Quantitative Trait Locus Mapping of Marsh Spot Disease Resistance in Cranberry Common Bean (<i>Phaseolus vulgaris</i> L.)
Common bean (<i>Phaseolus vulgaris</i> L.) is a food crop that is an important source of dietary proteins and carbohydrates. Marsh spot is a physiological disorder that diminishes seed quality in beans. Prior research suggested that this disease is likely caused by manganese (Mn) deficie...
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MDPI AG
2022-07-01
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| Series: | International Journal of Molecular Sciences |
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| author | Bosen Jia Robert L. Conner Waldo C. Penner Chunfang Zheng Sylvie Cloutier Anfu Hou Xuhua Xia Frank M. You |
| author_facet | Bosen Jia Robert L. Conner Waldo C. Penner Chunfang Zheng Sylvie Cloutier Anfu Hou Xuhua Xia Frank M. You |
| author_sort | Bosen Jia |
| collection | DOAJ |
| description | Common bean (<i>Phaseolus vulgaris</i> L.) is a food crop that is an important source of dietary proteins and carbohydrates. Marsh spot is a physiological disorder that diminishes seed quality in beans. Prior research suggested that this disease is likely caused by manganese (Mn) deficiency during seed development and that marsh spot resistance is controlled by at least four genes. In this study, genetic mapping was performed to identify quantitative trait loci (QTL) and the potential candidate genes associated with marsh spot resistance. All 138 recombinant inbred lines (RILs) from a bi-parental population were evaluated for marsh spot resistance during five years from 2015 to 2019 in sandy and heavy clay soils in Morden, Manitoba, Canada. The RILs were sequenced using a genotyping by sequencing approach. A total of 52,676 single nucleotide polymorphisms (SNPs) were identified and filtered to generate a high-quality set of 2066 SNPs for QTL mapping. A genetic map based on 1273 SNP markers distributed on 11 chromosomes and covering 1599 cm was constructed. A total of 12 stable and 4 environment-specific QTL were identified using additive effect models, and an additional two epistatic QTL interacting with two of the 16 QTL were identified using an epistasis model. Genome-wide scans of the candidate genes identified 13 metal transport-related candidate genes co-locating within six QTL regions. In particular, two QTL (<i>QTL.3.1</i> and <i>QTL.3.2</i>) with the highest <i>R</i><sup>2</sup> values (21.8% and 24.5%, respectively) harbored several metal transport genes <i>Phvul.003G086300</i>, <i>Phvul.003G092500</i>, <i>Phvul.003G104900</i>, <i>Phvul.003G099700</i>, and <i>Phvul.003G108900</i> in a large genomic region of 16.8–27.5 Mb on chromosome 3. These results advance the current understanding of the genetic mechanisms of marsh spot resistance in cranberry common bean and provide new genomic resources for use in genomics-assisted breeding and for candidate gene isolation and functional characterization. |
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| spelling | doaj.art-0f486c2e49f24cce8c31be047f01f3f42023-11-30T21:04:25ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672022-07-012314763910.3390/ijms23147639Quantitative Trait Locus Mapping of Marsh Spot Disease Resistance in Cranberry Common Bean (<i>Phaseolus vulgaris</i> L.)Bosen Jia0Robert L. Conner1Waldo C. Penner2Chunfang Zheng3Sylvie Cloutier4Anfu Hou5Xuhua Xia6Frank M. You7Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, CanadaMorden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, MB R6M 1Y5, CanadaMorden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, MB R6M 1Y5, CanadaOttawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, CanadaOttawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, CanadaMorden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, MB R6M 1Y5, CanadaDepartment of Biology, University of Ottawa, 30 Marie Curie, Ottawa, ON K1N 6N5, CanadaOttawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, CanadaCommon bean (<i>Phaseolus vulgaris</i> L.) is a food crop that is an important source of dietary proteins and carbohydrates. Marsh spot is a physiological disorder that diminishes seed quality in beans. Prior research suggested that this disease is likely caused by manganese (Mn) deficiency during seed development and that marsh spot resistance is controlled by at least four genes. In this study, genetic mapping was performed to identify quantitative trait loci (QTL) and the potential candidate genes associated with marsh spot resistance. All 138 recombinant inbred lines (RILs) from a bi-parental population were evaluated for marsh spot resistance during five years from 2015 to 2019 in sandy and heavy clay soils in Morden, Manitoba, Canada. The RILs were sequenced using a genotyping by sequencing approach. A total of 52,676 single nucleotide polymorphisms (SNPs) were identified and filtered to generate a high-quality set of 2066 SNPs for QTL mapping. A genetic map based on 1273 SNP markers distributed on 11 chromosomes and covering 1599 cm was constructed. A total of 12 stable and 4 environment-specific QTL were identified using additive effect models, and an additional two epistatic QTL interacting with two of the 16 QTL were identified using an epistasis model. Genome-wide scans of the candidate genes identified 13 metal transport-related candidate genes co-locating within six QTL regions. In particular, two QTL (<i>QTL.3.1</i> and <i>QTL.3.2</i>) with the highest <i>R</i><sup>2</sup> values (21.8% and 24.5%, respectively) harbored several metal transport genes <i>Phvul.003G086300</i>, <i>Phvul.003G092500</i>, <i>Phvul.003G104900</i>, <i>Phvul.003G099700</i>, and <i>Phvul.003G108900</i> in a large genomic region of 16.8–27.5 Mb on chromosome 3. These results advance the current understanding of the genetic mechanisms of marsh spot resistance in cranberry common bean and provide new genomic resources for use in genomics-assisted breeding and for candidate gene isolation and functional characterization.https://www.mdpi.com/1422-0067/23/14/7639marsh spot diseasecranberry common beanQTL mappinggenotyping by sequencing (GBS)single nucleotide polymorphisms (SNPs)genome-wide association study (GWAS) |
| spellingShingle | Bosen Jia Robert L. Conner Waldo C. Penner Chunfang Zheng Sylvie Cloutier Anfu Hou Xuhua Xia Frank M. You Quantitative Trait Locus Mapping of Marsh Spot Disease Resistance in Cranberry Common Bean (<i>Phaseolus vulgaris</i> L.) International Journal of Molecular Sciences marsh spot disease cranberry common bean QTL mapping genotyping by sequencing (GBS) single nucleotide polymorphisms (SNPs) genome-wide association study (GWAS) |
| title | Quantitative Trait Locus Mapping of Marsh Spot Disease Resistance in Cranberry Common Bean (<i>Phaseolus vulgaris</i> L.) |
| title_full | Quantitative Trait Locus Mapping of Marsh Spot Disease Resistance in Cranberry Common Bean (<i>Phaseolus vulgaris</i> L.) |
| title_fullStr | Quantitative Trait Locus Mapping of Marsh Spot Disease Resistance in Cranberry Common Bean (<i>Phaseolus vulgaris</i> L.) |
| title_full_unstemmed | Quantitative Trait Locus Mapping of Marsh Spot Disease Resistance in Cranberry Common Bean (<i>Phaseolus vulgaris</i> L.) |
| title_short | Quantitative Trait Locus Mapping of Marsh Spot Disease Resistance in Cranberry Common Bean (<i>Phaseolus vulgaris</i> L.) |
| title_sort | quantitative trait locus mapping of marsh spot disease resistance in cranberry common bean i phaseolus vulgaris i l |
| topic | marsh spot disease cranberry common bean QTL mapping genotyping by sequencing (GBS) single nucleotide polymorphisms (SNPs) genome-wide association study (GWAS) |
| url | https://www.mdpi.com/1422-0067/23/14/7639 |
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