci enrich our stripe rust resistance gene pool, and the linked SNPs should be useful for marker-assisted selection in breeding programs.
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Affiliation(s)
- Jianhui Wu
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Shaanxi 712100, P. R. China
| | - Xiaoting Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Shaanxi 712100, P. R. China
| | - Nan Chen
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Shaanxi 712100, P. R. China
| | - Rui Yu
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Shaanxi 712100, P. R. China
| | - Shizhou Yu
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Shaanxi 712100, P. R. China
| | - Qilin Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Shaanxi 712100, P. R. China
| | - Shuo Huang
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Shaanxi 712100, P. R. China
| | - Haiying Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Shaanxi 712100, P. R. China
| | - Ravi P Singh
- International Maize and Wheat Improvement Center, Texcoco, Mexico
| | - Sridhar Bhavani
- International Maize and Wheat Improvement Center, Texcoco, Mexico
| | - Zhensheng Kang
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Shaanxi 712100, P. R. China
| | - Dejun Han
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Shaanxi 712100, P. R. China
| | - Qingdong Zeng
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Shaanxi 712100, P. R. China
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20
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Liu Y, Qie Y, Li X, Wang M, Chen X. Genome-Wide Mapping of Quantitative Trait Loci Conferring All-Stage and High-Temperature Adult-Plant Resistance to Stripe Rust in Spring Wheat Landrace PI 181410. Int J Mol Sci 2020; 21:ijms21020478. [PMID: 31940871 PMCID: PMC7014124 DOI: 10.3390/ijms21020478] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 01/08/2020] [Accepted: 01/09/2020] [Indexed: 11/16/2022] Open
Abstract
Stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is one of the most destructive diseases of wheat in the world. Genetic resistance is the best strategy for control of the disease. Spring wheat landrace PI 181410 has shown high level resistance to stripe rust. The present study characterized the landrace to have both race-specific all-stage resistance and nonrace-specific high-temperature adult-plant (HTAP) resistance. To map quantitative trait loci (QTL) for the resistance in PI 181410, it was crossed with Avocet S (AvS), from which a recombinant inbred line population was developed. The F5–F8 populations were consecutively phenotyped for stripe rust response in multiple field environments under natural Pst infection, and the F7 population was phenotyped in seedlings at low temperature and in adult-plant stage with selected Pst races in the greenhouse. The F7 population was genotyped using the 90K wheat SNP chip. Three QTL, QYrPI181410.wgp-4AS, QYrPI181410.wgp-4BL, and QYrPI181410.wgp-5BL.1, from PI 181410 for all-stage resistance, were mapped on chromosome arms 4AS, 4BL, and 5BL, respectively. Four QTL, QYrPI181410.wgp-1BL, QYrPI181410.wgp-4BL, QYrPI181410.wgp-5AS, and QYrPI181410.wgp-5BL.2, were identified from PI 181410 for HTAP resistance and mapped to 1BL, 4BL, 5AS, and 5BL, respectively. Two QTL with minor effects on stripe rust response were identified from AvS and mapped to 2BS and 2BL. Four of the QTL from PI 181410 and one from AvS were potentially new. As the 4BL QTL was most effective and likely a new gene for stripe rust resistance, three kompetitive allele specific PCR (KASP) markers were developed for incorporating this gene into new wheat cultivars.
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Affiliation(s)
- Yan Liu
- Department of Plant Pathology, Washington State University, Pullman, WA 99164-6430, USA; (Y.L.); (Y.Q.); (X.L.); (M.W.)
| | - Yanmin Qie
- Department of Plant Pathology, Washington State University, Pullman, WA 99164-6430, USA; (Y.L.); (Y.Q.); (X.L.); (M.W.)
- Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences, 162 Hengshan Street, Gaoxin District, Shijiazhuang, Hebei 050035, China
| | - Xing Li
- Department of Plant Pathology, Washington State University, Pullman, WA 99164-6430, USA; (Y.L.); (Y.Q.); (X.L.); (M.W.)
- College of Plant Protection, Hebei Agricultural University, Baoding, Hebei 071001, China
| | - Meinan Wang
- Department of Plant Pathology, Washington State University, Pullman, WA 99164-6430, USA; (Y.L.); (Y.Q.); (X.L.); (M.W.)
| | - Xianming Chen
- Department of Plant Pathology, Washington State University, Pullman, WA 99164-6430, USA; (Y.L.); (Y.Q.); (X.L.); (M.W.)
- US Department of Agriculture, Agricultural Research Service, Wheat Health, Genetics, and Quality Research Unit, Pullman, WA 99164-6430, USA
- Correspondence: ; Tel.: +1-509-335-8086
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Mu J, Liu L, Liu Y, Wang M, See DR, Han D, Chen X. Genome-Wide Association Study and Gene Specific Markers Identified 51 Genes or QTL for Resistance to Stripe Rust in U.S. Winter Wheat Cultivars and Breeding Lines. FRONTIERS IN PLANT SCIENCE 2020; 11:998. [PMID: 32719705 PMCID: PMC7350909 DOI: 10.3389/fpls.2020.00998] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2020] [Accepted: 06/17/2020] [Indexed: 05/06/2023]
Abstract
Stripe (yellow) rust, caused by fungal pathogen Puccinia striiformis f. sp. tritici (Pst), is a serious disease of wheat in the United States and many other countries. Growing resistant cultivars has been approved to be the best approach for control of stripe rust. To determine stripe rust resistance genes in U.S. winter wheat cultivars and breeding lines, we analyzed a winter wheat panel of 857 cultivars and breeding lines in a genome-wide association study (GWAS) using genotyping by multiplexed sequencing (GMS) and by genotyping with molecular markers of 18 important stripe rust resistance genes or quantitative trait loci (QTL). The accessions were phenotyped for stripe rust response at adult-plant stage under natural infection in Pullman and Mount Vernon, Washington in 2018 and 2019, and in the seedling stage with six predominant or most virulent races of Pst. A total of 51 loci were identified to be related to stripe rust resistance, and at least 10 of them (QYrww.wgp.1D-3, QYrww.wgp.2B-2, QYrww.wgp.2B-3, QYrww.wgp.2B-4, QYrww.wgp.3A, QYrww.wgp.5A, QYrww.wgp.5B, QYrww.wgp.5D, QYrww.wgp.6A-2 and QYrww.wgp.7B-3) were previously reported. These genes or QTL were found to be present at different frequencies in breeding lines and cultivars developed by breeding programs in various winter wheat growing regions. Both Yr5 and Yr15, which are highly resistant to all races identified thus far in the U.S., as well as Yr46 providing resistance to many races, were found absent in the breeding lines and commercially grown cultivars. The identified genes or QTL and their markers are useful in breeding programs to improve the level and durability of resistance to stripe rust.
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Affiliation(s)
- Jingmei Mu
- Department of Plant Pathology, Washington State University, Pullman, WA, United States
- College of Life Science and Food Engineering, Hebei University of Engineering, Handan, China
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Agronomy, Northwest A&F University, Yangling, China
| | - Lu Liu
- Department of Plant Pathology, Washington State University, Pullman, WA, United States
| | - Yan Liu
- Department of Plant Pathology, Washington State University, Pullman, WA, United States
| | - Meinan Wang
- Department of Plant Pathology, Washington State University, Pullman, WA, United States
| | - Deven R. See
- Department of Plant Pathology, Washington State University, Pullman, WA, United States
- Wheat Health, Genetics and Quality Research Unit, Agricultural Research Service, U.S. Department of Agriculture, Pullman, WA, United States
| | - Dejun Han
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Agronomy, Northwest A&F University, Yangling, China
| | - Xianming Chen
- Department of Plant Pathology, Washington State University, Pullman, WA, United States
- Wheat Health, Genetics and Quality Research Unit, Agricultural Research Service, U.S. Department of Agriculture, Pullman, WA, United States
- *Correspondence: Xianming Chen,
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Liu L, Yuan C, Wang M, See DR, Chen X. Mapping Quantitative Trait Loci for High-Temperature Adult-Plant Resistance to Stripe Rust in Spring Wheat PI 197734 Using a Doubled Haploid Population and Genotyping by Multiplexed Sequencing. FRONTIERS IN PLANT SCIENCE 2020; 11:596962. [PMID: 33281855 PMCID: PMC7688900 DOI: 10.3389/fpls.2020.596962] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 10/15/2020] [Indexed: 05/13/2023]
Abstract
Stripe rust caused by Puccinia striiformis f. sp. tritici (Pst) is a global concern for wheat production. Spring wheat cultivar PI 197734, of Sweden origin, has shown high-temperature adult-plant resistance (APR) to stripe rust for many years. To map resistance quantitative trait loci (QTL), 178 doubled haploid lines were developed from a cross of PI 197734 with susceptible AvS. The DH lines and parents were tested in fields in 2017 and 2018 under natural infection of Pst and genotyped with genotyping by multiplexed sequencing (GMS). Kompetitive allele specific PCR (KASP) and simple sequence repeat (SSR) markers from specific chromosomal regions were also used to genotype the population to validate and saturate resistance QTL regions. Two major QTL on chromosomes 1AL and 3BL and one minor QTL on 2AL were identified. The two major QTL, QYrPI197734.wgp-1A and QYrPI197734.wgp-3B, were detected in all tested environments explaining up to 20.7 and 46.8% phenotypic variation, respectively. An awnletted gene mapped to the expected distal end of chromosome 5AL indicated the accuracy of linkage mapping. The KASP markers converted from the GMS-SNPs in the 1A and 3B QTL regions were used to genotype 95 US spring wheat cultivars and breeding lines, and they individually showed different percentages of polymorphisms. The haplotypes of the three markers for the 1A QTL and four markers for the 3B QTL identified 37.9 and 21.1% of the wheat cultivar/breeding lines possibly carrying these two QTL, indicating their usefulness in marker-assisted selection (MAS) for incorporating the two major QTL into new wheat cultivars.
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Affiliation(s)
- Lu Liu
- Department of Plant Pathology, Washington State University, Pullman, WA, United States
- Agriculture and Agri-Food Canada, Summerland Research and Development Centre, Summerland, BC, Canada
| | - Congying Yuan
- Department of Plant Pathology, Washington State University, Pullman, WA, United States
- College of Life Sciences, Luoyang Normal University, Luoyang, China
| | - Meinan Wang
- Department of Plant Pathology, Washington State University, Pullman, WA, United States
| | - Deven R. See
- Department of Plant Pathology, Washington State University, Pullman, WA, United States
- Wheat Health, Genetics, and Quality Research Unit, Agricultural Research Service, U.S. Department of Agriculture, Pullman, WA, United States
| | - Xianming Chen
- Department of Plant Pathology, Washington State University, Pullman, WA, United States
- Wheat Health, Genetics, and Quality Research Unit, Agricultural Research Service, U.S. Department of Agriculture, Pullman, WA, United States
- *Correspondence: Xianming Chen, ;
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Mu J, Wu J, Liu S, Dai M, Sun D, Huang S, Wang Q, Zeng Q, Yu S, Chen L, Kang Z, Han D. Genome-Wide Linkage Mapping Reveals Stripe Rust Resistance in Common Wheat ( Triticum aestivum) Xinong1376. PLANT DISEASE 2019; 103:2742-2750. [PMID: 31509495 DOI: 10.1094/pdis-12-18-2264-re] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Stripe rust, also known as yellow rust, is a significant threat to wheat yield worldwide. Adult plant resistance (APR) is the preferred way to obtain durable protection. Chinese winter wheat cultivar Xinong1376 has maintained acceptable APR to stripe rust in field environments. To characterize APR in this cultivar, 190 F10 recombinant inbred lines (RILs) developed from Xiaoyan81 × Xinong1376 were evaluated for infection type and disease severity in fields either artificially or naturally inoculated. The population along with parents were genotyped using the Illumina 90K single-nucleotide polymorphism arrays. Six quantitative trait loci (QTL) were detected using the inclusive composite interval mapping method. QYr.nwafu-4AL and QYr.nwafu-6BL.3 conferred stable resistance in all environments, and likely corresponded to a gene-rich region on the long arm of chromosomes 4A and 6B. QYr.nwafu-5AL, QYr.nwafu-5BL, QYr.nwafu-3BL.1, and QYr.nwafu-3BL.2 were detected only in some environments but enhanced the level of resistance conferred by QYr.nwafu-4AL and QYr.nwafu-6BL.3. Kompetitive allele-specific PCR (KASP) markers developed for QYr.nwafu-4AL and QYr.nwafu-6BL.3 were confirmed in a subset of RILs and 133 wheat genotypes. The QTL on 4AL and 6BL with their linked KASP markers would be useful for marker-assisted selection to improve stripe rust resistance in breeding programs.
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Affiliation(s)
- Jingmei Mu
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Jianhui Wu
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Shengjie Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Miaofei Dai
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Daojie Sun
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Shuo Huang
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Qilin Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Qingdong Zeng
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Shizhou Yu
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Li Chen
- Extension Center for Agriculture Technology, Agriculture Department of Tibetan Autonomous Region, China
| | - Zhensheng Kang
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Dejun Han
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, 712100, Shaanxi, China
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Liu L, Wang M, Feng J, See DR, Chen X. Whole-Genome Mapping of Stripe Rust Resistance Quantitative Trait Loci and Race Specificity Related to Resistance Reduction in Winter Wheat Cultivar Eltan. PHYTOPATHOLOGY 2019; 109:1226-1235. [PMID: 30730788 DOI: 10.1094/phyto-10-18-0385-r] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Winter wheat cultivar Eltan has been one of the most widely grown cultivars in the U.S. Pacific Northwest. It has shown variable levels of resistance to stripe rust in different years since it was released in 1990. To map all currently effective and defeated resistance genes in Eltan and understand the factors causing the resistance changes, 112 F2:5 recombinant inbred lines (RILs) were developed from a cross of Eltan with cultivar Avocet S. The RILs were evaluated in fields of Pullman, Washington in 2015, 2016, 2017, and 2018 and Mount Vernon, Washington in 2016 and 2017 under natural infections; they were also evaluated in the greenhouse with races PSTv-4 and PSTv-40 of Puccinia striiformis f. sp. tritici. The RILs were genotyped with the 90K Illumina iSelect wheat single-nucleotide polymorphism chip. A total of five quantitative trait loci (QTLs) were identified in Eltan. Two major QTLs on chromosome arms 2BS and 4AL were detected in the greenhouse tests, explaining up to 28.0 and 42.0% of phenotypic variation, respectively. The two race-specific QTLs were also detected in some field experiments but with reduced effects. A minor QTL on 5BS was detected in the greenhouse and field tests, explaining 10.0 to 14.8% of the phenotypic variation. The other two minor QTLs were mapped on 6AS and 7BL and detected only in field experiments, explaining up to 20.5 and 13.5% of phenotypic variation, respectively. All stripe rust samples collected in the experimental fields in 2015 and 2016 were identified as P. striiformis f. sp. tritici races virulent on seedlings of Eltan. The resistance reduction of Eltan was caused by changes of the P. striiformis f. sp. tritici population from avirulent to virulent, overcoming the race-specific all-stage resistance in Eltan.
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Affiliation(s)
- Lu Liu
- 1 Department of Plant Pathology, Washington State University, Pullman 99164-6430, WA, U.S.A
| | - Meinan Wang
- 1 Department of Plant Pathology, Washington State University, Pullman 99164-6430, WA, U.S.A
| | - Junyan Feng
- 1 Department of Plant Pathology, Washington State University, Pullman 99164-6430, WA, U.S.A
- 2 Institute of Biotechnology and Nuclear Technology Research, Sichuan Academy of Agricultural Sciences, Chengdu 610061, China; and
| | - Deven R See
- 1 Department of Plant Pathology, Washington State University, Pullman 99164-6430, WA, U.S.A
- 3 Wheat Health, Genetics and Quality Research Unit, U.S. Department of Agriculture Agricultural Research Service, Pullman 99164-6430, WA, U.S.A
| | - Xianming Chen
- 1 Department of Plant Pathology, Washington State University, Pullman 99164-6430, WA, U.S.A
- 3 Wheat Health, Genetics and Quality Research Unit, U.S. Department of Agriculture Agricultural Research Service, Pullman 99164-6430, WA, U.S.A
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25
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Liu L, Yuan CY, Wang MN, See DR, Zemetra RS, Chen XM. QTL analysis of durable stripe rust resistance in the North American winter wheat cultivar Skiles. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:1677-1691. [PMID: 30796480 DOI: 10.1007/s00122-019-03307-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2018] [Accepted: 02/05/2019] [Indexed: 05/19/2023]
Abstract
This study determined the effects of growth stage and temperature on expression of high-temperature adult-plant resistance to stripe rust, mapped six QTL for durable resistance in winter wheat Skiles using a doubled haploid population, and selected breeding lines with different combinations of the QTL using marker-assisted selection. The winter wheat cultivar Skiles has a high level of high-temperature adult-plant (HTAP) resistance to stripe rust caused by Puccinia striiformis f. sp. tritici (Pst). The Skiles HTAP resistance was highly effective at the adult-plant stage even under low temperatures, but high temperatures induced earlier expression and increased levels of resistance. To map resistance genes, Skiles was crossed with the susceptible cultivar Avocet S and a doubled haploid (DH) population was developed. The DH population was tested in fields at Pullman, WA, in 2016, 2017 and 2018, Mount Vernon, WA, in 2017 and 2018 under natural infection, and an environmentally controlled greenhouse at the adult-plant stage with the currently predominant race PSTv-37. The population was genotyped using the 90 K Illumina iSelect wheat SNP chip and selected SSR markers on specific chromosomes. In total, 2526 polymorphic markers were used for QTL mapping and six QTL were detected. Two of the six QTL had major effects across all environments, with one mapped on chromosome 3BS, explaining up to 28.2% of the phenotypic variation and the other on chromosome 4BL, explaining up to 41.8%. Minor QTL were mapped on chromosomes 1BL, 5AL, 6B and 7DL. Genotyping 140 wheat cultivars from the US Pacific Northwest revealed high polymorphism of markers for five of the QTL, and five highly resistant lines with the five QTL were selected from Skiles-derived breeding lines using the markers. This study demonstrated that multiple QTL with mostly additive effects contributed to the high-level HTAP resistance in Skiles.
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Affiliation(s)
- L Liu
- Department of Plant Pathology, Washington State University, Pullman, WA, 99164-6430, USA
| | - C Y Yuan
- Department of Plant Pathology, Washington State University, Pullman, WA, 99164-6430, USA
- College of Life Sciences, Luoyang Normal University, Luoyang, 471934, Henan, People's Republic of China
| | - M N Wang
- Department of Plant Pathology, Washington State University, Pullman, WA, 99164-6430, USA
| | - D R See
- Department of Plant Pathology, Washington State University, Pullman, WA, 99164-6430, USA
- USDA-ARS, Wheat Health, Genetics and Quality Research Unit, Pullman, WA, 99164-6430, USA
| | - R S Zemetra
- Department of Crop and Soil Sciences, Oregon State University, Corvallis, OR, 97331-3002, USA
| | - X M Chen
- Department of Plant Pathology, Washington State University, Pullman, WA, 99164-6430, USA.
- USDA-ARS, Wheat Health, Genetics and Quality Research Unit, Pullman, WA, 99164-6430, USA.
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Zeng Q, Wu J, Liu S, Huang S, Wang Q, Mu J, Yu S, Han D, Kang Z. A major QTL co-localized on chromosome 6BL and its epistatic interaction for enhanced wheat stripe rust resistance. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:1409-1424. [PMID: 30707240 DOI: 10.1007/s00122-019-03288-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2018] [Accepted: 01/16/2019] [Indexed: 05/27/2023]
Abstract
Co-localization of a major QTL for wheat stripe rust resistance to a 3.9-cM interval on chromosome 6BL across both populations and another QTL on chromosome 2B with epistatic interaction. Cultivars with diverse resistance are the optimal strategy to minimize yield losses caused by wheat stripe rust (Puccinia striiformis f. sp. tritici). Two wheat populations involving resistant wheat lines P10078 and Snb"S" from CIMMYT were evaluated for stripe rust response in multiple environments. Pool analysis by Wheat660K SNP array showed that the overlapping interval on chromosome 6B likely harbored a major QTL between two populations. Then, linkage maps were constructed using KASP markers, and a co-localized locus with large effect on chromosome 6BL was detected using QTL analysis in both populations. The coincident QTL, named QYr.nwafu-6BL.2, explained 59.7% of the phenotypic maximum variation in the Mingxian 169 × P10078 and 52.5% in the Zhengmai 9023 × Snb"S" populations, respectively. This co-localization interval spanning 3.9 cM corresponds to ~ 30.5-Mb genomic region of the newest common wheat reference genome (IWGSC RefSeq v.1.0). In addition, another QTL was also detected on chromosome 2B in Zhengmai 9023 × Snb"S" population and it can accelerate expression of QYr.nwafu-6BL.2 to enhance resistance with epistatic interaction. Allowing for Pst response, marker genotypes, pedigree analysis and relative genetic distance, QYr.nwafu-6BL.2 is likely to be a distinct adult plant resistance QTL. Haplotype analysis of QYr.nwafu-6BL.2 revealed specific SNPs or alleles in the target region from a diversity panel of 176 unrelated wheat accessions. This QTL region provides opportunity for further map-based cloning, and haplotypes analysis enables pyramiding favorable alleles into commercial cultivars by marker-assisted selection.
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Affiliation(s)
- Qingdong Zeng
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China
| | - Jianhui Wu
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China
| | - Shengjie Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China
- College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China
| | - Shuo Huang
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China
- College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China
| | - Qilin Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China
| | - Jingmei Mu
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China
- College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China
| | - Shizhou Yu
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China
- College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China
| | - Dejun Han
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China.
- College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China.
| | - Zhensheng Kang
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China.
- College of Plant Protection, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China.
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Yao F, Zhang X, Ye X, Li J, Long L, Yu C, Li J, Wang Y, Wu Y, Wang J, Jiang Q, Li W, Ma J, Wei Y, Zheng Y, Chen G. Characterization of molecular diversity and genome-wide association study of stripe rust resistance at the adult plant stage in Northern Chinese wheat landraces. BMC Genet 2019; 20:38. [PMID: 30914040 PMCID: PMC6434810 DOI: 10.1186/s12863-019-0736-x] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Accepted: 03/03/2019] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND Stripe rust is a serious fungal disease of wheat (Triticum aestivum L.) caused by Puccinia striiformis f. sp. tritici (Pst), which results in yield reduction and decreased grain quality. Breeding for genetic resistance to stripe rust is the most cost-effective method to control the disease. In the present study, a genome-wide association study (GWAS) was conducted to identify markers linked to stripe rust resistance genes (or loci) in 93 Northern Chinese wheat landraces, using Diversity Arrays Technology (DArT) and simple sequence repeat (SSR) molecular marker technology based on phenotypic data from two field locations over two growing seasons in China. RESULTS Seventeen accessions were verified to display stable and high levels of adult plant resistance (APR) to stripe rust via multi-environment field assessments. Significant correlations among environments and high heritability were observed for stripe rust infection type (IT) and disease severity (DS). Using mixed linear models (MLM) for the GWAS, a total of 32 significantly associated loci (P < 0.001) were detected. In combination with the linkage disequilibrium (LD) decay distance (6.4 cM), 25 quantitative trait loci (QTL) were identified. Based on the integrated map of previously reported genes and QTL, six QTL located on chromosomes 4A, 6A and 7D were mapped far from resistance regions identified previously, and represent potentially novel stripe rust resistance loci at the adult plant stage. CONCLUSIONS The present findings demonstrated that identification of genes or loci linked to significant markers in wheat by GWAS is feasible. Seventeen elite accessions conferred with stable and high resistance to stripe rust, and six putative newly detected APR loci were identified among the 93 Northern Chinese wheat landraces. The results illustrate the potential for acceleration of molecular breeding of wheat, and also provide novel sources of stripe rust resistance with potential utility in the breeding of improved wheat cultivars.
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Affiliation(s)
- Fangjie Yao
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130 People’s Republic of China
| | - Xuemei Zhang
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130 People’s Republic of China
| | - Xueling Ye
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130 People’s Republic of China
| | - Jian Li
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130 People’s Republic of China
| | - Li Long
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130 People’s Republic of China
| | - Can Yu
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130 People’s Republic of China
| | - Jing Li
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130 People’s Republic of China
| | - Yuqi Wang
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130 People’s Republic of China
| | - Yu Wu
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130 People’s Republic of China
| | - Jirui Wang
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130 People’s Republic of China
- State Key Laboratory of Crop Genetics of Disease Resistance and Disease Control, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130 People’s Republic of China
| | - Qiantao Jiang
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130 People’s Republic of China
| | - Wei Li
- College of Agronomy, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130 People’s Republic of China
| | - Jian Ma
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130 People’s Republic of China
| | - Yuming Wei
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130 People’s Republic of China
- State Key Laboratory of Crop Genetics of Disease Resistance and Disease Control, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130 People’s Republic of China
| | - Youliang Zheng
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130 People’s Republic of China
- State Key Laboratory of Crop Genetics of Disease Resistance and Disease Control, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130 People’s Republic of China
| | - Guoyue Chen
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130 People’s Republic of China
- State Key Laboratory of Crop Genetics of Disease Resistance and Disease Control, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130 People’s Republic of China
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Xu J, Dai X, Ramasamy RK, Wang L, Zhu T, McGuire PE, Jorgensen CM, Dehghani H, Gulick PJ, Luo MC, Müller HG, Dvorak J. Aegilops tauschii Genome Sequence: A Framework for Meta-analysis of Wheat QTLs. G3 (BETHESDA, MD.) 2019; 9:841-853. [PMID: 30670607 PMCID: PMC6404623 DOI: 10.1534/g3.118.200921] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 01/12/2019] [Indexed: 12/22/2022]
Abstract
Numerous quantitative trait loci (QTL) have been mapped in tetraploid and hexaploid wheat and wheat relatives, mostly with simple sequence repeat (SSR) or single nucleotide polymorphism (SNP) markers. To conduct meta-analysis of QTL requires projecting them onto a common genomic framework, either a consensus genetic map or genomic sequence. The latter strategy is pursued here. Of 774 QTL mapped in wheat and wheat relatives found in the literature, 585 (75.6%) were successfully projected onto the Aegilops tauschii pseudomolecules. QTL mapped with SNP markers were more successfully projected (92.2%) than those mapped with SSR markers (66.2%). The QTL were not distributed homogeneously along chromosome arms. Their frequencies increased in the proximal-to-distal direction but declined in the most distal regions and were weakly correlated with recombination rates along the chromosome arms. Databases for projected SSR markers and QTL were constructed and incorporated into the Ae. tauschii JBrowse. To facilitate meta-QTL analysis, eight clusters of QTL were used to estimate standard deviations ([Formula: see text]) of independently mapped QTL projected onto the Ae. tauschii genome sequence. The standard deviations [Formula: see text] were modeled as an exponential decay function of recombination rates along the Ae. tauschii chromosomes. We implemented four hypothesis tests for determining the membership of query QTL. The hypothesis tests and estimation procedure for [Formula: see text] were implemented in a web portal for meta-analysis of projected QTL. Twenty-one QTL for Fusarium head blight resistance mapped on wheat chromosomes 3A, 3B, and 3D were analyzed to illustrate the use of the portal for meta-QTL analyses.
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Affiliation(s)
- Jiale Xu
- Department of Plant Sciences, University of California, Davis, California
| | - Xiongtao Dai
- Department of Statistics, Iowa State University, Iowa
| | - Ramesh K Ramasamy
- Department of Plant Sciences, University of California, Davis, California
| | - Le Wang
- Department of Plant Sciences, University of California, Davis, California
| | - Tingting Zhu
- Department of Plant Sciences, University of California, Davis, California
| | - Patrick E McGuire
- Department of Plant Sciences, University of California, Davis, California
| | - Chad M Jorgensen
- Department of Plant Sciences, University of California, Davis, California
| | - Hamid Dehghani
- Department of Plant Sciences, University of California, Davis, California
- Department of Plant Breeding, Faculty of Agriculture, Tarbiat Modares University, Tehran, Iran, and
| | - Patrick J Gulick
- Department of Biology, Concordia University, Montreal, Quebec, Canada
| | - Ming-Cheng Luo
- Department of Plant Sciences, University of California, Davis, California
| | - Hans-Georg Müller
- Department of Statistics, University of California, Davis, California
| | - Jan Dvorak
- Department of Plant Sciences, University of California, Davis, California,
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29
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Zeng Q, Wu J, Liu S, Chen X, Yuan F, Su P, Wang Q, Huang S, Mu J, Han D, Kang Z, Chen XM. Genome-wide Mapping for Stripe Rust Resistance Loci in Common Wheat Cultivar Qinnong 142. PLANT DISEASE 2019; 103:439-447. [PMID: 30648483 DOI: 10.1094/pdis-05-18-0846-re] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [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 threatens worldwide wheat production. Growing resistant cultivars is the best way to control this disease. Chinese wheat cultivar Qinnong 142 (QN142) has a high level of adult-plant resistance to stripe rust. To identify quantitative trait loci (QTLs) related to stripe rust resistance, we developed a recombinant inbred line (RIL) population from a cross between QN142 and susceptible cultivar Avocet S. The parents and 165 F6 RILs were evaluated in terms of their stripe rust infection type and disease severity in replicated field tests with six site-year environments. The parents and RILs were genotyped with single-nucleotide polymorphism (SNP) markers. Four stable QTLs were identified in QN142 and mapped to chromosome arms 1BL, 2AL, 2BL, and 6BS. The 1BL QTL was probably the known resistance gene Yr29, the 2BL QTL was in a resistance gene-rich region, and the 2AL and 6BS QTLs might be new. Kompetitive allele specific polymerase chain reaction markers developed from the SNP markers flanking these QTLs were highly polymorphic in a panel of 150 wheat cultivars and breeding lines. These markers could be used in marker-assisted selection for incorporating the stripe rust resistance QTL into new wheat cultivars.
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Affiliation(s)
- Qingdong Zeng
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Shaanxi 712100, P.R. China
| | - Jianhui Wu
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Shaanxi 712100, P.R. China
| | - Shengjie Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Shaanxi 712100, P.R. China
| | - Xianming Chen
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Shaanxi 712100, P.R. China
| | - Fengping Yuan
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Shaanxi 712100, P.R. China
| | - Pingping Su
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Shaanxi 712100, P.R. China
| | - Qilin Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Shaanxi 712100, P.R. China
| | - Shuo Huang
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Shaanxi 712100, P.R. China
| | - Jingmei Mu
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Shaanxi 712100, P.R. China
| | - Dejun Han
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Shaanxi 712100, P.R. China
| | - Zhensheng Kang
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Shaanxi 712100, P.R. China
| | - X M Chen
- Wheat Health, Genetics, and Quality Research Unit, Agricultural Research Service, U.S. Department of Agriculture, Pullman, WA 99164; and Department of Plant Pathology, Washington State University, Pullman, WA 99164, U.S.A
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30
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Long L, Yao F, Yu C, Ye X, Cheng Y, Wang Y, Wu Y, Li J, Wang J, Jiang Q, Li W, Ma J, Liu Y, Deng M, Wei Y, Zheng Y, Chen G. Genome-Wide Association Study for Adult-Plant Resistance to Stripe Rust in Chinese Wheat Landraces ( Triticum aestivum L.) From the Yellow and Huai River Valleys. FRONTIERS IN PLANT SCIENCE 2019; 10:596. [PMID: 31156668 PMCID: PMC6532019 DOI: 10.3389/fpls.2019.00596] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Accepted: 04/24/2019] [Indexed: 05/21/2023]
Abstract
Stripe rust (also known as yellow rust), caused by the pathogen Puccinia striiformis f. sp. tritici (Pst), is a common and serious fungal disease of wheat (Triticum aestivum L.) worldwide. To identify effective stripe rust resistance loci, a genome-wide association study was performed using 152 wheat landraces from the Yellow and Huai River Valleys in China based on Diversity Arrays Technology and simple sequence repeat markers. Phenotypic evaluation of the degree of resistance to stripe rust at the adult-plant stage under field conditions was carried out in five environments. In total, 19 accessions displayed stable, high degrees of resistance to stripe rust development when exposed to mixed races of Pst at the adult-plant stage in multi-environment field assessments. A marker-trait association analysis indicated that 51 loci were significantly associated with adult-plant resistance to stripe rust. These loci included 40 quantitative trait loci (QTL) regions for adult-plant resistance. Twenty identified resistance QTL were linked closely to previously reported yellow rust resistance genes or QTL regions, which were distributed across chromosomes 1B, 1D, 2A, 2B, 3A, 3B, 4A, 4B, 5B, 6B, 7A, 7B, and 7D. Six multi-trait QTL were detected on chromosomes 1B, 1D, 2B, 3A, 3B, and 7D. Twenty QTL were mapped to chromosomes 1D, 2A, 2D, 4B, 5B, 6A, 6B, 6D, 7A, 7B, and 7D, distant from previously identified yellow rust resistance genes. Consequently, these QTL are potentially novel loci for stripe rust resistance. Among the 20 potentially novel QTL, five (QDS.sicau-2A, QIT.sicau-4B, QDS.sicau-4B.2, QDS.sicau-6A.3, and QYr.sicau-7D) were associated with field responses at the adult-plant stage in at least two environments, and may have large effects on stripe rust resistance. The novel effective QTL for adult-plant resistance to stripe rust will improve understanding of the genetic mechanisms that control the spread of stripe rust, and will aid in the molecular marker-assisted selection-based breeding of wheat for stripe rust resistance.
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Affiliation(s)
- Li Long
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
- State Key Laboratory of Crop Genetics of Disease Resistance and Disease Control, Sichuan Agricultural University, Chengdu, China
| | - Fangjie Yao
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
- State Key Laboratory of Crop Genetics of Disease Resistance and Disease Control, Sichuan Agricultural University, Chengdu, China
| | - Can Yu
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
- State Key Laboratory of Crop Genetics of Disease Resistance and Disease Control, Sichuan Agricultural University, Chengdu, China
| | - Xueling Ye
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
- State Key Laboratory of Crop Genetics of Disease Resistance and Disease Control, Sichuan Agricultural University, Chengdu, China
| | - Yukun Cheng
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
- State Key Laboratory of Crop Genetics of Disease Resistance and Disease Control, Sichuan Agricultural University, Chengdu, China
| | - Yuqi Wang
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
- State Key Laboratory of Crop Genetics of Disease Resistance and Disease Control, Sichuan Agricultural University, Chengdu, China
| | - Yu Wu
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
- State Key Laboratory of Crop Genetics of Disease Resistance and Disease Control, Sichuan Agricultural University, Chengdu, China
| | - Jing Li
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
- State Key Laboratory of Crop Genetics of Disease Resistance and Disease Control, Sichuan Agricultural University, Chengdu, China
| | - Jirui Wang
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Qiantao Jiang
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Wei Li
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
| | - Jian Ma
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
- State Key Laboratory of Crop Genetics of Disease Resistance and Disease Control, Sichuan Agricultural University, Chengdu, China
| | - YaXi Liu
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
- State Key Laboratory of Crop Genetics of Disease Resistance and Disease Control, Sichuan Agricultural University, Chengdu, China
| | - Mei Deng
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Yuming Wei
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
- State Key Laboratory of Crop Genetics of Disease Resistance and Disease Control, Sichuan Agricultural University, Chengdu, China
| | - Youliang Zheng
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Guoyue Chen
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
- State Key Laboratory of Crop Genetics of Disease Resistance and Disease Control, Sichuan Agricultural University, Chengdu, China
- *Correspondence: Guoyue Chen,
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Qie Y, Liu Y, Wang M, Li X, See DR, An D, Chen X. Development, Validation, and Re-selection of Wheat Lines with Pyramided Genes Yr64 and Yr15 Linked on the Short Arm of Chromosome 1B for Resistance to Stripe Rust. PLANT DISEASE 2019; 103:51-58. [PMID: 30387683 DOI: 10.1094/pdis-03-18-0470-re] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [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 (Pst), is one of the most destructive diseases of wheat worldwide. The disease is most preferably managed by developing and growing cultivars with high-level, durable resistance. To achieve high-level and long-lasting resistance, we developed a wheat line, RIL-Yr64/Yr15, by pyramiding Yr64 and Yr15, both on the chromosome 1BS and providing high resistance to all tested Pst races. To validate RIL-Yr64/Yr15 possessing both genes, we crossed it to Avocet S (AvS). The F4 RILs from this cross were phenotyped with Pst races under controlled greenhouse conditions and also under natural Pst infection in the field. The population was genotyped with SSR markers previously reported to be linked to the resistance gene loci and with additional SSR and SNP-KASP markers along chromosome 1B. Both phenotype and genotype data confirmed the copresence of Yr64 and Yr15 in RIL-Yr64/Yr15, and the high-resolution linkage map dissected the chromosomal regions and traced their origins. New lines possessing these genes were selected from the F5 population of cross AvS × RIL-Yr64/Yr15 by marker-assisted selection. These lines with the two highly effective genes should be more useful than individual gene lines for developing high-level, durable resistant wheat cultivars.
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Affiliation(s)
- Yanmin Qie
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, Hebei 050021; University of Chinese Academy of Sciences, Beijing, 100049, China; and Department of Plant Pathology, Washington State University, Pullman, WA 99164-6430
| | - Yan Liu
- Department of Plant Pathology, Washington State University, Pullman, WA 99164-6430
| | - Meinan Wang
- Department of Plant Pathology, Washington State University, Pullman, WA 99164-6430
| | - Xing Li
- College of Plant Protection, Hebei Agricultural University, Baoding, Hebei 071001, China and Department of Plant Pathology, Washington State University, Pullman, WA
| | - Deven R See
- USDA-ARS, Wheat Health, Genetics, and Quality Research Unit, Pullman, WA 99164-6430
| | - Diaoguo An
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, Hebei 050021, China
| | - Xianming Chen
- USDA-ARS, Wheat Health, Genetics, and Quality Research Unit, Pullman, WA 99164-6430
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32
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Liu L, Wang MN, Feng JY, See DR, Chao SM, Chen XM. Combination of all-stage and high-temperature adult-plant resistance QTL confers high-level, durable resistance to stripe rust in winter wheat cultivar Madsen. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2018; 131:1835-1849. [PMID: 29797034 DOI: 10.1007/s00122-018-3116-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 05/14/2018] [Indexed: 05/10/2023]
Abstract
Wheat cultivar Madsen has a new gene on the short arm of chromosome 1A and two QTL for all-stage resistance and three QTL for high-temperature adult-plant resistance that in combination confer high-level, durable resistance to stripe rust. Wheat cultivar Madsen has maintained a high-level resistance to stripe rust over 30 years. To map quantitative trait loci (QTL) underlying the high-level, durable resistance, 156 recombinant inbred lines (RILs) developed from cross Avocet S × Madsen were phenotyped with selected races of Puccinia striiformis f. sp. tritici in the greenhouse seedling tests, and in naturally infected fields during 2015-2017. The RILs were genotyped by SSR and SNP markers from genotyping by sequencing and the 90 K wheat SNP chip. Three QTL for all-stage resistance were mapped on chromosomes 1AS, 1BS and 2AS, and two QTL for high-temperature adult-plant (HTAP) resistance were mapped on 3BS and 6BS. The most effective QTL on 2AS, explaining 8.97-23.10% of the phenotypic variation in seedling tests and 8.60-71.23% in field tests, contained Yr17 for all-stage resistance and an additional gene for HTAP resistance. The 6BS QTL, detected in all field tests, was identified as Yr78. The 1AS QTL, conferring all-stage resistance, was identified as a new gene, which explained 20.45 and 30.23% of variation in resistance to races PSTv-37 and PSTv-40, respectively, and contributed significantly to field resistance at Pullman in 2015-2017, but was not detected at Mount Vernon. The interactions among QTL were mostly additive, and RILs with all five QTL had the highest level of resistance in the field, similar to Madsen. Genotyping 148 US Pacific Northwest wheat cultivars with markers for the 1AS, 2AS and 6BS QTL validated the genes and markers, and indicated their usefulness for marker-assisted selection.
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Affiliation(s)
- L Liu
- Department of Plant Pathology, Washington State University, Pullman, WA, 99164-6430, USA
| | - M N Wang
- Department of Plant Pathology, Washington State University, Pullman, WA, 99164-6430, USA
| | - J Y Feng
- Department of Plant Pathology, Washington State University, Pullman, WA, 99164-6430, USA
- Institute of Biotechnology and Nuclear Technology Research, Sichuan Academy of Agricultural Sciences, Chengdu, 610061, Sichuan, China
| | - D R See
- Department of Plant Pathology, Washington State University, Pullman, WA, 99164-6430, USA
- Wheat Health, Genetics and Quality Research Unit, USDA-ARS, Pullman, WA, 99164-6430, USA
| | - S M Chao
- Cereal Crops Research, USDA-ARS, Fargo, ND, 58102-2775, USA
| | - X M Chen
- Department of Plant Pathology, Washington State University, Pullman, WA, 99164-6430, USA.
- Wheat Health, Genetics and Quality Research Unit, USDA-ARS, Pullman, WA, 99164-6430, USA.
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Wu J, Huang S, Zeng Q, Liu S, Wang Q, Mu J, Yu S, Han D, Kang Z. Comparative genome-wide mapping versus extreme pool-genotyping and development of diagnostic SNP markers linked to QTL for adult plant resistance to stripe rust in common wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2018; 131:1777-1792. [PMID: 29909527 DOI: 10.1007/s00122-018-3113-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Accepted: 05/07/2018] [Indexed: 06/08/2023]
Abstract
A major stripe rust resistance QTL on chromosome 4BL was localized to a 4.5-Mb interval using comparative QTL mapping methods and validated in 276 wheat genotypes by haplotype analysis. CYMMIT-derived wheat line P10103 was previously identified to have adult plant resistance (APR) to stripe rust in the greenhouse and field. The conventional approach for QTL mapping in common wheat is laborious. Here, we performed QTL detection of APR using a combination of genome-wide scanning and extreme pool-genotyping. SNP-based genetic maps were constructed using the Wheat55 K SNP array to genotype a recombinant inbred line (RIL) population derived from the cross Mingxian 169 × P10103. Five stable QTL were detected across multiple environments. A fter comparing SNP profiles from contrasting, extreme DNA pools of RILs six putative QTL were located to approximate chromosome positions. A major QTL on chromosome 4B was identified in F2:4 contrasting pools from cross Zhengmai 9023 × P10103. A consensus QTL (LOD = 26-40, PVE = 42-55%), named QYr.nwafu-4BL, was defined and localized to a 4.5-Mb interval flanked by SNP markers AX-110963704 and AX-110519862 in chromosome arm 4BL. Based on stripe rust response, marker genotypes, pedigree analysis and mapping data, QYr.nwafu-4BL is likely to be a new APR QTL. The applicability of the SNP-based markers flanking QYr.nwafu-4BL was validated on a diversity panel of 276 wheat lines. The additional minor QTL on chromosomes 4A, 5A, 5B and 6A enhanced the level of resistance conferred by QYr.nwafu-4BL. Marker-assisted pyramiding of QYr.nwafu-4BL and other favorable minor QTL in new wheat cultivars should improve the level of APR to stripe rust.
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Affiliation(s)
- Jianhui Wu
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China
| | - Shuo Huang
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China
- College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China
| | - Qingdong Zeng
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China
| | - Shengjie Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China
- College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China
| | - Qilin Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China
| | - Jingmei Mu
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China
- College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China
| | - Shizhou Yu
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China
- College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China
| | - Dejun Han
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China.
- College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China.
| | - Zhensheng Kang
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China.
- College of Plant Protection, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China.
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34
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Feng J, Wang M, See DR, Chao S, Zheng Y, Chen X. Characterization of Novel Gene Yr79 and Four Additional Quantitative Trait Loci for All-Stage and High-Temperature Adult-Plant Resistance to Stripe Rust in Spring Wheat PI 182103. PHYTOPATHOLOGY 2018; 108:737-747. [PMID: 29303685 DOI: 10.1094/phyto-11-17-0375-r] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Stripe rust, caused by Puccinia striiformis f. sp. tritici, is an important disease of wheat worldwide. Exploring new resistance genes is essential for breeding resistant wheat cultivars. PI 182103, a spring wheat landrace originally from Pakistan, has shown a high level of resistance to stripe rust in fields for many years, but genes for resistance to stripe rust in the variety have not been studied. To map the resistance gene(s) in PI 182103, 185 recombinant inbred lines (RILs) were developed from a cross with Avocet Susceptible (AvS). The RIL population was genotyped with simple sequence repeat (SSR) and single nucleotide polymorphism markers and tested with races PST-100 and PST-114 at the seedling stage under controlled greenhouse conditions and at the adult-plant stage in fields at Pullman and Mt. Vernon, Washington under natural infection by the stripe rust pathogen in 2011, 2012, and 2013. A total of five quantitative trait loci (QTL) were detected. QyrPI182103.wgp-2AS and QyrPI182103.wgp-3AL were detected at the seedling stage, QyrPI182103.wgp-4DL was detected only in Mt. Vernon field tests, and QyrPI182103.wgp-5BS was detected in both seedling and field tests. QyrPI182103.wgp-7BL was identified as a high-temperature adult-plant resistance gene and detected in all field tests. Interactions among the QTL were mostly additive, but some negative interactions were detected. The 7BL QTL was mapped in chromosomal bin 7BL 0.40 to 0.45 and identified as a new gene, permanently designated as Yr79. SSR markers Xbarc72 and Xwmc335 flanking the Yr79 locus were highly polymorphic in various wheat genotypes, indicating that the molecular markers are useful for incorporating the new gene for potentially durable stripe rust resistance into new wheat cultivars.
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Affiliation(s)
- Junyan Feng
- First author: Biotechnology and Nuclear Technology Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan 610061, China; first, second, third, and sixth authors: Department of Plant Pathology, Washington State University, Pullman 99164-6430; first and fifth authors: Triticeae Research Institute, Sichuan Agricultural University, Northeast Road No. 555, Wenjiang, Chengdu, Sichuan 611130, China; third and sixth authors: U.S. Department of Agriculture, Agricultural Research Service, Wheat Health, Genetics, and Quality Research Unit, Pullman, WA 99164-6430; and fourth author: U.S. Department of Agriculture, Agricultural Research Service, Cereal Crops Research, Fargo, ND 58102-2775
| | - Meinan Wang
- First author: Biotechnology and Nuclear Technology Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan 610061, China; first, second, third, and sixth authors: Department of Plant Pathology, Washington State University, Pullman 99164-6430; first and fifth authors: Triticeae Research Institute, Sichuan Agricultural University, Northeast Road No. 555, Wenjiang, Chengdu, Sichuan 611130, China; third and sixth authors: U.S. Department of Agriculture, Agricultural Research Service, Wheat Health, Genetics, and Quality Research Unit, Pullman, WA 99164-6430; and fourth author: U.S. Department of Agriculture, Agricultural Research Service, Cereal Crops Research, Fargo, ND 58102-2775
| | - Deven R See
- First author: Biotechnology and Nuclear Technology Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan 610061, China; first, second, third, and sixth authors: Department of Plant Pathology, Washington State University, Pullman 99164-6430; first and fifth authors: Triticeae Research Institute, Sichuan Agricultural University, Northeast Road No. 555, Wenjiang, Chengdu, Sichuan 611130, China; third and sixth authors: U.S. Department of Agriculture, Agricultural Research Service, Wheat Health, Genetics, and Quality Research Unit, Pullman, WA 99164-6430; and fourth author: U.S. Department of Agriculture, Agricultural Research Service, Cereal Crops Research, Fargo, ND 58102-2775
| | - Shiaoman Chao
- First author: Biotechnology and Nuclear Technology Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan 610061, China; first, second, third, and sixth authors: Department of Plant Pathology, Washington State University, Pullman 99164-6430; first and fifth authors: Triticeae Research Institute, Sichuan Agricultural University, Northeast Road No. 555, Wenjiang, Chengdu, Sichuan 611130, China; third and sixth authors: U.S. Department of Agriculture, Agricultural Research Service, Wheat Health, Genetics, and Quality Research Unit, Pullman, WA 99164-6430; and fourth author: U.S. Department of Agriculture, Agricultural Research Service, Cereal Crops Research, Fargo, ND 58102-2775
| | - Youliang Zheng
- First author: Biotechnology and Nuclear Technology Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan 610061, China; first, second, third, and sixth authors: Department of Plant Pathology, Washington State University, Pullman 99164-6430; first and fifth authors: Triticeae Research Institute, Sichuan Agricultural University, Northeast Road No. 555, Wenjiang, Chengdu, Sichuan 611130, China; third and sixth authors: U.S. Department of Agriculture, Agricultural Research Service, Wheat Health, Genetics, and Quality Research Unit, Pullman, WA 99164-6430; and fourth author: U.S. Department of Agriculture, Agricultural Research Service, Cereal Crops Research, Fargo, ND 58102-2775
| | - Xianming Chen
- First author: Biotechnology and Nuclear Technology Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan 610061, China; first, second, third, and sixth authors: Department of Plant Pathology, Washington State University, Pullman 99164-6430; first and fifth authors: Triticeae Research Institute, Sichuan Agricultural University, Northeast Road No. 555, Wenjiang, Chengdu, Sichuan 611130, China; third and sixth authors: U.S. Department of Agriculture, Agricultural Research Service, Wheat Health, Genetics, and Quality Research Unit, Pullman, WA 99164-6430; and fourth author: U.S. Department of Agriculture, Agricultural Research Service, Cereal Crops Research, Fargo, ND 58102-2775
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Wu J, Liu S, Wang Q, Zeng Q, Mu J, Huang S, Yu S, Han D, Kang Z. Rapid identification of an adult plant stripe rust resistance gene in hexaploid wheat by high-throughput SNP array genotyping of pooled extremes. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2018; 131:43-58. [PMID: 28965125 DOI: 10.1007/s00122-017-2984-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 09/14/2017] [Indexed: 05/07/2023]
Abstract
High-throughput SNP array analysis of pooled extreme phenotypes in a segregating population by KASP marker genotyping permitted rapid, cost-effective location of a stripe rust resistance QTL in wheat. German wheat cultivar "Friedrichswerther" has exhibited high levels of adult plant resistance (APR) to stripe rust in field environments for many years. F2:3 lines and F6 recombinant inbred line (RILs) populations derived from a cross between Friedrichswerther and susceptible landrace Mingxian 169 were evaluated in the field in 2013, 2016 and 2017. Illumina 90K iSelect SNP arrays were used to genotype bulked extreme pools and parents; 286 of 1135 polymorphic SNPs were identified on chromosome 6B. Kompetitive Allele-Specific PCR (KASP) markers were used to verify the chromosome region associated with the resistance locus. A linkage map was constructed with 18 KASP-SNP markers, and a major effect QTL was identified within a 1.4 cM interval flanked by KASP markers IWB71602 and IWB55937 in the region 6BL3-0-0.36. The QTL, named QYr.nwafu-6BL, was stable across environments, and explained average 54.4 and 47.8% of the total phenotypic variation in F2:3 lines and F6 RILs, respectively. On the basis of marker genotypes, pedigree analysis and relative genetic distance QYr.nwafu-6BL is likely to be a new APR QTL. Combined high-throughput SNP array genotyping of pooled extremes and validation by KASP assays lowers sequencing costs compared to genome-wide association studies with SNP arrays, and more importantly, permits rapid isolation of major effect QTL in hexaploid wheat as well as improving accuracy of mapping in the QTL region. QYr.nwafu-6BL with flanking KASP markers developed and verified in a subset of 236 diverse lines can be used in marker-assisted selection to improve stripe rust resistance in breeding programs.
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Affiliation(s)
- Jianhui Wu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China
| | - Shengjie Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China
| | - Qilin Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China
| | - Qingdong Zeng
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China
| | - Jingmei Mu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China
| | - Shuo Huang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China
| | - Shizhou Yu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China
| | - Dejun Han
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China.
| | - Zhensheng Kang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China.
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36
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Bokore FE, Cuthbert RD, Knox RE, Randhawa HS, Hiebert CW, DePauw RM, Singh AK, Singh A, Sharpe AG, N'Diaye A, Pozniak CJ, McCartney C, Ruan Y, Berraies S, Meyer B, Munro C, Hay A, Ammar K, Huerta-Espino J, Bhavani S. Quantitative trait loci for resistance to stripe rust of wheat revealed using global field nurseries and opportunities for stacking resistance genes. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2017; 130:2617-2635. [PMID: 28913655 DOI: 10.1007/s00122-017-2980-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Accepted: 08/30/2017] [Indexed: 05/19/2023]
Abstract
Quantitative trait loci controlling stripe rust resistance were identified in adapted Canadian spring wheat cultivars providing opportunity for breeders to stack loci using marker-assisted breeding. Stripe rust or yellow rust, caused by Puccinia striiformis Westend. f. sp. tritici Erikss., is a devastating disease of common wheat (Triticum aestivum L.) in many regions of the world. The objectives of this research were to identify and map quantitative trait loci (QTL) associated with stripe rust resistance in adapted Canadian spring wheat cultivars that are effective globally, and investigate opportunities for stacking resistance. Doubled haploid (DH) populations from the crosses Vesper/Lillian, Vesper/Stettler, Carberry/Vesper, Stettler/Red Fife and Carberry/AC Cadillac were phenotyped for stripe rust severity and infection response in field nurseries in Canada (Lethbridge and Swift Current), New Zealand (Lincoln), Mexico (Toluca) and Kenya (Njoro), and genotyped with SNP markers. Six QTL for stripe rust resistance in the population of Vesper/Lillian, five in Vesper/Stettler, seven in Stettler/Red Fife, four in Carberry/Vesper and nine in Carberry/AC Cadillac were identified. Lillian contributed stripe rust resistance QTL on chromosomes 4B, 5A, 6B and 7D, AC Cadillac on 2A, 2B, 3B and 5B, Carberry on 1A, 1B, 4A, 4B, 7A and 7D, Stettler on 1A, 2A, 3D, 4A, 5B and 6A, Red Fife on 2D, 3B and 4B, and Vesper on 1B, 2B and 7A. QTL on 1A, 1B, 2A, 2B, 3B, 4A, 4B, 5B, 7A and 7D were observed in multiple parents. The populations are compelling sources of recombination of many stripe rust resistance QTL for stacking disease resistance. Gene pyramiding should be possible with little chance of linkage drag of detrimental genes as the source parents were mostly adapted cultivars widely grown in Canada.
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Affiliation(s)
- Firdissa E Bokore
- Swift Current Research and Development Center, Agriculture and Agri-Food Canada, Swift Current, SK, S9H 3X2, Canada.
| | - Richard D Cuthbert
- Swift Current Research and Development Center, Agriculture and Agri-Food Canada, Swift Current, SK, S9H 3X2, Canada.
| | - Ron E Knox
- Swift Current Research and Development Center, Agriculture and Agri-Food Canada, Swift Current, SK, S9H 3X2, Canada
| | - Harpinder S Randhawa
- Lethbridge Research and Development Center, Agriculture and Agri-Food Canada, 5403 1st Avenue South, Lethbridge, AB, T1J 4B1, Canada
| | - Colin W Hiebert
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, 101 Route 100, Morden, MB, R6M 1Y5, Canada
| | - Ron M DePauw
- Advancing Wheat Technologies, 870 Field Drive, Swift Current, SK, S9H 4N5, Canada
| | - Asheesh K Singh
- Department of Agronomy, Iowa State University, Ames, IA, USA
| | - Arti Singh
- Department of Agronomy, Iowa State University, Ames, IA, USA
| | - Andrew G Sharpe
- National Research Council of Canada, 110 Gymnasium Place, Saskatoon, SK, S7N 0W9, Canada
| | - Amidou N'Diaye
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK, S7N 5A8, Canada
| | - Curtis J Pozniak
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK, S7N 5A8, Canada
| | - Curt McCartney
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, 101 Route 100, Morden, MB, R6M 1Y5, Canada
| | - Yuefeng Ruan
- Swift Current Research and Development Center, Agriculture and Agri-Food Canada, Swift Current, SK, S9H 3X2, Canada
| | - Samia Berraies
- Swift Current Research and Development Center, Agriculture and Agri-Food Canada, Swift Current, SK, S9H 3X2, Canada
| | - Brad Meyer
- Swift Current Research and Development Center, Agriculture and Agri-Food Canada, Swift Current, SK, S9H 3X2, Canada
| | - Catherine Munro
- Plant and Food Research Canterbury Agriculture and Science Centre, Gerald St, Lincoln, 7608, New Zealand
| | - Andy Hay
- Plant and Food Research Canterbury Agriculture and Science Centre, Gerald St, Lincoln, 7608, New Zealand
| | - Karim Ammar
- International Maize and Wheat Improvement Center (CIMMYT), Apdo., Postal 6-6-41, 06600, Mexico, DF, Mexico
| | - Julio Huerta-Espino
- Campo Experimental Valle de México INIFAP, Apdo., Postal 10, 56230, Chapingo, Edo. de México, Mexico
| | - Sridhar Bhavani
- International Maize and Wheat Improvement Center (CIMMYT), Nairobi, Kenya
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Identification of novel EST-SSR markers by transcriptome sequencing in ridgetail white prawn Exopalaemon carinicauda. Genes Genomics 2017; 40:207-215. [PMID: 29892927 DOI: 10.1007/s13258-017-0571-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Accepted: 05/30/2017] [Indexed: 10/18/2022]
Abstract
The ridgetail white prawn Exopalaemon carinicauda is one of the major commercial mariculture species in eastern China. However, only limited molecular markers are currently available due to the lack of genome information, which hinders its genetic and breeding studies. In this study, we identified new simple sequence repeats from transcriptome sequences by Illumina Hiseq 2500 platform. A total of 14273 SSR loci were identified from 130,082 assembled transcripts, with 6590 pairs of PCR primers designed. A total of 12,155 sequences containing SSR were predicted; and 2764 (22.74%) transcripts had significant matches to the NCBI non redundant protein (Nr) database. 11,563 transcripts were assigned into gene ontology (GO) categories. A set of 200 primers selected randomly were synthesized, of which 152 (76.0%) were successfully amplified. Further test with 60 pairs of polymorphic SSR primers to evaluate the genetic diversity of 30 wild populations and 43 loci were polymorphic, which had a polymorphic information content between 0.204 and 0.911. The results enriched genomic resources of E. carinicauda and provided powerful information for future conservation and breeding researches.
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Liu T, Wan A, Liu D, Chen X. Changes of Races and Virulence Genes in Puccinia striiformis f. sp. tritici, the Wheat Stripe Rust Pathogen, in the United States from 1968 to 2009. PLANT DISEASE 2017; 101:1522-1532. [PMID: 30678601 DOI: 10.1094/pdis-12-16-1786-re] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Stripe (yellow) rust, caused by Puccinia striiformis f. sp. tritici, is a serious disease of wheat in the world. The obligate biotrophic fungal pathogen changes its virulence rapidly, which can circumvent resistance in wheat cultivars and cause severe epidemics. Because P. striiformis f. sp. tritici races have been identified in the United States using different wheat genotypes in different time periods, it is difficult to make direct comparisons of the current population with historical populations. The objective of this study was to characterize historical populations with 18 Yr single-gene lines that are currently used to differentiate P. striiformis f. sp. tritici races in order to understand virulence and race changes of the pathogen over 40 years in the United States. From 908 P. striiformis f. sp. tritici isolates collected from 1968 to 2009 in the United States, 171 races were identified and their frequencies were determined. More races, more new races, and races with more virulence genes were detected since the year 2000 than prior to 2000. None of the races were virulent to Yr5 and Yr15, indicating that these genes have been effective since the late 1960s. Virulence genes to the remaining 16 Yr genes were detected in different periods, and most of them increased in frequency over time. Some virulence genes such as those to Yr17, Yr27, Yr32, Yr43, Yr44, YrTr1, and YrExp2 appeared 14 to 37 years earlier than previously reported, indicating the greater value of using Yr single-gene lines as differentials. Positive and negative associations were detected between virulence genes. The continual information on virulence and races in the P. striiformis f. sp. tritici populations is useful for understanding the evolution of the pathogen and for breeding wheat cultivars with effective resistance to stripe rust.
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Affiliation(s)
- Tinglan Liu
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan 611130, China; and Department of Plant Pathology, Washington State University, Pullman 99164-6430
| | - Anmin Wan
- Department of Plant Pathology, Washington State University
| | - Dengcai Liu
- Triticeae Research Institute, Sichuan Agricultural University
| | - Xianming Chen
- United States Department of Agriculture-Agricultural Research Service, Wheat Health, Genetics, and Quality Research Unit and Department of Plant Pathology, Washington State University, Pullman 99164-6430
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Liu W, Maccaferri M, Rynearson S, Letta T, Zegeye H, Tuberosa R, Chen X, Pumphrey M. Novel Sources of Stripe Rust Resistance Identified by Genome-Wide Association Mapping in Ethiopian Durum Wheat ( Triticum turgidum ssp. durum). FRONTIERS IN PLANT SCIENCE 2017; 8:774. [PMID: 28553306 PMCID: PMC5427679 DOI: 10.3389/fpls.2017.00774] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Accepted: 04/25/2017] [Indexed: 05/22/2023]
Abstract
Stripe rust of wheat, caused by Puccinia striiformis f. sp. tritici (Pst), is a global concern for wheat production, and has been increasingly destructive in Ethiopia, as well as in the United States and in many other countries. As Ethiopia has a long history of stripe rust epidemics, its native wheat germplasm harbors potentially valuable resistance loci. Moreover, the Ethiopian germplasm has been historically underutilized in breeding of modern wheat worldwide and thus the resistance alleles from the Ethiopian germplasm represent potentially novel sources. The objective of this study was to identify loci conferring resistance to predominant Pst races in Ethiopia and the United States. Using a high-density 90 K wheat single nucleotide polymorphism array, a genome-wide association analysis (GWAS) was conducted on 182 durum wheat landrace accessions and contemporary varieties originating from Ethiopia. Landraces were detected to be more resistant at the seedling stage while cultivars were more resistant at the adult-plant stages. GWAS identified 68 loci associated with seedling resistance to one or more races. Six loci on chromosome arms 1AS, 1BS, 3AS, 4BL, and 5BL were associated with resistance against at least two races at the seedling stage, and five loci were previously undocumented. GWAS analysis of field resistance reactions identified 12 loci associated with resistance on chromosomes 1A, 1B, 2BS, 3BL, 4AL, 4B and 5AL, which were detected in at least two of six field screening nurseries at the adult-plant stage. Comparison with previously mapped resistance loci indicates that six of the 12 resistance loci are newly documented. This study reports effective sources of resistance to contemporary races in Ethiopia and the United States and reveals that Ethiopian durum wheat landraces are abundant in novel Pst resistance loci that may be transferred into adapted cultivars to provide resistance against Pst.
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Affiliation(s)
- Weizhen Liu
- Department of Crop and Soil Sciences, Washington State University, PullmanWA, USA
| | - Marco Maccaferri
- Department of Agricultural Sciences, University of BolognaBologna, Italy
| | - Sheri Rynearson
- Department of Crop and Soil Sciences, Washington State University, PullmanWA, USA
| | - Tesfaye Letta
- Sinana Agricultural Research CenterBale-Robe, Ethiopia
| | | | - Roberto Tuberosa
- Department of Agricultural Sciences, University of BolognaBologna, Italy
| | - Xianming Chen
- Wheat Health, Genetics, and Quality Research Unit, Agricultural Research Service (USDA), PullmanWA, USA
- Department of Plant Pathology, Washington State University, PullmanWA, USA
| | - Michael Pumphrey
- Department of Crop and Soil Sciences, Washington State University, PullmanWA, USA
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Wu J, Wang Q, Liu S, Huang S, Mu J, Zeng Q, Huang L, Han D, Kang Z. Saturation Mapping of a Major Effect QTL for Stripe Rust Resistance on Wheat Chromosome 2B in Cultivar Napo 63 Using SNP Genotyping Arrays. FRONTIERS IN PLANT SCIENCE 2017; 8:653. [PMID: 28491075 PMCID: PMC5405077 DOI: 10.3389/fpls.2017.00653] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Accepted: 04/10/2017] [Indexed: 05/18/2023]
Abstract
Stripe rust or yellow rust (YR), caused by Puccinia striiformis f. sp. tritici (Pst), is one of the most important diseases of wheat (Triticum aestivum L.). Widespread deployment of resistant cultivars is the best means of achieving durable disease control. The red grain, spring wheat cultivar Napo 63 produced by CIMMYT in the 1960s shows a high level of adult-plant resistance to stripe rust in the field. To elucidate the genetic basis of resistance in this cultivar we evaluated 224 F2:3 lines and 175 F2:6 recombinant inbred lines (RILs) derived from a cross between Napo 63 and the Pst-susceptible line Avocet S. The maximum disease severity (MDS) data of F2:3 lines and the relative area under the disease progress curve (rAUDPC) data of RILs were collected during the 2014-2015 and 2015-2016 wheat growing seasons, respectively. Combined bulked segregant analysis and 90K single nucleotide polymorphism (SNP) arrays placed 275 of 511 polymorphic SNPs on chromosome 2B. Sixty four KASP markers selected from the 275 SNPs and 76 SSR markers on 2B were used to identify a chromosome region associated with rust response. A major effect QTL, named Qyrnap.nwafu-2BS, was identified by inclusive composite interval mapping and was preliminarily mapped to a 5.46 cM interval flanked by KASP markers 90K-AN34 and 90K-AN36 in chromosome 2BS. Fourteen KASP markers more closely linked to the locus were developed following a 660K SNP array analysis. The QTL region was finally narrowed to a 0.9 cM interval flanked by KASP markers 660K-AN21 and 660K-AN57 in bin region 2BS-1-0.53. The resistance of Napo 63 was stable across all environments, and as a QTL, explained an average 66.1% of the phenotypic variance in MDS of F2:3 lines and 55.7% of the phenotypic variance in rAUDPC of F5:6 RILs. The short genetic interval and flanking KASP markers developed in the study will facilitate marker-assisted selection, gene pyramiding, and eventual positional cloning of Qyrnap.nwafu-2BS.
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Affiliation(s)
- Jianhui Wu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F UniversityYangling, China
| | - Qilin Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F UniversityYangling, China
| | - Shengjie Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F UniversityYangling, China
| | - Shuo Huang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F UniversityYangling, China
| | - Jingmei Mu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F UniversityYangling, China
| | - Qingdong Zeng
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F UniversityYangling, China
| | - Lili Huang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F UniversityYangling, China
| | - Dejun Han
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F UniversityYangling, China
| | - Zhensheng Kang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F UniversityYangling, China
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Pasam RK, Bansal U, Daetwyler HD, Forrest KL, Wong D, Petkowski J, Willey N, Randhawa M, Chhetri M, Miah H, Tibbits J, Bariana H, Hayden MJ. Detection and validation of genomic regions associated with resistance to rust diseases in a worldwide hexaploid wheat landrace collection using BayesR and mixed linear model approaches. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2017; 130:777-793. [PMID: 28255670 DOI: 10.1007/s00122-016-2851-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Accepted: 12/28/2016] [Indexed: 05/26/2023]
Abstract
BayesR and MLM association mapping approaches in common wheat landraces were used to identify genomic regions conferring resistance to Yr, Lr, and Sr diseases. Deployment of rust resistant cultivars is the most economically effective and environmentally friendly strategy to control rust diseases in wheat. However, the highly evolving nature of wheat rust pathogens demands continued identification, characterization, and transfer of new resistance alleles into new varieties to achieve durable rust control. In this study, we undertook genome-wide association studies (GWAS) using a mixed linear model (MLM) and the Bayesian multilocus method (BayesR) to identify QTL contributing to leaf rust (Lr), stem rust (Sr), and stripe rust (Yr) resistance. Our study included 676 pre-Green Revolution common wheat landrace accessions collected in the 1920-1930s by A.E. Watkins. We show that both methods produce similar results, although BayesR had reduced background signals, enabling clearer definition of QTL positions. For the three rust diseases, we found 5 (Lr), 14 (Yr), and 11 (Sr) SNPs significant in both methods above stringent false-discovery rate thresholds. Validation of marker-trait associations with known rust QTL from the literature and additional genotypic and phenotypic characterisation of biparental populations showed that the landraces harbour both previously mapped and potentially new genes for resistance to rust diseases. Our results demonstrate that pre-Green Revolution landraces provide a rich source of genes to increase genetic diversity for rust resistance to facilitate the development of wheat varieties with more durable rust resistance.
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Affiliation(s)
- Raj K Pasam
- Department of Economic Development, Jobs, Transport and Recourses, AgriBio Centre for AgriBioscience, Bundoora, VIC, 3083, Australia
| | - Urmil Bansal
- Faculty of Agriculture and Environment, Plant Breeding Institute-Cobbitty, The University of Sydney, PMB4011, Narellan, NSW, 2567, Australia
| | - Hans D Daetwyler
- Department of Economic Development, Jobs, Transport and Recourses, AgriBio Centre for AgriBioscience, Bundoora, VIC, 3083, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, 3083, Australia
| | - Kerrie L Forrest
- Department of Economic Development, Jobs, Transport and Recourses, AgriBio Centre for AgriBioscience, Bundoora, VIC, 3083, Australia
| | - Debbie Wong
- Department of Economic Development, Jobs, Transport and Recourses, AgriBio Centre for AgriBioscience, Bundoora, VIC, 3083, Australia
| | - Joanna Petkowski
- Department of Economic Development, Jobs, Transport and Recourses, AgriBio Centre for AgriBioscience, Bundoora, VIC, 3083, Australia
| | - Nicholas Willey
- Faculty of Agriculture and Environment, Plant Breeding Institute-Cobbitty, The University of Sydney, PMB4011, Narellan, NSW, 2567, Australia
- Dow AgroSciences Australia Ltd, Unit 12A, 84 Barnes Street, Tamworth, NSW, 2340, Australia
| | - Mandeep Randhawa
- Faculty of Agriculture and Environment, Plant Breeding Institute-Cobbitty, The University of Sydney, PMB4011, Narellan, NSW, 2567, Australia
- International Maize and Wheat Improvement Center (CIMMYT), Carretera México-Veracruz Km. 45, El Batán, Texcoco, México, C.P. 56237, Mexico
| | - Mumta Chhetri
- Faculty of Agriculture and Environment, Plant Breeding Institute-Cobbitty, The University of Sydney, PMB4011, Narellan, NSW, 2567, Australia
| | - Hanif Miah
- Faculty of Agriculture and Environment, Plant Breeding Institute-Cobbitty, The University of Sydney, PMB4011, Narellan, NSW, 2567, Australia
| | - Josquin Tibbits
- Department of Economic Development, Jobs, Transport and Recourses, AgriBio Centre for AgriBioscience, Bundoora, VIC, 3083, Australia
| | - Harbans Bariana
- Faculty of Agriculture and Environment, Plant Breeding Institute-Cobbitty, The University of Sydney, PMB4011, Narellan, NSW, 2567, Australia.
| | - Matthew J Hayden
- Department of Economic Development, Jobs, Transport and Recourses, AgriBio Centre for AgriBioscience, Bundoora, VIC, 3083, Australia.
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, 3083, Australia.
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42
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Farber DH, Mundt CC. Effect of Plant Age and Leaf Position on Susceptibility to Wheat Stripe Rust. PHYTOPATHOLOGY 2017; 107:412-417. [PMID: 27898264 DOI: 10.1094/phyto-07-16-0284-r] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
In addition to pathogen propagule dispersal, disease spread requires successful infection of host tissue. In plant disease epidemiology, susceptibility of host tissue is often assumed to be constant. This assumption ignores changes in host phenology due to developmental stage. To examine this assumption, 3-, 4-, and 5-week-old wheat plants were inoculated with equal quantities of urediniospores of Puccinia striiformis f. sp. tritici, the causal agent of wheat stripe rust (WSR). Disease severity on each leaf was assessed and fit by mixed-effect linear model as a function of leaf position and plant age. Younger plants had significantly greater disease severity than older plants, with mean severities of 50.4, 30.1, and 12.9% on plants that were 3, 4, and 5 weeks old, respectively, at time of inoculation. This effect was greater on leaves higher on the plant. Within same-aged plants, younger leaves had significantly greater disease severity than older leaves, with mean severities of 40.2, 34.8, and 17.7% on the uppermost, second, and third leaf, respectively. These results suggest that the vertical distribution of WSR lesions in agricultural fields could be driven by differences in host susceptibility more so than propagule dispersal.
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Affiliation(s)
- D H Farber
- Department of Botany and Plant Pathology, Oregon State University, 2082 Cordley Hall, Corvallis 97331-2902
| | - C C Mundt
- Department of Botany and Plant Pathology, Oregon State University, 2082 Cordley Hall, Corvallis 97331-2902
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Bulli P, Zhang J, Chao S, Chen X, Pumphrey M. Genetic Architecture of Resistance to Stripe Rust in a Global Winter Wheat Germplasm Collection. G3 (BETHESDA, MD.) 2016; 6:2237-53. [PMID: 27226168 PMCID: PMC4978880 DOI: 10.1534/g3.116.028407] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Accepted: 05/16/2016] [Indexed: 12/30/2022]
Abstract
Virulence shifts in populations of Puccinia striiformis f. sp. tritici (Pst), the causal pathogen of wheat stripe rust, are a major challenge to resistance breeding. The majority of known resistance genes are already ineffective against current races of Pst, necessitating the identification and introgression of new sources of resistance. Germplasm core collections that reflect the range of genetic and phenotypic diversity of crop species are ideal platforms for examining the genetic architecture of complex traits such as resistance to stripe rust. We report the results of genetic characterization and genome-wide association analysis (GWAS) for resistance to stripe rust in a core subset of 1175 accessions in the National Small Grains Collection (NSGC) winter wheat germplasm collection, based on genotyping with the wheat 9K single nucleotide polymorphism (SNP) iSelect assay and phenotyping of seedling and adult plants under natural disease epidemics in four environments. High correlations among the field data translated into high heritability values within and across locations. Population structure was evident when accessions were grouped by stripe rust reaction. GWAS identified 127 resistance loci that were effective across at least two environments, including 20 with significant genome-wide adjusted P-values. Based on relative map positions of previously reported genes and QTL, five of the QTL with significant genome-wide adjusted P-values in this study represent potentially new loci. This study provides an overview of the diversity of Pst resistance in the NSGC winter wheat germplasm core collection, which can be exploited for diversification of stripe rust resistance in breeding programs.
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Affiliation(s)
- Peter Bulli
- Department of Crop and Soil Sciences, Washington State University, Pullman, Washington 99164-6420
| | - Junli Zhang
- Department of Plant Sciences, University of California, Davis, California 95616
| | - Shiaoman Chao
- USDA-ARS Genotyping Laboratory, Biosciences Research Laboratory, Fargo, North Dakota 58102
| | - Xianming Chen
- USDA-ARS, Wheat Health, Genetics and Quality Research Unit, Washington State University, Pullman, Washington 99164 Department of Plant Pathology, Washington State University, Pullman, Washington 99164
| | - Michael Pumphrey
- Department of Crop and Soil Sciences, Washington State University, Pullman, Washington 99164-6420
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Qin Z, Wang Y, Wang Q, Li A, Hou F, Zhang L. Evolution Analysis of Simple Sequence Repeats in Plant Genome. PLoS One 2015; 10:e0144108. [PMID: 26630570 PMCID: PMC4668000 DOI: 10.1371/journal.pone.0144108] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Accepted: 11/13/2015] [Indexed: 01/30/2023] Open
Abstract
Simple sequence repeats (SSRs) are widespread units on genome sequences, and play many important roles in plants. In order to reveal the evolution of plant genomes, we investigated the evolutionary regularities of SSRs during the evolution of plant species and the plant kingdom by analysis of twelve sequenced plant genome sequences. First, in the twelve studied plant genomes, the main SSRs were those which contain repeats of 1–3 nucleotides combination. Second, in mononucleotide SSRs, the A/T percentage gradually increased along with the evolution of plants (except for P. patens). With the increase of SSRs repeat number the percentage of A/T in C. reinhardtii had no significant change, while the percentage of A/T in terrestrial plants species gradually declined. Third, in dinucleotide SSRs, the percentage of AT/TA increased along with the evolution of plant kingdom and the repeat number increased in terrestrial plants species. This trend was more obvious in dicotyledon than monocotyledon. The percentage of CG/GC showed the opposite pattern to the AT/TA. Forth, in trinucleotide SSRs, the percentages of combinations including two or three A/T were in a rising trend along with the evolution of plant kingdom; meanwhile with the increase of SSRs repeat number in plants species, different species chose different combinations as dominant SSRs. SSRs in C. reinhardtii, P. patens, Z. mays and A. thaliana showed their specific patterns related to evolutionary position or specific changes of genome sequences. The results showed that, SSRs not only had the general pattern in the evolution of plant kingdom, but also were associated with the evolution of the specific genome sequence. The study of the evolutionary regularities of SSRs provided new insights for the analysis of the plant genome evolution.
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Affiliation(s)
- Zhen Qin
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Yanping Wang
- Shandong Key Laboratory of Animal Disease Control and Breeding/Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Qingmei Wang
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Aixian Li
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Fuyun Hou
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Liming Zhang
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, China
- * E-mail:
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