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Kaur R, Vasistha NK, Ravat VK, Mishra VK, Sharma S, Joshi AK, Dhariwal R. Genome-Wide Association Study Reveals Novel Powdery Mildew Resistance Loci in Bread Wheat. PLANTS (BASEL, SWITZERLAND) 2023; 12:3864. [PMID: 38005757 PMCID: PMC10675159 DOI: 10.3390/plants12223864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 10/24/2023] [Accepted: 10/26/2023] [Indexed: 11/26/2023]
Abstract
Powdery mildew (PM), caused by the fungal pathogen Blumeria graminis f. sp. tritici (Bgt), significantly threatens global bread wheat production. Although the use of resistant cultivars is an effective strategy for managing PM, currently available wheat cultivars lack sufficient levels of resistance. To tackle this challenge, we conducted a comprehensive genome-wide association study (GWAS) using a diverse panel of 286 bread wheat genotypes. Over three consecutive years (2020-2021, 2021-2022, and 2022-2023), these genotypes were extensively evaluated for PM severity under field conditions following inoculation with virulent Bgt isolates. The panel was previously genotyped using the Illumina 90K Infinium iSelect assay to obtain genome-wide single-nucleotide polymorphism (SNP) marker coverage. By applying FarmCPU, a multilocus mixed model, we identified a total of 113 marker-trait associations (MTAs) located on chromosomes 1A, 1B, 2B, 3A, 3B, 4A, 4B, 5A, 5B, 6B, 7A, and 7B at a significance level of p ≤ 0.001. Notably, four novel MTAs on chromosome 6B were consistently detected in 2020-2021 and 2021-2022. Furthermore, within the confidence intervals of the identified SNPs, we identified 96 candidate genes belonging to different proteins including 12 disease resistance/host-pathogen interaction-related protein families. Among these, protein kinases, leucine-rich repeats, and zinc finger proteins were of particular interest due to their potential roles in PM resistance. These identified loci can serve as targets for breeding programs aimed at developing disease-resistant wheat cultivars.
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Affiliation(s)
- Ramandeep Kaur
- Department of Genetics-Plant Breeding and Biotechnology, Dr. Khem Sigh Gill Akal College of Agriculture, Eternal University, Baru Sahib, Sirmour 173101, India
| | - Neeraj Kumar Vasistha
- Department of Genetics-Plant Breeding and Biotechnology, Dr. Khem Sigh Gill Akal College of Agriculture, Eternal University, Baru Sahib, Sirmour 173101, India
- Department of Genetics and Plant Breeding, Rajiv Gandhi University, Rono Hills, Itanagar 791112, India
| | - Vikas Kumar Ravat
- Department of Plant Pathology, Rajiv Gandhi University, Rono Hills, Itanagar 791112, India
| | - Vinod Kumar Mishra
- Department of Genetics and Plant Breeding, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi 221005, India
| | - Sandeep Sharma
- Department of Genetics and Plant Breeding, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi 221005, India
| | - Arun Kumar Joshi
- Borlaug Institute for South Asia (BISA), NASC Complex, DPS Marg, New Delhi 110012, India
- International Maize and Wheat Improvement Center (CIMMYT) Regional Office, NASC Complex, DPS Marg, New Delhi 110012, India
| | - Raman Dhariwal
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, 5403 1 Avenue South, Lethbridge, AB T1J 4B1, Canada
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Xu X, Sun D, Ni Z, Zou X, Xu X, Sun M, Cao Q, Tong J, Ding F, Zhang Y, Wang F, Dong Y, Zhang L, Wang J, Xia X, He Z, Hao Y. Molecular identification and validation of four stable QTL for adult-plant resistance to powdery mildew in Chinese wheat cultivar Bainong 64. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:232. [PMID: 37875655 DOI: 10.1007/s00122-023-04481-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Accepted: 10/04/2023] [Indexed: 10/26/2023]
Abstract
KEY MESSAGE Four stable QTL for adult-plant resistance (APR) to powdery mildew were identified on chromosome arms 1DL, 2BS, 2DL, and 6BL in the widely grown Chinese wheat cultivar Bainong 64. These QTL had no effect on response to stripe rust or leaf rust. Wheat powdery mildew, caused by Blumeria graminis f. sp. tritici (Bgt), is a devastating fungal disease. Seedlings of Chinese wheat Bainong 64 are susceptible to Bgt, but adult plants have maintained resistance since it was released in 1996. A population of 171 recombinant inbred lines (RILs) developed from cross Jingshuang 16/Bainong 64 (JS16/BN64) was used to dissect genetic components of powdery mildew resistance. A genetic map comprising 5383 polymorphic markers was constructed using the 15 K SNP chip and kompetitive allele-specific PCR (KASP) markers. Composite interval mapping identified four stable QTL with favorable alleles all from BN64 on chromosome arms 1DL, 2BS, 2DL, and 6BL in at least four environments. They accounted for 8.3%, 13.8%, 14.4%, and 9.0% of the total phenotypic variation explained (PVE) in maximum, respectively. QPmjbr.caas-1DL, situated about 22 Mb from centromere, is probably a new QTL. QPmjbr.caas-2DL located near the end of arm 2DL and explained the largest PVE. Using genetic maps populated with KASP markers, QPmjbr.caas-2BS and QPmjbr.caas-6BL were fine mapped to a 1.8 cM genetic intervals spanning 13.6 Mb (76.0-89.6 Mb) and 1.7 cM and 4.9 Mb (659.9-664.8 Mb), respectively. The four QTL independent of stripe rust and leaf rust resistance were validated for powdery mildew resistance in another RIL population related to BN64 and a cultivar panel using representative KASP markers. Since BN64 has been a leading cultivar and an important breeding parent in China, the QTL and markers reported in this study will be useful for marker-assisted selection of APR.
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Affiliation(s)
- Xiaowan Xu
- College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
| | - Daojie Sun
- College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China.
| | - Zhongqiu Ni
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
| | - Xinyu Zou
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
| | - Xiaoting Xu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
| | - Mengjing Sun
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
| | - Qiang Cao
- College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
| | - Jingyang Tong
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
| | - Fugong Ding
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
| | - Yelun Zhang
- Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences/The Key Laboratory of Crop Genetics and Breeding of Hebei Province, Shijiazhuang, 050035, Hebei, China
| | - Fengju Wang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
| | - Yachao Dong
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
| | - Luyan Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
| | - Jiankang Wang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
| | - Xianchun Xia
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
| | - Zhonghu He
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
- International Maize and Wheat Improvement Center (CIMMYT) China Office, c/o CAAS, 12 Zhongguancun South Street, Beijing, 100081, China
| | - Yuanfeng Hao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China.
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He L, Sui Y, Che Y, Wang H, Rashid KY, Cloutier S, You FM. Genome-wide association studies using multi-models and multi-SNP datasets provide new insights into pasmo resistance in flax. FRONTIERS IN PLANT SCIENCE 2023; 14:1229457. [PMID: 37954993 PMCID: PMC10634603 DOI: 10.3389/fpls.2023.1229457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 07/24/2023] [Indexed: 11/14/2023]
Abstract
Introduction Flax (Linum usitatissimum L.) is an economically important crop due to its oil and fiber. However, it is prone to various diseases, including pasmo caused by the fungus Septoria linicola. Methods In this study, we conducted field evaluations of 445 flax accessions over a five-year period (2012-2016) to assess their resistance to pasmo A total of 246,035 single nucleotide polymorphisms (SNPs) were used for genetic analysis. Four statistical models, including the single-locus model GEMMA and the multi-locus models FarmCPU, mrMLM, and 3VmrMLM, were assessed to identify quantitative trait nucleotides (QTNs) associated with pasmo resistance. Results We identified 372 significant QTNs or 132 tag QTNs associated with pasmo resistance from five pasmo resistance datasets (PAS2012-PAS2016 and the 5-year average, namely PASmean) and three genotypic datasets (the all SNPs/ALL, the gene-based SNPs/GB and the RGA-based SNPs/RGAB). The tag QTNs had R2 values of 0.66-16.98% from the ALL SNP dataset, 0.68-20.54%from the GB SNP dataset, and 0.52-22.42% from the RGAB SNP dataset. Of these tag QTNs, 93 were novel. Additionally, 37 resistance gene analogs (RGAs)co-localizing with 39 tag QTNs were considered as potential candidates for controlling pasmo resistance in flax and 50 QTN-by-environment interactions(QEIs) were identified to account for genes by environmental interactions. Nine RGAs were predicted as candidate genes for ten QEIs. Discussion Our results suggest that pasmo resistance in flax is polygenic and potentially influenced by environmental factors. The identified QTNs provide potential targets for improving pasmo resistance in flax breeding programs. This study sheds light on the genetic basis of pasmo resistance and highlights the importance of considering both genetic and environmental factors in breeding programs for flax.
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Affiliation(s)
- Liqiang He
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
- School of Tropical Agriculture and Forestry, School of Tropical Crops, Hainan University, Haikou, China
| | - Yao Sui
- School of Tropical Agriculture and Forestry, School of Tropical Crops, Hainan University, Haikou, China
| | - Yanru Che
- School of Tropical Agriculture and Forestry, School of Tropical Crops, Hainan University, Haikou, China
| | - Huixian Wang
- School of Tropical Agriculture and Forestry, School of Tropical Crops, Hainan University, Haikou, China
| | - Khalid Y. Rashid
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - Sylvie Cloutier
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - Frank M. You
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
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Xu X, Ni Z, Zou X, Zhang Y, Tong J, Xu X, Dong Y, Han B, Li S, Wang D, Xia X, He Z, Hao Y. QTL Mapping Reveals Both All-Stage and Adult-Plant Resistance to Powdery Mildew in Chinese Elite Wheat Cultivars. PLANT DISEASE 2023; 107:3230-3237. [PMID: 37018212 DOI: 10.1094/pdis-02-23-0399-re] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Powdery mildew caused by Blumeria graminis f. sp. tritici is a threat to wheat production in China. Mapping quantitative trait loci (QTL) for resistance to powdery mildew and developing breeder-friendly markers are important initial steps in breeding resistant cultivars. An all-stage resistance gene and several QTL were identified using a population of 254 recombinant inbred lines developed from a Jingdong 8/Aikang 58 cross. The population was evaluated for powdery mildew resistance across six field environments over three consecutive growing seasons utilizing two different mixtures of B. graminis f. sp. tritici isolates, named #Bgt-HB and #Bgt-BJ. Using genotypic data obtained from the Wheat TraitBreed 50K single-nucleotide polymorphism array, seven stable QTL were identified on chromosome arms 1DL, 2AL, 2DS, 4DL, 5AL, 6BL.1, and 6BL.2. The QTL on 2AL conferred all-stage resistance to B. graminis f. sp. tritici race E20 in greenhouse tests and explained up to 52% of the phenotypic variance in field trials but was resistant only against #Bgt-HB. The gene involved in this QTL was predicted to be Pm4a based on genome location and gene sequence. QPmja.caas-1DL, QPmja.caas-4DL, and QPmja.caas-6BL.1 were identified as potentially new QTL for powdery mildew resistance. QPmja.caas-2DS and QPmja.caas-6BL.1 were effective against both B. graminis f. sp. tritici mixtures, indicating their probable broad-spectrum resistance. A Kompetitive allele-specific PCR marker closely linked to QPmja.caas-2DS was developed and validated in a panel of 286 wheat cultivars. Because both Jingdong 8 and Aikang 58 have been leading cultivars and breeding parents, the QTL and marker reported represent valuable resources for wheat researchers and breeders.
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Affiliation(s)
- Xiaoting Xu
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China
| | - Zhongqiu Ni
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China
| | - Xinyu Zou
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China
| | - Yelun Zhang
- Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences/Hebei Laboratory of Crop Genetics and Breeding, Shijiazhuang 050031, Hebei, China
| | - Jingyang Tong
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China
| | - Xiaowan Xu
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China
| | - Yachao Dong
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China
| | - Bin Han
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China
| | - Simin Li
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China
| | - Desen Wang
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China
| | - Xianchun Xia
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China
| | - Zhonghu He
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China
- International Maize and Wheat Improvement Center (CIMMYT) China Office, Beijing 100081, China
| | - Yuanfeng Hao
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China
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Kumar S, Saini DK, Jan F, Jan S, Tahir M, Djalovic I, Latkovic D, Khan MA, Kumar S, Vikas VK, Kumar U, Kumar S, Dhaka NS, Dhankher OP, Rustgi S, Mir RR. Comprehensive meta-QTL analysis for dissecting the genetic architecture of stripe rust resistance in bread wheat. BMC Genomics 2023; 24:259. [PMID: 37173660 PMCID: PMC10182688 DOI: 10.1186/s12864-023-09336-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Accepted: 04/26/2023] [Indexed: 05/15/2023] Open
Abstract
BACKGROUND Yellow or stripe rust, caused by the fungus Puccinia striiformis f. sp. tritici (Pst) is an important disease of wheat that threatens wheat production. Since developing resistant cultivars offers a viable solution for disease management, it is essential to understand the genetic basis of stripe rust resistance. In recent years, meta-QTL analysis of identified QTLs has gained popularity as a way to dissect the genetic architecture underpinning quantitative traits, including disease resistance. RESULTS Systematic meta-QTL analysis involving 505 QTLs from 101 linkage-based interval mapping studies was conducted for stripe rust resistance in wheat. For this purpose, publicly available high-quality genetic maps were used to create a consensus linkage map involving 138,574 markers. This map was used to project the QTLs and conduct meta-QTL analysis. A total of 67 important meta-QTLs (MQTLs) were identified which were refined to 29 high-confidence MQTLs. The confidence interval (CI) of MQTLs ranged from 0 to 11.68 cM with a mean of 1.97 cM. The mean physical CI of MQTLs was 24.01 Mb, ranging from 0.0749 to 216.23 Mb per MQTL. As many as 44 MQTLs colocalized with marker-trait associations or SNP peaks associated with stripe rust resistance in wheat. Some MQTLs also included the following major genes- Yr5, Yr7, Yr16, Yr26, Yr30, Yr43, Yr44, Yr64, YrCH52, and YrH52. Candidate gene mining in high-confidence MQTLs identified 1,562 gene models. Examining these gene models for differential expressions yielded 123 differentially expressed genes, including the 59 most promising CGs. We also studied how these genes were expressed in wheat tissues at different phases of development. CONCLUSION The most promising MQTLs identified in this study may facilitate marker-assisted breeding for stripe rust resistance in wheat. Information on markers flanking the MQTLs can be utilized in genomic selection models to increase the prediction accuracy for stripe rust resistance. The candidate genes identified can also be utilized for enhancing the wheat resistance against stripe rust after in vivo confirmation/validation using one or more of the following methods: gene cloning, reverse genetic methods, and omics approaches.
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Affiliation(s)
- Sandeep Kumar
- Division of Genetics and Plant Breeding, Faculty of Agriculture, SKUAST-Kashmir, Wadura, 193201, India
| | - Dinesh Kumar Saini
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, 141004, Punjab, India
| | - Farkhandah Jan
- Division of Genetics and Plant Breeding, Faculty of Agriculture, SKUAST-Kashmir, Wadura, 193201, India
| | - Sofora Jan
- Division of Genetics and Plant Breeding, Faculty of Agriculture, SKUAST-Kashmir, Wadura, 193201, India
| | - Mohd Tahir
- Division of Genetics and Plant Breeding, Faculty of Agriculture, SKUAST-Kashmir, Wadura, 193201, India
| | - Ivica Djalovic
- Institute of Field and Vegetable Crops, National Institute of the Republic of Serbia, Maxim Gorki 30, Novi Sad, Serbia
| | - Dragana Latkovic
- Department of Field and Vegetable Crops, Faculty of Agriculture, University of Novi Sad, Trg Dositeja Obradovića 8, 21000, Novi Sad, Serbia
| | - Mohd Anwar Khan
- Division of Genetics and Plant Breeding, Faculty of Agriculture, SKUAST-Kashmir, Wadura, 193201, India
| | - Sundeep Kumar
- Indian Council of Agricultural Research-National Bureau of Plant Genetic Resources, New Delhi, India
| | - V K Vikas
- ICAR-IARI, Regional Station, Wellington, 643 231, The Nilgiris, India
| | - Upendra Kumar
- Department of Molecular Biology & Biotechnology., CCS Haryana Agriculture University, Hisar, India
| | - Sundip Kumar
- Department of Molecular Biology and Genetic Engineering, Molecular Cytogenetics Laboratory, College of Basic Science and Humanities, G. B. Pant University of Agriculture and Technology, Pantnagar-263145, U.S. Nagar, Uttarakhand, India
| | - Narendra Singh Dhaka
- Department of Genetics and Plant Breeding, College of Agriculture, G. B. Pant, University of Agriculture & Technology, Pantnagar-263145, U. S. Nagar, Uttarakhand, India
| | - Om Parkash Dhankher
- School of Agriculture, University of Massachusetts Amherst, Stockbridge Amherst, MA, 01003, USA
| | - Sachin Rustgi
- Department of Plant and Environmental Sciences, Clemson University, 2200 Pocket Road, Florence, SC, 29506, USA
| | - Reyazul Rouf Mir
- Division of Genetics and Plant Breeding, Faculty of Agriculture, SKUAST-Kashmir, Wadura, 193201, India.
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Berraies S, Cuthbert R, Knox R, Singh A, DePauw R, Ruan Y, Bokore F, Henriquez MA, Kumar S, Burt A, Pozniak C, N’Diaye A, Meyer B. High-density genetic mapping of Fusarium head blight resistance and agronomic traits in spring wheat. FRONTIERS IN PLANT SCIENCE 2023; 14:1134132. [PMID: 37284725 PMCID: PMC10241073 DOI: 10.3389/fpls.2023.1134132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Accepted: 04/03/2023] [Indexed: 06/08/2023]
Abstract
Fusarium head blight (FHB) has rapidly become a major challenge to successful wheat production and competitive end-use quality in western Canada. Continuous effort is required to develop germplasm with improved FHB resistance and understand how to incorporate the material into crossing schemes for marker-assisted selection and genomic selection. The aim of this study was to map quantitative trait loci (QTL) responsible for the expression of FHB resistance in two adapted cultivars and to evaluate their co-localization with plant height, days to maturity, days to heading, and awnedness. A large doubled haploid population of 775 lines developed from cultivars Carberry and AC Cadillac was assessed for FHB incidence and severity in nurseries near Portage la Prairie, Brandon, and Morden in different years, and for plant height, awnedness, days to heading, and days to maturity near Swift Current. An initial linkage map using a subset of 261 lines was constructed using 634 polymorphic DArT and SSR markers. QTL analysis revealed five resistance QTL on chromosomes 2A, 3B (two loci), 4B, and 5A. A second genetic map with increased marker density was constructed using the Infinium iSelect 90k SNP wheat array in addition to the previous DArT and SSR markers, which revealed two additional QTL on 6A and 6D. The complete population was genotyped, and a total of 6,806 Infinium iSelect 90k SNP polymorphic markers were used to identify 17 putative resistance QTL on 14 different chromosomes. As with the smaller population size and fewer markers, large-effect QTL were detected on 3B, 4B, and 5A that were consistently expressed across environments. FHB resistance QTL were co-localized with plant height QTL on chromosomes 4B, 6D, and 7D; days to heading on 2B, 3A, 4A, 4B, and 5A; and maturity on 3A, 4B, and 7D. A major QTL for awnedness was identified as being associated with FHB resistance on chromosome 5A. Nine small-effect QTL were not associated with any of the agronomic traits, whereas 13 QTL that were associated with agronomic traits did not co-localize with any of the FHB traits. There is an opportunity to select for improved FHB resistance within adapted cultivars by using markers associated with complementary QTL.
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Affiliation(s)
- Samia Berraies
- Swift Current Research and Development Center, Agriculture and Agri-Food Canada, Swift Current, SK, Canada
| | - Richard Cuthbert
- Swift Current Research and Development Center, Agriculture and Agri-Food Canada, Swift Current, SK, Canada
| | - Ron Knox
- Swift Current Research and Development Center, Agriculture and Agri-Food Canada, Swift Current, SK, Canada
| | - Arti Singh
- Department of Agronomy, Iowa State University, Ames, IA, United States
| | | | - Yuefeng Ruan
- Swift Current Research and Development Center, Agriculture and Agri-Food Canada, Swift Current, SK, Canada
| | - Firdissa Bokore
- Swift Current Research and Development Center, Agriculture and Agri-Food Canada, Swift Current, SK, Canada
| | - Maria Antonia Henriquez
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, MB, Canada
| | - Santosh Kumar
- Brandon Research and Development Centre, Agriculture and Agri-Food Canada, Brandon, MB, Canada
| | - Andrew Burt
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - Curtis Pozniak
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK, Canada
| | - Amidou N’Diaye
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK, Canada
| | - Brad Meyer
- Swift Current Research and Development Center, Agriculture and Agri-Food Canada, Swift Current, SK, Canada
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Singh S, Gaurav SS, Vasistha NK, Kumar U, Joshi AK, Mishra VK, Chand R, Gupta PK. Genetics of spot blotch resistance in bread wheat ( Triticum aestivum L.) using five models for GWAS. FRONTIERS IN PLANT SCIENCE 2023; 13:1036064. [PMID: 36743576 PMCID: PMC9891466 DOI: 10.3389/fpls.2022.1036064] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Accepted: 12/28/2022] [Indexed: 06/18/2023]
Abstract
Genetic architecture of resistance to spot blotch in wheat was examined using a Genome-Wide Association Study (GWAS) involving an association panel comprising 303 diverse genotypes. The association panel was evaluated at two different locations in India including Banaras Hindu University (BHU), Varanasi (Uttar Pradesh), and Borlaug Institute for South Asia (BISA), Pusa, Samastipur (Bihar) for two consecutive years (2017-2018 and 2018-2019), thus making four environments (E1, BHU 2017-18; E2, BHU 2018-19; E3, PUSA, 2017-18; E4, PUSA, 2018-19). The panel was genotyped for 12,196 SNPs based on DArT-seq (outsourced to DArT Ltd by CIMMYT); these SNPs included 5,400 SNPs, which could not be assigned to individual chromosomes and were therefore, described as unassigned by the vendor. Phenotypic data was recorded on the following three disease-related traits: (i) Area Under Disease Progress Curve (AUDPC), (ii) Incubation Period (IP), and (iii) Lesion Number (LN). GWAS was conducted using each of five different models, which included two single-locus models (CMLM and SUPER) and three multi-locus models (MLMM, FarmCPU, and BLINK). This exercise gave 306 MTAs, but only 89 MTAs (33 for AUDPC, 30 for IP and 26 for LN) including a solitary MTA detected using all the five models and 88 identified using four of the five models (barring SUPER) were considered to be important. These were used for further analysis, which included identification of candidate genes (CGs) and their annotation. A majority of these MTAs were novel. Only 70 of the 89 MTAs were assigned to individual chromosomes; the remaining 19 MTAs belonged to unassigned SNPs, for which chromosomes were not known. Seven MTAs were selected on the basis of minimum P value, number of models, number of environments and location on chromosomes with respect to QTLs reported earlier. These 7 MTAs, which included five main effect MTAs and two for epistatic interactions, were considered to be important for marker-assisted selection (MAS). The present study thus improved our understanding of the genetics of resistance against spot blotch in wheat and provided seven MTAs, which may be used for MAS after due validation.
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Affiliation(s)
- Sahadev Singh
- Molecular Biology Laboratory, Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, India
| | - Shailendra Singh Gaurav
- Molecular Biology Laboratory, Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, India
| | - Neeraj Kumar Vasistha
- Department of Genetics-Plant Breeding and Biotechnology, Dr Khem Singh Gill, Akal College of Agriculture, Eternal University, Sirmaur, India
| | - Uttam Kumar
- Borlaug Institute for South Asia (BISA), Ludhiana, India
| | - Arun Kumar Joshi
- The International Maize and Wheat Improvement Center (CIMMYT), Borlaug Institute for South Asia (BISA), G-2, B-Block, NASC Complex, DPS Marg, New Delhi, India
| | - Vinod Kumar Mishra
- Department of Genetics and Plant Breeding, Indian Institute of Agricultural Science, Banaras Hindu University, Varanasi, India
| | - Ramesh Chand
- Department of Mycology and Plant Pathology, Indian Institute of Agricultural Science Banaras Hindu University, Varanasi, India
| | - Pushpendra Kumar Gupta
- Molecular Biology Laboratory, Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, India
- Borlaug Institute for South Asia (BISA), Ludhiana, India
- Murdoch’s Centre for Crop & Food Innovation, Murdoch University, Murdoch, WA, Australia
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Saini P, Sheikh I, Saini DK, Mir RR, Dhaliwal HS, Tyagi V. Consensus genomic regions associated with grain protein content in hexaploid and tetraploid wheat. Front Genet 2022; 13:1021180. [PMID: 36246648 PMCID: PMC9554612 DOI: 10.3389/fgene.2022.1021180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 09/13/2022] [Indexed: 11/13/2022] Open
Abstract
A meta-analysis of QTLs associated with grain protein content (GPC) was conducted in hexaploid and tetraploid wheat to identify robust and stable meta-QTLs (MQTLs). For this purpose, as many as 459 GPC-related QTLs retrieved from 48 linkage-based QTL mapping studies were projected onto the newly developed wheat consensus map. The analysis resulted in the prediction of 57 MQTLs and 7 QTL hotspots located on all wheat chromosomes (except chromosomes 1D and 4D) and the average confidence interval reduced 2.71-fold in the MQTLs and QTL hotspots compared to the initial QTLs. The physical regions occupied by the MQTLs ranged from 140 bp to 224.02 Mb with an average of 15.2 Mb, whereas the physical regions occupied by QTL hotspots ranged from 1.81 Mb to 36.03 Mb with a mean of 8.82 Mb. Nineteen MQTLs and two QTL hotspots were also found to be co-localized with 45 significant SNPs identified in 16 previously published genome-wide association studies in wheat. Candidate gene (CG) investigation within some selected MQTLs led to the identification of 705 gene models which also included 96 high-confidence CGs showing significant expressions in different grain-related tissues and having probable roles in GPC regulation. These significantly expressed CGs mainly involved the genes/gene families encoding for the following proteins: aminotransferases, early nodulin 93, glutamine synthetases, invertase/pectin methylesterase inhibitors, protein BIG GRAIN 1-like, cytochrome P450, glycosyl transferases, hexokinases, small GTPases, UDP-glucuronosyl/UDP-glucosyltransferases, and EamA, SANT/Myb, GNAT, thioredoxin, phytocyanin, and homeobox domains containing proteins. Further, eight genes including GPC-B1, Glu-B1-1b, Glu-1By9, TaBiP1, GSr, TaNAC019-A, TaNAC019-D, and bZIP-TF SPA already known to be associated with GPC were also detected within some of the MQTL regions confirming the efficacy of MQTLs predicted during the current study.
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Affiliation(s)
- Pooja Saini
- Department of Genetics-Plant Breeding and Biotechnology, Dr. Khem Singh Gill Akal College of Agriculture, Eternal University, Baru Sahib, India
| | - Imran Sheikh
- Department of Genetics-Plant Breeding and Biotechnology, Dr. Khem Singh Gill Akal College of Agriculture, Eternal University, Baru Sahib, India
| | - Dinesh Kumar Saini
- Department of Plant Breeding and Genetics, Punajb Agricultural University, Ludhiana, India
| | - Reyazul Rouf Mir
- Division of Genetics and Plant Breeding, Faculty of Agriculture SKUAST-Kashmir, Srinagar, India
| | - Harcharan Singh Dhaliwal
- Department of Genetics-Plant Breeding and Biotechnology, Dr. Khem Singh Gill Akal College of Agriculture, Eternal University, Baru Sahib, India
| | - Vikrant Tyagi
- Department of Genetics-Plant Breeding and Biotechnology, Dr. Khem Singh Gill Akal College of Agriculture, Eternal University, Baru Sahib, India
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Pal N, Jan I, Saini DK, Kumar K, Kumar A, Sharma PK, Kumar S, Balyan HS, Gupta PK. Meta-QTLs for multiple disease resistance involving three rusts in common wheat (Triticum aestivum L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:2385-2405. [PMID: 35699741 DOI: 10.1007/s00122-022-04119-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 04/28/2022] [Indexed: 05/20/2023]
Abstract
In wheat, multiple disease resistance meta-QTLs (MDR-MQTLs) and underlying candidate genes for the three rusts were identified which may prove useful for development of resistant cultivars. Rust diseases in wheat are a major threat to global food security. Therefore, development of multiple disease-resistant cultivars (resistant to all three rusts) is a major goal in all wheat breeding programs worldwide. In the present study, meta-QTLs and candidate genes for multiple disease resistance (MDR) involving all three rusts were identified using 152 individual QTL mapping studies for resistance to leaf rust (LR), stem rust (SR), and yellow rust (YR). From these 152 studies, a total of 1,146 QTLs for resistance to three rusts were retrieved, which included 368 QTLs for LR, 291 QTLs for SR, and 487 QTLs for YR. Of these 1,146 QTLs, only 718 QTLs could be projected onto the consensus map saturated with 2, 34,619 markers. Meta-analysis of the projected QTLs resulted in the identification of 86 MQTLs, which included 71 MDR-MQTLs. Ten of these MDR-MQTLs were referred to as the 'Breeders' MQTLs'. Seventy-eight of the 86 MQTLs could also be anchored to the physical map of the wheat genome, and 54 MQTLs were validated by marker-trait associations identified during earlier genome-wide association studies. Twenty MQTLs (including 17 MDR-MQTLs) identified in the present study were co-localized with 44 known R genes. In silico expression analysis allowed identification of several differentially expressed candidate genes (DECGs) encoding proteins carrying different domains including the following: NBS-LRR, WRKY domains, F-box domains, sugar transporters, transferases, etc. The introgression of these MDR loci into high-yielding cultivars should prove useful for developing high yielding cultivars with resistance to all the three rusts.
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Affiliation(s)
- Neeraj Pal
- Department of Molecular Biology and Genetic Engineering, G. B. Pant University of Agriculture and Technology, Pantnagar, Uttrakhand, 263145, India
| | - Irfat Jan
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, 250004, India
| | - Dinesh Kumar Saini
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, 141004, India
| | - Kuldeep Kumar
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, 250004, India
| | - Anuj Kumar
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, 250004, India
| | - P K Sharma
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, 250004, India
| | - Sundip Kumar
- Department of Molecular Biology and Genetic Engineering, G. B. Pant University of Agriculture and Technology, Pantnagar, Uttrakhand, 263145, India
| | - H S Balyan
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, 250004, India
| | - P K Gupta
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, 250004, India.
- Murdoch's Centre for Crop & Food Innovation, Murdoch University, Murdoch, Perth, WA 6150, Australia.
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Gudi S, Saini DK, Singh G, Halladakeri P, Kumar P, Shamshad M, Tanin MJ, Singh S, Sharma A. Unravelling consensus genomic regions associated with quality traits in wheat using meta-analysis of quantitative trait loci. PLANTA 2022; 255:115. [PMID: 35508739 DOI: 10.1007/s00425-022-03904-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 04/26/2022] [Indexed: 05/03/2023]
Abstract
Meta-analysis in wheat for three major quality traits identified 110 meta-QTL (MQTL) with reduced confidence interval (CI). Five GWAS validated MQTL (viz., 1A.1, 1B.2, 3B.4, 5B.2, and 6B.2), each involving more than 20 initial QTL and reduced CI (95%) (< 2 cM), were selected for quality breeding programmes. Functional characterization including candidate gene mining and expression analysis discovered 44 high confidence candidate genes associated with quality traits. A meta-analysis of quantitative trait loci (QTL) associated with dough rheology properties, nutritional traits, and processing quality traits was conducted in wheat. For this purpose, as many as 2458 QTL were collected from 50 interval mapping studies published during 2013-2020. Of the total QTL, 1126 QTL were projected onto the consensus map saturated with 249,603 markers which led to the identification of 110 meta-QTL (MQTL). These MQTL exhibited an 18.84-fold reduction in the average CI compared to the average CI of the initial QTL (ranging from 14.87 to 95.55 cM with an average of 40.35 cM). Of the 110, 108 MQTL were physically anchored to the wheat reference genome, including 51 MQTL verified with marker-trait associations (MTAs) reported from earlier genome-wide association studies. Candidate gene (CG) mining allowed the identification of 2533 unique gene models from the MQTL regions. In-silico expression analysis discovered 439 differentially expressed gene models with > 2 transcripts per million expressions in grains and related tissues, which also included 44 high-confidence CGs involved in the various cellular and biochemical processes related to quality traits. Nine functionally characterized wheat genes associated with grain protein content, high-molecular-weight glutenin, and starch synthase enzymes were also found to be co-localized with some of the MQTL. Synteny analysis between wheat and rice MQTL regions identified 23 wheat MQTL syntenic to 16 rice MQTL associated with quality traits. Furthermore, 64 wheat orthologues of 30 known rice genes were detected in 44 MQTL regions. Markers flanking the MQTL identified in the present study can be used for marker-assisted breeding and as fixed effects in the genomic selection models for improving the prediction accuracy during quality breeding. Wheat orthologues of rice genes and other CGs available from MQTLs can be promising targets for further functional validation and to better understand the molecular mechanism underlying the quality traits in wheat.
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Affiliation(s)
- Santosh Gudi
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India.
| | - Dinesh Kumar Saini
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Gurjeet Singh
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Priyanka Halladakeri
- Department of Genetics and Plant Breeding, Anand Agricultural University, Gujarat, India
| | - Pradeep Kumar
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Mohammad Shamshad
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Mohammad Jafar Tanin
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Satinder Singh
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Achla Sharma
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
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You FM, Rashid KY, Zheng C, Khan N, Li P, Xiao J, He L, Yao Z, Cloutier S. Insights into the Genetic Architecture and Genomic Prediction of Powdery Mildew Resistance in Flax ( Linum usitatissimum L.). Int J Mol Sci 2022; 23:ijms23094960. [PMID: 35563347 PMCID: PMC9104541 DOI: 10.3390/ijms23094960] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 04/28/2022] [Accepted: 04/28/2022] [Indexed: 12/29/2022] Open
Abstract
Powdery mildew (PM), caused by the fungus Oidium lini in flax, can cause defoliation and reduce seed yield and quality. To date, one major dominant gene (Pm1) and three quantitative trait loci (QTL) on chromosomes 1, 7 and 9 have been reported for PM resistance. To fully dissect the genetic architecture of PM resistance and identify QTL, a diverse flax core collection of 372 accessions augmented with an additional 75 breeding lines were sequenced, and PM resistance was evaluated in the field for eight years (2010–2017) in Morden, Manitoba, Canada. Genome-wide association studies (GWAS) were performed using two single-locus and seven multi-locus statistical models with 247,160 single nucleotide polymorphisms (SNPs) and the phenotypes of the 447 individuals for each year separately as well as the means over years. A total of 349 quantitative trait nucleotides (QTNs) were identified, of which 44 large-effect QTNs (R2 = 10–30%) were highly stable over years. The total number of favourable alleles per accession was significantly correlated with PM resistance (r = 0.74), and genomic selection (GS) models using all identified QTNs generated significantly higher predictive ability (r = 0.93) than those constructed using the 247,160 genome-wide random SNP (r = 0.69), validating the overall reliability of the QTNs and showing the additivity of PM resistance in flax. The QTNs were clustered on the distal ends of all 15 chromosomes, especially on chromosome 5 (0.4–5.6 Mb and 9.4–16.9 Mb) and 13 (4.7–5.2 Mb). To identify candidate genes, a dataset of 3230 SNPs located in resistance gene analogues (RGAs) was used as input for GWAS, from which an additional 39 RGA-specific QTNs were identified. Overall, 269 QTN loci harboured 445 RGAs within the 200 Kb regions spanning the QTNs, including 45 QTNs located within the RGAs. These RGAs supported by significant QTN/SNP allele effects were mostly nucleotide binding site and leucine-rich repeat receptors (NLRs) belonging to either coiled-coil (CC) NLR (CNL) or toll interleukin-1 (TIR) NLR (TNL), receptor-like kinase (RLK), receptor-like protein kinase (RLP), transmembrane-coiled-coil (TM-CC), WRKY, and mildew locus O (MLO) genes. These results constitute an important genomic tool for resistance breeding and gene cloning for PM in flax.
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Affiliation(s)
- Frank M. You
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, Canada; (C.Z.); (N.K.); (P.L.); (L.H.)
- Correspondence: (F.M.Y.); (S.C.); Tel.: +1-613-759-1539 (F.M.Y.); +1-613-759-1744 (S.C.)
| | - Khalid Y. Rashid
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, MB R6M 1Y5, Canada; (K.Y.R.); (Z.Y.)
| | - Chunfang Zheng
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, Canada; (C.Z.); (N.K.); (P.L.); (L.H.)
| | - Nadeem Khan
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, Canada; (C.Z.); (N.K.); (P.L.); (L.H.)
- Department of Biology, University of Ottawa, 30 Marie Curie, Ottawa, ON K1N 6N5, Canada
| | - Pingchuan Li
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, Canada; (C.Z.); (N.K.); (P.L.); (L.H.)
| | - Jin Xiao
- Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Nanjing Agricultural University/JCIC-MCP, Nanjing 210095, China;
| | - Liqiang He
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, Canada; (C.Z.); (N.K.); (P.L.); (L.H.)
- Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Nanjing Agricultural University/JCIC-MCP, Nanjing 210095, China;
| | - Zhen Yao
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, MB R6M 1Y5, Canada; (K.Y.R.); (Z.Y.)
| | - Sylvie Cloutier
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, Canada; (C.Z.); (N.K.); (P.L.); (L.H.)
- Correspondence: (F.M.Y.); (S.C.); Tel.: +1-613-759-1539 (F.M.Y.); +1-613-759-1744 (S.C.)
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Saini DK, Srivastava P, Pal N, Gupta PK. Meta-QTLs, ortho-meta-QTLs and candidate genes for grain yield and associated traits in wheat (Triticum aestivum L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:1049-1081. [PMID: 34985537 DOI: 10.1007/s00122-021-04018-3] [Citation(s) in RCA: 43] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 12/10/2021] [Indexed: 05/03/2023]
Abstract
In wheat, 2852 major QTLs of 8998 QTLs available for yield and related traits were used for meta-analysis; 141 meta-QTLs were identified, which included 13 breeder's MQTLs and 24 ortho-MQTLs; 1202 candidate genes and 50 homologues of genes for yield from other cereals were also identified. Meta-QTL analysis was conducted using 2852 of the 8998 known QTLs, retrieved from 230 reports published during 1999-2020 (including 19 studies on tetraploid wheat) for grain yield (GY) and the following ten component traits: (i) grain weight (GWei), (ii) grain morphology-related traits (GMRTs), (iii) grain number (GN), (iv) spikes-related traits (SRTs), (v) plant height (PH), (vi) tiller number (TN), (vii) harvest index (HI), (viii) biomass yield (BY), (ix) days to heading/flowering and maturity (DTH/F/M), and (x) grain filling duration (GFD). The study resulted in the identification of 141 meta-QTLs (MQTLs), with an average confidence interval (CI) of 1.4 cM as against a CI of > 12.1 cM (8.8 fold reduction) in the QTLs that were used. The corresponding physical length of CI ranged from 0.01 Mb to 661.9 Mb (mean, 31.5 Mb). Seventy-seven (77) of these 141 MQTLs overlapped marker-trait associations (MTAs) reported in genome-wide association studies. Also, 63 MQTLs (each based on at least 10 QTLs) were considered stable and robust, with 13 MQTLs described as breeder's MQTLs (selected based on small CI, large LOD, and high level of phenotypic variation explained). Thirty-five yield-related genes from rice, barley, and maize were also utilized to identify 50 wheat homologues in MQTLs. Further, the use of synteny and collinearity allowed the identification of 24 ortho-MQTLs which were common among the wheat, barley, rice, and maize. The results of the present study should prove useful for wheat breeding and future basic research in cereals including wheat, barley, rice, and maize.
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Affiliation(s)
- Dinesh Kumar Saini
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, 141004, India
| | - Puja Srivastava
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, 141004, India.
| | - Neeraj Pal
- Department of Molecular Biology and Genetic Engineering, G. B. Pant University of Agriculture and Technology, Pantnagar, Uttarakhand, 263145, India
| | - P K Gupta
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, 250004, India
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Saini DK, Chahal A, Pal N, Srivastava P, Gupta PK. Meta-analysis reveals consensus genomic regions associated with multiple disease resistance in wheat ( Triticum aestivum L.). MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2022; 42:11. [PMID: 37309411 PMCID: PMC10248701 DOI: 10.1007/s11032-022-01282-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 02/07/2022] [Indexed: 06/14/2023]
Abstract
In wheat, meta-QTLs (MQTLs) and candidate genes (CGs) were identified for multiple disease resistance (MDR). For this purpose, information was collected from 58 studies for mapping QTLs for resistance to one or more of the five diseases. As many as 493 QTLs were available from these studies, which were distributed in five diseases as follows: septoria tritici blotch (STB) 126 QTLs; septoria nodorum blotch (SNB), 103 QTLs; fusarium head blight (FHB), 184 QTLs; karnal bunt (KB), 66 QTLs; and loose smut (LS), 14 QTLs. Of these 493 QTLs, only 291 QTLs could be projected onto a consensus genetic map, giving 63 MQTLs. The CI of the MQTLs ranged from 0.04 to 15.31 cM with an average of 3.09 cM per MQTL. This is a ~ 4.39 fold reduction from the CI of QTLs, which ranged from 0 to 197.6 cM, with a mean of 13.57 cM. Of 63 MQTLs, 60 were anchored to the reference physical map of wheat (the physical interval of these MQTLs ranged from 0.30 to 726.01 Mb with an average of 74.09 Mb). Thirty-eight (38) of these MQTLs were verified using marker-trait associations (MTAs) derived from genome-wide association studies. As many as 874 CGs were also identified which were further investigated for differential expression using data from five transcriptome studies, resulting in 194 differentially expressed candidate genes (DECGs). Among the DECGs, 85 genes had functions previously reported to be associated with disease resistance. These results should prove useful for fine mapping and cloning of MDR genes and marker-assisted breeding. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-022-01282-z.
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Affiliation(s)
- Dinesh Kumar Saini
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab-141004 India
| | - Amneek Chahal
- College of Agriculture, Punjab Agricultural University, Ludhiana, Punjab-141004 India
| | - Neeraj Pal
- Department of Molecular Biology and Genetic Engineering, G. B. Pant, University of Agriculture and Technology, Pantnagar, Uttrakhand-263145 India
| | - Puja Srivastava
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab-141004 India
| | - Pushpendra Kumar Gupta
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, 250004 India
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Hinterberger V, Douchkov D, Lück S, Kale S, Mascher M, Stein N, Reif JC, Schulthess AW. Mining for New Sources of Resistance to Powdery Mildew in Genetic Resources of Winter Wheat. FRONTIERS IN PLANT SCIENCE 2022; 13:836723. [PMID: 35300015 PMCID: PMC8922026 DOI: 10.3389/fpls.2022.836723] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 01/31/2022] [Indexed: 05/02/2023]
Abstract
Genetic pathogen control is an economical and sustainable alternative to the use of chemicals. In order to breed resistant varieties, information about potentially unused genetic resistance mechanisms is of high value. We phenotyped 8,316 genotypes of the winter wheat collection of the German Federal ex situ gene bank for Agricultural and Horticultural Crops, Germany, for resistance to powdery mildew (PM), Blumeria graminis f. sp. tritici, one of the most important biotrophic pathogens in wheat. To achieve this, we used a semi-automatic phenotyping facility to perform high-throughput detached leaf assays. This data set, combined with genotyping-by-sequencing (GBS) marker data, was used to perform a genome-wide association study (GWAS). Alleles of significantly associated markers were compared with SNP profiles of 171 widely grown wheat varieties in Germany to identify currently unexploited resistance conferring genes. We also used the Chinese Spring reference genome annotation and various domain prediction algorithms to perform a domain enrichment analysis and produced a list of candidate genes for further investigation. We identified 51 significantly associated regions. In most of these, the susceptible allele was fixed in the tested commonly grown wheat varieties. Eleven of these were located on chromosomes for which no resistance conferring genes have been previously reported. In addition to enrichment of leucine-rich repeats (LRR), we saw enrichment of several domain types so far not reported as relevant to PM resistance, thus, indicating potentially novel candidate genes for the disease resistance research and prebreeding in wheat.
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Affiliation(s)
| | - Dimitar Douchkov
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany
| | - Stefanie Lück
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany
| | - Sandip Kale
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany
| | - Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany
- Center for Integrated Breeding Research (CiBreed), Georg-August-University, Göttingen, Germany
| | - Jochen C. Reif
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany
| | - Albert W. Schulthess
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany
- *Correspondence: Albert W. Schulthess
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Pal N, Saini DK, Kumar S. Meta-QTLs, ortho-MQTLs and candidate genes for the traits contributing to salinity stress tolerance in common wheat ( Triticum aestivum L.). PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2021; 27:2767-2786. [PMID: 35035135 PMCID: PMC8720133 DOI: 10.1007/s12298-021-01112-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 12/04/2021] [Accepted: 12/07/2021] [Indexed: 05/20/2023]
Abstract
A meta-analysis of QTLs associated with the traits contributing to salinity tolerance was undertaken in wheat to detect consensus and robust meta-QTLs (MQTLs) using 844 known QTLs retrieved from 26 earlier studies. A consensus map with a total length of 4621.56 cM including 7710 markers was constructed using 21 individual linkage maps and three previously published integrated genetic maps. Out of 844 QTLs, 571 QTLs were projected on the consensus map which gave origin to 100 MQTLs. Interestingly, 49 MQTLs were co-located with marker-trait associations reported in wheat genome-wide association studies for the traits contributing to salinity stress tolerance. Five potential MQTLs associated with the major salinity-responsive traits were also identified to be utilized in the breeding programme. In the resulted MQTLs, the average confidence interval (CI, 3.58 cM) was reduced up to 4.16 folds compared to the mean CI of the initial QTLs. Furthermore, as many as 617 gene models including 81 most likely candidate genes (CGs) were identified in the high confidence MQTL regions. These most likely CGs encoded proteins mainly belonging to the following families: B-box-type zinc finger, cytochrome P450 protein, pentatricopeptide repeat, phospholipid/glycerol acyltransferase, F-box protein, small auxin-up RNA, UDP-glucosyltransferase, glutathione S-transferase protein, etc. In addition, ortho-MQTL analysis based on synteny among wheat, rice and barley was also performed which permitted the identification of six ortho-MQTLs among these three cereals. This meta-analysis defines a genome-wide landscape on the most stable and consistent loci associated with reliable molecular markers and candidate genes for salinity tolerance in wheat. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s12298-021-01112-0.
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Affiliation(s)
- Neeraj Pal
- Department of Molecular Biology and Genetic Engineering, G. B. Pant, University of Agriculture and Technology, Pantnagar, Uttarakhand 263145 India
| | - Dinesh Kumar Saini
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab 141004 India
| | - Sundip Kumar
- Department of Molecular Biology and Genetic Engineering, G. B. Pant, University of Agriculture and Technology, Pantnagar, Uttarakhand 263145 India
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Jan I, Saripalli G, Kumar K, Kumar A, Singh R, Batra R, Sharma PK, Balyan HS, Gupta PK. Meta-QTLs and candidate genes for stripe rust resistance in wheat. Sci Rep 2021; 11:22923. [PMID: 34824302 PMCID: PMC8617266 DOI: 10.1038/s41598-021-02049-w] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 11/02/2021] [Indexed: 11/15/2022] Open
Abstract
In bread wheat, meta-QTL analysis was conducted using 353 QTLs that were available from earlier studies. When projected onto a dense consensus map comprising 76,753 markers, only 184 QTLs with the required information, could be utilized leading to identification of 61 MQTLs spread over 18 of the 21 chromosomes (barring 5D, 6D and 7D). The range for mean R2 (PVE %) was 1.9% to 48.1%, and that of CI was 0.02 to 11.47 cM; these CIs also carried 37 Yr genes. Using these MQTLs, 385 candidate genes (CGs) were also identified. Out of these CGs, 241 encoded known R proteins and 120 showed differential expression due to stripe rust infection at the seedling stage; the remaining 24 CGs were common in the sense that they encoded R proteins as well as showed differential expression. The proteins encoded by CGs carried the following widely known domains: NBS-LRR domain, WRKY domains, ankyrin repeat domains, sugar transport domains, etc. Thirteen breeders' MQTLs (PVE > 20%) including four pairs of closely linked MQTLs are recommended for use in wheat molecular breeding, for future studies to understand the molecular mechanism of stripe rust resistance and for gene cloning.
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Grants
- BT/PR21024/AGIII/103/925/2016 Department of Biotechnology, Ministry of Science and Technology, India
- BT/PR21024/AGIII/103/925/2016 Department of Biotechnology, Ministry of Science and Technology, India
- BT/PR21024/AGIII/103/925/2016 Department of Biotechnology, Ministry of Science and Technology, India
- BT/PR21024/AGIII/103/925/2016 Department of Biotechnology, Ministry of Science and Technology, India
- BT/PR21024/AGIII/103/925/2016 Department of Biotechnology, Ministry of Science and Technology, India
- Indian National Science Academy
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Affiliation(s)
- Irfat Jan
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, 250004, India
| | - Gautam Saripalli
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, 250004, India
| | - Kuldeep Kumar
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, 250004, India
| | - Anuj Kumar
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, 250004, India
| | - Rakhi Singh
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, 250004, India
| | - Ritu Batra
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, 250004, India
| | - Pradeep Kumar Sharma
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, 250004, India
| | - Harindra Singh Balyan
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, 250004, India
| | - Pushpendra Kumar Gupta
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, 250004, India.
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Kumar S, Singh VP, Saini DK, Sharma H, Saripalli G, Kumar S, Balyan HS, Gupta PK. Meta-QTLs, ortho-MQTLs, and candidate genes for thermotolerance in wheat ( Triticum aestivum L.). MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2021; 41:69. [PMID: 37309361 PMCID: PMC10236124 DOI: 10.1007/s11032-021-01264-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 11/04/2021] [Indexed: 06/14/2023]
Abstract
Meta-QTL analysis for thermotolerance in wheat was conducted to identify robust meta-QTLs (MQTLs). In this study, 441 QTLs related to 31 heat-responsive traits were projected on the consensus map with 50,310 markers. This exercise resulted in the identification of 85 MQTLs with confidence interval (CI) ranging from 0.11 to 34.9 cM with an average of 5.6 cM. This amounted to a 2.96-fold reduction relative to the mean CI (16.5 cM) of the QTLs used. Seventy-seven (77) of these MQTLs were also compared and verified with the results of recent genome-wide association studies (GWAS). The 85 MQTLs included seven MQTLs that are particularly useful for breeding purposes (we called them breeders' MQTLs). Seven ortho-MQTLs between wheat and rice genomes were also identified using synteny and collinearity. The MQTLs were used for the identification of 1,704 candidate genes (CGs). In silico expression analysis of these CGs permitted identification of 182 differentially expressed genes (DEGs), which included 36 high confidence CGs with known functions previously reported to be important for thermotolerance. These high confidence CGs encoded proteins belonging to the following families: protein kinase, WD40 repeat, glycosyltransferase, ribosomal protein, SNARE associated Golgi protein, GDSL lipase/esterase, SANT/Myb domain, K homology domain, etc. Thus, the present study resulted in the identification of MQTLs (including breeders' MQTLs), ortho-MQTLs, and underlying CGs, which could prove useful not only for molecular breeding for the development of thermotolerant wheat cultivars but also for future studies focused on understanding the molecular basis of thermotolerance. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-021-01264-7.
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Affiliation(s)
- Sourabh Kumar
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, UP India
| | - Vivudh Pratap Singh
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, UP India
| | - Dinesh Kumar Saini
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab India
| | - Hemant Sharma
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, UP India
| | - Gautam Saripalli
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, UP India
| | - Sachin Kumar
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, UP India
| | - Harindra Singh Balyan
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, UP India
| | - Pushpendra Kumar Gupta
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, UP India
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18
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Semagn K, Iqbal M, Chen H, Perez-Lara E, Bemister DH, Xiang R, Zou J, Asif M, Kamran A, N'Diaye A, Randhawa H, Beres BL, Pozniak C, Spaner D. Physical mapping of QTL associated with agronomic and end-use quality traits in spring wheat under conventional and organic management systems. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:3699-3719. [PMID: 34333664 DOI: 10.1007/s00122-021-03923-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 07/20/2021] [Indexed: 06/13/2023]
Abstract
Using phenotypic data of four biparental spring wheat populations evaluated at multiple environments under two management systems, we discovered 152 QTL and 22 QTL hotspots, of which two QTL accounted for up to 37% and 58% of the phenotypic variance, consistently detected in all environments, and fell within genomic regions harboring known genes. Identification of the physical positions of quantitative trait loci (QTL) would be highly useful for developing functional markers and comparing QTL results across multiple independent studies. The objectives of the present study were to map and characterize QTL associated with nine agronomic and end-use quality traits (tillering ability, plant height, lodging, grain yield, grain protein content, thousand kernel weight, test weight, sedimentation volume, and falling number) in hard red spring wheat recombinant inbred lines (RILs) using the International Wheat Genome Sequencing Consortium (IWGSC) RefSeq v2.0 physical map. We evaluated a total of 698 RILs from four populations derived from crosses involving seven parents at 3-8 conventionally (high N) and organically (low N) managed field environments. Using the phenotypic data combined across all environments per management, and the physical map between 1058 and 6526 markers per population, we identified 152 QTL associated with the nine traits, of which 29 had moderate and 2 with major effects. Forty-nine of the 152 QTL mapped across 22 QTL hotspot regions with each region coincident to 2-6 traits. Some of the QTL hotspots were physically located close to known genes. QSv.dms-1A and QPht.dms-4B.1 individually explained up to 37% and 58% of the variation in sedimentation volume and plant height, respectively, and had very large LOD scores that varied from 19.0 to 35.7 and from 16.7 to 55.9, respectively. We consistently detected both QTL in the combined and all individual environments, laying solid ground for further characterization and possibly for cloning.
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Affiliation(s)
- Kassa Semagn
- Department of Agricultural, Food and Nutritional Science, 4-10 Agriculture-Forestry Centre, University of Alberta, Edmonton, AB, T6G 2P5, Canada
| | - Muhammad Iqbal
- Department of Agricultural, Food and Nutritional Science, 4-10 Agriculture-Forestry Centre, University of Alberta, Edmonton, AB, T6G 2P5, Canada
| | - Hua Chen
- Department of Agricultural, Food and Nutritional Science, 4-10 Agriculture-Forestry Centre, University of Alberta, Edmonton, AB, T6G 2P5, Canada
- Department of Agronomy, School of Life Science and Engineering, Southwest University of Science and Technology, 59 Qinglong Road, Mianyang, 621010, Sichuan, China
| | - Enid Perez-Lara
- Department of Agricultural, Food and Nutritional Science, 4-10 Agriculture-Forestry Centre, University of Alberta, Edmonton, AB, T6G 2P5, Canada
| | - Darcy H Bemister
- Department of Agricultural, Food and Nutritional Science, 4-10 Agriculture-Forestry Centre, University of Alberta, Edmonton, AB, T6G 2P5, Canada
| | - Rongrong Xiang
- Department of Agricultural, Food and Nutritional Science, 4-10 Agriculture-Forestry Centre, University of Alberta, Edmonton, AB, T6G 2P5, Canada
| | - Jun Zou
- Department of Agricultural, Food and Nutritional Science, 4-10 Agriculture-Forestry Centre, University of Alberta, Edmonton, AB, T6G 2P5, Canada
| | - Muhammad Asif
- Department of Agricultural, Food and Nutritional Science, 4-10 Agriculture-Forestry Centre, University of Alberta, Edmonton, AB, T6G 2P5, Canada
- Department of Agronomy, 2004 Throckmorton Plant Science Center, Kansas State University, Manhattan, KS, 66506, USA
- Heartland Plant Innovations, Kansas Wheat Innovation Center, 1990 Kimball Avenue, Manhattan, KS, 66502, USA
| | - Atif Kamran
- Department of Agricultural, Food and Nutritional Science, 4-10 Agriculture-Forestry Centre, University of Alberta, Edmonton, AB, T6G 2P5, Canada
- Department of Botany, Seed Centre, The University of Punjab, New Campus, Lahore, 54590, Pakistan
| | - Amidou N'Diaye
- Crop Development Centre and Department of Plant Sciences, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK, S7N 5A8, Canada
| | - Harpinder Randhawa
- Agriculture, and Agri-Food Canada, 5403-1st Avenue South, Lethbridge, AB, T1J 4B1, Canada
| | - Brian L Beres
- Agriculture, and Agri-Food Canada, 5403-1st Avenue South, Lethbridge, AB, T1J 4B1, Canada
| | - Curtis Pozniak
- Crop Development Centre and Department of Plant Sciences, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK, S7N 5A8, Canada
| | - Dean Spaner
- Department of Agricultural, Food and Nutritional Science, 4-10 Agriculture-Forestry Centre, University of Alberta, Edmonton, AB, T6G 2P5, Canada.
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19
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Arif MAR, Shokat S, Plieske J, Ganal M, Lohwasser U, Chesnokov YV, Kocherina NV, Kulwal P, Kumar N, McGuire PE, Sorrells ME, Qualset CO, Börner A. A SNP-based genetic dissection of versatile traits in bread wheat (Triticum aestivum L.). THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 108:960-976. [PMID: 34218494 DOI: 10.1111/tpj.15407] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 06/14/2021] [Indexed: 05/20/2023]
Abstract
The continuous increase in global population prompts increased wheat production. Future wheat (Triticum aestivum L.) breeding will heavily rely on dissecting molecular and genetic bases of wheat yield and related traits which is possible through the discovery of quantitative trait loci (QTLs) in constructed populations, such as recombinant inbred lines (RILs). Here, we present an evaluation of 92 RILs in a bi-parental RIL mapping population (the International Triticeae Mapping Initiative Mapping Population [ITMI/MP]) using newly generated phenotypic data in 3-year experiments (2015), older phenotypic data (1997-2009), and newly created single nucleotide polymorphism (SNP) marker data based on 92 of the original RILs to search for novel and stable QTLs. Our analyses of more than 15 unique traits observed in multiple experiments included analyses of 46 traits in three environments in the USA, 69 traits in eight environments in Germany, 149 traits in 10 environments in Russia, and 28 traits in four environments in India (292 traits in 25 environments) with 7584 SNPs (292 × 7584 = 2 214 528 data points). A total of 874 QTLs were detected with limit of detection (LOD) scores of 2.01-3.0 and 432 QTLs were detected with LOD > 3.0. Moreover, 769 QTLs could be assigned to 183 clusters based on the common markers and relative proximity of related QTLs, indicating gene-rich regions throughout the A, B, and D genomes of common wheat. This upgraded genotype-phenotype information of ITMI/MP can assist breeders and geneticists who can make crosses with suitable RILs to improve or investigate traits of interest.
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Affiliation(s)
- Mian Abdur Rehman Arif
- Wheat Breeding Group, Plant Breeding and Genetics Division, Nuclear Institute for Agriculture and Biology (NIAB), Faisalabad, Pakistan
| | - Sajid Shokat
- Wheat Breeding Group, Plant Breeding and Genetics Division, Nuclear Institute for Agriculture and Biology (NIAB), Faisalabad, Pakistan
| | - Jörg Plieske
- SGS Institut Fresenius GmbH TraitGenetics Section, Am Schwabeplan 1b, Stadt Seeland, OT Gatersleben, 06466, Germany
| | - Martin Ganal
- SGS Institut Fresenius GmbH TraitGenetics Section, Am Schwabeplan 1b, Stadt Seeland, OT Gatersleben, 06466, Germany
| | - Ulrike Lohwasser
- Resources Genetics and Reproduction Group, Leibniz Institute of Plant Genetics and Crop Plant Research, Corrensstr. 3, Seeland, OT Gatersleben, 06466, Germany
| | - Yuriy V Chesnokov
- Laboratory of Ecological Genetics and Plant Breeding, Agrophysical Research Institute, Grazhdanskiy pr. 14, St. Petersburg, 195220, Russia
| | - Nataliya V Kocherina
- Laboratory of Ecological Genetics and Plant Breeding, Agrophysical Research Institute, Grazhdanskiy pr. 14, St. Petersburg, 195220, Russia
| | - Pawan Kulwal
- State Level Biotechnology Centre, Mahatma Phule Krishi Vidyapeeth, Rahuri, Ahmednagar, Maharashtra, 413 722, India
| | - Neeraj Kumar
- Department of Plant and Environmental Sciences, Clemson University, 100C Biosystems Research Complex 105 Collings Street, Clemson, SC, 29634-0141, USA
| | - Patrick E McGuire
- Plant Sciences Department, University of California, Mail Stop 3, One Shields Avenue, Davis, CA, 95616, USA
| | - Mark E Sorrells
- Department of Plant Breeding and Genetics, Cornell University, Ithaca, NY, 14853, USA
| | - Calvin O Qualset
- Plant Sciences Department, University of California, Mail Stop 3, One Shields Avenue, Davis, CA, 95616, USA
| | - Andreas Börner
- Resources Genetics and Reproduction Group, Leibniz Institute of Plant Genetics and Crop Plant Research, Corrensstr. 3, Seeland, OT Gatersleben, 06466, Germany
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20
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Saini DK, Chopra Y, Pal N, Chahal A, Srivastava P, Gupta PK. Meta-QTLs, ortho-MQTLs and candidate genes for nitrogen use efficiency and root system architecture in bread wheat ( Triticum aestivum L.). PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2021; 27:2245-2267. [PMID: 34744364 PMCID: PMC8526679 DOI: 10.1007/s12298-021-01085-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 09/26/2021] [Accepted: 09/27/2021] [Indexed: 05/04/2023]
Abstract
In wheat, meta-QTLs (MQTLs), ortho-MQTLs, and candidate genes (CGs) were identified for nitrogen use efficiency and root system architecture. For this purpose, 1788 QTLs were available from 24 studies published during 2006-2020. Of these, 1098 QTLs were projected onto the consensus map resulting in 118 MQTLs. The average confidence interval (CI) of MQTLs was reduced up to 8.56 folds in comparison to the average CI of QTLs. Of the 118 MQTLs, 112 were anchored to the physical map of the wheat reference genome. The physical interval of MQTLs ranged from 0.02 to 666.18 Mb with a mean of 94.36 Mb. Eighty-eight of these 112 MQTLs were verified by marker-trait associations (MTAs) identified in published genome-wide association studies (GWAS); the MQTLs that were verified using GWAS also included 9 most robust MQTLs, which are particularly useful for breeders; we call them 'Breeder's QTLs'. Some selected wheat MQTLs were further utilized for the identification of ortho-MQTLs for wheat and maize; 9 such ortho-MQTLs were available. As many as 1991 candidate genes (CGs) were also detected, which included 930 CGs with an expression level of > 2 transcripts per million in relevant organs/tissues. Among the CGs, 97 CGs with functions previously reported as important for the traits under study were selected. Based on homology analysis and expression patterns, 49 orthologues of 35 rice genes were also identified in MQTL regions. The results of the present study may prove useful for the improvement of selection strategy for yield potential, stability, and performance under N-limiting conditions. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s12298-021-01085-0.
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Affiliation(s)
- Dinesh Kumar Saini
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, 141004 India
| | - Yuvraj Chopra
- College of Agriculture, Punjab Agricultural University, Ludhiana, 141004 India
- Present Address: Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE 68583 USA
| | - Neeraj Pal
- Department of Molecular Biology and Genetic Engineering, G. B. Pant, University of Agriculture and Technology, Pantnagar, Uttarakhand 263145 India
| | - Amneek Chahal
- College of Agriculture, Punjab Agricultural University, Ludhiana, 141004 India
| | - Puja Srivastava
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, 141004 India
| | - Pushpendra Kumar Gupta
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, 250004 India
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21
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Dyda M, Tyrka M, Gołębiowska G, Rapacz M, Wędzony M. Genetic mapping of adult-plant resistance genes to powdery mildew in triticale. J Appl Genet 2021; 63:73-86. [PMID: 34561842 PMCID: PMC8755695 DOI: 10.1007/s13353-021-00664-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 09/03/2021] [Accepted: 09/13/2021] [Indexed: 11/21/2022]
Abstract
Triticale is a cereal of high economic importance; however, along with the increase in the area of this cereal, it is more often infected by the fungal pathogen Blumeria graminis, which causes powdery mildew. The rapid development of molecular biology techniques, in particular methods based on molecular markers may be an important tool used in modern plant breeding. Development of genetic maps, location of the QTLs defining the region of the genome associated with resistance and selection of markers linked to particular trait can be used to select resistant genotypes as well as to pyramidize several resistance genes in one variety. In this paper, we present a new, high-density genetic map of triticale doubled haploids (DH) population “Grenado” × “Zorro” composed of DArT, silicoDArT, and SNP markers. Composite interval mapping method was used to detect eight QTL regions associated with the area under disease progress curve (AUDPC) and 15 regions with the average value of powdery mildew infection (avPM) based on observation conducted in 3-year period in three different locations across the Poland. Two regions on rye chromosome 4R, and single loci on 5R and 6R were reported for the first time as regions associated with powdery mildew resistance. Among all QTLs, 14 candidate genes were identified coded cyclin-dependent kinase, serine/threonine-protein kinase-like protein as well as AMEIOTIC 1 homolog DYAD-like protein, DETOXIFICATION 16-like protein, and putative disease resistance protein RGA3. Three of identified candidate genes were found among newly described QTL regions associated with powdery mildew resistance in triticale.
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Affiliation(s)
- Mateusz Dyda
- Chair of Genetics, Institute of Biology, Pedagogical University of Cracow, Podchorążych 2, 30-084, Kraków, Poland.
| | - Mirosław Tyrka
- Department of Biotechnology and Bioinformatics, Faculty of Chemistry, Rzeszów University of Technology, Rzeszów, Poland
| | - Gabriela Gołębiowska
- Chair of Genetics, Institute of Biology, Pedagogical University of Cracow, Podchorążych 2, 30-084, Kraków, Poland
| | - Marcin Rapacz
- Department of Plant Breeding, Physiology and Seed Science, University of Agriculture in Kraków, Podłużna 3, 30-239, Krakow, Poland
| | - Maria Wędzony
- Chair of Genetics, Institute of Biology, Pedagogical University of Cracow, Podchorążych 2, 30-084, Kraków, Poland
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22
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Mores A, Borrelli GM, Laidò G, Petruzzino G, Pecchioni N, Amoroso LGM, Desiderio F, Mazzucotelli E, Mastrangelo AM, Marone D. Genomic Approaches to Identify Molecular Bases of Crop Resistance to Diseases and to Develop Future Breeding Strategies. Int J Mol Sci 2021; 22:5423. [PMID: 34063853 PMCID: PMC8196592 DOI: 10.3390/ijms22115423] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 04/30/2021] [Accepted: 05/15/2021] [Indexed: 12/16/2022] Open
Abstract
Plant diseases are responsible for substantial crop losses each year and affect food security and agricultural sustainability. The improvement of crop resistance to pathogens through breeding represents an environmentally sound method for managing disease and minimizing these losses. The challenge is to breed varieties with a stable and broad-spectrum resistance. Different approaches, from markers to recent genomic and 'post-genomic era' technologies, will be reviewed in order to contribute to a better understanding of the complexity of host-pathogen interactions and genes, including those with small phenotypic effects and mechanisms that underlie resistance. An efficient combination of these approaches is herein proposed as the basis to develop a successful breeding strategy to obtain resistant crop varieties that yield higher in increasing disease scenarios.
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Affiliation(s)
- Antonia Mores
- Council for Agricultural Research and Economics, Research Centre for Cereal and Industrial Crops, S.S. 673, Km 25,200, 71122 Foggia, Italy; (A.M.); (G.M.B.); (G.L.); (G.P.); (N.P.); (A.M.M.)
| | - Grazia Maria Borrelli
- Council for Agricultural Research and Economics, Research Centre for Cereal and Industrial Crops, S.S. 673, Km 25,200, 71122 Foggia, Italy; (A.M.); (G.M.B.); (G.L.); (G.P.); (N.P.); (A.M.M.)
| | - Giovanni Laidò
- Council for Agricultural Research and Economics, Research Centre for Cereal and Industrial Crops, S.S. 673, Km 25,200, 71122 Foggia, Italy; (A.M.); (G.M.B.); (G.L.); (G.P.); (N.P.); (A.M.M.)
| | - Giuseppe Petruzzino
- Council for Agricultural Research and Economics, Research Centre for Cereal and Industrial Crops, S.S. 673, Km 25,200, 71122 Foggia, Italy; (A.M.); (G.M.B.); (G.L.); (G.P.); (N.P.); (A.M.M.)
| | - Nicola Pecchioni
- Council for Agricultural Research and Economics, Research Centre for Cereal and Industrial Crops, S.S. 673, Km 25,200, 71122 Foggia, Italy; (A.M.); (G.M.B.); (G.L.); (G.P.); (N.P.); (A.M.M.)
| | | | - Francesca Desiderio
- Council for Agricultural Research and Economics, Genomics and Bioinformatics Research Center, Via San Protaso 302, 29017 Fiorenzuola d’Arda, Italy; (F.D.); (E.M.)
| | - Elisabetta Mazzucotelli
- Council for Agricultural Research and Economics, Genomics and Bioinformatics Research Center, Via San Protaso 302, 29017 Fiorenzuola d’Arda, Italy; (F.D.); (E.M.)
| | - Anna Maria Mastrangelo
- Council for Agricultural Research and Economics, Research Centre for Cereal and Industrial Crops, S.S. 673, Km 25,200, 71122 Foggia, Italy; (A.M.); (G.M.B.); (G.L.); (G.P.); (N.P.); (A.M.M.)
| | - Daniela Marone
- Council for Agricultural Research and Economics, Research Centre for Cereal and Industrial Crops, S.S. 673, Km 25,200, 71122 Foggia, Italy; (A.M.); (G.M.B.); (G.L.); (G.P.); (N.P.); (A.M.M.)
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23
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Alemu A, Brazauskas G, Gaikpa DS, Henriksson T, Islamov B, Jørgensen LN, Koppel M, Koppel R, Liatukas Ž, Svensson JT, Chawade A. Genome-Wide Association Analysis and Genomic Prediction for Adult-Plant Resistance to Septoria Tritici Blotch and Powdery Mildew in Winter Wheat. Front Genet 2021; 12:661742. [PMID: 34054924 PMCID: PMC8149967 DOI: 10.3389/fgene.2021.661742] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Accepted: 04/06/2021] [Indexed: 11/29/2022] Open
Abstract
Septoria tritici blotch (STB) caused by the fungal pathogen Zymoseptoria tritici and powdery mildew (PM) caused by Blumeria graminis f.sp tritici (Bgt) are among the forefront foliar diseases of wheat that lead to a significant loss of grain yield and quality. Resistance breeding aimed at developing varieties with inherent resistance to STB and PM diseases has been the most sustainable and environment-friendly approach. In this study, 175 winter wheat landraces and historical cultivars originated from the Nordic region were evaluated for adult-plant resistance (APR) to STB and PM in Denmark, Estonia, Lithuania, and Sweden. Genome-wide association study (GWAS) and genomic prediction (GP) were performed based on the adult-plant response to STB and PM in field conditions using 7,401 single-nucleotide polymorphism (SNP) markers generated by 20K SNP chip. Genotype-by-environment interaction was significant for both disease scores. GWAS detected stable and environment-specific quantitative trait locis (QTLs) on chromosomes 1A, 1B, 1D, 2B, 3B, 4A, 5A, 6A, and 6B for STB and 2A, 2D, 3A, 4B, 5A, 6B, 7A, and 7B for PM adult-plant disease resistance. GP accuracy was improved when assisted with QTL from GWAS as a fixed effect. The GWAS-assisted GP accuracy ranged within 0.53–0.75 and 0.36–0.83 for STB and PM, respectively, across the tested environments. This study highlights that landraces and historical cultivars are a valuable source of APR to STB and PM. Such germplasm could be used to identify and introgress novel resistance genes to modern breeding lines.
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Affiliation(s)
- Admas Alemu
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | - Gintaras Brazauskas
- Institute of Agriculture, Lithuanian Research Centre for Agriculture and Forestry (LAMMC), Kėdainiai, Lithuania
| | - David S Gaikpa
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | | | | | | | - Mati Koppel
- Estonian University of Life Sciences, Tartu, Estonia
| | - Reine Koppel
- Estonian Crop Research Institute, Jõgeva, Estonia
| | - Žilvinas Liatukas
- Institute of Agriculture, Lithuanian Research Centre for Agriculture and Forestry (LAMMC), Kėdainiai, Lithuania
| | | | - Aakash Chawade
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
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24
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Colasuonno P, Marcotuli I, Gadaleta A, Soriano JM. From Genetic Maps to QTL Cloning: An Overview for Durum Wheat. PLANTS (BASEL, SWITZERLAND) 2021; 10:315. [PMID: 33562160 PMCID: PMC7914919 DOI: 10.3390/plants10020315] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 01/26/2021] [Accepted: 02/02/2021] [Indexed: 12/17/2022]
Abstract
Durum wheat is one of the most important cultivated cereal crops, providing nutrients to humans and domestic animals. Durum breeding programs prioritize the improvement of its main agronomic traits; however, the majority of these traits involve complex characteristics with a quantitative inheritance (quantitative trait loci, QTL). This can be solved with the use of genetic maps, new molecular markers, phenotyping data of segregating populations, and increased accessibility to sequences from next-generation sequencing (NGS) technologies. This allows for high-density genetic maps to be developed for localizing candidate loci within a few Kb in a complex genome, such as durum wheat. Here, we review the identified QTL, fine mapping, and cloning of QTL or candidate genes involved in the main traits regarding the quality and biotic and abiotic stresses of durum wheat. The current knowledge on the used molecular markers, sequence data, and how they changed the development of genetic maps and the characterization of QTL is summarized. A deeper understanding of the trait architecture useful in accelerating durum wheat breeding programs is envisioned.
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Affiliation(s)
- Pasqualina Colasuonno
- Department of Agricultural and Environmental Science, University of Bari ‘Aldo Moro’, Via G. Amendola 165/A, 70126 Bari, Italy; (P.C.); (I.M.)
| | - Ilaria Marcotuli
- Department of Agricultural and Environmental Science, University of Bari ‘Aldo Moro’, Via G. Amendola 165/A, 70126 Bari, Italy; (P.C.); (I.M.)
| | - Agata Gadaleta
- Department of Agricultural and Environmental Science, University of Bari ‘Aldo Moro’, Via G. Amendola 165/A, 70126 Bari, Italy; (P.C.); (I.M.)
| | - Jose Miguel Soriano
- Sustainable Field Crops Programme, IRTA (Institute for Food and Agricultural Research and Technology), 25198 Lleida, Spain
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25
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Tomar V, Singh D, Dhillon GS, Singh RP, Poland J, Joshi AK, Singh PK, Bhati PK, Kumar S, Rahman M, Tiwari BS, Kumar U. New QTLs for Spot Blotch Disease Resistance in Wheat ( Triticum aestivum L.) Using Genome-Wide Association Mapping. Front Genet 2021; 11:613217. [PMID: 33519916 PMCID: PMC7841440 DOI: 10.3389/fgene.2020.613217] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 12/10/2020] [Indexed: 11/13/2022] Open
Abstract
Spot blotch disease caused by Bipolaris sorokiniana is a major constraint for wheat production in tropics and subtropics. The introgression of spot blotch resistance alleles to the disease susceptible lines is critical to securing the wheat production in these regions. Although genome-wide association studies (GWASs) for spot blotch were attempted earlier, the present study focused on identifying new quantitative trait loci (QTLs) for spot blotch under natural disease pressure in diverse field conditions. A total of 139 advanced spring wheat lines were evaluated in three environments (three years and two locations) in India and Bangladesh. The GWAS using 14,063 polymorphic genotyping-by-sequencing (GBS) markers identified eight QTLs associated with spot blotch disease resistance belonging to eight chromosomes across the wheat genome. Here, we report the identified marker–trait associations (MTAs), along with the allele effects associated with the disease. The functional annotation of the significant markers identified NBS-LRR, MADS-box transcription factor, and 34 other plant-related protein families across multiple chromosomal regions. The results indicate four promising new QTLs on chromosomes 1A (497.2 Mb), 1D (89.84 Mb), 2B (421.92 Mb), and 6D (6.84 Mb) associated with several disease resistance protein families. These results provide insights into new genomic regions associated with spot blotch disease, and with additional validation, could be utilized in disease resistance breeding efforts in wheat development.
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Affiliation(s)
- Vipin Tomar
- Borlaug Institute for South Asia, Ludhiana, India.,Institute of Advanced Research, Gandhinagar, Gujarat, India
| | - Daljit Singh
- The Climate Corporation, Bayer Crop Science, Creve Coeur, MO, United States
| | - Guriqbal Singh Dhillon
- Department of Biotechnology, Thapar Institute of Engineering and Technology, Patiala, India
| | - Ravi Prakash Singh
- Global Wheat Program, International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
| | - Jesse Poland
- Department of Plant Pathology, Kansas State University, Manhattan, KS, United States
| | - Arun Kumar Joshi
- Borlaug Institute for South Asia, Ludhiana, India.,International Maize and Wheat Improvement Centre, New Delhi, India
| | - Pawan Kumar Singh
- Global Wheat Program, International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
| | | | - Suneel Kumar
- Borlaug Institute for South Asia, Ludhiana, India
| | - Mokhlesur Rahman
- Wheat Research Center, Regional Agricultural Research Station, Bangladesh Agricultural Research Institute, Jamalpur, Bangladesh
| | | | - Uttam Kumar
- Borlaug Institute for South Asia, Ludhiana, India.,Global Wheat Program, International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
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26
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Mapping Powdery Mildew ( Blumeria graminis f. sp. tritici) Resistance in Wild and Cultivated Tetraploid Wheats. Int J Mol Sci 2020; 21:ijms21217910. [PMID: 33114422 PMCID: PMC7662567 DOI: 10.3390/ijms21217910] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 10/19/2020] [Accepted: 10/20/2020] [Indexed: 01/22/2023] Open
Abstract
Wheat is the most widely grown crop and represents the staple food for one third of the world’s population. Wheat is attacked by a large variety of pathogens and the use of resistant cultivars is an effective and environmentally safe strategy for controlling diseases and eliminating the use of fungicides. In this study, a collection of wild and cultivated tetraploid wheats (Triticum turgidum) were evaluated for seedling resistance (SR) and adult plant resistance (APR) to powdery mildew (Blumeria graminis) and genotyped with a 90K single nucleotide polymorphism (SNP) array to identify new sources of resistance genes. The genome-wide association mapping detected 18 quantitative trait loci (QTL) for APR and 8 QTL for SR, four of which were identical or at least closely linked to four QTL for APR. Thirteen candidate genes, containing nucleotide binding sites and leucine-rich repeats, were localized in the confidence intervals of the QTL-tagging SNPs. The marker IWB6155, associated to QPm.mgb-1AS, was located within the gene TRITD1Av1G004560 coding for a disease resistance protein. While most of the identified QTL were described previously, five QTL for APR (QPm.mgb-1AS, QPm.mgb-2BS, QPm.mgb-3BL.1, QPm.mgb-4BL, QPm.mgb-7BS.1) and three QTL for SR (QPm.mgb-3BL.3, QPm.mgb-5AL.2, QPm.mgb-7BS.2) were mapped on chromosome regions where no resistance gene was reported before. The novel QTL/genes can contribute to enriching the resistance sources available to breeders.
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27
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Genome-wide association mapping for adult resistance to powdery mildew in common wheat. Mol Biol Rep 2019; 47:1241-1256. [PMID: 31813131 DOI: 10.1007/s11033-019-05225-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 12/04/2019] [Indexed: 12/23/2022]
Abstract
Blumeria graminis f. sp. tritici, the causal agent of wheat powdery mildew disease, can occur at all stages of the crop and constantly threatens wheat production. To identify candidate resistance genes for powdery mildew, we performed GWAS (genome-wide association studies) on a total set of 329 wheat varieties obtained from different origins. These wheat materials were genotyped using wheat 90K SNP array and evaluated for their resistance in either field or glasshouse condition from 2016 to 2018. Using a mixed linear model, 33 SNP markers of which 14 QTL (quantitative trait loci) were later defined were observed to associate with powdery mildew resistance. Among these, QTL on chromosome 3A, 3B, 6D and 7D were concluded as potentially new QTL. Exploration of candidate genes for new QTL suggested roles of these genes involved in encoding disease resistance and defence-related proteins, and regulating early immune response to the pathogen. Overall, the results reveal that GWAS can be an effective means of identifying marker-trait associations, though further functional validation and fine-mapping of gene candidates are required before creating opportunities for developing new resistant genotypes.
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28
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Mohler V, Stadlmeier M. Dynamic QTL for adult plant resistance to powdery mildew in common wheat (Triticum aestivum L.). J Appl Genet 2019; 60:291-300. [PMID: 31506777 DOI: 10.1007/s13353-019-00518-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Revised: 08/13/2019] [Accepted: 08/21/2019] [Indexed: 01/21/2023]
Abstract
Agriculture will benefit from a rigorous characterization of genes for adult plant resistance (APR) since this gene class was recognized to provide more durable protection from plant diseases. The present study reports the identification of APR loci to powdery mildew in German winter wheat cultivars Cortez and Atlantis. Cortez was previously shown to carry all-stage resistance gene Pm3e. To avoid interference of Pm3e in APR studies, line 6037 that lacked Pm3e but showed field resistance from doubled-haploid (DH) population Atlantis/Cortez was used in two backcrosses to Atlantis for the establishment of DH population 6037/Atlantis//Atlantis. APR was assessed in the greenhouse 10, 15, and 20 days after inoculation (dai) from the 4-leaf stage onwards and combined with single-nucleotide polymorphism data in a genome-wide association study (GWAS) and a linkage map-based quantitative trait loci (QTL) analysis. In GWAS, two QTL were detected: one on chromosome 1BL 10 dai, the other on chromosome 2BL 20 dai. In conventional QTL analysis, both QTL were detected with all three disease ratings: the QTL on chromosome 1BL explained a maximum of 35.2% of the phenotypic variation 10 dai, whereas the QTL on chromosome 2BL explained a maximum of 43.5% of the phenotypic variation 20 dai. Compared with GWAS, linkage map-based QTL analysis allowed following the dynamics of QTL action. The two large-effect QTL for APR to powdery mildew with dynamic gene action can be useful for the enhancement of wheat germplasm.
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Affiliation(s)
- Volker Mohler
- Institute for Crop Science and Plant Breeding, Bavarian State Research Center for Agriculture (LfL), Am Gereuth 6, 85354, Freising, Germany.
| | - Melanie Stadlmeier
- Institute for Crop Science and Plant Breeding, Bavarian State Research Center for Agriculture (LfL), Am Gereuth 6, 85354, Freising, Germany
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29
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Soriano JM, Alvaro F. Discovering consensus genomic regions in wheat for root-related traits by QTL meta-analysis. Sci Rep 2019; 9:10537. [PMID: 31332216 PMCID: PMC6646344 DOI: 10.1038/s41598-019-47038-2] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Accepted: 07/09/2019] [Indexed: 11/25/2022] Open
Abstract
Root system architecture is crucial for wheat adaptation to drought stress, but phenotyping for root traits in breeding programmes is difficult and time-consuming owing to the belowground characteristics of the system. Identifying quantitative trait loci (QTLs) and linked molecular markers and using marker-assisted selection is an efficient way to increase selection efficiency and boost genetic gains in breeding programmes. Hundreds of QTLs have been identified for different root traits in the last few years. In the current study, consensus QTL regions were identified through QTL meta-analysis. First, a consensus map comprising 7352 markers was constructed. For the meta-analysis, 754 QTLs were retrieved from the literature and 634 of them were projected onto the consensus map. Meta-analysis grouped 557 QTLs in 94 consensus QTL regions, or meta-QTLs (MQTLs), and 18 QTLs remained as singletons. The recently published genome sequence of wheat was used to search for gene models within the MQTL peaks. As a result, gene models for 68 of the 94 Root_MQTLs were found, 35 of them related to root architecture and/or drought stress response. This work will facilitate QTL cloning and pyramiding to develop new cultivars with specific root architecture for coping with environmental constraints.
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Affiliation(s)
- Jose Miguel Soriano
- Sustainable Field Crops Programme, IRTA (Institute for Food and Agricultural Research and Technology), Lleida, Spain.
| | - Fanny Alvaro
- Sustainable Field Crops Programme, IRTA (Institute for Food and Agricultural Research and Technology), Lleida, Spain
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30
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Saccomanno A, Matny O, Marone D, Laidò G, Petruzzino G, Mazzucotelli E, Desiderio F, Blanco A, Gadaleta A, Pecchioni N, De Vita P, Steffenson B, Mastrangelo AM. Genetic Mapping of Loci for Resistance to Stem Rust in a Tetraploid Wheat Collection. Int J Mol Sci 2018; 19:E3907. [PMID: 30563213 PMCID: PMC6321032 DOI: 10.3390/ijms19123907] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Revised: 12/04/2018] [Accepted: 12/04/2018] [Indexed: 01/31/2023] Open
Abstract
Stem rust, caused by Puccinia graminis f. sp. tritici (Pgt), is a major biotic constraint to wheat production worldwide. Disease resistant cultivars are a sustainable means for the efficient control of this disease. To identify quantitative trait loci (QTLs) conferring resistance to stem rust at the seedling stage, an association mapping panel consisting of 230 tetraploid wheat accessions were evaluated for reaction to five Pgt races under greenhouse conditions. A high level of phenotypic variation was observed in the panel in response to all of the races, allowing for genome-wide association mapping of resistance QTLs in wild, landrace, and cultivated tetraploid wheats. Twenty-two resistance QTLs were identified, which were characterized by at least two marker-trait associations. Most of the identified resistance loci were coincident with previously identified rust resistance genes/QTLs; however, six regions detected on chromosomes 1B, 5A, 5B, 6B, and 7B may be novel. Availability of the reference genome sequence of wild emmer wheat accession Zavitan facilitated the search for candidate resistance genes in the regions where QTLs were identified, and many of them were annotated as NOD (nucleotide binding oligomerization domain)-like receptor (NLR) genes or genes related to broad spectrum resistance.
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Affiliation(s)
- Antonietta Saccomanno
- Council for Agricultural Research and Economics, Research Centre for Cereal and Industrial Crops, 71122 Foggia (FG), Italy.
| | - Oadi Matny
- Department of Plant Pathology, University of Minnesota, Saint Paul, MN 55108, USA.
| | - Daniela Marone
- Council for Agricultural Research and Economics, Research Centre for Cereal and Industrial Crops, 71122 Foggia (FG), Italy.
| | - Giovanni Laidò
- Council for Agricultural Research and Economics, Research Centre for Cereal and Industrial Crops, 71122 Foggia (FG), Italy.
| | - Giuseppe Petruzzino
- Council for Agricultural Research and Economics, Research Centre for Cereal and Industrial Crops, 71122 Foggia (FG), Italy.
| | - Elisabetta Mazzucotelli
- Council for Agricultural Research and Economics, Research Centre for Genomics and Bioinfomatics, 29017 Fiorenzuola d'Arda (PC), Italy.
| | - Francesca Desiderio
- Council for Agricultural Research and Economics, Research Centre for Genomics and Bioinfomatics, 29017 Fiorenzuola d'Arda (PC), Italy.
| | - Antonio Blanco
- Department of Agricultural & Environmental Science, Research Unit of "Genetics and Plant Biotechnology", University of Bari, 70126 Bari, Italy.
| | - Agata Gadaleta
- Department of Agricultural & Environmental Science, Research Unit of "Genetics and Plant Biotechnology", University of Bari, 70126 Bari, Italy.
| | - Nicola Pecchioni
- Council for Agricultural Research and Economics, Research Centre for Cereal and Industrial Crops, 71122 Foggia (FG), Italy.
| | - Pasquale De Vita
- Council for Agricultural Research and Economics, Research Centre for Cereal and Industrial Crops, 71122 Foggia (FG), Italy.
| | - Brian Steffenson
- Department of Plant Pathology, University of Minnesota, Saint Paul, MN 55108, USA.
| | - Anna Maria Mastrangelo
- Council for Agricultural Research and Economics, Research Centre for Cereal and Industrial Crops, 24126 Bergamo (BG), Italy.
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31
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Fan X, Zhang W, Zhang N, Chen M, Zheng S, Zhao C, Han J, Liu J, Zhang X, Song L, Ji J, Liu X, Ling H, Tong Y, Cui F, Wang T, Li J. Identification of QTL regions for seedling root traits and their effect on nitrogen use efficiency in wheat (Triticum aestivum L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2018; 131:2677-2698. [PMID: 30255337 DOI: 10.1007/s00122-018-3183-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 09/08/2018] [Indexed: 05/26/2023]
Abstract
QTL for a wheat ideotype root system and its plasticity to nitrogen deficiency were characterized. Root system architecture-related traits (RRTs) and their plasticity to nitrogen availability are important for nitrogen acquisition and yield formation in wheat (Triticum aestivum L.). In this study, quantitative trait loci (QTL) analysis was conducted under different nitrogen conditions, using the seedlings of 188 recombinant inbred lines derived from a cross between Kenong 9204 and Jing 411. Fifty-three QTL for seven RRTs and fourteen QTL for the plasticity of these RRTs to nitrogen deficiency were detected. Thirty of these QTL were mapped in nine clusters on chromosomes 2B, 2D, 3A, 3D, 6B, 6D, 7A and 7B. Six of these nine clusters were also colocated with loci for nitrogen use efficiency (NUE)-related traits (NRTs). Among them, three QTL clusters (C2B, C6D and C7B) were highlighted, considering that they individually harbored three stable robust QTL (i.e., QMrl-2B.1, QdRs-6D and QMrl-7B). C2B and C7B stably contributed to the optimal root system, and C6D greatly affected the plasticity of RRTs in response to nitrogen deficiency. However, strong artificial selection was only observed for C7B in 574 derivatives of Kenong 9204. Covariance analysis identified QMrl-7B as the major contributor in C7B that affected the investigated NRTs in mature plants. Phenotypic analysis indicated that thousand kernel weight might represent a "concomitant" above-ground trait of the "hidden" RRTs controlled by C7B, which are used for breeding selection. Dissecting these QTL regions with potential breeding value will ultimately facilitate the selection of donor lines with both high yield and NUE in wheat breeding programs.
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Affiliation(s)
- Xiaoli Fan
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Wei Zhang
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, 050022, China
- State Key Laboratory of Plant Cell and Chromosome Engineering, Chinese Academy of Sciences, Beijing, 100101, China
| | - Na Zhang
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, 050022, China
- State Key Laboratory of Plant Cell and Chromosome Engineering, Chinese Academy of Sciences, Beijing, 100101, China
| | - Mei Chen
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, 050022, China
| | - Shusong Zheng
- State Key Laboratory of Plant Cell and Chromosome Engineering, Chinese Academy of Sciences, Beijing, 100101, China
| | - Chunhua Zhao
- Genetic Improvement Centre of Agricultural and Forest Crops, College of Agriculture, Ludong University, Yantai, 264025, China
| | - Jie Han
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, 050022, China
| | - Jiajia Liu
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, 050022, China
| | - Xilan Zhang
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, 050022, China
| | - Liqiang Song
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, 050022, China
- State Key Laboratory of Plant Cell and Chromosome Engineering, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jun Ji
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, 050022, China
- State Key Laboratory of Plant Cell and Chromosome Engineering, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xigang Liu
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, 050022, China
- State Key Laboratory of Plant Cell and Chromosome Engineering, Chinese Academy of Sciences, Beijing, 100101, China
| | - Hongqing Ling
- State Key Laboratory of Plant Cell and Chromosome Engineering, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yiping Tong
- State Key Laboratory of Plant Cell and Chromosome Engineering, Chinese Academy of Sciences, Beijing, 100101, China
| | - Fa Cui
- Genetic Improvement Centre of Agricultural and Forest Crops, College of Agriculture, Ludong University, Yantai, 264025, China.
| | - Tao Wang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China.
| | - Junming Li
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, 050022, China.
- State Key Laboratory of Plant Cell and Chromosome Engineering, Chinese Academy of Sciences, Beijing, 100101, China.
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32
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De Vita P, Avio L, Sbrana C, Laidò G, Marone D, Mastrangelo AM, Cattivelli L, Giovannetti M. Genetic markers associated to arbuscular mycorrhizal colonization in durum wheat. Sci Rep 2018; 8:10612. [PMID: 30006562 PMCID: PMC6045686 DOI: 10.1038/s41598-018-29020-6] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 07/04/2018] [Indexed: 11/09/2022] Open
Abstract
In this work we investigated the variability and the genetic basis of susceptibility to arbuscular mycorrhizal (AM) colonization of wheat roots. The mycorrhizal status of wild, domesticated and cultivated tetraploid wheat accessions, inoculated with the AM species Funneliformis mosseae, was evaluated. In addition, to detect genetic markers in linkage with chromosome regions involved in AM root colonization, a genome wide association analysis was carried out on 108 durum wheat varieties and two AM fungal species (F. mosseae and Rhizoglomus irregulare). Our findings showed that a century of breeding on durum wheat and the introgression of Reduced height (Rht) genes associated with increased grain yields did not select against AM symbiosis in durum wheat. Seven putative Quantitative Trait Loci (QTLs) linked with durum wheat mycorrhizal susceptibility in both experiments, located on chromosomes 1A, 2B, 5A, 6A, 7A and 7B, were detected. The individual QTL effects (r2) ranged from 7 to 16%, suggesting a genetic basis for this trait. Marker functional analysis identified predicted proteins with potential roles in host-parasite interactions, degradation of cellular proteins, homeostasis regulation, plant growth and disease/defence. The results of this work emphasize the potential for further enhancement of root colonization exploiting the genetic variability present in wheat.
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Affiliation(s)
- Pasquale De Vita
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria, Centro di Ricerca Cerealicoltura e Colture Industriali, S.S. 673 km 25 + 200, 71121, Foggia, Italy.
| | - Luciano Avio
- Dipartimento di Scienze Agrarie, Alimentari e Agro-Ambientali, Università di Pisa, Via del Borghetto 80, 56124, Pisa, Italy
| | | | - Giovanni Laidò
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria, Centro di Ricerca Cerealicoltura e Colture Industriali, S.S. 673 km 25 + 200, 71121, Foggia, Italy
| | - Daniela Marone
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria, Centro di Ricerca Cerealicoltura e Colture Industriali, S.S. 673 km 25 + 200, 71121, Foggia, Italy
| | - Anna M Mastrangelo
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria, Centro di Ricerca Cerealicoltura e Colture Industriali, S.S. 673 km 25 + 200, 71121, Foggia, Italy
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria, Centro di Ricerca Cerealicoltura e Colture Industriali, Via Stezzano 24, 24126, Bergamo, Italy
| | - Luigi Cattivelli
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria, Centro di Ricerca Genomica e Bioinformatica, Via San Protaso 302, 29017, Fiorenzuola d'Arda, (PC), Italy
| | - Manuela Giovannetti
- Dipartimento di Scienze Agrarie, Alimentari e Agro-Ambientali, Università di Pisa, Via del Borghetto 80, 56124, Pisa, Italy
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33
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Tyrka M, Oleszczuk S, Rabiza-Swider J, Wos H, Wedzony M, Zimny J, Ponitka A, Ślusarkiewicz-Jarzina A, Metzger RJ, Baenziger PS, Lukaszewski AJ. Populations of doubled haploids for genetic mapping in hexaploid winter triticale. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2018; 38:46. [PMID: 29623004 PMCID: PMC5878199 DOI: 10.1007/s11032-018-0804-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Accepted: 03/13/2018] [Indexed: 06/08/2023]
Abstract
To create a framework for genetic dissection of hexaploid triticale, six populations of doubled haploid (DH) lines were developed from pairwise hybrids of high-yielding winter triticale cultivars. The six populations comprise between 97 and 231 genotyped DH lines each, totaling 957 DH lines. A consensus genetic map spans 4593.9 cM is composed of 1576 unique DArT markers. The maps reveal several structural rearrangements in triticale genomes. In preliminary tests of the populations and maps, markers specific to wheat segments of the engineered rye chromosome 1R (RM1B) were identified. Example QTL mapping of days to heading in cv. Krakowiak revealed loci on chromosomes 2BL and 2R responsible for extended vernalization requirement, and candidate genes were identified. The material is available to all parties interested in triticale genetics.
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Affiliation(s)
- M. Tyrka
- Department of Biotechnology and Bioinformatics, Rzeszow University of Technology, Rzeszow, Poland
| | - S. Oleszczuk
- Institute of Plant Breeding and Acclimatization, National Research Institute, Radzikow, Poland
| | - J. Rabiza-Swider
- Department of Ornamental Plants, Warsaw University of Life Sciences, Warsaw, Poland
| | - H. Wos
- Plant Breeding Strzelce Ltd., Co. - IHAR-PIB Group, Strzelce, Poland
| | - M. Wedzony
- Department of Cell Biology and Genetics, Pedagogical University of Cracow, Kraków, Poland
| | - J. Zimny
- Institute of Plant Breeding and Acclimatization, National Research Institute, Radzikow, Poland
| | - A. Ponitka
- Institute of Plant Genetics, Poznan, Poland
| | | | - R. J. Metzger
- Department of Crop and Soil Science, Oregon State University, Corvallis, OR 97331-3002 USA
| | - P. S. Baenziger
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE USA
| | - A. J. Lukaszewski
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92521 USA
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Qian C, Cui C, Wang X, Zhou C, Hu P, Li M, Li R, Xiao J, Wang X, Chen P, Xing L, Cao A. Molecular characterisation of the broad-spectrum resistance to powdery mildew conferred by the Stpk-V gene from the wild species Haynaldia villosa. PLANT BIOLOGY (STUTTGART, GERMANY) 2017; 19:875-885. [PMID: 28881082 DOI: 10.1111/plb.12625] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 08/30/2017] [Indexed: 06/07/2023]
Abstract
A key member of the Pm21 resistance gene locus, Stpk-V, derived from Haynaldia villosa, was shown to confer broad-spectrum resistance to wheat powdery mildew. The present study was planned to investigate the resistance mechanism mediated by Stpk-V. Transcriptome analysis was performed in Stpk-V transgenic plants and recipient Yangmai158 upon Bgt infection, and detailed histochemical observations were conducted. Chromosome location of Stpk-V orthologous genes in Triticeae species was conducted for evolutionary study and over-expression of Stpk-V both in barley and Arabidopsis was performed for functional study. The transcriptome results indicate, at the early infection stage, the ROS pathway, JA pathway and some PR proteins associated with the SA pathway were activated in both the resistant Stpk-V transgenic plants and susceptible Yangmai158. However, at the later infection stage, the genes up-regulated at the early stage were continuously held only in the transgenic plants, and a large number of new genes were also activated in the transgenic plants but not in Yangmai158. Results indicate that sustained activation of the early response genes combined with later-activated genes mediated by Stpk-V is critical for resistance in Stpk-V transgenic plants. Stpk-V orthologous genes in the representative grass species are all located on homologous group six chromosomes, indicating that Stpk-V is an ancient gene in the grasses. Over-expression of Stpk-V enhanced host resistance to powdery mildew in barley but not in Arabidopsis. Our results enable a better understanding of the resistance mechanism mediated by Stpk-V, and establish a solid foundation for its use in cereal breeding as a gene resource.
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Affiliation(s)
- C Qian
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, China
- Laboratory of Forage Breeding, Institute of Animal Science, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - C Cui
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, China
| | - X Wang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, China
| | - C Zhou
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, China
| | - P Hu
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, China
| | - M Li
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, China
| | - R Li
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, China
| | - J Xiao
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, China
| | - X Wang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, China
| | - P Chen
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, China
| | - L Xing
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, China
| | - A Cao
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, China
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Iannucci A, Marone D, Russo MA, De Vita P, Miullo V, Ferragonio P, Blanco A, Gadaleta A, Mastrangelo AM. Mapping QTL for Root and Shoot Morphological Traits in a Durum Wheat × T. dicoccum Segregating Population at Seedling Stage. Int J Genomics 2017; 2017:6876393. [PMID: 28845431 PMCID: PMC5563412 DOI: 10.1155/2017/6876393] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Revised: 05/12/2017] [Accepted: 06/21/2017] [Indexed: 01/27/2023] Open
Abstract
A segregating population of 136 recombinant inbred lines derived from a cross between the durum wheat cv. "Simeto" and the T. dicoccum accession "Molise Colli" was grown in soil and evaluated for a number of shoot and root morphological traits. A total of 17 quantitative trait loci (QTL) were identified for shoot dry weight, number of culms, and plant height and for root dry weight, volume, length, surface area, and number of forks and tips, on chromosomes 1B, 2A, 3A, 4B, 5B, 6A, 6B, and 7B. LODs were 2.1 to 21.6, with percent of explained phenotypic variability between 0.07 and 52. Three QTL were mapped to chromosome 4B, one of which corresponds to the Rht-B1 locus and has a large impact on both shoot and root traits (LOD 21.6). Other QTL that have specific effects on root morphological traits were also identified. Moreover, meta-QTL analysis was performed to compare the QTL identified in the "Simeto" × "Molise Colli" segregating population with those described in previous studies in wheat, with three novel QTL defined. Due to the complexity of phenotyping for root traits, further studies will be helpful to validate these regions as targets for breeding programs for optimization of root function for field performance.
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Affiliation(s)
- Anna Iannucci
- Consiglio per la Ricerca in Agricoltura e l'analisi dell'economia Agraria-Centro Cerealicoltura e Colture Industriali (CREA-CI), SS 673 km 25.2, 71122 Foggia, Italy
| | - Daniela Marone
- Consiglio per la Ricerca in Agricoltura e l'analisi dell'economia Agraria-Centro Cerealicoltura e Colture Industriali (CREA-CI), SS 673 km 25.2, 71122 Foggia, Italy
| | - Maria Anna Russo
- Consiglio per la Ricerca in Agricoltura e l'analisi dell'economia Agraria-Centro Cerealicoltura e Colture Industriali (CREA-CI), SS 673 km 25.2, 71122 Foggia, Italy
| | - Pasquale De Vita
- Consiglio per la Ricerca in Agricoltura e l'analisi dell'economia Agraria-Centro Cerealicoltura e Colture Industriali (CREA-CI), SS 673 km 25.2, 71122 Foggia, Italy
| | - Vito Miullo
- Consiglio per la Ricerca in Agricoltura e l'analisi dell'economia Agraria-Centro Cerealicoltura e Colture Industriali (CREA-CI), SS 673 km 25.2, 71122 Foggia, Italy
| | - Pina Ferragonio
- Consiglio per la Ricerca in Agricoltura e l'analisi dell'economia Agraria-Centro Cerealicoltura e Colture Industriali (CREA-CI), SS 673 km 25.2, 71122 Foggia, Italy
| | - Antonio Blanco
- Department of Soil, Plant and Food Sciences, Section of Genetic and Plant Breeding, University of Bari Aldo Moro, Via G. Amendola 165/A, 70126 Bari, Italy
| | - Agata Gadaleta
- Department of Soil, Plant and Food Sciences, Section of Genetic and Plant Breeding, University of Bari Aldo Moro, Via G. Amendola 165/A, 70126 Bari, Italy
| | - Anna Maria Mastrangelo
- Consiglio per la Ricerca in Agricoltura e l'analisi dell'economia Agraria-Centro Cerealicoltura e Colture Industriali (CREA-CI), SS 673 km 25.2, 71122 Foggia, Italy
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Ren Y, Hou W, Lan C, Basnet BR, Singh RP, Zhu W, Cheng X, Cui D, Chen F. QTL Analysis and Nested Association Mapping for Adult Plant Resistance to Powdery Mildew in Two Bread Wheat Populations. FRONTIERS IN PLANT SCIENCE 2017; 8:1212. [PMID: 28798752 PMCID: PMC5529384 DOI: 10.3389/fpls.2017.01212] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Accepted: 06/27/2017] [Indexed: 05/20/2023]
Abstract
CIMMYT wheat (Triticum aestivum L.) lines Francolin#1 and Quaiu#3 displayed effective and stable adult plant resistance (APR) to Chinese Blumeria graminis f. sp. tritici isolates in the field. To elucidate their genetic basis of resistance, two recombinant inbred line (RIL) populations of their crosses with Avocet, the susceptible parent, were phenotyped in Zhengzhou and Shangqiu in the 2014-2015 and 2015-2016 cropping seasons. These populations were also genotyped with SSR (simple sequence repeat markers) and DArT (diversity arrays technology) markers. Two common significant quantitative trait loci (QTL) on wheat chromosomes 1BL and 4BL were detected in both populations by joint and individual inclusive composite interval mapping, explaining 20.3-28.7% and 9.6-15.9% of the phenotypic variance in Avocet × Francolin#1 and 4.8-11.5% and 10.8-18.9% in Avocet × Quaiu#3, respectively. Additional QTL were mapped on chromosomes 1DL and 5BL in Avocet × Francolin#1 and on 2DL and 6BS in Avocet × Quaiu#3. Among these, QPm.heau-1DL is probably a novel APR gene contributing 6.1-8.5% of total phenotypic variance. The QTL on 1BL corresponds to the pleiotropic multi-pathogen resistance gene Yr29/Lr46/Pm39, whereas the QTL on 2DL maps to a similar region where stripe rust resistance gene Yr54 is located. The QTL identified can potentially be used for the improvement of powdery mildew and rust resistance in wheat breeding.
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Affiliation(s)
- Yan Ren
- Collaborative Innovation Center of Henan Grain Crops/National Key Laboratory of Wheat and Maize Crop Science/Agronomy College, Henan Agricultural UniversityZhengzhou, China
| | - Weixiu Hou
- Collaborative Innovation Center of Henan Grain Crops/National Key Laboratory of Wheat and Maize Crop Science/Agronomy College, Henan Agricultural UniversityZhengzhou, China
| | - Caixia Lan
- International Maize and Wheat Improvement Center (CIMMYT)Mexico, Mexico
| | - Bhoja R. Basnet
- International Maize and Wheat Improvement Center (CIMMYT)Mexico, Mexico
| | - Ravi P. Singh
- International Maize and Wheat Improvement Center (CIMMYT)Mexico, Mexico
| | - Wei Zhu
- Shangqiu Academy of Agricultural and Forestry SciencesShangqiu, China
| | - Xiyong Cheng
- Collaborative Innovation Center of Henan Grain Crops/National Key Laboratory of Wheat and Maize Crop Science/Agronomy College, Henan Agricultural UniversityZhengzhou, China
| | - Dangqun Cui
- Collaborative Innovation Center of Henan Grain Crops/National Key Laboratory of Wheat and Maize Crop Science/Agronomy College, Henan Agricultural UniversityZhengzhou, China
| | - Feng Chen
- Collaborative Innovation Center of Henan Grain Crops/National Key Laboratory of Wheat and Maize Crop Science/Agronomy College, Henan Agricultural UniversityZhengzhou, China
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Chandra S, Kazmi AZ, Ahmed Z, Roychowdhury G, Kumari V, Kumar M, Mukhopadhyay K. Genome-wide identification and characterization of NB-ARC resistant genes in wheat (Triticum aestivum L.) and their expression during leaf rust infection. PLANT CELL REPORTS 2017; 36:1097-1112. [PMID: 28401336 DOI: 10.1007/s00299-017-2141-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Accepted: 04/04/2017] [Indexed: 05/06/2023]
Abstract
NB-ARC domain-containing resistance genes from the wheat genome were identified, characterized and localized on chromosome arms that displayed differential yet positive response during incompatible and compatible leaf rust interactions. Wheat (Triticum aestivum L.) is an important cereal crop; however, its production is affected severely by numerous diseases including rusts. An efficient, cost-effective and ecologically viable approach to control pathogens is through host resistance. In wheat, high numbers of resistance loci are present but only few have been identified and cloned. A comprehensive analysis of the NB-ARC-containing genes in complete wheat genome was accomplished in this study. Complete NB-ARC encoding genes were mined from the Ensembl Plants database to predict 604 NB-ARC containing sequences using the HMM approach. Genome-wide analysis of orthologous clusters in the NB-ARC-containing sequences of wheat and other members of the Poaceae family revealed maximum homology with Oryza sativa indica and Brachypodium distachyon. The identification of overlap between orthologous clusters enabled the elucidation of the function and evolution of resistance proteins. The distributions of the NB-ARC domain-containing sequences were found to be balanced among the three wheat sub-genomes. Wheat chromosome arms 4AL and 7BL had the most NB-ARC domain-containing contigs. The spatio-temporal expression profiling studies exemplified the positive role of these genes in resistant and susceptible wheat plants during incompatible and compatible interaction in response to the leaf rust pathogen Puccinia triticina. Two NB-ARC domain-containing sequences were modelled in silico, cloned and sequenced to analyze their fine structures. The data obtained in this study will augment isolation, characterization and application NB-ARC resistance genes in marker-assisted selection based breeding programs for improving rust resistance in wheat.
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Affiliation(s)
- Saket Chandra
- Department of Bio-Engineering, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, 835215, India
| | - Andaleeb Z Kazmi
- Department of Bio-Engineering, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, 835215, India
| | - Zainab Ahmed
- Department of Bio-Engineering, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, 835215, India
| | - Gargi Roychowdhury
- Department of Bio-Engineering, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, 835215, India
| | - Veena Kumari
- Department of Bio-Engineering, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, 835215, India
| | - Manish Kumar
- Department of Bio-Engineering, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, 835215, India
| | - Kunal Mukhopadhyay
- Department of Bio-Engineering, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, 835215, India.
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38
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Soriano JM, Malosetti M, Roselló M, Sorrells ME, Royo C. Dissecting the old Mediterranean durum wheat genetic architecture for phenology, biomass and yield formation by association mapping and QTL meta-analysis. PLoS One 2017; 12:e0178290. [PMID: 28542488 PMCID: PMC5444813 DOI: 10.1371/journal.pone.0178290] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Accepted: 05/10/2017] [Indexed: 12/01/2022] Open
Abstract
Association mapping was used to identify genome regions affecting yield formation, crop phenology and crop biomass in a collection of 172 durum wheat landraces representative of the genetic diversity of ancient local durum varieties from the Mediterranean Basin. The collection was genotyped with 1,149 DArT markers and phenotyped in Spanish northern and southern locations during three years. A total of 245 significant marker trait associations (MTAs) (P<0.01) were detected. Some of these associations confirmed previously identified quantitative trait loci (QTL) and/or candidate genes, and others are reported for the first time here. Eighty-six MTAs corresponded with yield and yield component traits, 70 to phenology and 89 to biomass production. Twelve genomic regions harbouring stable MTAs (significant in three or more environments) were identified, while five and two regions showed specific MTAs for northern and southern environments, respectively. Sixty per cent of MTAs were located on the B genome and 29% on the A genome. The marker wPt-9859 was detected in 12 MTAs, associated with six traits in four environments and the mean across years. To refine QTL positions, a meta-analysis was performed. A total of 477 unique QTLs were projected onto a durum wheat consensus map and were condensed to 71 meta-QTLs and left 13 QTLs as singletons. Sixty-one percent of QTLs explained less than 10% of the phenotypic variance confirming the high genetic complexity of the traits analysed.
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Affiliation(s)
- Jose Miguel Soriano
- Field Crops Programme, IRTA (Institute for Food and Agricultural Research and Technology), Lleida, Spain
| | - Marcos Malosetti
- Biometrics, Wageningen University and Research Centre, Wageningen, The Netherlands
| | - Martina Roselló
- Field Crops Programme, IRTA (Institute for Food and Agricultural Research and Technology), Lleida, Spain
| | - Mark Earl Sorrells
- Department of Plant Breeding and Genetics, Cornell University, Ithaca, NY, United States of America
| | - Conxita Royo
- Field Crops Programme, IRTA (Institute for Food and Agricultural Research and Technology), Lleida, Spain
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Corwin JA, Kliebenstein DJ. Quantitative Resistance: More Than Just Perception of a Pathogen. THE PLANT CELL 2017; 29:655-665. [PMID: 28302676 PMCID: PMC5435431 DOI: 10.1105/tpc.16.00915] [Citation(s) in RCA: 102] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Revised: 02/26/2017] [Accepted: 03/16/2017] [Indexed: 05/20/2023]
Abstract
Molecular plant pathology has focused on studying large-effect qualitative resistance loci that predominantly function in detecting pathogens and/or transmitting signals resulting from pathogen detection. By contrast, less is known about quantitative resistance loci, particularly the molecular mechanisms controlling variation in quantitative resistance. Recent studies have provided insight into these mechanisms, showing that genetic variation at hundreds of causal genes may underpin quantitative resistance. Loci controlling quantitative resistance contain some of the same causal genes that mediate qualitative resistance, but the predominant mechanisms of quantitative resistance extend beyond pathogen recognition. Indeed, most causal genes for quantitative resistance encode specific defense-related outputs such as strengthening of the cell wall or defense compound biosynthesis. Extending previous work on qualitative resistance to focus on the mechanisms of quantitative resistance, such as the link between perception of microbe-associated molecular patterns and growth, has shown that the mechanisms underlying these defense outputs are also highly polygenic. Studies that include genetic variation in the pathogen have begun to highlight a potential need to rethink how the field considers broad-spectrum resistance and how it is affected by genetic variation within pathogen species and between pathogen species. These studies are broadening our understanding of quantitative resistance and highlighting the potentially vast scale of the genetic basis of quantitative resistance.
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Affiliation(s)
- Jason A Corwin
- Department of Plant Sciences, University of California, Davis, California 95616
| | - Daniel J Kliebenstein
- Department of Plant Sciences, University of California, Davis, California 95616
- DynaMo Center of Excellence, University of Copenhagen, DK-1871 Frederiksberg C, Denmark
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40
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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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41
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Kuhn H, Kwaaitaal M, Kusch S, Acevedo-Garcia J, Wu H, Panstruga R. Biotrophy at Its Best: Novel Findings and Unsolved Mysteries of the Arabidopsis-Powdery Mildew Pathosystem. THE ARABIDOPSIS BOOK 2016; 14:e0184. [PMID: 27489521 PMCID: PMC4957506 DOI: 10.1199/tab.0184] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
It is generally accepted in plant-microbe interactions research that disease is the exception rather than a common outcome of pathogen attack. However, in nature, plants with symptoms that signify colonization by obligate biotrophic powdery mildew fungi are omnipresent. The pervasiveness of the disease and the fact that many economically important plants are prone to infection by powdery mildew fungi drives research on this interaction. The competence of powdery mildew fungi to establish and maintain true biotrophic relationships renders the interaction a paramount example of a pathogenic plant-microbe biotrophy. However, molecular details underlying the interaction are in many respects still a mystery. Since its introduction in 1990, the Arabidopsis-powdery mildew pathosystem has become a popular model to study molecular processes governing powdery mildew infection. Due to the many advantages that the host Arabidopsis offers in terms of molecular and genetic tools this pathosystem has great capacity to answer some of the questions of how biotrophic pathogens overcome plant defense and establish a persistent interaction that nourishes the invader while in parallel maintaining viability of the plant host.
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Affiliation(s)
- Hannah Kuhn
- RWTH Aachen University, Institute for Biology I, Unit of Plant
Molecular Cell Biology, Worringerweg 1, D-52056 Aachen, Germany
- Address correspondence to
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Barabaschi D, Tondelli A, Desiderio F, Volante A, Vaccino P, Valè G, Cattivelli L. Next generation breeding. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2016; 242:3-13. [PMID: 26566820 DOI: 10.1016/j.plantsci.2015.07.010] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Revised: 07/10/2015] [Accepted: 07/11/2015] [Indexed: 05/18/2023]
Abstract
The genomic revolution of the past decade has greatly improved our understanding of the genetic make-up of living organisms. The sequencing of crop genomes has completely changed our vision and interpretation of genome organization and evolution. Re-sequencing allows the identification of an unlimited number of markers as well as the analysis of germplasm allelic diversity based on allele mining approaches. High throughput marker technologies coupled with advanced phenotyping platforms provide new opportunities for discovering marker-trait associations which can sustain genomic-assisted breeding. The availability of genome sequencing information is enabling genome editing (site-specific mutagenesis), to obtain gene sequences desired by breeders. This review illustrates how next generation sequencing-derived information can be used to tailor genomic tools for different breeders' needs to revolutionize crop improvement.
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Affiliation(s)
- Delfina Barabaschi
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria, Genomics Research Centre, Via San Protaso 302, 29017 Fiorenzuola d'Arda, Italy
| | - Alessandro Tondelli
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria, Genomics Research Centre, Via San Protaso 302, 29017 Fiorenzuola d'Arda, Italy
| | - Francesca Desiderio
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria, Genomics Research Centre, Via San Protaso 302, 29017 Fiorenzuola d'Arda, Italy
| | - Andrea Volante
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria, Rice Research Unit, SS 11 to Torino Km 2.5, 13100 Vercelli, Italy
| | - Patrizia Vaccino
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria, Research Unit for Cereal Selection in Continental areas, via R. Forlani, e, 26866 S. Angelo Lodigiano, Italy
| | - Giampiero Valè
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria, Rice Research Unit, SS 11 to Torino Km 2.5, 13100 Vercelli, Italy
| | - Luigi Cattivelli
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria, Genomics Research Centre, Via San Protaso 302, 29017 Fiorenzuola d'Arda, Italy.
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Laidò G, Panio G, Marone D, Russo MA, Ficco DBM, Giovanniello V, Cattivelli L, Steffenson B, de Vita P, Mastrangelo AM. Identification of New Resistance Loci to African Stem Rust Race TTKSK in Tetraploid Wheats Based on Linkage and Genome-Wide Association Mapping. FRONTIERS IN PLANT SCIENCE 2015; 6:1033. [PMID: 26697025 PMCID: PMC4673868 DOI: 10.3389/fpls.2015.01033] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Accepted: 11/06/2015] [Indexed: 05/22/2023]
Abstract
Stem rust, caused by Puccinia graminis Pers. f. sp. tritici Eriks. and E. Henn. (Pgt), is one of the most destructive diseases of wheat. Races of the pathogen in the "Ug99 lineage" are of international concern due to their virulence for widely used stem rust resistance genes and their spread throughout Africa. Disease resistant cultivars provide one of the best means for controlling stem rust. To identify quantitative trait loci (QTL) conferring resistance to African stem rust race TTKSK at the seedling stage, we evaluated an association mapping (AM) panel consisting of 230 tetraploid wheat accessions under greenhouse conditions. A high level of phenotypic variation was observed in response to race TTKSK in the AM panel, allowing for genome-wide association mapping of resistance QTL in wild, landrace, and cultivated tetraploid wheats. Thirty-five resistance QTL were identified on all chromosomes, and seventeen are of particular interest as identified by multiple associations. Many of the identified resistance loci were coincident with previously identified rust resistance genes; however, nine on chromosomes 1AL, 2AL, 4AL, 5BL, and 7BS may be novel. To validate AM results, a biparental population of 146 recombinant inbred lines was also considered, which derived from a cross between the resistant cultivar "Cirillo" and susceptible "Neodur." The stem rust resistance of Cirillo was conferred by a single gene on the distal region of chromosome arm 6AL in an interval map coincident with the resistance gene Sr13, and confirmed one of the resistance loci identified by AM. A search for candidate resistance genes was carried out in the regions where QTL were identified, and many of them corresponded to NBS-LRR genes and protein kinases with LRR domains. The results obtained in the present study are of great interest as a high level of genetic variability for resistance to race TTKSK was described in a germplasm panel comprising most of the tetraploid wheat sub-species.
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Affiliation(s)
- Giovanni Laidò
- Cereal Research Centre, Council for Agricultural Research and EconomicsFoggia, Italy
| | - Giosuè Panio
- Cereal Research Centre, Council for Agricultural Research and EconomicsFoggia, Italy
| | - Daniela Marone
- Cereal Research Centre, Council for Agricultural Research and EconomicsFoggia, Italy
| | - Maria A. Russo
- Cereal Research Centre, Council for Agricultural Research and EconomicsFoggia, Italy
| | - Donatella B. M. Ficco
- Cereal Research Centre, Council for Agricultural Research and EconomicsFoggia, Italy
| | | | - Luigi Cattivelli
- Cereal Research Centre, Council for Agricultural Research and EconomicsFoggia, Italy
- Genomics Research Centre, Council for Agricultural Research and EconomicsFiorenzuola d'Arda, Italy
| | - Brian Steffenson
- Department of Plant Pathology, University of Minnesota Twin CitiesMinneapolis, MN, USA
| | - Pasquale de Vita
- Cereal Research Centre, Council for Agricultural Research and EconomicsFoggia, Italy
| | - Anna M. Mastrangelo
- Cereal Research Centre, Council for Agricultural Research and EconomicsFoggia, Italy
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Soriano JM, Royo C. Dissecting the Genetic Architecture of Leaf Rust Resistance in Wheat by QTL Meta-Analysis. PHYTOPATHOLOGY 2015; 105:1585-93. [PMID: 26571424 DOI: 10.1094/phyto-05-15-0130-r] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Leaf rust is an important disease that causes significant yield losses in wheat. Many studies have reported the identification of quantitative trait loci (QTL) controlling leaf rust resistance; therefore, QTL meta-analysis has become a useful tool for identifying consensus QTL and refining QTL positions among them. In this study, QTL meta-analysis was conducted using reported results on the number, position, and effects of QTL for leaf rust resistance in bread and durum wheat. Investigation of 14 leaf rust resistance traits from 19 studies involving 20 mapping populations and 33 different parental lines provided information for 144 unique QTL that were projected onto the Wheat Composite 2004 reference map. In total, 35 meta-QTL for leaf rust resistance traits were identified in 17 wheat chromosomes and 13 QTL remained as unique QTL. The results will facilitate further work on the cloning of QTL for pyramiding minor- and partial-effect resistance genes to develop varieties with durable resistance to leaf rust.
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Affiliation(s)
- Jose Miguel Soriano
- Field Crops Programme, IRTA (Institute for Food and Agricultural Research and Technology), 25198 Lleida, Spain
| | - Conxita Royo
- Field Crops Programme, IRTA (Institute for Food and Agricultural Research and Technology), 25198 Lleida, Spain
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45
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Hou L, Zhang X, Li X, Jia J, Yang H, Zhan H, Qiao L, Guo H, Chang Z. Mapping of Powdery Mildew Resistance Gene pmCH89 in a Putative Wheat-Thinopyrum intermedium Introgression Line. Int J Mol Sci 2015. [PMID: 26225967 PMCID: PMC4581190 DOI: 10.3390/ijms160817231] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Powdery mildew, caused by Blumeria graminis f. sp. tritici (Bgt), is a globally serious disease adversely affecting wheat production. The Bgt-resistant wheat breeding line CH09W89 was derived after backcrossing a Bgt resistant wheat-Thinopyrum intermedium partial amphiploid TAI7045 with susceptible wheat cultivars. At the seedling stage, CH09W89 exhibited immunity or high resistance to Bgt pathotypes E09, E20, E21, E23, E26, Bg1, and Bg2, similar to its donor line TAI7045 and Th. intermedium. No Th. intermedium chromatin was detected based on genomic in situ hybridization of mitotic chromosomes. To determine the mode of inheritance of the Bgt resistance and the chromosomal location of the resistance gene, CH09W89 was crossed with two susceptible wheat cultivars. The results of the genetic analysis showed that the adult resistance to Bgt E09 in CH09W89 was controlled by a single recessive gene, which was tentatively designated as pmCH89. Two polymorphic SSR markers, Xwmc310 and Xwmc125, were linked to the resistance gene with genetic distances 3.1 and 2.7 cM, respectively. Using the Chinese Spring aneuploid and deletion lines, the resistance gene and its linked markers were assigned to chromosome arm 4BL in the bin 0.68–0.78. Due to its unique position on chromosome 4BL, pmCH89 appears to be a new locus for resistance to powdery mildew. These results will be of benefit for improving powdery mildew resistance in wheat breeding programs.
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Affiliation(s)
- Liyuan Hou
- College of Life Science, Shanxi University, Taiyuan 030006, Shanxi, China.
| | - Xiaojun Zhang
- Institute of Crop Science, Shanxi Academy of Agricultural Sciences, Taiyuan 030031, Shanxi, China.
- Key Laboratory for Crop Gene Resources and Germplasm Enhancement on the Loess Plateau, Ministry of Agriculture, Taiyuan 030031, Shanxi, China.
| | - Xin Li
- Institute of Crop Science, Shanxi Academy of Agricultural Sciences, Taiyuan 030031, Shanxi, China.
- Key Laboratory for Crop Gene Resources and Germplasm Enhancement on the Loess Plateau, Ministry of Agriculture, Taiyuan 030031, Shanxi, China.
| | - Juqing Jia
- College of Agronomy, Shanxi Agricultural University, Taigu 030801, Shanxi, China.
| | - Huizhen Yang
- Institute of Crop Science, Shanxi Academy of Agricultural Sciences, Taiyuan 030031, Shanxi, China.
| | - Haixian Zhan
- Institute of Crop Science, Shanxi Academy of Agricultural Sciences, Taiyuan 030031, Shanxi, China.
- Key Laboratory for Crop Gene Resources and Germplasm Enhancement on the Loess Plateau, Ministry of Agriculture, Taiyuan 030031, Shanxi, China.
| | - Linyi Qiao
- Institute of Crop Science, Shanxi Academy of Agricultural Sciences, Taiyuan 030031, Shanxi, China.
- Key Laboratory for Crop Gene Resources and Germplasm Enhancement on the Loess Plateau, Ministry of Agriculture, Taiyuan 030031, Shanxi, China.
| | - Huijuan Guo
- Institute of Crop Science, Shanxi Academy of Agricultural Sciences, Taiyuan 030031, Shanxi, China.
- Key Laboratory for Crop Gene Resources and Germplasm Enhancement on the Loess Plateau, Ministry of Agriculture, Taiyuan 030031, Shanxi, China.
| | - Zhijian Chang
- Institute of Crop Science, Shanxi Academy of Agricultural Sciences, Taiyuan 030031, Shanxi, China.
- Key Laboratory for Crop Gene Resources and Germplasm Enhancement on the Loess Plateau, Ministry of Agriculture, Taiyuan 030031, Shanxi, China.
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Elkot AFA, Chhuneja P, Kaur S, Saluja M, Keller B, Singh K. Marker Assisted Transfer of Two Powdery Mildew Resistance Genes PmTb7A.1 and PmTb7A.2 from Triticum boeoticum (Boiss.) to Triticum aestivum (L.). PLoS One 2015; 10:e0128297. [PMID: 26066332 PMCID: PMC4466026 DOI: 10.1371/journal.pone.0128297] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2015] [Accepted: 04/27/2015] [Indexed: 11/24/2022] Open
Abstract
Powdery mildew (PM), caused by Blumeria graminis f. sp. tritici, is one of the important wheat diseases, worldwide. Two PM resistance genes, designated as PmTb7A.1 and PmTb7A.2, were identified in T. boeoticum acc. pau5088 and mapped on chromosome 7AL approximately 48cM apart. Two resistance gene analogue (RGA)-STS markers Ta7AL-4556232 and 7AL-4426363 were identified to be linked to the PmTb7A.1 and PmTb7A.2, at a distance of 0.6cM and 6.0cM, respectively. In the present study, following marker assisted selection (MAS), the two genes were transferred to T. aestivum using T. durum as bridging species. As many as 12,317 florets of F1 of the cross T. durum /T. boeoticum were pollinated with T. aestivum lines PBW343-IL and PBW621 to produce 61 and 65 seeds, respectively, of three-way F1. The resulting F1s of the cross T. durum/T. boeoticum//T. aestivum were screened with marker flanking both the PM resistance genes PmTb7A.1 and PmTb7A.2 (foreground selection) and the selected plants were backcrossed to generate BC1F1. Marker assisted selection was carried both in BC1F1 and the BC2F1 generations. Introgression of alien chromatin in BC2F1 plants varied from 15.4-62.9 percent. Out of more than 110 BC2F1 plants showing introgression for markers linked to the two PM resistance genes, 40 agronomically desirable plants were selected for background selection for the carrier chromosome to identify the plants with minimum of the alien introgression. Cytological analysis showed that most plants have chromosome number ranging from 40-42. The BC2F2 plants homozygous for the two genes have been identified. These will be crossed to generate lines combining both the PM resistance genes but with minimal of the alien introgression. The PM resistance gene PmTb7A.1 maps in a region very close to Sr22, a stem rust resistance gene effective against the race Ug99. Analysis of selected plants with markers linked to Sr22 showed introgression of Sr22 from T. boeoticum in several BC2F1 plants. Thus, in addition to PM resistance, these progeny might also carry resistance to stem rust race Ug99.
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Affiliation(s)
| | - Parveen Chhuneja
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, 141 004, India
| | - Satinder Kaur
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, 141 004, India
| | - Manny Saluja
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, 141 004, India
| | - Beat Keller
- Institute of Plant Biology, University of Zurich, Zurich, Switzerland
| | - Kuldeep Singh
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, 141 004, India
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47
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Petrarulo M, Marone D, Ferragonio P, Cattivelli L, Rubiales D, De Vita P, Mastrangelo AM. Genetic analysis of root morphological traits in wheat. Mol Genet Genomics 2014; 290:785-806. [PMID: 25416422 DOI: 10.1007/s00438-014-0957-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Accepted: 11/11/2014] [Indexed: 02/05/2023]
Abstract
Traits related to root architecture are of great importance for yield performance of crop species, although they remain poorly understood. The present study is aimed at identifying the genomic regions involved in the control of root morphological traits in durum wheat (Triticum durum Desf.). A set of 123 recombinant inbred lines derived from the durum wheat cross of cvs. 'Creso' × 'Pedroso' were grown hydroponically to two growth stages, and were phenotypically evaluated for a number of root traits. In addition, meta-(M)QTL analysis was performed that considered the results of other root traits studies in wheat, to compare with the 'Creso' × 'Pedroso' cross and to increase the QTL detection power. Eight quantitative trait loci (QTL) for traits related to root morphology were identified on chromosomes 1A, 1B, 2A, 3A, 6A and 6B in the 'Creso' × 'Pedroso' segregating population. Twenty-two MQTL that comprised from two to six individual QTL that had widely varying confidence intervals were found on 14 chromosomes. The data from the present study provide a detailed analysis of the genetic basis of morphological root traits in wheat. This study of the 'Creso' × 'Pedroso' durum-wheat population has revealed some QTL that had not been previously identified.
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Affiliation(s)
- Maria Petrarulo
- Consiglio per la Ricerca e la Sperimentazione in Agricoltura-Cereal Research Centre, SS 673 km 25.200, 71122, Foggia, Italy
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48
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Maccaferri M, Cane' MA, Sanguineti MC, Salvi S, Colalongo MC, Massi A, Clarke F, Knox R, Pozniak CJ, Clarke JM, Fahima T, Dubcovsky J, Xu S, Ammar K, Karsai I, Vida G, Tuberosa R. A consensus framework map of durum wheat (Triticum durum Desf.) suitable for linkage disequilibrium analysis and genome-wide association mapping. BMC Genomics 2014; 15:873. [PMID: 25293821 PMCID: PMC4287192 DOI: 10.1186/1471-2164-15-873] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2014] [Accepted: 09/23/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Durum wheat (Triticum durum Desf.) is a tetraploid cereal grown in the medium to low-precipitation areas of the Mediterranean Basin, North America and South-West Asia. Genomics applications in durum wheat have the potential to boost exploitation of genetic resources and to advance understanding of the genetics of important complex traits (e.g. resilience to environmental and biotic stresses). A dense and accurate consensus map specific for T. durum will greatly facilitate genetic mapping, functional genomics and marker-assisted improvement. RESULTS High quality genotypic data from six core recombinant inbred line populations were used to obtain a consensus framework map of 598 simple sequence repeats (SSR) and Diversity Array Technology® (DArT) anchor markers (common across populations). Interpolation of unique markers from 14 maps allowed us to position a total of 2,575 markers in a consensus map of 2,463 cM. The T. durum A and B genomes were covered in their near totality based on the reference SSR hexaploid wheat map. The consensus locus order compared to those of the single component maps showed good correspondence, (average Spearman's rank correlation rho ρ value of 0.96). Differences in marker order and local recombination rate were observed between the durum and hexaploid wheat consensus maps. The consensus map was used to carry out a whole-genome search for genetic differentiation signatures and association to heading date in a panel of 183 accessions adapted to the Mediterranean areas. Linkage disequilibrium was found to decay below the r2 threshold=0.3 within 2.20 cM, on average. Strong molecular differentiations among sub-populations were mapped to 87 chromosome regions. A genome-wide association scan for heading date from 27 field trials in the Mediterranean Basin and in Mexico yielded 50 chromosome regions with evidences of association in multiple environments. CONCLUSIONS The consensus map presented here was used as a reference for genetic diversity and mapping analyses in T. durum, providing nearly complete genome coverage and even marker density. Markers previously mapped in hexaploid wheat constitute a strong link between the two species. The consensus map provides the basis for high-density single nucleotide polymorphic (SNP) marker implementation in durum wheat.
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Affiliation(s)
- Marco Maccaferri
- Department of Agricultural Sciences (DipSA), Viale Fanin 44, University of Bologna, 40127 Bologna, Italy.
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49
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Bouktila D, Khalfallah Y, Habachi-Houimli Y, Mezghani-Khemakhem M, Makni M, Makni H. Full-genome identification and characterization of NBS-encoding disease resistance genes in wheat. Mol Genet Genomics 2014; 290:257-71. [PMID: 25231182 DOI: 10.1007/s00438-014-0909-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2014] [Accepted: 08/26/2014] [Indexed: 11/25/2022]
Abstract
Host resistance is the most economical, effective and ecologically sustainable method of controlling diseases in crop plants. In bread wheat, despite the high number of resistance loci that have been cataloged to date, only few have been cloned, underlying the need for genomics-guided investigations capable of providing a prompt and acute knowledge on the identity of effective resistance genes that can be used in breeding programs. Proteins with a nucleotide-binding site (NBS) encoded by the major plant disease resistance (R) genes play an important role in the responses of plants to various pathogens. In this study, a comprehensive analysis of NBS-encoding genes within the whole wheat genome was performed, and the genome scale characterization of this gene family was established. From the recently published wheat genome sequence, we used a data mining and automatic prediction pipeline to identify 580 complete ORF candidate NBS-encoding genes and 1,099 partial-ORF ones. Among complete gene models, 464 were longer than 200 aa, among them 436 had less than 70 % of sequence identity to each other. This gene models set was deeply characterized. (1) First, we have analyzed domain architecture and identified, in addition to typical domain combinations, the presence of particular domains like signal peptides, zinc fingers, kinases, heavy-metal-associated and WRKY DNA-binding domains. (2) Functional and expression annotation via homology searches in protein and transcript databases, based on sufficient criteria, enabled identifying similar proteins for 60 % of the studied gene models and expression evidence for 13 % of them. (3) Shared orthologous groups were defined using NBS-domain proteins of rice and Brachypodium distachyon. (4) Finally, alignment of the 436 NBS-containing gene models to the full set of scaffolds from the IWGSC's wheat chromosome survey sequence enabled high-stringence anchoring to chromosome arms. The distribution of the R genes was found balanced on the three wheat sub-genomes. In contrast, at chromosome scale, 50 % of members of this gene family were localized on 6 of the 21 wheat chromosomes and ~22 % of them were localized on homeologous group 7. The results of this study provide a detailed analysis of the largest family of plant disease resistance genes in allohexaploid wheat. Some structural traits reported had not been previously identified and the genome-derived data were confronted with those stored in databases outlining the functional specialization of members of this family. The large reservoir of NBS-type genes presented and discussed will, firstly, form an important framework for marker-assisted improvement of resistance in wheat, and, secondly, open up new perspectives for a better understanding of the evolution dynamics of this gene family in grass species and in polyploid systems.
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Affiliation(s)
- Dhia Bouktila
- Unité de Recherche "Génomique des Insectes Ravageurs des Cultures d'intérêt agronomique" (GIRC, UR11ES10), Faculté des Sciences de Tunis, Université de Tunis El Manar, El Manar, 2092, Tunis, Tunisia,
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50
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Zegeye H, Rasheed A, Makdis F, Badebo A, Ogbonnaya FC. Genome-wide association mapping for seedling and adult plant resistance to stripe rust in synthetic hexaploid wheat. PLoS One 2014; 9:e105593. [PMID: 25153126 PMCID: PMC4143293 DOI: 10.1371/journal.pone.0105593] [Citation(s) in RCA: 112] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2014] [Accepted: 07/23/2014] [Indexed: 01/08/2023] Open
Abstract
Use of genetic diversity from related wild and domesticated species has made a significant contribution to improving wheat productivity. Synthetic hexaploid wheats (SHWs) exhibit natural genetic variation for resistance and/or tolerance to biotic and abiotic stresses. Stripe rust caused by (Puccinia striiformis f. sp. tritici; Pst), is an important disease of wheat worldwide. To characterise loci conferring resistance to stripe rust in SHWs, we conducted a genome-wide association study (GWAS) with a panel of 181 SHWs using the wheat 9 K SNP iSelect array. The SHWs were evaluated for their response to the prevailing races of Pst at the seedling and adult plant stages, the latter in replicated field trials at two sites in Ethiopia in 2011. About 28% of the SHWs exhibited immunity at the seedling stage while 56% and 83% were resistant to Pst at the adult plant stage at Meraro and Arsi Robe, respectively. A total of 27 SNPs in nine genomic regions (1 BS, 2 AS, 2 BL, 3 BL, 3 DL, 5A, 5 BL, 6DS and 7A) were linked with resistance to Pst at the seedling stage, while 38 SNPs on 18 genomic regions were associated with resistance at the adult plant stage. Six genomic regions were commonly detected at both locations using a mixed linear model corrected for population structure, kinship relatedness and adjusted for false discovery rate (FDR). The loci on chromosome regions 1 AS, 3 DL, 6 DS and 7 AL appeared to be novel QTL; our results confirm that resynthesized wheat involving its progenitor species is a rich source of new stripe (yellow) rust resistance that may be useful in choosing SHWs and incorporating diverse yellow rust (YR) resistance loci into locally adapted wheat cultivars.
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Affiliation(s)
| | - Awais Rasheed
- Crop Science Research Institute/National Wheat Improvement Centre, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
- Department of Plant Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Farid Makdis
- Department of Field Crops, Faculty of Agriculture, University of Aleppo, Aleppo, Syria
- Research Program, Grains Research and Development Corporation, Barton, Australian Capital Territory, Canberra, Australia
| | - Ayele Badebo
- Ethiopian Institute of Agricultural Research, Addis Ababa, Ethiopia
| | - Francis C. Ogbonnaya
- International Centre for Agricultural Research in the Dry Areas (ICARDA), Aleppo, Syria
- Research Program, Grains Research and Development Corporation, Barton, Australian Capital Territory, Canberra, Australia
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