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Ramesh GV, Kaur J, Singla D, Chhuneja P, Saharan A, Gangwar OP, Bala R, Mir RR, Tak PS. Use of Field pathogenomics approach for Puccinia striiformis f. sp. tritici race identification and phylogenomic delineation in North India. World J Microbiol Biotechnol 2025; 41:166. [PMID: 40325275 DOI: 10.1007/s11274-025-04391-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2025] [Accepted: 04/28/2025] [Indexed: 05/07/2025]
Abstract
Stripe rust of wheat caused by Puccinia striiformis f. sp. tritici (Pst) is among the top 10 most important fungal phytopathogens in the world, threatening the global wheat production. Continuous pathogen evolution and air borne nature of the pathogen, increased the importance of pathogen population structure studies in case of wheat-Puccinia pathosystem. The current study aimed to characterize the Pst pathotype distribution in North India. A total of 61 stripe rust infected samples were collected from sub-mountainous areas of Punjab (50), Himachal Pradesh (HP) (8) and Jammu & Kashmir (J&K) (3) during 2021-24. Virulence profiling results of 58 samples using Indian stripe rust differentials revealed the prevalence of five pathotypes (238S119, 110S119, 46S119, 47S103 and 6S0) in North India. Among which 238S119 was the most predominant (51.72%) one followed by 110S119 (27.59%) and 46S119 (17.24%). No virulence was found against stripe rust resistant Yr5, Yr10, Yr15, Yr24 and YrSP genes indicating these genes are the most effective resistant genes in North India providing complete resistance till date. A total of 23 field infected samples were used for transcriptome analysis (RNA-seq) generating an average of 31.77 million raw reads. The clustered assembly generated mean assembly size of ∼ 45.10 Mb containing 7,587-2,49,571 contigs with 47.99% GC content, N50 value of 749.87 with 7.48-94.90% BUSCO score. Phylogenomic analysis of farmer's field samples revealed the existence of three different Pst lineages in North India i.e., Punjab lineage, Himachal lineage and Kashmir lineage, where Himachal lineage exhibited highest genetic diversity. A total of three (3) SSR and 14 KASP markers developed in previous studies were tested on farmer's field isolates for pathotype identification. Eight KASP markers showed reproducible polymorphism for pathotype specific detection. Correlating the KASP assay with results of virulence profiling revealed that these markers have the ability to detect the virulence change from five established pathotypes under field conditions. The findings of present study provided better understanding in Pst pathotype distribution in North India and pathotype detection using consistent polymorphic markers along with deciphering the behaviour of Pst under field conditions and deducing their evolutionary relationship in North India.
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Affiliation(s)
- Gutha Venkata Ramesh
- Department of Plant Pathology, Punjab Agricultural University, Ludhiana, Punjab, 141004, India
| | - Jaspal Kaur
- Department of Plant Breeding & Genetics, Punjab Agricultural University, Ludhiana, Punjab, 141004, India.
| | - Deepak Singla
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, Punjab, 141004, India
| | - Parveen Chhuneja
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, Punjab, 141004, India
| | - Anurag Saharan
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, Punjab, 141004, India
| | - O P Gangwar
- Regional Station, ICAR-Indian Institute of Wheat and Barley Research, Flowerdale, Shimla, Himachal Pradesh, 171002, India
| | - Ritu Bala
- Department of Plant Breeding & Genetics, Punjab Agricultural University, Ludhiana, Punjab, 141004, India
| | - Reyazul Rouf Mir
- Division of Genetics and Plant Breeding, Sher-e-Kashmir University of Agricultural Sciences & Technology of Kashmir, Wadura, Jammu & Kashmir, 193201, India
| | - Parminder Singh Tak
- Department of Plant Pathology, Punjab Agricultural University, Ludhiana, Punjab, 141004, India
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Wei B, Gourlie R, Celoy R, Amundsen E, Aboukhaddour R. Stripe Rust Virulence and Host Reaction Assessment Protocols: From Lab to Field. Methods Mol Biol 2025; 2898:41-61. [PMID: 40198549 DOI: 10.1007/978-1-0716-4378-5_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/10/2025]
Abstract
Puccinia striiformis, the causal agent of stripe rust disease, poses a significant threat to cereal crops worldwide. Since 2000, the emergence of heat-adapted races/lineages of the wheat-infecting form P. striiformis f. sp. tritici (Pst) has enabled the disease to spread beyond its traditional high-elevation, cool, and moist regions. It can now occur wherever wheat is cultivated, making it a pandemic concern. This chapter provides an overview of the methodologies and practices established in our lab for working with this pathogen. These methodologies include isolate collection, recovery, purification, increase, and storage, as well as the evaluation of virulence in a greenhouse setting, and the fundamentals of running a large-scale yearly disease nursery under field conditions. This comprehensive guide, based on our lab's experience with stripe rust, aims to provide researchers with the knowledge and tools necessary for effective and informed studies on P. striiformis.
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Affiliation(s)
- Bohan Wei
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada
| | - Ryan Gourlie
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada
| | - Rhodesia Celoy
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada
| | - Eric Amundsen
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada
| | - Reem Aboukhaddour
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada.
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Gogoleva OA, Ryazanov EA, Murzagulova GS, Ponomarev SN, Chastukhina IB, Sakhabutdinov IT, Osipova EV, Mannapova GS, Korzun VN, Ponomareva ML, Gorshkov VY. Intra- and Interpopulation Diversity of the Phytopathogenic Fungi of the Microdochium nivale Species. J Fungi (Basel) 2024; 10:841. [PMID: 39728337 DOI: 10.3390/jof10120841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2024] [Revised: 11/29/2024] [Accepted: 12/03/2024] [Indexed: 12/28/2024] Open
Abstract
Our study investigates the intra- and interpopulation diversity of phytopathogenic fungi, using Microdochium nivale as a model organism. A total of 136 strains, representing two populations, were collected from different winter cereal crops (rye, wheat, and triticale) across two agrocenoses. In these strains, we analyzed and compared genetic and phenotypic traits, exploring potential relationships between them. Significant genetic and phenotypic diversity was revealed among the assayed strains, with most exhibiting distinctive genetic features compared to previously characterized strains from other countries. Both populations included highly virulent and lowly virulent strains, with the majority displaying similar virulence levels across different cereal crops. Some strains demonstrated differential virulence toward different crops, and some even exhibited a plant-beneficial effect on rye while being virulent to wheat and triticale. The percentages of strains with specific genetic traits were different in the two analyzed populations. Our study lays the groundwork for identifying genetic markers associated with phenotypic traits in the studied strains, which will aid in developing reliable diagnostics for predicting crop loss risk and improving disease management. Furthermore, it will assist in identifying reliable sources of resistance to M. nivale-induced diseases within the winter cereal gene pool.
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Affiliation(s)
- Olga A Gogoleva
- Federal Research Center "Kazan Scientific Center of the Russian Academy of Sciences", 420111 Kazan, Russia
| | - Egor A Ryazanov
- Federal Research Center "Kazan Scientific Center of the Russian Academy of Sciences", 420111 Kazan, Russia
- Faculty of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Guzalia Sh Murzagulova
- Federal Research Center "Kazan Scientific Center of the Russian Academy of Sciences", 420111 Kazan, Russia
| | - Sergey N Ponomarev
- Federal Research Center "Kazan Scientific Center of the Russian Academy of Sciences", 420111 Kazan, Russia
| | - Inna B Chastukhina
- Federal Research Center "Kazan Scientific Center of the Russian Academy of Sciences", 420111 Kazan, Russia
| | - Ildar T Sakhabutdinov
- Federal Research Center "Kazan Scientific Center of the Russian Academy of Sciences", 420111 Kazan, Russia
| | - Elena V Osipova
- Federal Research Center "Kazan Scientific Center of the Russian Academy of Sciences", 420111 Kazan, Russia
| | - Gulnaz S Mannapova
- Federal Research Center "Kazan Scientific Center of the Russian Academy of Sciences", 420111 Kazan, Russia
| | - Viktor N Korzun
- KWS SAAT SE & Co. KGaA, Grimsehlstr. 31, 37555 Einbeck, Germany
| | - Mira L Ponomareva
- Federal Research Center "Kazan Scientific Center of the Russian Academy of Sciences", 420111 Kazan, Russia
| | - Vladimir Yu Gorshkov
- Federal Research Center "Kazan Scientific Center of the Russian Academy of Sciences", 420111 Kazan, Russia
- Institute of Fundamental Medicine and Biology, Kazan Federal University, 420008 Kazan, Russia
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Li Y, Wang M, Hu X, Chen X. Identification of a Locus for High-Temperature Adult-Plant Resistance to Stripe Rust in the Wheat Yr8 Near-Isogenic Line Through Mutagenesis and Molecular Mapping. PLANT DISEASE 2024; 108:1261-1269. [PMID: 37938905 DOI: 10.1094/pdis-10-23-2037-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2023]
Abstract
Aegilops species are wheat relatives that harbor valuable disease resistance genes for wheat breeding. The wheat Yr8 near-isogenic line AvSYr8NIL has long been believed to carry only Yr8 for race-specific all-stage resistance to stripe rust, caused by Puccinia striiformis f. sp. tritici, derived from Aegilops comosa. However, AvSYr8NIL has been found to have high-temperature adult-plant (HTAP) resistance in our field and greenhouse tests. To confirm both HTAP and Yr8 resistance, seeds from AvSYr8NIL were treated with ethyl methanesulfonate to generate mutant lines. The mutant lines with only Yr8 (M641) and only HTAP resistance (M488) were crossed with the susceptible recurrent parent Avocet S (AvS). The F1 and F4 lines of AvS/M641 were phenotyped with Yr8-avirulent races in the seedling stage at the low-temperature (4 to 20°C) profile, while the F1, F2, F4, and F5 lines of AvS/M488 were phenotyped with Yr8-virulent races in the adult-plant stage at the high-temperature (10 to 30°C) profile. Both Yr8 and the HTAP resistance gene (YrM488) were recessive. The F4 populations of AvS/M641 and AvS/M488 were genotyped using polymorphic Kompetitive allele-specific PCR markers converted from single-nucleotide polymorphisms. Yr8 was mapped to a 0.66-cM fragment, and YrM488 was mapped to a 1.22-cM interval on chromosome 2D. The physical distance between the two resistance genes was estimated to be more than 500 Mb, indicating their distinct loci. The mutant lines with separated resistance genes would be useful in enhancing our understanding of different types of resistance and in further studying the interactions between wheat and the stripe rust pathogen.
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Affiliation(s)
- Yuxiang Li
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
- Department of Plant Pathology, Washington State University, Pullman, WA 99164, U.S.A
| | - Meinan Wang
- Department of Plant Pathology, Washington State University, Pullman, WA 99164, U.S.A
| | - Xiaoping Hu
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xianming Chen
- Department of Plant Pathology, Washington State University, Pullman, WA 99164, U.S.A
- U.S. Department of Agriculture, Agricultural Research Service, Wheat Health, Genetics, and Quality Research Unit, Pullman, WA 99164, U.S.A
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Gebremariam TG, Wang F, Lin R, Li H. Comparative Analysis of Virulence and Molecular Diversity of Puccinia striiformis f. sp. tritici Isolates Collected in 2016 and 2023 in the Western Region of China. Genes (Basel) 2024; 15:542. [PMID: 38790172 PMCID: PMC11121451 DOI: 10.3390/genes15050542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Revised: 04/15/2024] [Accepted: 04/20/2024] [Indexed: 05/26/2024] Open
Abstract
Puccinia striiformis f. sp. tritici (Pst) is adept at overcoming resistance in wheat cultivars, through variations in virulence in the western provinces of China. To apply disease management strategies, it is essential to understand the temporal and spatial dynamics of Pst populations. This study aimed to evaluate the virulence and molecular diversity of 84 old Pst isolates, in comparison to 59 newer ones. By using 19 Chinese wheat differentials, we identified 98 pathotypes, showing virulence complexity ranging from 0 to 16. Associations between 23 Yr gene pairs showed linkage disequilibrium and have the potential for gene pyramiding. The new Pst isolates had a higher number of polymorphic alleles (1.97), while the older isolates had a slightly higher number of effective alleles, Shannon's information, and diversity. The Gansu Pst population had the highest diversity (uh = 0.35), while the Guizhou population was the least diverse. Analysis of molecular variance revealed that 94% of the observed variation occurred within Pst populations across the four provinces, while 6% was attributed to differences among populations. Overall, Pst populations displayed a higher pathotypic diversity of H > 2.5 and a genotypic diversity of 96%. This underscores the need to develop gene-pyramided cultivars to enhance the durability of resistance.
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Affiliation(s)
- Tesfay Gebrekirstos Gebremariam
- The National Engineering Laboratory of Crop Molecular Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China;
- Tigray Agricultural Research Institute, Mekelle P.O. Box 492, Ethiopia
| | - Fengtao Wang
- State Key Laboratory for Biology of Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China;
| | - Ruiming Lin
- State Key Laboratory for Biology of Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China;
| | - Hongjie Li
- The National Engineering Laboratory of Crop Molecular Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China;
- Institute of Biotechnology, Xianghu Laboratory, Hangzhou 311231, China
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Holden S, Bakkeren G, Hubensky J, Bamrah R, Abbasi M, Qutob D, de Graaf ML, Kim SH, Kutcher HR, McCallum BD, Randhawa HS, Iqbal M, Uloth K, Burlakoti RR, Brar GS. Uncovering the history of recombination and population structure in western Canadian stripe rust populations through mating type alleles. BMC Biol 2023; 21:233. [PMID: 37880702 PMCID: PMC10601111 DOI: 10.1186/s12915-023-01717-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 09/27/2023] [Indexed: 10/27/2023] Open
Abstract
BACKGROUND The population structure of crop pathogens such as Puccinia striiformis f. sp. tritici (Pst), the cause of wheat stripe rust, is of interest to researchers looking to understand these pathogens on a molecular level as well as those with an applied focus such as disease epidemiology. Cereal rusts can reproduce sexually or asexually, and the emergence of novel lineages has the potential to cause serious epidemics such as the one caused by the 'Warrior' lineage in Europe. In a global context, Pst lineages in Canada were not well-characterized and the origin of foreign incursions was not known. Additionally, while some Pst mating type genes have been identified in published genomes, there has been no rigorous assessment of mating type diversity and distribution across the species. RESULTS We used a whole-genome/transcriptome sequencing approach for the Canadian Pst population to identify lineages in their global context and evidence tracing foreign incursions. More importantly: for the first time ever, we identified nine alleles of the homeodomain mating type locus in the worldwide Pst population and show that previously identified lineages exhibit a single pair of these alleles. Consistently with the literature, we find only two pheromone receptor mating type alleles. We show that the recent population shift from the 'PstS1' lineage to the 'PstS1-related' lineage is also associated with the introduction of a novel mating type allele (Pst-b3-HD) to the Canadian population. We also show evidence for high levels of mating type diversity in samples associated with the Himalayan center of diversity for Pst, including a single Canadian race previously identified as 'PstPr' (probable recombinant) which we identify as a foreign incursion, most closely related to isolates sampled from China circa 2015. CONCLUSIONS These data describe a recent shift in the population of Canadian Pst field isolates and characterize homeodomain-locus mating type alleles in the global Pst population which can now be utilized in testing several research questions and hypotheses around sexuality and hybridization in rust fungi.
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Affiliation(s)
- Samuel Holden
- Faculty of Land and Food Systems, The University of British Columbia (UBC), Vancouver, BC, Canada.
| | - Guus Bakkeren
- Agriculture and Agri-Food Canada (AAFC), Summerland Research and Development Center, Summerland, BC, Canada
| | - John Hubensky
- Faculty of Land and Food Systems, The University of British Columbia (UBC), Vancouver, BC, Canada
| | - Ramandeep Bamrah
- Faculty of Land and Food Systems, The University of British Columbia (UBC), Vancouver, BC, Canada
| | - Mehrdad Abbasi
- Faculty of Land and Food Systems, The University of British Columbia (UBC), Vancouver, BC, Canada
| | - Dinah Qutob
- Kent State University, Stark Campus, North Canton, OH, USA
| | - Mei-Lan de Graaf
- Agriculture and Agri-Food Canada (AAFC), Summerland Research and Development Center, Summerland, BC, Canada
| | - Sang Hu Kim
- Agriculture and Agri-Food Canada (AAFC), Summerland Research and Development Center, Summerland, BC, Canada
| | - Hadley R Kutcher
- Department of Plant Science/Crop Development Centre, University of Saskatchewan, Saskatoon, SK, Canada
| | - Brent D McCallum
- Agriculture and Agri-Food Canada (AAFC), Brandon Research and Development Center, Brandon, MB, Canada
| | - Harpinder S Randhawa
- Agriculture and Agri-Food Canada (AAFC), Lethbridge Research and Development Center, Lethbridge, AB, Canada
| | - Muhammad Iqbal
- Faculty of Agricultural, Life & Environmental Sciences, University of Alberta, Edmonton, AB, Canada
| | - Keith Uloth
- British Columbia Pest Monitoring Network, Dawson Creek, BC, Canada
| | - Rishi R Burlakoti
- Agriculture and Agri-Food Canada (AAFC), Agassiz Research and Development Center, Agassiz, BC, Canada
| | - Gurcharn S Brar
- Faculty of Land and Food Systems, The University of British Columbia (UBC), Vancouver, BC, Canada.
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Michel S, Löschenberger F, Ametz C, Bürstmayr H. Toward combining qualitative race-specific and quantitative race-nonspecific disease resistance by genomic selection. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:79. [PMID: 36952008 PMCID: PMC10036288 DOI: 10.1007/s00122-023-04312-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 01/27/2023] [Indexed: 06/17/2023]
Abstract
A novel genomic selection strategy offers the unique opportunity to develop qualitative race-specific resistant varieties that possess high levels of the more durable quantitative race-nonspecific resistance in their genetic background. Race-specific qualitative resistance genes (R-genes) are conferring complete resistance in many pathosystems, but are frequently overcome by new virulent pathogen races. Once the deployed R-genes are overcome, a wide variation of quantitative disease resistance (QDR) can be observed in a set of previously race-specific, i.e., completely resistant genotypes-a phenomenon known as "vertifolia effect." This race-nonspecific QDR is considered to be more durable in the long term, but provides merely a partial protection against pathogens. This simulation study aimed to detangle race-specific R-gene-mediated resistance of pending selection candidates and the QDR in their genetic background by employing different genomic selection strategies. True breeding values that reflected performance data for rust resistance in wheat were simulated, and used in a recurrent genomic selection based on several prediction models and training population designs. Using training populations that were devoid of race-specific R-genes was thereby pivotal for an efficient improvement of QDR in the long term. Marker-assisted preselection for the presence of R-genes followed by a genomic prediction for accumulating the many small to medium effect loci underlying QDR in the genetic background of race-specific resistant genotypes appeared furthermore to be a promising approach to select simultaneously for both types of resistance. The practical application of such a knowledge-driven genomic breeding strategy offers the opportunity to develop varieties with multiple layers of resistance, which have the potential to prevent intolerable crop losses under epidemic situations by displaying a high level of QDR even when race-specific R-genes have been overcome by evolving pathogen populations.
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Affiliation(s)
- Sebastian Michel
- Department of Agrobiotechnology, IFA-Tulln, University of Natural Resources and Life Sciences Vienna, Konrad-Lorenz-Str. 20, 3430, Tulln, Austria.
| | | | - Christian Ametz
- Saatzucht Donau GesmbH & CoKG, Saatzuchtstrasse 11, 2301, Probstdorf, Austria
| | - Hermann Bürstmayr
- Department of Agrobiotechnology, IFA-Tulln, University of Natural Resources and Life Sciences Vienna, Konrad-Lorenz-Str. 20, 3430, Tulln, Austria
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Semagn K, Iqbal M, Jarquin D, Randhawa H, Aboukhaddour R, Howard R, Ciechanowska I, Farzand M, Dhariwal R, Hiebert CW, N’Diaye A, Pozniak C, Spaner D. Genomic Prediction Accuracy of Stripe Rust in Six Spring Wheat Populations by Modeling Genotype by Environment Interaction. PLANTS (BASEL, SWITZERLAND) 2022; 11:1736. [PMID: 35807690 PMCID: PMC9269065 DOI: 10.3390/plants11131736] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 06/27/2022] [Accepted: 06/28/2022] [Indexed: 11/17/2022]
Abstract
Some previous studies have assessed the predictive ability of genome-wide selection on stripe (yellow) rust resistance in wheat, but the effect of genotype by environment interaction (GEI) in prediction accuracies has not been well studied in diverse genetic backgrounds. Here, we compared the predictive ability of a model based on phenotypic data only (M1), the main effect of phenotype and molecular markers (M2), and a model that incorporated GEI (M3) using three cross-validations (CV1, CV2, and CV0) scenarios of interest to breeders in six spring wheat populations. Each population was evaluated at three to eight field nurseries and genotyped with either the DArTseq technology or the wheat 90K single nucleotide polymorphism arrays, of which a subset of 1,058- 23,795 polymorphic markers were used for the analyses. In the CV1 scenario, the mean prediction accuracies of the M1, M2, and M3 models across the six populations varied from -0.11 to -0.07, from 0.22 to 0.49, and from 0.19 to 0.48, respectively. Mean accuracies obtained using the M3 model in the CV1 scenario were significantly greater than the M2 model in two populations, the same in three populations, and smaller in one population. In both the CV2 and CV0 scenarios, the mean prediction accuracies of the three models varied from 0.53 to 0.84 and were not significantly different in all populations, except the Attila/CDC Go in the CV2, where the M3 model gave greater accuracy than both the M1 and M2 models. Overall, the M3 model increased prediction accuracies in some populations by up to 12.4% and decreased accuracy in others by up to 17.4%, demonstrating inconsistent results among genetic backgrounds that require considering each population separately. This is the first comprehensive genome-wide prediction study that investigated details of the effect of GEI on stripe rust resistance across diverse spring wheat populations.
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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; (M.I.); (I.C.); (M.F.)
| | - Muhammad Iqbal
- Department of Agricultural, Food and Nutritional Science, 4-10 Agriculture-Forestry Centre, University of Alberta, Edmonton, AB T6G 2P5, Canada; (M.I.); (I.C.); (M.F.)
| | - Diego Jarquin
- Agronomy Department, University of Florida, Gainesville, FL 32611, USA;
| | - Harpinder Randhawa
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, 5403-1st Avenue South, Lethbridge, AB T1J 4B1, Canada; (H.R.); (R.A.); (R.D.)
| | - Reem Aboukhaddour
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, 5403-1st Avenue South, Lethbridge, AB T1J 4B1, Canada; (H.R.); (R.A.); (R.D.)
| | - Reka Howard
- Department of Statistics, University of Nebraska–Lincoln, Lincoln, NE 68583, USA;
| | - Izabela Ciechanowska
- Department of Agricultural, Food and Nutritional Science, 4-10 Agriculture-Forestry Centre, University of Alberta, Edmonton, AB T6G 2P5, Canada; (M.I.); (I.C.); (M.F.)
| | - Momna Farzand
- Department of Agricultural, Food and Nutritional Science, 4-10 Agriculture-Forestry Centre, University of Alberta, Edmonton, AB T6G 2P5, Canada; (M.I.); (I.C.); (M.F.)
| | - Raman Dhariwal
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, 5403-1st Avenue South, Lethbridge, AB T1J 4B1, Canada; (H.R.); (R.A.); (R.D.)
| | - Colin W. Hiebert
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, 101 Route 100, Morden, MB R6M 1Y5, Canada;
| | - Amidou N’Diaye
- Crop Development Centre and Department of Plant Sciences, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK S7N 5A8, Canada; (A.N.); (C.P.)
| | - Curtis Pozniak
- Crop Development Centre and Department of Plant Sciences, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK S7N 5A8, Canada; (A.N.); (C.P.)
| | - Dean Spaner
- Department of Agricultural, Food and Nutritional Science, 4-10 Agriculture-Forestry Centre, University of Alberta, Edmonton, AB T6G 2P5, Canada; (M.I.); (I.C.); (M.F.)
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