Genome-Wide Association Study and Genomic Prediction of Fusarium Wilt Resistance in Common Bean Core Collection

Authors

Kenani Chiwina, University of Arkansas-FayettevilleFollow
Haizheng Xiong, University of Arkansas, FayettevilleFollow
Gehendra Bhattarai, University of Arkansas, FayettevilleFollow
Ryan Dickson, University of Arkansas, FayettevilleFollow
Theresa Makawa Phiri, University of Arkansas-FayettevilleFollow
Yilin Chen, University of Arkansas, FayettevilleFollow
Ibtisam Alatawi, University of Arkansas, FayettevilleFollow
Derek Dean, University of Arkansas, FayettevilleFollow
Neelendra K. Joshi, University of Arkansas, FayettevilleFollow
Yuyan Chen, University of Arkansas, FayettevilleFollow
Awais Riaz, University of Arkansas, FayettevilleFollow
Paul Gepts, University of California, DavisFollow
Mark Brick, Colorado State UniversityFollow
Patrick Byrne, Colorado State UniversityFollow
Howard Schwartz, Colorado State UniversityFollow
James B. Ogg, Colorado State UniversityFollow
Kristen Otto, Colorado State UniversityFollow
Amy Fall, Colorado State UniversityFollow
Jeremy Gilbert, Colorado State UniversityFollow
Ainong Shi, University of Arkansas, FayettevilleFollow

Document Type

Article

Publication Date

10-2023

Keywords

common bean; genome-wide association study; fusarium wilt; genomic prediction

Abstract

The common bean (Phaseolus vulgaris L.) is a globally cultivated leguminous crop. Fusarium wilt (FW), caused by Fusarium oxysporum f. sp. phaseoli (Fop), 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 Fop 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 Fop race 1 resistance, 23 SNPs on chromosomes Pv03, Pv04, Pv05, Pv07, Pv09, Pv10, and Pv11 associated with Fop race 4 resistance, and 7 SNPs on chromosomes Pv04 and Pv09 correlated with both Fop 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 Fop 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 Fop resistance.

Citation

Chiwina, K., Xiong, H., Bhattarai, G., Dickson, R., Makawa Phiri, T., Chen, Y., Alatawi, I., Dean, D., Joshi, N. K., Chen, Y., Riaz, A., Gepts, P., Brick, M., Byrne, P., Schwartz, H., Ogg, J. B., Otto, K., Fall, A., Gilbert, J., & Shi, A. (2023). Genome-Wide Association Study and Genomic Prediction of Fusarium Wilt Resistance in Common Bean Core Collection. International Journal of Molecular Sciences, 24, 15300. https://doi.org/10.3390/ijms242015300

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This work is licensed under a Creative Commons Attribution 4.0 International License.