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Genome-wide association studies using multi-models and multi-SNP datasets provide new insights into pasmo resistance in flax
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 per...
Autores principales: | , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Frontiers Media S.A.
2023
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10634603/ https://www.ncbi.nlm.nih.gov/pubmed/37954993 http://dx.doi.org/10.3389/fpls.2023.1229457 |
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author | He, Liqiang Sui, Yao Che, Yanru Wang, Huixian Rashid, Khalid Y. Cloutier, Sylvie You, Frank M. |
author_facet | He, Liqiang Sui, Yao Che, Yanru Wang, Huixian Rashid, Khalid Y. Cloutier, Sylvie You, Frank M. |
author_sort | He, Liqiang |
collection | PubMed |
description | 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 R(2) 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. |
format | Online Article Text |
id | pubmed-10634603 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | Frontiers Media S.A. |
record_format | MEDLINE/PubMed |
spelling | pubmed-106346032023-11-10 Genome-wide association studies using multi-models and multi-SNP datasets provide new insights into pasmo resistance in flax He, Liqiang Sui, Yao Che, Yanru Wang, Huixian Rashid, Khalid Y. Cloutier, Sylvie You, Frank M. Front Plant Sci Plant Science 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 R(2) 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. Frontiers Media S.A. 2023-10-25 /pmc/articles/PMC10634603/ /pubmed/37954993 http://dx.doi.org/10.3389/fpls.2023.1229457 Text en Copyright © 2023 Yao Sui, Yanru Che, Huixian Wang, and His Majesty the King in Right of Canada, as represented by the Minister of Agriculture and Agri-Food Canada for the contribution of Liqiang He, Khalid Y. Rashid, Sylvie Cloutier and Frank M. You https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. |
spellingShingle | Plant Science He, Liqiang Sui, Yao Che, Yanru Wang, Huixian Rashid, Khalid Y. Cloutier, Sylvie You, Frank M. Genome-wide association studies using multi-models and multi-SNP datasets provide new insights into pasmo resistance in flax |
title | Genome-wide association studies using multi-models and multi-SNP datasets provide new insights into pasmo resistance in flax |
title_full | Genome-wide association studies using multi-models and multi-SNP datasets provide new insights into pasmo resistance in flax |
title_fullStr | Genome-wide association studies using multi-models and multi-SNP datasets provide new insights into pasmo resistance in flax |
title_full_unstemmed | Genome-wide association studies using multi-models and multi-SNP datasets provide new insights into pasmo resistance in flax |
title_short | Genome-wide association studies using multi-models and multi-SNP datasets provide new insights into pasmo resistance in flax |
title_sort | genome-wide association studies using multi-models and multi-snp datasets provide new insights into pasmo resistance in flax |
topic | Plant Science |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10634603/ https://www.ncbi.nlm.nih.gov/pubmed/37954993 http://dx.doi.org/10.3389/fpls.2023.1229457 |
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