Genome-Wide Mapping of Loci Associated With Resistance to Clubroot in Brassica napus ssp. napobrassica (Rutabaga) Accessions From Nordic Countries
Rutabaga [Brassica napus ssp. napobrassica (L.) Hanelt] is reported to be an excellent source of clubroot (Plasmodiophora brassicae) resistance genes. In this study, 124 rutabaga accessions from the Nordic countries (Norway, Sweden, Finland, Denmark, and Iceland) were evaluated for their reaction to...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2020-06-01
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| Series: | Frontiers in Plant Science |
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| Online Access: | https://www.frontiersin.org/article/10.3389/fpls.2020.00742/full |
| _version_ | 1811206539718950912 |
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| author | Rudolph Fredua-Agyeman Zhiyu Yu Sheau-Fang Hwang Stephen E. Strelkov |
| author_facet | Rudolph Fredua-Agyeman Zhiyu Yu Sheau-Fang Hwang Stephen E. Strelkov |
| author_sort | Rudolph Fredua-Agyeman |
| collection | DOAJ |
| description | Rutabaga [Brassica napus ssp. napobrassica (L.) Hanelt] is reported to be an excellent source of clubroot (Plasmodiophora brassicae) resistance genes. In this study, 124 rutabaga accessions from the Nordic countries (Norway, Sweden, Finland, Denmark, and Iceland) were evaluated for their reaction to five single-spore isolates representing P. brassicae pathotypes 2F, 3H, 5I, 6M, and 8N and 12 field isolates representing pathotypes 2B, 3A, 3O, 5C, 5G, 5K, 5L, 5X (two isolates, L-G2 and L-G3), 8E, 8J, and 8P. The accessions were also genotyped using a 15K Brassica SNP array and 60 PCR-based primers linked to previously identified clubroot resistance genes. Six thousand eight hundred sixty-one SNP markers were retained after filtering with TASSEL 5.0, and used to evaluate four general linear models (GLM) and four mixed linear models (MLM). The PCA + K and Q + K MLM models gave the minimal deviance of the observed from the expected distribution in quantile-quantile plots, and hence were used for SNP-clubroot association analyses. In addition, 108 alleles derived from the PCR-based markers and the phenotypic data were analyzed with the PCA + K model. Forty-five SNPs and four PCR-based markers were identified to be associated strongly with resistance to isolates representing 13 pathotypes (2F, 3H, 5I, 6M, 8N, 2B, 3A, 3O, 5C, 5G, 5K, 5L, and 8P). These markers revealed the top and bottom segments of rutabaga chromosome A03 and the middle segment of chromosome A08 as genomic hotspots associated with resistance to the different P. brassicae pathotypes. |
| first_indexed | 2024-04-12T03:48:54Z |
| format | Article |
| id | doaj.art-bac14da85e06402fa53360eecbee0a00 |
| institution | Directory Open Access Journal |
| issn | 1664-462X |
| language | English |
| last_indexed | 2024-04-12T03:48:54Z |
| publishDate | 2020-06-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Plant Science |
| spelling | doaj.art-bac14da85e06402fa53360eecbee0a002022-12-22T03:49:02ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2020-06-011110.3389/fpls.2020.00742491849Genome-Wide Mapping of Loci Associated With Resistance to Clubroot in Brassica napus ssp. napobrassica (Rutabaga) Accessions From Nordic CountriesRudolph Fredua-AgyemanZhiyu YuSheau-Fang HwangStephen E. StrelkovRutabaga [Brassica napus ssp. napobrassica (L.) Hanelt] is reported to be an excellent source of clubroot (Plasmodiophora brassicae) resistance genes. In this study, 124 rutabaga accessions from the Nordic countries (Norway, Sweden, Finland, Denmark, and Iceland) were evaluated for their reaction to five single-spore isolates representing P. brassicae pathotypes 2F, 3H, 5I, 6M, and 8N and 12 field isolates representing pathotypes 2B, 3A, 3O, 5C, 5G, 5K, 5L, 5X (two isolates, L-G2 and L-G3), 8E, 8J, and 8P. The accessions were also genotyped using a 15K Brassica SNP array and 60 PCR-based primers linked to previously identified clubroot resistance genes. Six thousand eight hundred sixty-one SNP markers were retained after filtering with TASSEL 5.0, and used to evaluate four general linear models (GLM) and four mixed linear models (MLM). The PCA + K and Q + K MLM models gave the minimal deviance of the observed from the expected distribution in quantile-quantile plots, and hence were used for SNP-clubroot association analyses. In addition, 108 alleles derived from the PCR-based markers and the phenotypic data were analyzed with the PCA + K model. Forty-five SNPs and four PCR-based markers were identified to be associated strongly with resistance to isolates representing 13 pathotypes (2F, 3H, 5I, 6M, 8N, 2B, 3A, 3O, 5C, 5G, 5K, 5L, and 8P). These markers revealed the top and bottom segments of rutabaga chromosome A03 and the middle segment of chromosome A08 as genomic hotspots associated with resistance to the different P. brassicae pathotypes.https://www.frontiersin.org/article/10.3389/fpls.2020.00742/fullrutabagamarker-clubroot associationPlasmodiophora brassicaepathotypesgenomic hotspot |
| spellingShingle | Rudolph Fredua-Agyeman Zhiyu Yu Sheau-Fang Hwang Stephen E. Strelkov Genome-Wide Mapping of Loci Associated With Resistance to Clubroot in Brassica napus ssp. napobrassica (Rutabaga) Accessions From Nordic Countries Frontiers in Plant Science rutabaga marker-clubroot association Plasmodiophora brassicae pathotypes genomic hotspot |
| title | Genome-Wide Mapping of Loci Associated With Resistance to Clubroot in Brassica napus ssp. napobrassica (Rutabaga) Accessions From Nordic Countries |
| title_full | Genome-Wide Mapping of Loci Associated With Resistance to Clubroot in Brassica napus ssp. napobrassica (Rutabaga) Accessions From Nordic Countries |
| title_fullStr | Genome-Wide Mapping of Loci Associated With Resistance to Clubroot in Brassica napus ssp. napobrassica (Rutabaga) Accessions From Nordic Countries |
| title_full_unstemmed | Genome-Wide Mapping of Loci Associated With Resistance to Clubroot in Brassica napus ssp. napobrassica (Rutabaga) Accessions From Nordic Countries |
| title_short | Genome-Wide Mapping of Loci Associated With Resistance to Clubroot in Brassica napus ssp. napobrassica (Rutabaga) Accessions From Nordic Countries |
| title_sort | genome wide mapping of loci associated with resistance to clubroot in brassica napus ssp napobrassica rutabaga accessions from nordic countries |
| topic | rutabaga marker-clubroot association Plasmodiophora brassicae pathotypes genomic hotspot |
| url | https://www.frontiersin.org/article/10.3389/fpls.2020.00742/full |
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