Genome Wide Association Studies in Multiple Spinach Breeding Populations Refine Downy Mildew Race 13 Resistance Genes
Downy mildew, caused by the oomycete Peronospora effusa, is the most economically important disease on spinach. Fourteen new races of P. effusa have been identified in the last three decades. The frequent emergence of new races of P. effusa continually overcome the genetic resistance to the pathogen...
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| Format: | Article |
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Frontiers Media S.A.
2020-10-01
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| Series: | Frontiers in Plant Science |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fpls.2020.563187/full |
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| author | Gehendra Bhattarai Ainong Shi Chunda Feng Braham Dhillon Braham Dhillon Beiquan Mou James C. Correll |
| author_facet | Gehendra Bhattarai Ainong Shi Chunda Feng Braham Dhillon Braham Dhillon Beiquan Mou James C. Correll |
| author_sort | Gehendra Bhattarai |
| collection | DOAJ |
| description | Downy mildew, caused by the oomycete Peronospora effusa, is the most economically important disease on spinach. Fourteen new races of P. effusa have been identified in the last three decades. The frequent emergence of new races of P. effusa continually overcome the genetic resistance to the pathogen. The objectives of this research were to more clearly map the downy mildew resistance locus RPF1 in spinach, to identify single nucleotide polymorphism (SNP) markers associated with the resistance, and to refine the candidate genes responsible for the resistance. Progeny from populations generated from crosses of cultivars resistant (due to RPF1) to race 13 of P. effusa (Swan, T-Bird, Squirrel, and Tonga) with race 13 susceptible cultivars (Whale and Polka) were inoculated and the downy mildew disease response determined. Association analysis was performed in TASSEL, GAPIT, PLINK, and GENESIS programs using SNP markers identified from genotyping by sequencing (GBS). Association analysis mapped the race 13 resistance loci (RPF1) to positions 0.39, 0.69, 0.94-0.98, and 1.2 Mb of chromosome 3. The associated SNPs were within 1–7 kb of the disease resistance genes Spo12784, Spo12719, Spo12905, and Spo12821, and 11–18 Kb from Spo12903. This study extended our understanding of the genetic basis of downy mildew resistance in spinach and provided the most promising candidate genes Spo12784 and Spo12903 near the RPF1 locus, to pursue functional validation. The SNP markers may be used to select for the resistant lines to improve genetic resistance against the downy mildew pathogen and in developing durably resistant cultivars. |
| first_indexed | 2024-12-14T01:02:29Z |
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| institution | Directory Open Access Journal |
| issn | 1664-462X |
| language | English |
| last_indexed | 2024-12-14T01:02:29Z |
| publishDate | 2020-10-01 |
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| series | Frontiers in Plant Science |
| spelling | doaj.art-2ff3fc5c037f4a26ba0196389fa7f6502022-12-21T23:23:09ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2020-10-011110.3389/fpls.2020.563187563187Genome Wide Association Studies in Multiple Spinach Breeding Populations Refine Downy Mildew Race 13 Resistance GenesGehendra Bhattarai0Ainong Shi1Chunda Feng2Braham Dhillon3Braham Dhillon4Beiquan Mou5James C. Correll6Department of Horticulture, University of Arkansas, Fayetteville, AR, United StatesDepartment of Horticulture, University of Arkansas, Fayetteville, AR, United StatesDepartment of Plant Pathology, University of Arkansas, Fayetteville, AR, United StatesDepartment of Plant Pathology, University of Arkansas, Fayetteville, AR, United StatesDepartment of Plant Pathology, Fort Lauderdale Research and Education Center, University of Florida, Davie, FL, United StatesCrop Improvement and Protection Research Unit, United States Department of Agriculture, Agricultural Research Service, Salinas, CA, United StatesDepartment of Plant Pathology, University of Arkansas, Fayetteville, AR, United StatesDowny mildew, caused by the oomycete Peronospora effusa, is the most economically important disease on spinach. Fourteen new races of P. effusa have been identified in the last three decades. The frequent emergence of new races of P. effusa continually overcome the genetic resistance to the pathogen. The objectives of this research were to more clearly map the downy mildew resistance locus RPF1 in spinach, to identify single nucleotide polymorphism (SNP) markers associated with the resistance, and to refine the candidate genes responsible for the resistance. Progeny from populations generated from crosses of cultivars resistant (due to RPF1) to race 13 of P. effusa (Swan, T-Bird, Squirrel, and Tonga) with race 13 susceptible cultivars (Whale and Polka) were inoculated and the downy mildew disease response determined. Association analysis was performed in TASSEL, GAPIT, PLINK, and GENESIS programs using SNP markers identified from genotyping by sequencing (GBS). Association analysis mapped the race 13 resistance loci (RPF1) to positions 0.39, 0.69, 0.94-0.98, and 1.2 Mb of chromosome 3. The associated SNPs were within 1–7 kb of the disease resistance genes Spo12784, Spo12719, Spo12905, and Spo12821, and 11–18 Kb from Spo12903. This study extended our understanding of the genetic basis of downy mildew resistance in spinach and provided the most promising candidate genes Spo12784 and Spo12903 near the RPF1 locus, to pursue functional validation. The SNP markers may be used to select for the resistant lines to improve genetic resistance against the downy mildew pathogen and in developing durably resistant cultivars.https://www.frontiersin.org/articles/10.3389/fpls.2020.563187/fullspinachdowny mildewoomycetedisease resistancemappingGWAS |
| spellingShingle | Gehendra Bhattarai Ainong Shi Chunda Feng Braham Dhillon Braham Dhillon Beiquan Mou James C. Correll Genome Wide Association Studies in Multiple Spinach Breeding Populations Refine Downy Mildew Race 13 Resistance Genes Frontiers in Plant Science spinach downy mildew oomycete disease resistance mapping GWAS |
| title | Genome Wide Association Studies in Multiple Spinach Breeding Populations Refine Downy Mildew Race 13 Resistance Genes |
| title_full | Genome Wide Association Studies in Multiple Spinach Breeding Populations Refine Downy Mildew Race 13 Resistance Genes |
| title_fullStr | Genome Wide Association Studies in Multiple Spinach Breeding Populations Refine Downy Mildew Race 13 Resistance Genes |
| title_full_unstemmed | Genome Wide Association Studies in Multiple Spinach Breeding Populations Refine Downy Mildew Race 13 Resistance Genes |
| title_short | Genome Wide Association Studies in Multiple Spinach Breeding Populations Refine Downy Mildew Race 13 Resistance Genes |
| title_sort | genome wide association studies in multiple spinach breeding populations refine downy mildew race 13 resistance genes |
| topic | spinach downy mildew oomycete disease resistance mapping GWAS |
| url | https://www.frontiersin.org/articles/10.3389/fpls.2020.563187/full |
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