Genome-Wide Association Study of QTLs Conferring Resistance to Bacterial Leaf Streak in Rice
Bacterial leaf streak (BLS) is a devastating rice disease caused by the bacterial pathogen, <i>Xanthomonas oryzae</i> pv. <i>oryzicola</i> (<i>Xoc</i>), which can result in severe damage to rice production worldwide. Based on a total of 510 rice accessions, triale...
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MDPI AG
2021-09-01
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| Online Access: | https://www.mdpi.com/2223-7747/10/10/2039 |
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| author | Xiaofang Xie Yan Zheng Libin Lu Jiazheng Yuan Jie Hu Suhong Bu Yanyi Lin Yinsong Liu Huazhong Guan Weiren Wu |
| author_facet | Xiaofang Xie Yan Zheng Libin Lu Jiazheng Yuan Jie Hu Suhong Bu Yanyi Lin Yinsong Liu Huazhong Guan Weiren Wu |
| author_sort | Xiaofang Xie |
| collection | DOAJ |
| description | Bacterial leaf streak (BLS) is a devastating rice disease caused by the bacterial pathogen, <i>Xanthomonas oryzae</i> pv. <i>oryzicola</i> (<i>Xoc</i>), which can result in severe damage to rice production worldwide. Based on a total of 510 rice accessions, trialed in two seasons and using six different multi-locus GWAS methods (mrMLM, ISIS EM-BLASSO, pLARmEB, FASTmrMLM, FASTmrEMMA and pKWmEB), 79 quantitative trait nucleotides (QTNs) reflecting 69 QTLs for BLS resistance were identified (LOD > 3). The QTNs were distributed on all chromosomes, with the most distributed on chromosome 11, followed by chromosomes 1 and 5. Each QTN had an additive effect of 0.20 (cm) and explained, on average, 2.44% of the phenotypic variance, varying from 0.00–0.92 (cm) and from 0.00–9.86%, respectively. Twenty-five QTNs were detected by at least two methods. Among them, <i>qnBLS11.17</i> was detected by as many as five methods. Most of the QTNs showed a significant interaction with their environment, but no QTNs were detected in both seasons. By defining the QTL range for each QTN according to the LD half-decay distance, a total of 848 candidate genes were found for nine top QTNs. Among them, more than 10% were annotated to be related to biotic stress resistance, and five showed a significant response to <i>Xoc</i> infection. Our results could facilitate the in-depth study and marker-assisted improvement of rice resistance to BLS. |
| first_indexed | 2024-03-10T06:15:34Z |
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| last_indexed | 2024-03-10T06:15:34Z |
| publishDate | 2021-09-01 |
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| series | Plants |
| spelling | doaj.art-bdfc5b3f19ab4b64b61047ddb01fac112023-11-22T19:42:47ZengMDPI AGPlants2223-77472021-09-011010203910.3390/plants10102039Genome-Wide Association Study of QTLs Conferring Resistance to Bacterial Leaf Streak in RiceXiaofang Xie0Yan Zheng1Libin Lu2Jiazheng Yuan3Jie Hu4Suhong Bu5Yanyi Lin6Yinsong Liu7Huazhong Guan8Weiren Wu9College of Life Sciences, Fujian Agriculture & Forestry University, Fuzhou 350002, ChinaCollege of Life Sciences, Fujian Agriculture & Forestry University, Fuzhou 350002, ChinaFujian Academy of Agricultural Sciences, Fuzhou 350000, ChinaDepartment of Biological and Forensic Sciences, Fayetteville State University, Fayetteville, NC 28301, USAFujian Key Laboratory of Crop Breeding by Design, Fujian Agriculture & Forestry University, Fuzhou 350002, ChinaCollege of Agriculturem, South China Agricultural University, Guangzhou 510342, ChinaCollege of Arts College of Landscape Architecture, Fujian Agriculture & Forestry University, Fuzhou 350002, ChinaCollege of Life Sciences, Fujian Agriculture & Forestry University, Fuzhou 350002, ChinaFujian Key Laboratory of Crop Breeding by Design, Fujian Agriculture & Forestry University, Fuzhou 350002, ChinaFujian Key Laboratory of Crop Breeding by Design, Fujian Agriculture & Forestry University, Fuzhou 350002, ChinaBacterial leaf streak (BLS) is a devastating rice disease caused by the bacterial pathogen, <i>Xanthomonas oryzae</i> pv. <i>oryzicola</i> (<i>Xoc</i>), which can result in severe damage to rice production worldwide. Based on a total of 510 rice accessions, trialed in two seasons and using six different multi-locus GWAS methods (mrMLM, ISIS EM-BLASSO, pLARmEB, FASTmrMLM, FASTmrEMMA and pKWmEB), 79 quantitative trait nucleotides (QTNs) reflecting 69 QTLs for BLS resistance were identified (LOD > 3). The QTNs were distributed on all chromosomes, with the most distributed on chromosome 11, followed by chromosomes 1 and 5. Each QTN had an additive effect of 0.20 (cm) and explained, on average, 2.44% of the phenotypic variance, varying from 0.00–0.92 (cm) and from 0.00–9.86%, respectively. Twenty-five QTNs were detected by at least two methods. Among them, <i>qnBLS11.17</i> was detected by as many as five methods. Most of the QTNs showed a significant interaction with their environment, but no QTNs were detected in both seasons. By defining the QTL range for each QTN according to the LD half-decay distance, a total of 848 candidate genes were found for nine top QTNs. Among them, more than 10% were annotated to be related to biotic stress resistance, and five showed a significant response to <i>Xoc</i> infection. Our results could facilitate the in-depth study and marker-assisted improvement of rice resistance to BLS.https://www.mdpi.com/2223-7747/10/10/2039ricebacterial leaf streakdisease resistancemulti-locus GWASQTN |
| spellingShingle | Xiaofang Xie Yan Zheng Libin Lu Jiazheng Yuan Jie Hu Suhong Bu Yanyi Lin Yinsong Liu Huazhong Guan Weiren Wu Genome-Wide Association Study of QTLs Conferring Resistance to Bacterial Leaf Streak in Rice Plants rice bacterial leaf streak disease resistance multi-locus GWAS QTN |
| title | Genome-Wide Association Study of QTLs Conferring Resistance to Bacterial Leaf Streak in Rice |
| title_full | Genome-Wide Association Study of QTLs Conferring Resistance to Bacterial Leaf Streak in Rice |
| title_fullStr | Genome-Wide Association Study of QTLs Conferring Resistance to Bacterial Leaf Streak in Rice |
| title_full_unstemmed | Genome-Wide Association Study of QTLs Conferring Resistance to Bacterial Leaf Streak in Rice |
| title_short | Genome-Wide Association Study of QTLs Conferring Resistance to Bacterial Leaf Streak in Rice |
| title_sort | genome wide association study of qtls conferring resistance to bacterial leaf streak in rice |
| topic | rice bacterial leaf streak disease resistance multi-locus GWAS QTN |
| url | https://www.mdpi.com/2223-7747/10/10/2039 |
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