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

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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Bibliographic Details
Main Authors:	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
Format:	Article
Language:	English
Published:	MDPI AG 2023-10-01
Series:	International Journal of Molecular Sciences
Subjects:	common bean genome-wide association study fusarium wilt genomic prediction
Online Access:	https://www.mdpi.com/1422-0067/24/20/15300

Description
Summary:	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.
ISSN:	1661-6596 1422-0067