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. 2022 May 31:13:853114.
doi: 10.3389/fgene.2022.853114. eCollection 2022.

Genome-Wide Association Study and Genomic Prediction for Bacterial Wilt Resistance in Common Bean (Phaseolus vulgaris) Core Collection

Bazgha Zia  1 , Ainong Shi  1 , Dotun Olaoye  1 , Haizheng Xiong  1 , Waltram Ravelombola  2 , Paul Gepts  3 , Howard F Schwartz  4 , Mark A Brick  5 , Kristen Otto  4 , Barry Ogg  5 , Senyu Chen  6
Affiliations

Genome-Wide Association Study and Genomic Prediction for Bacterial Wilt Resistance in Common Bean (Phaseolus vulgaris) Core Collection

Bazgha Zia et al. Front Genet. .

Abstract

Common bean (Phaseolus vulgaris) is one of the major legume crops cultivated worldwide. Bacterial wilt (BW) of common bean (Curtobacterium flaccumfaciens pv. flaccumfaciens), being a seed-borne disease, has been a challenge in common bean producing regions. A genome-wide association study (GWAS) was conducted to identify SNP markers associated with BW resistance in the USDA common bean core collection. A total of 168 accessions were evaluated for resistance against three different isolates of BW. Our study identified a total of 14 single nucleotide polymorphism (SNP) markers associated with the resistance to BW isolates 528, 557, and 597 using mixed linear models (MLMs) in BLINK, FarmCPU, GAPIT, and TASSEL 5. These SNPs were located on chromosomes Phaseolus vulgaris [Pv]02, Pv04, Pv08, and Pv09 for isolate 528; Pv07, Pv10, and Pv11 for isolate 557; and Pv04, Pv08, and Pv10 for isolate 597. The genomic prediction accuracy was assessed by utilizing seven GP models with 1) all the 4,568 SNPs and 2) the 14 SNP markers. The overall prediction accuracy (PA) ranged from 0.30 to 0.56 for resistance against the three BW isolates. A total of 14 candidate genes were discovered for BW resistance located on chromosomes Pv02, Pv04, Pv07, Pv08, and Pv09. This study revealed vital information for developing genetic resistance against the BW pathogen in common bean. Accordingly, the identified SNP markers and candidate genes can be utilized in common bean molecular breeding programs to develop novel resistant cultivars.

Keywords: Curtobacterium flaccumfaciens pv. flaccumfaciens; Phaseolus vulgaris; bacterial wilt; common bean; genome-wide association study; genomic prediction; single nucleotide polymorphism.

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Conflict of interest statement

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Figures

FIGURE 1
FIGURE 1
Distribution of bacterial wilt (BW) disease scale (0–4 rate) in 168 USDA common bean germplasm accessions.
FIGURE 2
FIGURE 2
Population genetic diversity analysis in the association panel consisted of 168 USDA common bean germplasm accessions. Phylogenetic trees drawn by using the neighbor-joining (NJ) method in three subpopulation (left) and 3D graphical plot of the principal component analysis (PCA) (right) drawn by using GAPIT 3. A large phylogenetic tree of the three subpopulation for each of the 168 common bean accessions is shown in Supplementary Table S1.
FIGURE 3
FIGURE 3
Phylogenetic tree among 21 common bean accessions of bacterial wilt resistance drawn using Mega 7. In the tree, the taxon name consists of the accession ID and the accession original country.
See this image and copyright information in PMC

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