Unravelling the Genetic Architecture of Rust Resistance in the Common Bean (<i>Phaseolus vulgaris</i> L.) by Combining QTL-Seq and GWAS Analysis
The common bean (<i>Phaseolus vulgaris</i> L.) is the most important legume crop directly used for human consumption worldwide. Bean rust, caused by <i>Uromyces appendiculatus</i>, is a devastating disease and usually causes severe loss of seed yield and pod quality. Deployme...
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MDPI AG
2022-03-01
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| Series: | Plants |
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| Online Access: | https://www.mdpi.com/2223-7747/11/7/953 |
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| author | Xinyi Wu Baogen Wang Yan Xin Ying Wang Shuo Tian Jian Wang Xiaohua Wu Zhongfu Lu Xinjiang Qi Liming Xu Guojing Li |
| author_facet | Xinyi Wu Baogen Wang Yan Xin Ying Wang Shuo Tian Jian Wang Xiaohua Wu Zhongfu Lu Xinjiang Qi Liming Xu Guojing Li |
| author_sort | Xinyi Wu |
| collection | DOAJ |
| description | The common bean (<i>Phaseolus vulgaris</i> L.) is the most important legume crop directly used for human consumption worldwide. Bean rust, caused by <i>Uromyces appendiculatus</i>, is a devastating disease and usually causes severe loss of seed yield and pod quality. Deployment of resistant cultivars is the best strategy to combat this disease. However, despite being the largest snap bean-producing country, the genetic basis research of rust resistance has largely lagged in China. In this study, an RIL population and a diversity panel were evaluated for rust resistance against a purified rust isolate <i>Cua-LS</i> using a detached leaf assay. Deploying a QTL-Seq analysis in the RIL population, a 1.81 Mb interval on chromosome 4, a 2.73 Mb interval on chromosome 5 and a 1.26 Mb interval on chromosome 6 were identified as major QTLs for rust resistance, designated as <i>Qur-1</i>, <i>Qur-2</i> and <i>Qur-3</i>, respectively. Through a GWAS diversity panel, 64 significant SNPs associated with rust resistance were detected, distributed in all 11 chromosomes and explaining 19–49% of the phenotypic variation. Synteny analysis showed that <i>Qur-2</i> was validated in GWAS, but the rust QTL/SNPs detected in our study were different from the known genes, except <i>Ur-11</i>. A total of 114 candidate genes, including the typical NBS-LRR genes, protein kinase superfamily proteins and ABC transporter family proteins, were identified and proposed as the likely candidates. The identified 17 resistant accessions will enrich the resistant germplasm resources, and the detected QTLs/SNPs will facilitate the molecular breeding of rust resistance in the common bean. |
| first_indexed | 2024-03-09T11:31:37Z |
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| institution | Directory Open Access Journal |
| issn | 2223-7747 |
| language | English |
| last_indexed | 2024-03-09T11:31:37Z |
| publishDate | 2022-03-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Plants |
| spelling | doaj.art-758e8c39192d4baab16b339cbf4959b02023-11-30T23:51:22ZengMDPI AGPlants2223-77472022-03-0111795310.3390/plants11070953Unravelling the Genetic Architecture of Rust Resistance in the Common Bean (<i>Phaseolus vulgaris</i> L.) by Combining QTL-Seq and GWAS AnalysisXinyi Wu0Baogen Wang1Yan Xin2Ying Wang3Shuo Tian4Jian Wang5Xiaohua Wu6Zhongfu Lu7Xinjiang Qi8Liming Xu9Guojing Li10Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, ChinaInstitute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, ChinaJilin Academy of Vegetables and Flower Sciences, Changchun 130119, ChinaInstitute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, ChinaJilin Academy of Vegetables and Flower Sciences, Changchun 130119, ChinaInstitute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, ChinaInstitute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, ChinaInstitute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, ChinaInstitute of Horticultural, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, ChinaJilin Academy of Vegetables and Flower Sciences, Changchun 130119, ChinaInstitute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, ChinaThe common bean (<i>Phaseolus vulgaris</i> L.) is the most important legume crop directly used for human consumption worldwide. Bean rust, caused by <i>Uromyces appendiculatus</i>, is a devastating disease and usually causes severe loss of seed yield and pod quality. Deployment of resistant cultivars is the best strategy to combat this disease. However, despite being the largest snap bean-producing country, the genetic basis research of rust resistance has largely lagged in China. In this study, an RIL population and a diversity panel were evaluated for rust resistance against a purified rust isolate <i>Cua-LS</i> using a detached leaf assay. Deploying a QTL-Seq analysis in the RIL population, a 1.81 Mb interval on chromosome 4, a 2.73 Mb interval on chromosome 5 and a 1.26 Mb interval on chromosome 6 were identified as major QTLs for rust resistance, designated as <i>Qur-1</i>, <i>Qur-2</i> and <i>Qur-3</i>, respectively. Through a GWAS diversity panel, 64 significant SNPs associated with rust resistance were detected, distributed in all 11 chromosomes and explaining 19–49% of the phenotypic variation. Synteny analysis showed that <i>Qur-2</i> was validated in GWAS, but the rust QTL/SNPs detected in our study were different from the known genes, except <i>Ur-11</i>. A total of 114 candidate genes, including the typical NBS-LRR genes, protein kinase superfamily proteins and ABC transporter family proteins, were identified and proposed as the likely candidates. The identified 17 resistant accessions will enrich the resistant germplasm resources, and the detected QTLs/SNPs will facilitate the molecular breeding of rust resistance in the common bean.https://www.mdpi.com/2223-7747/11/7/953QTL-SeqGWASrustsyntenycommon bean |
| spellingShingle | Xinyi Wu Baogen Wang Yan Xin Ying Wang Shuo Tian Jian Wang Xiaohua Wu Zhongfu Lu Xinjiang Qi Liming Xu Guojing Li Unravelling the Genetic Architecture of Rust Resistance in the Common Bean (<i>Phaseolus vulgaris</i> L.) by Combining QTL-Seq and GWAS Analysis Plants QTL-Seq GWAS rust synteny common bean |
| title | Unravelling the Genetic Architecture of Rust Resistance in the Common Bean (<i>Phaseolus vulgaris</i> L.) by Combining QTL-Seq and GWAS Analysis |
| title_full | Unravelling the Genetic Architecture of Rust Resistance in the Common Bean (<i>Phaseolus vulgaris</i> L.) by Combining QTL-Seq and GWAS Analysis |
| title_fullStr | Unravelling the Genetic Architecture of Rust Resistance in the Common Bean (<i>Phaseolus vulgaris</i> L.) by Combining QTL-Seq and GWAS Analysis |
| title_full_unstemmed | Unravelling the Genetic Architecture of Rust Resistance in the Common Bean (<i>Phaseolus vulgaris</i> L.) by Combining QTL-Seq and GWAS Analysis |
| title_short | Unravelling the Genetic Architecture of Rust Resistance in the Common Bean (<i>Phaseolus vulgaris</i> L.) by Combining QTL-Seq and GWAS Analysis |
| title_sort | unravelling the genetic architecture of rust resistance in the common bean i phaseolus vulgaris i l by combining qtl seq and gwas analysis |
| topic | QTL-Seq GWAS rust synteny common bean |
| url | https://www.mdpi.com/2223-7747/11/7/953 |
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