Genome-Wide Association Study and Genomic Prediction of Fusarium Wilt Resistance in Common Bean Core Collection
The common bean (<i>Phaseolus vulgaris</i> L.) is a globally cultivated leguminous crop. Fusarium wilt (FW), caused by <i>Fusarium oxysporum</i> f. sp. <i>phaseoli</i> (<i>Fop</i>), is a significant disease leading to substantial yield loss in common b...
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MDPI AG
2023-10-01
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| Series: | International Journal of Molecular Sciences |
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| Online Access: | https://www.mdpi.com/1422-0067/24/20/15300 |
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| author | Kenani Chiwina Haizheng Xiong Gehendra Bhattarai Ryan William Dickson Theresa Makawa Phiri Yilin Chen Ibtisam Alatawi Derek Dean Neelendra K. Joshi Yuyan Chen Awais Riaz Paul Gepts Mark Brick Patrick F. Byrne Howard Schwartz James B. Ogg Kristin Otto Amy Fall Jeremy Gilbert Ainong Shi |
| author_facet | Kenani Chiwina Haizheng Xiong Gehendra Bhattarai Ryan William Dickson Theresa Makawa Phiri Yilin Chen Ibtisam Alatawi Derek Dean Neelendra K. Joshi Yuyan Chen Awais Riaz Paul Gepts Mark Brick Patrick F. Byrne Howard Schwartz James B. Ogg Kristin Otto Amy Fall Jeremy Gilbert Ainong Shi |
| author_sort | Kenani Chiwina |
| collection | DOAJ |
| description | The common bean (<i>Phaseolus vulgaris</i> L.) is a globally cultivated leguminous crop. Fusarium wilt (FW), caused by <i>Fusarium oxysporum</i> f. sp. <i>phaseoli</i> (<i>Fop</i>), is a significant disease leading to substantial yield loss in common beans. Disease-resistant cultivars are recommended to counteract this. The objective of this investigation was to identify single nucleotide polymorphism (SNP) markers associated with FW resistance and to pinpoint potential resistant common bean accessions within a core collection, utilizing a panel of 157 accessions through the Genome-wide association study (GWAS) approach with TASSEL 5 and GAPIT 3. Phenotypes for <i>Fop</i> race 1 and race 4 were matched with genotypic data from 4740 SNPs of BARCBean6K_3 Infinium Bea Chips. After ranking the 157-accession panel and revealing 21 Fusarium wilt-resistant accessions, the GWAS pinpointed 16 SNPs on chromosomes Pv04, Pv05, Pv07, Pv8, and Pv09 linked to <i>Fop</i> race 1 resistance, 23 SNPs on chromosomes Pv03, Pv04, Pv05, Pv07, Pv09, Pv10, and Pv11 associated with <i>Fop</i> race 4 resistance, and 7 SNPs on chromosomes Pv04 and Pv09 correlated with both <i>Fop</i> race 1 and race 4 resistances. Furthermore, within a 30 kb flanking region of these associated SNPs, a total of 17 candidate genes were identified. Some of these genes were annotated as classical disease resistance protein/enzymes, including NB-ARC domain proteins, Leucine-rich repeat protein kinase family proteins, zinc finger family proteins, P-loopcontaining nucleoside triphosphate hydrolase superfamily, etc. Genomic prediction (GP) accuracy for <i>Fop</i> race resistances ranged from 0.26 to 0.55. This study advanced common bean genetic enhancement through marker-assisted selection (MAS) and genomic selection (GS) strategies, paving the way for improved <i>Fop</i> resistance. |
| first_indexed | 2024-03-10T21:11:29Z |
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| issn | 1661-6596 1422-0067 |
| language | English |
| last_indexed | 2024-03-10T21:11:29Z |
| publishDate | 2023-10-01 |
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| spelling | doaj.art-1d9cbe1206e84300b25d7c2b75811d632023-11-19T16:44:41ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672023-10-0124201530010.3390/ijms242015300Genome-Wide Association Study and Genomic Prediction of Fusarium Wilt Resistance in Common Bean Core CollectionKenani Chiwina0Haizheng Xiong1Gehendra Bhattarai2Ryan William Dickson3Theresa Makawa Phiri4Yilin Chen5Ibtisam Alatawi6Derek Dean7Neelendra K. Joshi8Yuyan Chen9Awais Riaz10Paul Gepts11Mark Brick12Patrick F. Byrne13Howard Schwartz14James B. Ogg15Kristin Otto16Amy Fall17Jeremy Gilbert18Ainong Shi19Department of Horticulture, University of Arkansas, Fayetteville, AR 72701, USADepartment of Horticulture, University of Arkansas, Fayetteville, AR 72701, USADepartment of Horticulture, University of Arkansas, Fayetteville, AR 72701, USADepartment of Horticulture, University of Arkansas, Fayetteville, AR 72701, USADepartment of Horticulture, University of Arkansas, Fayetteville, AR 72701, USADepartment of Horticulture, University of Arkansas, Fayetteville, AR 72701, USADepartment of Horticulture, University of Arkansas, Fayetteville, AR 72701, USADepartment of Horticulture, University of Arkansas, Fayetteville, AR 72701, USADepartment of Entomology and Plant Pathology, University of Arkansas, Fayetteville, AR 72701, USADepartment of Biological Sciences, University of Arkansas, Fayetteville, AR 72701, USADepartment of Crop, Soil and Environmental Sciences, University of Arkansas, Fayetteville, AR 72701, USADepartment of Plant Sciences, University of California, 1 Shields Avenue, Davis, CA 95616, USADepartment of Soil and Crop Sciences, Colorado State University, Fort Collins, CO 80523, USADepartment of Soil and Crop Sciences, Colorado State University, Fort Collins, CO 80523, USADepartment of Agricultural Biology, Colorado State University, Fort Collins, CO 80523, USADepartment of Soil and Crop Sciences, Colorado State University, Fort Collins, CO 80523, USADepartment of Agricultural Biology, Colorado State University, Fort Collins, CO 80523, USADepartment of Soil and Crop Sciences, Colorado State University, Fort Collins, CO 80523, USADepartment of Soil and Crop Sciences, Colorado State University, Fort Collins, CO 80523, USADepartment of Horticulture, University of Arkansas, Fayetteville, AR 72701, USAThe common bean (<i>Phaseolus vulgaris</i> L.) is a globally cultivated leguminous crop. Fusarium wilt (FW), caused by <i>Fusarium oxysporum</i> f. sp. <i>phaseoli</i> (<i>Fop</i>), is a significant disease leading to substantial yield loss in common beans. Disease-resistant cultivars are recommended to counteract this. The objective of this investigation was to identify single nucleotide polymorphism (SNP) markers associated with FW resistance and to pinpoint potential resistant common bean accessions within a core collection, utilizing a panel of 157 accessions through the Genome-wide association study (GWAS) approach with TASSEL 5 and GAPIT 3. Phenotypes for <i>Fop</i> race 1 and race 4 were matched with genotypic data from 4740 SNPs of BARCBean6K_3 Infinium Bea Chips. After ranking the 157-accession panel and revealing 21 Fusarium wilt-resistant accessions, the GWAS pinpointed 16 SNPs on chromosomes Pv04, Pv05, Pv07, Pv8, and Pv09 linked to <i>Fop</i> race 1 resistance, 23 SNPs on chromosomes Pv03, Pv04, Pv05, Pv07, Pv09, Pv10, and Pv11 associated with <i>Fop</i> race 4 resistance, and 7 SNPs on chromosomes Pv04 and Pv09 correlated with both <i>Fop</i> race 1 and race 4 resistances. Furthermore, within a 30 kb flanking region of these associated SNPs, a total of 17 candidate genes were identified. Some of these genes were annotated as classical disease resistance protein/enzymes, including NB-ARC domain proteins, Leucine-rich repeat protein kinase family proteins, zinc finger family proteins, P-loopcontaining nucleoside triphosphate hydrolase superfamily, etc. Genomic prediction (GP) accuracy for <i>Fop</i> race resistances ranged from 0.26 to 0.55. This study advanced common bean genetic enhancement through marker-assisted selection (MAS) and genomic selection (GS) strategies, paving the way for improved <i>Fop</i> resistance.https://www.mdpi.com/1422-0067/24/20/15300common beangenome-wide association studyfusarium wiltgenomic prediction |
| spellingShingle | Kenani Chiwina Haizheng Xiong Gehendra Bhattarai Ryan William Dickson Theresa Makawa Phiri Yilin Chen Ibtisam Alatawi Derek Dean Neelendra K. Joshi Yuyan Chen Awais Riaz Paul Gepts Mark Brick Patrick F. Byrne Howard Schwartz James B. Ogg Kristin Otto Amy Fall Jeremy Gilbert Ainong Shi Genome-Wide Association Study and Genomic Prediction of Fusarium Wilt Resistance in Common Bean Core Collection International Journal of Molecular Sciences common bean genome-wide association study fusarium wilt genomic prediction |
| title | Genome-Wide Association Study and Genomic Prediction of Fusarium Wilt Resistance in Common Bean Core Collection |
| title_full | Genome-Wide Association Study and Genomic Prediction of Fusarium Wilt Resistance in Common Bean Core Collection |
| title_fullStr | Genome-Wide Association Study and Genomic Prediction of Fusarium Wilt Resistance in Common Bean Core Collection |
| title_full_unstemmed | Genome-Wide Association Study and Genomic Prediction of Fusarium Wilt Resistance in Common Bean Core Collection |
| title_short | Genome-Wide Association Study and Genomic Prediction of Fusarium Wilt Resistance in Common Bean Core Collection |
| title_sort | genome wide association study and genomic prediction of fusarium wilt resistance in common bean core collection |
| topic | common bean genome-wide association study fusarium wilt genomic prediction |
| url | https://www.mdpi.com/1422-0067/24/20/15300 |
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