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

Authors

Bazgha Zia, University of Arkansas, FayettevilleFollow
Ainong Shi, University of Arkansas, FayettevilleFollow
Dotun Olaoye, University of Arkansas, FayettevilleFollow
Haizheng Xiong, University of Arkansas, FayettevilleFollow
Waltram Ravelombola, Texas A & M UniversityFollow
Paul Gepts, University of California, Davis
Howard F. Schwartz, Colorado State University
Mark A. Brick, Colorado State University
Kristen Otto, Colorado State University
Barry Ogg, Colorado State University
Senyu Chen, University of MinnesotaFollow

Document Type

Article

Publication Date

5-2022

Keywords

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

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.

Citation

Zia, B., Shi, A., Olaoye, D., Xiong, H., Ravelombola, W., Gepts, P., Schwartz, H. F., Brick, M. A., Otto, K., Ogg, B., & Chen, S. (2022). Genome-Wide Association Study and Genomic Prediction for Bacterial Wilt Resistance in Common Bean (Phaseolus vulgaris) Core Collection. Frontiers in Genetics, 13, 853114. https://doi.org/10.3389/fgene.2022.853114

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