Genome-Wide Association Studies for Pasmo Resistance in Flax (Linum usitatissimum L.)
Pasmo is one of the most widespread diseases threatening flax production. To identify genetic regions associated with pasmo resistance (PR), a genome-wide association study was performed on 370 accessions from the flax core collection. Evaluation of pasmo severity was performed in the field from 201...
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Frontiers Media S.A.
2019-01-01
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| Series: | Frontiers in Plant Science |
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| Online Access: | https://www.frontiersin.org/article/10.3389/fpls.2018.01982/full |
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| author | Liqiang He Liqiang He Jin Xiao Khalid Y. Rashid Zhen Yao Pingchuan Li Gaofeng Jia Xiue Wang Sylvie Cloutier Frank M. You Frank M. You |
| author_facet | Liqiang He Liqiang He Jin Xiao Khalid Y. Rashid Zhen Yao Pingchuan Li Gaofeng Jia Xiue Wang Sylvie Cloutier Frank M. You Frank M. You |
| author_sort | Liqiang He |
| collection | DOAJ |
| description | Pasmo is one of the most widespread diseases threatening flax production. To identify genetic regions associated with pasmo resistance (PR), a genome-wide association study was performed on 370 accessions from the flax core collection. Evaluation of pasmo severity was performed in the field from 2012 to 2016 in Morden, MB, Canada. Genotyping-by-sequencing has identified 258,873 single nucleotide polymorphisms (SNPs) distributed on all 15 flax chromosomes. Marker-trait associations were identified using ten different statistical models. A total of 692 unique quantitative trait nucleotides (QTNs) associated with 500 putative quantitative trait loci (QTL) were detected from six phenotypic PR datasets (five individual years and average across years). Different QTNs were identified with various statistical models and from individual PR datasets, indicative of the complementation between analytical methods and/or genotype × environment interactions of the QTL effects. The single-locus models tended to identify large-effect QTNs while the multi-loci models were able to detect QTNs with smaller effects. Among the putative QTL, 67 had large effects (3–23%), were stable across all datasets and explained 32–64% of the total variation for PR in the various datasets. Forty-five of these QTL spanned 85 resistance gene analogs including a large toll interleukin receptor, nucleotide-binding site, leucine-rich repeat (TNL) type gene cluster on chromosome 8. The number of QTL with positive-effect or favorite alleles (NPQTL) in accessions was significantly correlated with PR (R2 = 0.55), suggesting that these QTL effects are mainly additive. NPQTL was also significantly associated with morphotype (R2 = 0.52) and major QTL with positive effect alleles were present in the fiber type accessions. The 67 large effect QTL are suited for marker-assisted selection and the 500 QTL for effective genomic prediction in PR molecular breeding. |
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| institution | Directory Open Access Journal |
| issn | 1664-462X |
| language | English |
| last_indexed | 2024-12-11T09:34:31Z |
| publishDate | 2019-01-01 |
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| series | Frontiers in Plant Science |
| spelling | doaj.art-d35588c7f9a54554a175b088489c9f5c2022-12-22T01:12:56ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2019-01-01910.3389/fpls.2018.01982435554Genome-Wide Association Studies for Pasmo Resistance in Flax (Linum usitatissimum L.)Liqiang He0Liqiang He1Jin Xiao2Khalid Y. Rashid3Zhen Yao4Pingchuan Li5Gaofeng Jia6Xiue Wang7Sylvie Cloutier8Frank M. You9Frank M. You10Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, CanadaKey Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Nanjing Agricultural University/JCIC-MCP, Nanjing, ChinaKey Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Nanjing Agricultural University/JCIC-MCP, Nanjing, ChinaMorden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, MB, CanadaMorden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, MB, CanadaMorden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, MB, CanadaCrop Development Centre, University of Saskatchewan, Saskatoon, SK, CanadaKey Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Nanjing Agricultural University/JCIC-MCP, Nanjing, ChinaOttawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, CanadaOttawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, CanadaKey Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Nanjing Agricultural University/JCIC-MCP, Nanjing, ChinaPasmo is one of the most widespread diseases threatening flax production. To identify genetic regions associated with pasmo resistance (PR), a genome-wide association study was performed on 370 accessions from the flax core collection. Evaluation of pasmo severity was performed in the field from 2012 to 2016 in Morden, MB, Canada. Genotyping-by-sequencing has identified 258,873 single nucleotide polymorphisms (SNPs) distributed on all 15 flax chromosomes. Marker-trait associations were identified using ten different statistical models. A total of 692 unique quantitative trait nucleotides (QTNs) associated with 500 putative quantitative trait loci (QTL) were detected from six phenotypic PR datasets (five individual years and average across years). Different QTNs were identified with various statistical models and from individual PR datasets, indicative of the complementation between analytical methods and/or genotype × environment interactions of the QTL effects. The single-locus models tended to identify large-effect QTNs while the multi-loci models were able to detect QTNs with smaller effects. Among the putative QTL, 67 had large effects (3–23%), were stable across all datasets and explained 32–64% of the total variation for PR in the various datasets. Forty-five of these QTL spanned 85 resistance gene analogs including a large toll interleukin receptor, nucleotide-binding site, leucine-rich repeat (TNL) type gene cluster on chromosome 8. The number of QTL with positive-effect or favorite alleles (NPQTL) in accessions was significantly correlated with PR (R2 = 0.55), suggesting that these QTL effects are mainly additive. NPQTL was also significantly associated with morphotype (R2 = 0.52) and major QTL with positive effect alleles were present in the fiber type accessions. The 67 large effect QTL are suited for marker-assisted selection and the 500 QTL for effective genomic prediction in PR molecular breeding.https://www.frontiersin.org/article/10.3389/fpls.2018.01982/fullpasmo resistancequantitative trait loci (QTL)quantitative trait nucleotides (QTNs)fiberlinseedcore collection |
| spellingShingle | Liqiang He Liqiang He Jin Xiao Khalid Y. Rashid Zhen Yao Pingchuan Li Gaofeng Jia Xiue Wang Sylvie Cloutier Frank M. You Frank M. You Genome-Wide Association Studies for Pasmo Resistance in Flax (Linum usitatissimum L.) Frontiers in Plant Science pasmo resistance quantitative trait loci (QTL) quantitative trait nucleotides (QTNs) fiber linseed core collection |
| title | Genome-Wide Association Studies for Pasmo Resistance in Flax (Linum usitatissimum L.) |
| title_full | Genome-Wide Association Studies for Pasmo Resistance in Flax (Linum usitatissimum L.) |
| title_fullStr | Genome-Wide Association Studies for Pasmo Resistance in Flax (Linum usitatissimum L.) |
| title_full_unstemmed | Genome-Wide Association Studies for Pasmo Resistance in Flax (Linum usitatissimum L.) |
| title_short | Genome-Wide Association Studies for Pasmo Resistance in Flax (Linum usitatissimum L.) |
| title_sort | genome wide association studies for pasmo resistance in flax linum usitatissimum l |
| topic | pasmo resistance quantitative trait loci (QTL) quantitative trait nucleotides (QTNs) fiber linseed core collection |
| url | https://www.frontiersin.org/article/10.3389/fpls.2018.01982/full |
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